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Hontani Y, Ganapathy S, Frehan S, Kloz M, de Grip WJ, Kennis JTM. Strong pH-Dependent Near-Infrared Fluorescence in a Microbial Rhodopsin Reconstituted with a Red-Shifting Retinal Analogue. J Phys Chem Lett 2018; 9:6469-6474. [PMID: 30376338 PMCID: PMC6240888 DOI: 10.1021/acs.jpclett.8b02780] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 10/30/2018] [Indexed: 06/08/2023]
Abstract
Near-infrared (NIR)-driven rhodopsins are of great interest in optogenetics and other optobiotechnological developments such as artificial photosynthesis and deep-tissue voltage imaging. Here we report that the proton pump proteorhodopsin (PR) containing a NIR-active retinal analogue (PR:MMAR) exhibits intense NIR fluorescence at a quantum yield of 3.3%. This is 130 times higher than native PR ( Lenz , M. O. ; Biophys J. 2006 , 91 , 255 - 262 ) and 3-8 times higher than the QuasAr and PROPS voltage sensors ( Kralj , J. ; Science 2011 , 333 , 345 - 348 ; Hochbaum , D. R. ; Nat. Methods 2014 , 11 , 825 - 833 ). The NIR fluorescence strongly depends on the pH in the range of 6-8.5, suggesting potential application of MMAR-binding proteins as ultrasensitive NIR-driven pH and/or voltage sensors. Femtosecond transient absorption spectroscopy showed that upon near-IR excitation, PR:MMAR features an unusually long fluorescence lifetime of 310 ps and the absence of isomerized photoproducts, consistent with the high fluorescence quantum yield. Stimulated Raman analysis indicates that the NIR-absorbing species develops upon protonation of a conserved aspartate, which promotes charge delocalization and bond length leveling due to an additional methylamino group in MMAR, in essence providing a secondary protonated Schiff base. This results in much smaller bond length alteration along the conjugated backbone, thereby conferring significant single-bond character to the C13═C14 bond and structural deformation of the chromophore, which interferes with photoinduced isomerization and extends the lifetime for fluorescence. Hence, our studies allow for a molecular understanding of the relation between absorption/emission wavelength, isomerization, and fluorescence in PR:MMAR. As acidification enhances the resonance state, this explains the strong pH dependence of the NIR emission.
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Affiliation(s)
- Yusaku Hontani
- Department
of Physics and Astronomy, Vrije Universiteit, Amsterdam 1081 HV, The Netherlands
| | - Srividya Ganapathy
- Department
of Biophysical Organic Chemistry, Leiden Institute of
Chemistry, Gorlaeus Laboratories, Leiden University, Leiden 2300 RA, The Netherlands
| | - Sean Frehan
- Department
of Physics and Astronomy, Vrije Universiteit, Amsterdam 1081 HV, The Netherlands
| | - Miroslav Kloz
- Department
of Physics and Astronomy, Vrije Universiteit, Amsterdam 1081 HV, The Netherlands
- ELI-Beamlines,
Institute of Physics, Na Slovance 2, 182 21 Praha 8, Czech Republic
| | - Willem J. de Grip
- Department
of Biophysical Organic Chemistry, Leiden Institute of
Chemistry, Gorlaeus Laboratories, Leiden University, Leiden 2300 RA, The Netherlands
- Department
of Biochemistry, Radboud University Medical
Center, Nijmegen 6500 HB, The Netherlands
| | - John T. M. Kennis
- Department
of Physics and Astronomy, Vrije Universiteit, Amsterdam 1081 HV, The Netherlands
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202
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Chen X, Mu Y, Hu Y, Kuan AT, Nikitchenko M, Randlett O, Chen AB, Gavornik JP, Sompolinsky H, Engert F, Ahrens MB. Brain-wide Organization of Neuronal Activity and Convergent Sensorimotor Transformations in Larval Zebrafish. Neuron 2018; 100:876-890.e5. [PMID: 30473013 DOI: 10.1016/j.neuron.2018.09.042] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 07/30/2018] [Accepted: 09/25/2018] [Indexed: 11/30/2022]
Abstract
Simultaneous recordings of large populations of neurons in behaving animals allow detailed observation of high-dimensional, complex brain activity. However, experimental approaches often focus on singular behavioral paradigms or brain areas. Here, we recorded whole-brain neuronal activity of larval zebrafish presented with a battery of visual stimuli while recording fictive motor output. We identified neurons tuned to each stimulus type and motor output and discovered groups of neurons in the anterior hindbrain that respond to different stimuli eliciting similar behavioral responses. These convergent sensorimotor representations were only weakly correlated to instantaneous motor activity, suggesting that they critically inform, but do not directly generate, behavioral choices. To catalog brain-wide activity beyond explicit sensorimotor processing, we developed an unsupervised clustering technique that organizes neurons into functional groups. These analyses enabled a broad overview of the functional organization of the brain and revealed numerous brain nuclei whose neurons exhibit concerted activity patterns.
