1
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Brooks FP, Davis HC, Park P, Qi Y, Cohen AE. Photophysics-informed two-photon voltage imaging using FRET-opsin voltage indicators. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.01.587540. [PMID: 38617370 PMCID: PMC11014499 DOI: 10.1101/2024.04.01.587540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Microbial rhodopsin-derived genetically encoded voltage indicators (GEVIs) are powerful tools for mapping bioelectrical dynamics in cell culture and in live animals. Förster resonance energy transfer (FRET)-opsin GEVIs use voltage-dependent changes in opsin absorption to modulate the fluorescence of an attached fluorophore, achieving high brightness, speed, and voltage sensitivity. However, the voltage sensitivity of most FRET-opsin GEVIs has been reported to decrease or vanish under two-photon (2P) excitation. Here we investigated the photophysics of the FRET-opsin GEVIs Voltron1 and 2. We found that the voltage sensitivity came from a photocycle intermediate, not from the opsin ground state. The voltage sensitivities of both GEVIs were nonlinear functions of illumination intensity; for Voltron1, the sensitivity reversed sign under low-intensity illumination. Using photocycle-optimized 2P illumination protocols, we demonstrate 2P voltage imaging with Voltron2 in barrel cortex of a live mouse. These results open the door to high-speed 2P voltage imaging of FRET-opsin GEVIs in vivo.
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Affiliation(s)
| | | | - Pojeong Park
- Department of Chemistry and Chemical Biology, Harvard University
| | - Yitong Qi
- Department of Chemistry and Chemical Biology, Harvard University
| | - Adam E. Cohen
- Department of Chemistry and Chemical Biology, Harvard University
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2
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Berndt A, Cai D, Cohen A, Juarez B, Iglesias JT, Xiong H, Qin Z, Tian L, Slesinger PA. Current Status and Future Strategies for Advancing Functional Circuit Mapping In Vivo. J Neurosci 2023; 43:7587-7598. [PMID: 37940594 PMCID: PMC10634581 DOI: 10.1523/jneurosci.1391-23.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 08/24/2023] [Accepted: 08/25/2023] [Indexed: 11/10/2023] Open
Abstract
The human brain represents one of the most complex biological systems, containing billions of neurons interconnected through trillions of synapses. Inherent to the brain is a biochemical complexity involving ions, signaling molecules, and peptides that regulate neuronal activity and allow for short- and long-term adaptations. Large-scale and noninvasive imaging techniques, such as fMRI and EEG, have highlighted brain regions involved in specific functions and visualized connections between different brain areas. A major shortcoming, however, is the need for more information on specific cell types and neurotransmitters involved, as well as poor spatial and temporal resolution. Recent technologies have been advanced for neuronal circuit mapping and implemented in behaving model organisms to address this. Here, we highlight strategies for targeting specific neuronal subtypes, identifying, and releasing signaling molecules, controlling gene expression, and monitoring neuronal circuits in real-time in vivo Combined, these approaches allow us to establish direct causal links from genes and molecules to the systems level and ultimately to cognitive processes.
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Affiliation(s)
| | - Denise Cai
- Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | | | | | | | | | - Zhenpeng Qin
- University of Texas-Dallas, Richardson, TX 75080
| | - Lin Tian
- University of California-Davis, Davis, CA 95616
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3
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Hayward RF, Brooks FP, Yang S, Gao S, Cohen AE. Diminishing neuronal acidification by channelrhodopsins with low proton conduction. eLife 2023; 12:RP86833. [PMID: 37801078 PMCID: PMC10558203 DOI: 10.7554/elife.86833] [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: 10/07/2023] Open
Abstract
Many channelrhodopsins are permeable to protons. We found that in neurons, activation of a high-current channelrhodopsin, CheRiff, led to significant acidification, with faster acidification in the dendrites than in the soma. Experiments with patterned optogenetic stimulation in monolayers of HEK cells established that the acidification was due to proton transport through the opsin, rather than through other voltage-dependent channels. We identified and characterized two opsins which showed large photocurrents, but small proton permeability, PsCatCh2.0 and ChR2-3M. PsCatCh2.0 showed excellent response kinetics and was also spectrally compatible with simultaneous voltage imaging with QuasAr6a. Stimulation-evoked acidification is a possible source of disruptions to cell health in scientific and prospective therapeutic applications of optogenetics. Channelrhodopsins with low proton permeability are a promising strategy for avoiding these problems.