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Affiliation(s)
- Xiuye Chen
- Harvard University, Molecular and Cellular Biology, Cambridge, MA, 02138, USA; Harvard University, Center for Brain Science, Cambridge, MA, 02138, USA; Boston University, Department of Biology, Boston, MA, 02115, USA.
| | - Yu Mu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, 20147, USA
| | - Yu Hu
- Harvard University, Center for Brain Science, Cambridge, MA, 02138, USA; Hebrew University, The Edmond and Lily Safra Center for Brain Sciences, Jerusalem, Israel
| | - Aaron T Kuan
- Harvard Medical School, Department of Neurobiology, Boston, MA, 02115, USA
| | - Maxim Nikitchenko
- Harvard University, Center for Brain Science, Cambridge, MA, 02138, USA
| | - Owen Randlett
- Harvard University, Center for Brain Science, Cambridge, MA, 02138, USA
| | - Alex B Chen
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, 20147, USA
| | | | - Haim Sompolinsky
- Harvard University, Center for Brain Science, Cambridge, MA, 02138, USA; Hebrew University, The Edmond and Lily Safra Center for Brain Sciences, Jerusalem, Israel
| | - Florian Engert
- Harvard University, Molecular and Cellular Biology, Cambridge, MA, 02138, USA; Harvard University, Center for Brain Science, Cambridge, MA, 02138, USA
| | - Misha B Ahrens
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, 20147, USA.
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203
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Wanner AA, Vishwanathan A. Methods for Mapping Neuronal Activity to Synaptic Connectivity: Lessons From Larval Zebrafish. Front Neural Circuits 2018; 12:89. [PMID: 30410437 PMCID: PMC6209671 DOI: 10.3389/fncir.2018.00089] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 09/28/2018] [Indexed: 12/29/2022] Open
Abstract
For a mechanistic understanding of neuronal circuits in the brain, a detailed description of information flow is necessary. Thereby it is crucial to link neuron function to the underlying circuit structure. Multiphoton calcium imaging is the standard technique to record the activity of hundreds of neurons simultaneously. Similarly, recent advances in high-throughput electron microscopy techniques allow for the reconstruction of synaptic resolution wiring diagrams. These two methods can be combined to study both function and structure in the same specimen. Due to its small size and optical transparency, the larval zebrafish brain is one of the very few vertebrate systems where both, activity and connectivity of all neurons from entire, anatomically defined brain regions, can be analyzed. Here, we describe different methods and the tools required for combining multiphoton microscopy with dense circuit reconstruction from electron microscopy stacks of entire brain regions in the larval zebrafish.