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Affiliation(s)
- Rebecca Frank Hayward
- School of Engineering and Applied Sciences, Harvard UniversityCambridgeUnited States
| | - F Phil Brooks
- Department of Chemistry, Harvard UniversityCambridgeUnited States
| | - Shang Yang
- Department of Neurophysiology, University of WurzburgWurzburgGermany
| | - Shiqiang Gao
- Department of Neurophysiology, University of WurzburgWurzburgGermany
| | - Adam E Cohen
- Department of Chemistry, Harvard UniversityCambridgeUnited States
- Department of Physics, Harvard UniversityCambridgeUnited States
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4
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Hayward RF, Brooks FP, Yang S, Gao S, Cohen AE. Diminishing neuronal acidification by channelrhodopsins with low proton conduction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.07.527404. [PMID: 36798192 PMCID: PMC9934520 DOI: 10.1101/2023.02.07.527404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Many channelrhodopsins are permeable to protons. We found that in neurons, activation of a high-current channelrhodopsin, CheRiff, led to significant acidification, with faster acidification in the dendrites than in the soma. Experiments with patterned optogenetic stimulation in monolayers of HEK cells established that the acidification was due to proton transport through the opsin, rather than through other voltage-dependent channels. We identified and characterized two opsins which showed large photocurrents, but small proton permeability, PsCatCh2.0 and ChR2-3M. PsCatCh2.0 showed excellent response kinetics and was also spectrally compatible with simultaneous voltage imaging with QuasAr6a. Stimulation-evoked acidification is a possible source of disruptions to cell health in scientific and prospective therapeutic applications of optogenetics. Channelrhodopsins with low proton permeability are a promising strategy for avoiding these problems. Statement of Significance Acidification is an undesirable artifact of optogenetic stimulation. Low proton-permeability opsins minimize this artifact while still allowing robust optogenetic control.
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Affiliation(s)
| | - F. Phil Brooks
- Department of Chemistry, Harvard University, Cambridge, MA 02138
| | - Shang Yang
- Department of Neurophysiology, University of Wurzburg, Germany
| | - Shiqiang Gao
- Department of Neurophysiology, University of Wurzburg, Germany
| | - Adam E Cohen
- Department of Chemistry, Harvard University, Cambridge, MA 02138
- Department of Physics, Harvard University, Cambridge, MA 02138
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5
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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: 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: 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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6
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Zheng JS, Liang J, Shi WW, Li Y, Hu HG, Tian CL, Liu L. A mirror-image protein-based information barcoding and storage technology. Sci Bull (Beijing) 2021; 66:1542-1549. [PMID: 36654283 DOI: 10.1016/j.scib.2021.03.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 02/12/2021] [Accepted: 03/02/2021] [Indexed: 02/03/2023]
Abstract
A mirror-image protein-based information barcoding and storage technology wherein D-amino acids are used to encode information into mirror-image proteins that are chemically synthesized is described. These mirror-image proteins were then fused into various materials from which information-encoded objects were produced. Subsequently, the mirror-image proteins were extracted from the objects using biotin-streptavidin resin-mediated specific enrichment and cleaved using an Ni(II)-mediated selective peptide cleavage. Protein sequencing was accomplished using liquid chromatography/tandem mass spectrometry (LC-MS/MS) and then transcoded into the recorded information. We demonstrated the use of this technology to encode Chinese words into mirror-image proteins, which were then fused onto a poly(ethylene terephthalate) (PET) film and retrieved and decoded by LC-MS/MS sequencing. Compared to information barcoding and storage technologies using natural biopolymers, the mirror-image biopolymers used in our technology may be more stable and durable.
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Affiliation(s)
- Ji-Shen Zheng
- Tsinghua-Peking Joint Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China; Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Jun Liang
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Wei-Wei Shi
- Tsinghua-Peking Joint Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Ying Li
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Hong-Gang Hu
- Institute of Translational Medicine, Shanghai University, Shanghai 200444, China
| | - Chang-Lin Tian
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Lei Liu
- Tsinghua-Peking Joint Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China.
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7
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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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8
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Penzkofer A, Silapetere A, Hegemann P. Photocycle Dynamics of the Archaerhodopsin 3 Based Fluorescent Voltage Sensor QuasAr1. Int J Mol Sci 2019; 21:ijms21010160. [PMID: 31881701 PMCID: PMC6982170 DOI: 10.3390/ijms21010160] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 12/18/2019] [Accepted: 12/19/2019] [Indexed: 11/16/2022] Open
Abstract
The retinal photocycle dynamics of the fluorescent voltage sensor QuasAr1 (Archaerhodopsin 3 P60S-T80S-D95H-D106H-F161V mutant from Halorubrum sodomense) in pH 8 Tris buffer was studied. The samples were photoexcited to the first absorption band of the protonated retinal Schiff base (PRSB) Ret_580 (absorption maximum at λmax ≈ 580 nm), and the retinal Schiff base photoisomerization and protonation state changes were followed by absorption spectra recordings during light exposure and after light exposure. Ret_580 turned out to be composed of two protonated retinal Schiff base isomers, namely Ret_580I and Ret_580II. Photoexcitation of Ret_580I resulted in barrier-involved isomerization to Ret_540 (quantum yield ≈ 0.056) and subsequent retinal proton release leading to Ret_410 deprotonated retinal Schiff base (RSB). In the dark, Ret_410 partially recovered to Ret_580I and partially stabilized to irreversible Ret_400 due to apoprotein restructuring (Ret_410 lifetime ≈ 2 h). Photoexcitation of Ret_580II resulted in barrier-involved isomerization to Ret_640 (quantum yield ≈ 0.00135) and subsequent deprotonation to Ret_370 (RSB). In the dark, Ret_370 partially recovered to Ret_580II and partially stabilized to irreversible Ret_350 due to apoprotein restructuring (Ret_370 lifetime ≈ 10 h). Photocycle schemes and reaction coordinate diagrams for Ret_580I and Ret_580II were developed and photocyle parameters were determined.
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Affiliation(s)
- Alfons Penzkofer
- Fakultät für Physik, Universität Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
- Correspondence: ; Tel.: +49-941-943-2107
| | - Arita Silapetere
- Experimentelle Biophysik, Institut für Biologie, Humboldt Universität zu Berlin, Invalidenstraße 42, D-10115 Berlin, Germany; (A.S.); (P.H.)
| | - Peter Hegemann
- Experimentelle Biophysik, Institut für Biologie, Humboldt Universität zu Berlin, Invalidenstraße 42, D-10115 Berlin, Germany; (A.S.); (P.H.)
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9
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Penzkofer A, Silapetere A, Hegemann P. Absorption and Emission Spectroscopic Investigation of the Thermal Dynamics of the Archaerhodopsin 3 Based Fluorescent Voltage Sensor QuasAr1. Int J Mol Sci 2019; 20:E4086. [PMID: 31438573 PMCID: PMC6747118 DOI: 10.3390/ijms20174086] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 08/15/2019] [Accepted: 08/16/2019] [Indexed: 12/13/2022] Open
Abstract
QuasAr1 is a fluorescent voltage sensor derived from Archaerhodopsin 3 (Arch) of Halorubrum sodomense by directed evolution. Here we report absorption and emission spectroscopic studies of QuasAr1 in Tris buffer at pH 8. Absorption cross-section spectra, fluorescence quantum distributions, fluorescence quantum yields, and fluorescence excitation spectra were determined. The thermal stability of QuasAr1 was studied by long-time attenuation coefficient measurements at room temperature (23 ± 2 °C) and at 2.5 ± 0.5 °C. The apparent melting temperature was determined by stepwise sample heating up and cooling down (obtained apparent melting temperature: 65 ± 3 °C). In the protein melting process the originally present protonated retinal Schiff base (PRSB) with absorption maximum at 580 nm converted to de-protonated retinal Schiff base (RSB) with absorption maximum at 380 nm. Long-time storage of QuasAr1 at temperatures around 2.5 °C and around 23 °C caused gradual protonated retinal Schiff base isomer changes to other isomer conformations, de-protonation to retinal Schiff base isomers, and apoprotein structure changes showing up in ultraviolet absorption increase. Reaction coordinate schemes are presented for the thermal protonated retinal Schiff base isomerizations and deprotonations in parallel with the dynamic apoprotein restructurings.
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Affiliation(s)
- Alfons Penzkofer
- Fakultät für Physik, Universität Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany.
| | - Arita Silapetere
- Experimentelle Biophysik, Institut für Biologie, Humboldt Universität zu Berlin, Invalidenstraße 42, D-10115 Berlin, Germany
| | - Peter Hegemann
- Experimentelle Biophysik, Institut für Biologie, Humboldt Universität zu Berlin, Invalidenstraße 42, D-10115 Berlin, Germany
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10
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Deo C, Lavis LD. Synthetic and genetically encoded fluorescent neural activity indicators. Curr Opin Neurobiol 2018; 50:101-108. [DOI: 10.1016/j.conb.2018.01.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 12/19/2017] [Accepted: 01/10/2018] [Indexed: 10/18/2022]
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11
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Kiskinis E, Kralj JM, Zou P, Weinstein EN, Zhang H, Tsioras K, Wiskow O, Ortega JA, Eggan K, Cohen AE. All-Optical Electrophysiology for High-Throughput Functional Characterization of a Human iPSC-Derived Motor Neuron Model of ALS. Stem Cell Reports 2018; 10:1991-2004. [PMID: 29779896 PMCID: PMC5993648 DOI: 10.1016/j.stemcr.2018.04.020] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 04/20/2018] [Accepted: 04/22/2018] [Indexed: 11/26/2022] Open
Abstract
Human induced pluripotent stem cell (iPSC)-derived neurons are an attractive substrate for modeling disease, yet the heterogeneity of these cultures presents a challenge for functional characterization by manual patch-clamp electrophysiology. Here, we describe an optimized all-optical electrophysiology, “Optopatch,” pipeline for high-throughput functional characterization of human iPSC-derived neuronal cultures. We demonstrate the method in a human iPSC-derived motor neuron (iPSC-MN) model of amyotrophic lateral sclerosis (ALS). In a comparison of iPSC-MNs with an ALS-causing mutation (SOD1 A4V) with their genome-corrected controls, the mutants showed elevated spike rates under weak or no stimulus and greater likelihood of entering depolarization block under strong optogenetic stimulus. We compared these results with numerical simulations of simple conductance-based neuronal models and with literature results in this and other iPSC-based models of ALS. Our data and simulations suggest that deficits in slowly activating potassium channels may underlie the changes in electrophysiology in the SOD1 A4V mutation. All-optical electrophysiology enables high-throughput assays in hiPSC-derived neurons Neurons derived from ALS patients fire differently from genome-corrected controls A deficit in the Kv7 potassium current can explain the difference in firing
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Affiliation(s)
- Evangelos Kiskinis
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Joel M Kralj
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Peng Zou
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Eli N Weinstein
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Department of Physics, Harvard University, Cambridge, MA 02138, USA
| | - Hongkang Zhang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Konstantinos Tsioras
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Ole Wiskow
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - J Alberto Ortega
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Kevin Eggan
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.