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Affiliation(s)
- Adrian A Wanner
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, United States
| | - Ashwin Vishwanathan
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, United States
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204
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Kang BE, Lee S, Baker BJ. Optical consequences of a genetically-encoded voltage indicator with a pH sensitive fluorescent protein. Neurosci Res 2018; 146:13-21. [PMID: 30342069 DOI: 10.1016/j.neures.2018.10.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 09/20/2018] [Accepted: 10/16/2018] [Indexed: 12/31/2022]
Abstract
Genetically-Encoded Voltage Indicators (GEVIs) are capable of converting changes in membrane potential into an optical signal. Here, we focus on recent insights into the mechanism of ArcLight-type probes and the consequences of utilizing a pH-dependent Fluorescent Protein (FP). A negative charge on the exterior of the β-can of the FP combined with a pH-sensitive FP enables voltage-dependent conformational changes to affect the fluorescence of the probe. This hypothesis implies that interaction/dimerization of the FP creates a microenvironment for the probe that is altered via conformational changes. This mechanism explains why a pH sensitive FP with a negative charge on the outside of the β-can is needed, but also suggests that pH could affect the optical signal as well. To better understand the effects of pH on the voltage-dependent signal of ArcLight, the intracellular pH (pHi) was tested at pH 6.8, 7.2, or 7.8. The resting fluorescence of ArcLight gets brighter as the pHi increases, yet only pH 7.8 significantly affected the ΔF/F. ArcLight could also simultaneously report voltage and pH changes during the acidification of a neuron firing multiple action potentials revealing different buffering capacities of the soma versus the processes of the cell.
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Affiliation(s)
- Bok Eum Kang
- Center for Functional Connectomics, Korea Institute of Science and Technology, Seoul, Republic of Korea; Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology, Seoul 02792, Republic of Korea
| | - Sungmoo Lee
- Center for Functional Connectomics, Korea Institute of Science and Technology, Seoul, Republic of Korea; Program in Nanoscience and Technology, Department of Transdisciplinary Studies, Graduate School of Convergence Science and Technology, Seoul National University. Suwon, Republic of Korea
| | - Bradley J Baker
- Center for Functional Connectomics, Korea Institute of Science and Technology, Seoul, Republic of Korea; Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology, Seoul 02792, Republic of Korea.
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205
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Yi B, Kang BE, Lee S, Braubach S, Baker BJ. A dimeric fluorescent protein yields a bright, red-shifted GEVI capable of population signals in brain slice. Sci Rep 2018; 8:15199. [PMID: 30315245 PMCID: PMC6185910 DOI: 10.1038/s41598-018-33297-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 09/24/2018] [Indexed: 12/21/2022] Open
Abstract
A bright, red-shifted Genetically Encoded Voltage Indicator (GEVI) was developed using a modified version of the fluorescent protein, tdTomato. Dimerization of the fluorescent domain for ArcLight-type GEVIs has been shown to affect the signal size of the voltage-dependent optical signal. For red-shifted GEVI development, tdTomato was split fusing a single dTomato chromophore to the voltage sensing domain. Optimization of the amino acid length and charge composition of the linker region between the voltage sensing domain and the fluorescent protein resulted in a probe that is an order of magnitude brighter than FlicR1 at a resting potential of -70 mV and exhibits a ten-fold larger change in fluorescence (ΔF) upon 100 mV depolarization of the plasma membrane in HEK 293 cells. Unlike ArcLight, the introduction of charged residues to the exterior of dTomato did not substantially improve the dynamic range of the optical signal. As a result, this new GEVI, Ilmol, yields a 3-fold improvement in the signal-to-noise ratio compared to FlicR1 despite a smaller fractional change in fluorescence of 4% per 100 mV depolarization of the plasma membrane. Ilmol expresses well in neurons resolving action potentials in neuronal cultures and reporting population signals in mouse hippocampal acute brain slice recordings. Ilmol is the brightest red-shifted GEVI to date enabling imaging with 160-fold less light than Archon1 for primary neuron recordings (50 mW/cm2 versus 8 W/cm2) and 600-fold less light than QuasAr2 for mouse brain slice recordings (500 mW/cm2 versus 300 W/cm2). This new GEVI uses a distinct mechanism from other approaches, opening an alternate engineering path to improve sensitivity and speed.