| | - Adam E Cohen
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Department of Physics, Harvard University, Cambridge, MA 02138, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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12
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Abstract
Microbial rhodopsins (MRs) are a large family of photoactive membrane proteins, found in microorganisms belonging to all kingdoms of life, with new members being constantly discovered. Among the MRs are light-driven proton, cation and anion pumps, light-gated cation and anion channels, and various photoreceptors. Due to their abundance and amenability to studies, MRs served as model systems for a great variety of biophysical techniques, and recently found a great application as optogenetic tools. While the basic aspects of microbial rhodopsins functioning have been known for some time, there is still a plenty of unanswered questions. This chapter presents and summarizes the available knowledge, focusing on the functional and structural studies.
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Affiliation(s)
- Ivan Gushchin
- Moscow Institute of Physics and Technology, Dolgoprudniy, Russia.
| | - Valentin Gordeliy
- Moscow Institute of Physics and Technology, Dolgoprudniy, Russia.
- University of Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France.
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, Jülich, Germany.
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13
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Urban A, Golgher L, Brunner C, Gdalyahu A, Har-Gil H, Kain D, Montaldo G, Sironi L, Blinder P. Understanding the neurovascular unit at multiple scales: Advantages and limitations of multi-photon and functional ultrasound imaging. Adv Drug Deliv Rev 2017; 119:73-100. [PMID: 28778714 DOI: 10.1016/j.addr.2017.07.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 07/17/2017] [Accepted: 07/22/2017] [Indexed: 02/07/2023]
Abstract
Developing efficient brain imaging technologies by combining a high spatiotemporal resolution and a large penetration depth is a key step for better understanding the neurovascular interface that emerges as a main pathway to neurodegeneration in many pathologies such as dementia. This review focuses on the advances in two complementary techniques: multi-photon laser scanning microscopy (MPLSM) and functional ultrasound imaging (fUSi). MPLSM has become the gold standard for in vivo imaging of cellular dynamics and morphology, together with cerebral blood flow. fUSi is an innovative imaging modality based on Doppler ultrasound, capable of recording vascular brain activity over large scales (i.e., tens of cubic millimeters) at unprecedented spatial and temporal resolution for such volumes (up to 10μm pixel size at 10kHz). By merging these two technologies, researchers may have access to a more detailed view of the various processes taking place at the neurovascular interface. MPLSM and fUSi are also good candidates for addressing the major challenge of real-time delivery, monitoring, and in vivo evaluation of drugs in neuronal tissue.
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Affiliation(s)
- Alan Urban
- Neuroelectronics Research Flanders, Leuven, Belgium; VIB, Leuven, Belgium and/or IMEC, Leuven, Belgium; Department of Neurosciences, KU Leuven, Leuven, Belgium; Neurobiology Dept., Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Lior Golgher
- Sagol School of Neuroscience, Tel-Aviv University, Tel-Aviv, Israel
| | - Clément Brunner
- Neuroelectronics Research Flanders, Leuven, Belgium; VIB, Leuven, Belgium and/or IMEC, Leuven, Belgium
| | - Amos Gdalyahu
- Neurobiology Dept., Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Hagai Har-Gil
- Sagol School of Neuroscience, Tel-Aviv University, Tel-Aviv, Israel
| | - David Kain
- Neurobiology Dept., Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Gabriel Montaldo
- Neuroelectronics Research Flanders, Leuven, Belgium; VIB, Leuven, Belgium and/or IMEC, Leuven, Belgium
| | - Laura Sironi
- Physics Dept., Universita degli Studi di Milano Bicocca, Italy
| | - Pablo Blinder
- Neurobiology Dept., Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel; Sagol School of Neuroscience, Tel-Aviv University, Tel-Aviv, Israel.
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14
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Xu Y, Zou P, Cohen AE. Voltage imaging with genetically encoded indicators. Curr Opin Chem Biol 2017; 39:1-10. [PMID: 28460291 PMCID: PMC5581692 DOI: 10.1016/j.cbpa.2017.04.005] [Citation(s) in RCA: 114] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 04/03/2017] [Accepted: 04/07/2017] [Indexed: 02/06/2023]
Abstract
Membrane voltages are ubiquitous throughout cell biology. Voltage is most commonly associated with excitable cells such as neurons and cardiomyocytes, although many other cell types and organelles also support electrical signaling. Voltage imaging in vivo would offer unique capabilities in reporting the spatial pattern and temporal dynamics of electrical signaling at the cellular and circuit levels. Voltage is not directly visible, and so a longstanding challenge has been to develop genetically encoded fluorescent voltage indicator proteins. Recent advances have led to a profusion of new voltage indicators, based on different scaffolds and with different tradeoffs between voltage sensitivity, speed, brightness, and spectrum. In this review, we describe recent advances in design and applications of genetically-encoded voltage indicators (GEVIs). We also highlight the protein engineering strategies employed to improve the dynamic range and kinetics of GEVIs and opportunities for future advances.
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Affiliation(s)
- Yongxian Xu
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, PKU-IDG/McGovern Institute for Brain Research, Peking University, Beijing 100871, China
| | - Peng Zou
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, PKU-IDG/McGovern Institute for Brain Research, Peking University, Beijing 100871, China.
| | - Adam E Cohen
- Departments of Chemistry and Chemical Biology and of Physics, Harvard University, Cambridge, MA 02138, USA; Howard Hughes Medical Institute.
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15
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Wen-qi S, Li-wei Q. Synthesis of l -phenylalanine imprinted hydrogels with anti-biofouling capability by using a novel zwitterionic functional monomer. Sep Purif Technol 2017. [DOI: 10.1016/j.seppur.2017.03.055] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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16
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Brinks D, Adam Y, Kheifets S, Cohen AE. Painting with Rainbows: Patterning Light in Space, Time, and Wavelength for Multiphoton Optogenetic Sensing and Control. Acc Chem Res 2016; 49:2518-2526. [PMID: 27786461 DOI: 10.1021/acs.accounts.6b00415] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Photons are a fascinating reagent, flowing and reacting quite differently compared to more massive and less ephemeral particles of matter. The optogenetic palette comprises an ever growing set of light-responsive proteins, which open the possibility of using light to perturb and to measure biological processes with great precision in space and time. Yet there are limits on what light can achieve. Diffraction limits the smallest features, and scattering in tissue limits the largest. Photobleaching, diffusion of photogenerated products, and optical crosstalk between overlapping absorption spectra further muddy the optogenetic picture, particularly when one wants to use multiple optogenetic tools simultaneously. But these obstacles are surmountable. Most light-responsive proteins and small molecules undergo more than one light-driven transition, often with different action spectra and kinetics. By overlapping multiple laser beams, carefully patterned in space, time, and wavelength, one can steer molecules into fluorescent or nonfluorescent, active or inactive conformations. By doing so, one can often circumvent the limitations of simple one-photon excitation and achieve new imaging and stimulation capabilities. These include subdiffraction spatial resolution, optical sectioning, robustness to light scattering, and multiplexing of more channels than can be achieved with simple one-photon excitation. The microbial rhodopsins are a particularly rich substrate for this type of multiphoton optical control. The natural diversity of these proteins presents a huge range of starting materials. The spectroscopy and photocycles of microbial rhodopsins are relatively well understood, providing states with absorption maxima across the visible spectrum, which can be accessed on experimentally convenient time scales. A long history of mutational studies in microbial rhodopsins allows semirational protein engineering. Mutants of Archaerhodopsin 3 (Arch) come in all the colors of the rainbow. In a solution of purified Arch-eGFP, a focused green laser excites eGFP fluorescence throughout the laser path, while a focused red laser excites fluorescence of Arch only near the focus, indicative of multiphoton fluorescence. This nonlinearity occurs at a laser intensity ∼1010-fold lower than in conventional two-photon microscopy! The mutant Arch(D95H) shows photoswitchable optical bistability. In a lawn of E. coli expressing this mutant, illumination with patterned blue light converts the molecule into a state that is fluorescent. Illumination with red light excites this fluorescence, and gradually resets the molecules back to the non-fluorescent state. This review describes the new types of molecular logic that can be implemented with multi-photon control of microbial rhodopsins, from whole-brain activity mapping to measurements of absolute membrane voltage. Part of our goal in this Account is to describe recent work in nonlinear optogenetics, but we also present a variety of interesting things one could do if only the right optogenetic molecules were available. This latter component is intended to inspire future spectroscopic, protein discovery, and protein engineering work.
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Affiliation(s)
- Daan Brinks
- Department
of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Yoav Adam
- Department
of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Simon Kheifets
- Department
of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Adam E. Cohen
- Department
of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
- Department
of Physics, Harvard University, Cambridge, Massachusetts 02138, United States
- Howard
Hughes Medical Institute, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
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17
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Cho YK, Zheng G, Augustine GJ, Hochbaum D, Cohen A, Knöpfel T, Pisanello F, Pavone FS, Vellekoop IM, Booth MJ, Hu S, Zhu J, Chen Z, Hoshi Y. Roadmap on neurophotonics. JOURNAL OF OPTICS (2010) 2016; 18:093007. [PMID: 28386392 PMCID: PMC5378317 DOI: 10.1088/2040-8978/18/9/093007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Mechanistic understanding of how the brain gives rise to complex behavioral and cognitive functions is one of science's grand challenges. The technical challenges that we face as we attempt to gain a systems-level understanding of the brain are manifold. The brain's structural complexity requires us to push the limit of imaging resolution and depth, while being able to cover large areas, resulting in enormous data acquisition and processing needs. Furthermore, it is necessary to detect functional activities and 'map' them onto the structural features. The functional activity occurs at multiple levels, using electrical and chemical signals. Certain electrical signals are only decipherable with sub-millisecond timescale resolution, while other modes of signals occur in minutes to hours. For these reasons, there is a wide consensus that new tools are necessary to undertake this daunting task. Optical techniques, due to their versatile and scalable nature, have great potentials to answer these challenges. Optical microscopy can now image beyond the diffraction limit, record multiple types of brain activity, and trace structural features across large areas of tissue. Genetically encoded molecular tools opened doors to controlling and detecting neural activity using light in specific cell types within the intact brain. Novel sample preparation methods that reduce light scattering have been developed, allowing whole brain imaging in rodent models. Adaptive optical methods have the potential to resolve images from deep brain regions. In this roadmap article, we showcase a few major advances in this area, survey the current challenges, and identify potential future needs that may be used as a guideline for the next steps to be taken.