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Affiliation(s)
- Bumjun Yi
- The Center for Functional Connectomics, Korea Institute of Science and Technology, Seoul, Republic of Korea.,Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology (UST), Seoul, Republic of Korea
| | - Bok Eum Kang
- The Center for Functional Connectomics, Korea Institute of Science and Technology, Seoul, Republic of Korea.,Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology (UST), Seoul, Republic of Korea
| | - Sungmoo Lee
- The Center for Functional Connectomics, Korea Institute of Science and Technology, Seoul, Republic of Korea.,Department of Transdisciplinary Studies, Graduate school of Convergence Science and Technology, Seoul National University, Suwon, Republic of Korea
| | - Sophie Braubach
- The Center for Functional Connectomics, Korea Institute of Science and Technology, Seoul, Republic of Korea
| | - Bradley J Baker
- The Center for Functional Connectomics, Korea Institute of Science and Technology, Seoul, Republic of Korea. .,Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology (UST), Seoul, Republic of Korea.
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206
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A new way to capture the brain's electrical symphony. Nature 2018; 561:300-302. [PMID: 30232440 DOI: 10.1038/d41586-018-06694-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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207
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Manna P, Hung ST, Mukherjee S, Friis P, Simpson DM, Lo MN, Palmer AE, Jimenez R. Directed evolution of excited state lifetime and brightness in FusionRed using a microfluidic sorter. Integr Biol (Camb) 2018; 10:516-526. [PMID: 30094420 PMCID: PMC6141309 DOI: 10.1039/c8ib00103k] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Green fluorescent proteins (GFP) and their blue, cyan and red counterparts offer unprecedented advantages as biological markers owing to their genetic encodability and straightforward expression in different organisms. Although significant advancements have been made towards engineering the key photo-physical properties of red fluorescent proteins (RFPs), they continue to perform sub-optimally relative to GFP variants. Advanced engineering strategies are needed for further evolution of RFPs in the pursuit of improving their photo-physics. In this report, a microfluidic sorter that discriminates members of a cell-based library based on their excited state lifetime and fluorescence intensity is used for the directed evolution of the photo-physical properties of FusionRed. In-flow measurements of the fluorescence lifetime are performed in a frequency-domain approach with sub-millisecond sampling times. Promising clones are sorted by optical force trapping with an infrared laser. Using this microfluidic sorter, mutants are generated with longer lifetimes than their precursor, FusionRed. This improvement in the excited state lifetime of the mutants leads to an increase in their fluorescence quantum yield up to 1.8-fold. In the course of evolution, we also identified one key mutation (L177M), which generated a mutant (FusionRed-M) that displayed ∼2-fold higher brightness than its precursor upon expression in mammalian (HeLa) cells. Photo-physical and mutational analyses of clones isolated at the different stages of mutagenesis reveal the photo-physical evolution towards higher in vivo brightness.
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Affiliation(s)
- Premashis Manna
- JILA, NIST and University of Colorado, Boulder, Colorado 80309, USA.
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208
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Nitta N, Sugimura T, Isozaki A, Mikami H, Hiraki K, Sakuma S, Iino T, Arai F, Endo T, Fujiwaki Y, Fukuzawa H, Hase M, Hayakawa T, Hiramatsu K, Hoshino Y, Inaba M, Ito T, Karakawa H, Kasai Y, Koizumi K, Lee S, Lei C, Li M, Maeno T, Matsusaka S, Murakami D, Nakagawa A, Oguchi Y, Oikawa M, Ota T, Shiba K, Shintaku H, Shirasaki Y, Suga K, Suzuki Y, Suzuki N, Tanaka Y, Tezuka H, Toyokawa C, Yalikun Y, Yamada M, Yamagishi M, Yamano T, Yasumoto A, Yatomi Y, Yazawa M, Di Carlo D, Hosokawa Y, Uemura S, Ozeki Y, Goda K. Intelligent Image-Activated Cell Sorting. Cell 2018; 175:266-276.e13. [DOI: 10.1016/j.cell.2018.08.028] [Citation(s) in RCA: 298] [Impact Index Per Article: 49.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Revised: 08/09/2018] [Accepted: 08/15/2018] [Indexed: 11/27/2022]
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209
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Lillis KP, Staley KJ. Optogenetic dissection of ictogenesis: in search of a targeted anti-epileptic therapy. J Neural Eng 2018; 15:041001. [PMID: 29536948 PMCID: PMC6257979 DOI: 10.1088/1741-2552/aab66a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
For over a century, epileptic seizures have been characterized as a state of pathological, hypersynchronous brain activity. Anti-epileptic therapies have been developed largely based on the dogma that the altered brain rhythms result from an overabundance of glutamatergic activity or insufficient GABAergic inhibition. The most effective drugs in use today act to globally decrease excitation, increase inhibition, or decrease all activity. Unfortunately, such broad alterations to brain activity often lead to impactful side effects such as drowsiness, cognitive impairment, and sleep disruption. Recent advances in optical imaging, optogenetics, and chemogenetics have made it feasible to record and alter neuronal activity with single neuron resolution and genetically directed targeting. The goal of this review it to summarize the usage of these research tools in the study of ictogenesis (seizure generation) and propose a translational pathway by which these studies could result in novel clinical therapies. This manuscript is not intended to serve as an exhaustive list of optogenetic tools nor as a summary of all optogenetic manipulations in epilepsy research. Rather, we will focus on the tools and research aimed at dissecting the basic neuron-level interactions underlying ictogenesis.