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Affiliation(s)
- Yong Ku Cho
- Department of Chemical and Biomolecular Engineering, Institute for Systems Genomics, University of Connecticut, 191 Auditorium Rd, Storrs, CT 06269-3222, USA
| | - Guoan Zheng
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT 06269, USA
| | - George J Augustine
- Lee Kong Chian School of Medicine, Nanyang Technological University, 50 Nanyang Drive, Research Techno Plaza, Singapore 637553, Singapore
| | - Daniel Hochbaum
- Departments of Chemistry and Chemical Biology and Physics, Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Adam Cohen
- Departments of Chemistry and Chemical Biology and Physics, Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA; Howard Hughes Medical Institute, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
| | - Thomas Knöpfel
- Division of Brain Sciences, Department of Medicine, Imperial College London, London W12 0NN, UK
| | - Ferruccio Pisanello
- Istituto Italiano di Tecnologia (IIT), Center for Biomolecular Nanotechnologies, Via Barsanti sn, I-73010 Arnesano (Lecce), Italy
| | - Francesco S Pavone
- European Laboratory for Non Linear Spectroscopy, University of Florence, Via N. Carrara 1, I-50019 Sesto Fiorentino (FI), Italy; Department of Physics, University of Florence, Via G. Sansone 1, I-50019 Sesto Fiorentino, Italy; Istituto Nazionale di Ottica, L.go E. fermi 2, I-50100 Firenze, Italy
| | - Ivo M Vellekoop
- Biomedical Photonic Imaging group, MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, PO Box 217, 7500 AE Enschede, The Netherlands
| | - Martin J Booth
- Centre for Neural Circuits and Behaviour, University of Oxford, Mansfield Road, Oxford OX1 3SR, UK; Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, UK
| | - Song Hu
- Department of Biomedical Engineering, University of Virginia, 415 Lane Road, Charlottesville, VA 22908, USA
| | - Jiang Zhu
- Beckman Laser Institute, University of California, Irvine, 1002 Health Sciences Road East, Irvine, CA 92617, USA
| | - Zhongping Chen
- Beckman Laser Institute, University of California, Irvine, 1002 Health Sciences Road East, Irvine, CA 92617, USA
| | - Yoko Hoshi
- Department of Biomedical Optics, Institute for Medical Photonics Research, Preeminent Medical Photonics Education & Research Center, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu 431-3192, Japan
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18
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Heckman LM, Grimm JB, Schreiter ER, Kim C, Verdecia MA, Shields BC, Lavis LD. Design and Synthesis of a Calcium-Sensitive Photocage. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201602941] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Laurel M. Heckman
- Janelia Research Campus; Howard Hughes Medical Institute; 19700 Helix Drive Ashburn VA USA
| | - Jonathan B. Grimm
- Janelia Research Campus; Howard Hughes Medical Institute; 19700 Helix Drive Ashburn VA USA
| | - Eric R. Schreiter
- Janelia Research Campus; Howard Hughes Medical Institute; 19700 Helix Drive Ashburn VA USA
| | - Charles Kim
- Janelia Research Campus; Howard Hughes Medical Institute; 19700 Helix Drive Ashburn VA USA
| | - Mark A. Verdecia
- Janelia Research Campus; Howard Hughes Medical Institute; 19700 Helix Drive Ashburn VA USA
| | - Brenda C. Shields
- Janelia Research Campus; Howard Hughes Medical Institute; 19700 Helix Drive Ashburn VA USA
| | - Luke D. Lavis
- Janelia Research Campus; Howard Hughes Medical Institute; 19700 Helix Drive Ashburn VA USA
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19
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Heckman LM, Grimm JB, Schreiter ER, Kim C, Verdecia MA, Shields BC, Lavis LD. Design and Synthesis of a Calcium-Sensitive Photocage. Angew Chem Int Ed Engl 2016; 55:8363-6. [PMID: 27218487 PMCID: PMC6680284 DOI: 10.1002/anie.201602941] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Indexed: 12/12/2022]
Abstract
Photolabile protecting groups (or "photocages") enable precise spatiotemporal control of chemical functionality and facilitate advanced biological experiments. Extant photocages exhibit a simple input-output relationship, however, where application of light elicits a photochemical reaction irrespective of the environment. Herein, we refine and extend the concept of photolabile groups, synthesizing the first Ca(2+) -sensitive photocage. This system functions as a chemical coincidence detector, releasing small molecules only in the presence of both light and elevated [Ca(2+) ]. Caging a fluorophore with this ion-sensitive moiety yields an "ion integrator" that permanently marks cells undergoing high Ca(2+) flux during an illumination-defined time period. Our general design concept demonstrates a new class of light-sensitive material for cellular imaging, sensing, and targeted molecular delivery.
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Affiliation(s)
- Laurel M Heckman
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA, USA
| | - Jonathan B Grimm
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA, USA
| | - Eric R Schreiter
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA, USA
| | - Charles Kim
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA, USA
| | - Mark A Verdecia
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA, USA
| | - Brenda C Shields
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA, USA
| | - Luke D Lavis
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA, USA.
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20
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Treweek JB, Gradinaru V. Extracting structural and functional features of widely distributed biological circuits with single cell resolution via tissue clearing and delivery vectors. Curr Opin Biotechnol 2016; 40:193-207. [PMID: 27393829 DOI: 10.1016/j.copbio.2016.03.012] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 03/10/2016] [Accepted: 03/15/2016] [Indexed: 12/13/2022]
Abstract
The scientific community has learned a great deal from imaging small and naturally transparent organisms such as nematodes and zebrafish. The consequences of genetic mutations on their organ development and survival can be visualized easily and with high-throughput at the organism-wide scale. In contrast, three-dimensional information is less accessible in mammalian subjects because the heterogeneity of light-scattering tissue elements renders their organs opaque. Likewise, genetically labeling desired circuits across mammalian bodies is prohibitively slow and costly via the transgenic route. Emerging breakthroughs in viral vector engineering, genome editing tools, and tissue clearing can render larger opaque organisms genetically tractable and transparent for whole-organ cell phenotyping, tract tracing and imaging at depth.
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Affiliation(s)
- Jennifer Brooke Treweek
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Viviana Gradinaru
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
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21
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Brinks D, Klein AJ, Cohen AE. Two-Photon Lifetime Imaging of Voltage Indicating Proteins as a Probe of Absolute Membrane Voltage. Biophys J 2016; 109:914-21. [PMID: 26331249 DOI: 10.1016/j.bpj.2015.07.038] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 06/15/2015] [Accepted: 07/28/2015] [Indexed: 01/03/2023] Open
Abstract
Genetically encoded voltage indicators (GEVIs) can report cellular electrophysiology with high resolution in space and time. Two-photon (2P) fluorescence has been explored as a means to image voltage in tissue. Here, we used the 2P electronic excited-state lifetime to probe absolute membrane voltage in a manner that is insensitive to the protein expression level, illumination intensity, or photon detection efficiency. First, we tested several GEVIs for 2P brightness, response speed, and voltage sensitivity. ASAP1 and a previously described citrine-Arch electrochromic Förster resonance energy transfer sensor (dubbed CAESR) showed the best characteristics. We then characterized the voltage-dependent lifetime of ASAP1, CAESR, and ArcLight under voltage-clamp conditions. ASAP1 and CAESR showed voltage-dependent lifetimes, whereas ArcLight did not. These results establish 2P fluorescence lifetime imaging as a viable means of measuring absolute membrane voltage. We discuss the prospects and improvements necessary for applications in tissue.
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Affiliation(s)
- Daan Brinks
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts
| | - Aaron J Klein
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts
| | - Adam E Cohen
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts; Department of Physics, Harvard University, Cambridge, Massachusetts; Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts.
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22
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Mikutis G, Mora CA, Puddu M, Paunescu D, Grass RN, Stark WJ. DNA-Based Sensor Particles Enable Measuring Light Intensity in Single Cells. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2016; 28:2765-2770. [PMID: 26866714 DOI: 10.1002/adma.201504892] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 12/04/2015] [Indexed: 06/05/2023]
Abstract
"Lab on a particle" architecture is employed in designing a light nanosensor. Light-sensitive protecting groups are installed on DNA, which is encapsulated in silica particles, qualifying as a self-sufficient light sensor. The nanosensors allow measuring light intensity and duration in very small volumes, such as single cells, and store the irradiation information until readout.
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Affiliation(s)
- Gediminas Mikutis
- Institute for Chemical and Bioengineering, ETH Zürich, Vladimir-Prelog-Weg 1, 8093, Zürich, Switzerland
| | - Carlos A Mora
- Institute for Chemical and Bioengineering, ETH Zürich, Vladimir-Prelog-Weg 1, 8093, Zürich, Switzerland
| | - Michela Puddu
- Institute for Chemical and Bioengineering, ETH Zürich, Vladimir-Prelog-Weg 1, 8093, Zürich, Switzerland
| | - Daniela Paunescu
- Institute for Chemical and Bioengineering, ETH Zürich, Vladimir-Prelog-Weg 1, 8093, Zürich, Switzerland
| | - Robert N Grass
- Institute for Chemical and Bioengineering, ETH Zürich, Vladimir-Prelog-Weg 1, 8093, Zürich, Switzerland
| | - Wendelin J Stark
- Institute for Chemical and Bioengineering, ETH Zürich, Vladimir-Prelog-Weg 1, 8093, Zürich, Switzerland
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23
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Nadeau JL. Initial photophysical characterization of the proteorhodopsin optical proton sensor (PROPS). Front Neurosci 2015; 9:315. [PMID: 26388725 PMCID: PMC4559597 DOI: 10.3389/fnins.2015.00315] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 08/21/2015] [Indexed: 12/23/2022] Open
Abstract
Fluorescence is not frequently used as a tool for investigating the photocycles of rhodopsins, largely because of the low quantum yield of the retinal chromophore. However, a new class of genetically encoded voltage sensors is based upon rhodopsins and their fluorescence. The first such sensor reported in the literature was the proteorhodopsin optical proton sensor (PROPS), which is capable of indicating membrane voltage changes in bacteria by means of changes in fluorescence. However, the properties of this fluorescence, such as its lifetime decay components and its origin in the protein photocycle, remain unknown. This paper reports steady-state and nanosecond time-resolved emission of this protein expressed in two strains of Escherichia coli, before and after membrane depolarization. The voltage-dependence of a particularly long lifetime component is established. Additional work to improve quantum yields and improve the general utility of PROPS is suggested.