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210
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Patriarchi T, Cho JR, Merten K, Howe MW, Marley A, Xiong WH, Folk RW, Broussard GJ, Liang R, Jang MJ, Zhong H, Dombeck D, von Zastrow M, Nimmerjahn A, Gradinaru V, Williams JT, Tian L. Ultrafast neuronal imaging of dopamine dynamics with designed genetically encoded sensors. Science 2018; 360:eaat4422. [PMID: 29853555 PMCID: PMC6287765 DOI: 10.1126/science.aat4422] [Citation(s) in RCA: 601] [Impact Index Per Article: 100.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Accepted: 05/17/2018] [Indexed: 12/12/2022]
Abstract
Neuromodulatory systems exert profound influences on brain function. Understanding how these systems modify the operating mode of target circuits requires spatiotemporally precise measurement of neuromodulator release. We developed dLight1, an intensity-based genetically encoded dopamine indicator, to enable optical recording of dopamine dynamics with high spatiotemporal resolution in behaving mice. We demonstrated the utility of dLight1 by imaging dopamine dynamics simultaneously with pharmacological manipulation, electrophysiological or optogenetic stimulation, and calcium imaging of local neuronal activity. dLight1 enabled chronic tracking of learning-induced changes in millisecond dopamine transients in mouse striatum. Further, we used dLight1 to image spatially distinct, functionally heterogeneous dopamine transients relevant to learning and motor control in mouse cortex. We also validated our sensor design platform for developing norepinephrine, serotonin, melatonin, and opioid neuropeptide indicators.
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Affiliation(s)
- Tommaso Patriarchi
- Department of Biochemistry and Molecular Medicine, University of California, Davis, 2700 Stockton Boulevard, Sacramento, CA 95817, USA
| | - Jounhong Ryan Cho
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Katharina Merten
- Waitt Advanced Biophotonics Center, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Mark W Howe
- Department of Neurobiology, Northwestern University, Evanston, IL 60208, USA
| | - Aaron Marley
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94131, USA
| | - Wei-Hong Xiong
- Vollum Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Robert W Folk
- Waitt Advanced Biophotonics Center, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Gerard Joey Broussard
- Department of Biochemistry and Molecular Medicine, University of California, Davis, 2700 Stockton Boulevard, Sacramento, CA 95817, USA
| | - Ruqiang Liang
- Department of Biochemistry and Molecular Medicine, University of California, Davis, 2700 Stockton Boulevard, Sacramento, CA 95817, USA
| | - Min Jee Jang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Haining Zhong
- Vollum Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Daniel Dombeck
- Department of Neurobiology, Northwestern University, Evanston, IL 60208, USA
| | - Mark von Zastrow
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94131, USA
| | - Axel Nimmerjahn
- Waitt Advanced Biophotonics Center, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Viviana Gradinaru
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - John T Williams
- Vollum Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Lin Tian
- Department of Biochemistry and Molecular Medicine, University of California, Davis, 2700 Stockton Boulevard, Sacramento, CA 95817, USA.
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