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Affiliation(s)
- Jay L. Nadeau
- Graduate Aerospace Laboratories, California Institute of TechnologyPasadena, CA, USA
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24
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Gong Y. The evolving capabilities of rhodopsin-based genetically encoded voltage indicators. Curr Opin Chem Biol 2015; 27:84-9. [PMID: 26143170 DOI: 10.1016/j.cbpa.2015.05.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Accepted: 05/07/2015] [Indexed: 01/16/2023]
Abstract
Protein engineering over the past four years has made rhodopsin-based genetically encoded voltage indicators a leading candidate to achieve the task of reporting action potentials from a population of genetically targeted neurons in vivo. Rational design and large-scale screening efforts have steadily improved the dynamic range and kinetics of the rhodopsin voltage-sensing domain, and coupling these rhodopsins to bright fluorescent proteins has supported bright fluorescence readout of the large and rapid rhodopsin voltage response. The rhodopsin-fluorescent protein fusions have the highest achieved signal-to-noise ratios for detecting action potentials in neuronal cultures to date, and have successfully reported single spike events in vivo. Given the rapid pace of current development, the genetically encoded voltage indicator class is nearing the goal of robust spike imaging during live-animal behavioral experiments.
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Affiliation(s)
- Yiyang Gong
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, United States.
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25
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Venkatachalam V, Cohen AE. Imaging GFP-based reporters in neurons with multiwavelength optogenetic control. Biophys J 2015; 107:1554-63. [PMID: 25296307 DOI: 10.1016/j.bpj.2014.08.020] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 08/02/2014] [Accepted: 08/07/2014] [Indexed: 12/20/2022] Open
Abstract
To study the impact of neural activity on cellular physiology, one would like to combine precise control of firing patterns with highly sensitive probes of cellular physiology. Light-gated ion channels, e.g., Channelrhodopsin-2, enable precise control of firing patterns; green fluorescent protein-based reporters, e.g., the GCaMP6f Ca(2+) reporter, enable highly sensitive probing of cellular physiology. However, for most actuator-reporter combinations, spectral overlap prevents straightforward combination within a single cell. Here we explore multiwavelength control of channelrhodopsins to circumvent this limitation. The "stoplight" technique described in this article uses channelrhodopsin variants that are opened by blue light and closed by orange light. Cells are illuminated with constant blue light to excite fluorescence of a green fluorescent protein-based reporter. Modulated illumination with orange light negatively regulates activation of the channelrhodopsin. We performed detailed photophysical characterization and kinetic modeling of four candidate stoplight channelrhodopsins. The variant with the highest contrast, sdChR(C138S,E154A), enabled all-optical measurements of activity-induced calcium transients in cultured rat hippocampal neurons, although cell-to-cell variation in expression levels presents a challenge for quantification.
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Affiliation(s)
- Veena Venkatachalam
- Biophysics Program, Harvard Stem Cell Institute, Harvard University, Cambridge, Massachusetts
| | - Adam E Cohen
- Departments of Chemistry and Chemical Biology and Physics, Harvard Stem Cell Institute, Harvard University, Cambridge, Massachusetts; Howard Hughes Medical Institute, Chevy Chase, Maryland.
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26
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Qian L, Hu X, Guan P, Wang D, Li J, Du C, Song R. An effective way to imprint protein with the preservation of template structure by using a macromolecule as the functional monomer. RSC Adv 2015. [DOI: 10.1039/c5ra08246c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
A novel strategy of using a macromolecular functional monomer to stabilize and imprint protein was proposed for the first time.
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Affiliation(s)
- Liwei Qian
- School of Natural and Applied Science
- Northwestern Polytechnical University
- Xi'an 710072
- China
| | - Xiaoling Hu
- School of Natural and Applied Science
- Northwestern Polytechnical University
- Xi'an 710072
- China
| | - Ping Guan
- School of Natural and Applied Science
- Northwestern Polytechnical University
- Xi'an 710072
- China
| | - Dan Wang
- School of Natural and Applied Science
- Northwestern Polytechnical University
- Xi'an 710072
- China
| | - Ji Li
- School of Natural and Applied Science
- Northwestern Polytechnical University
- Xi'an 710072
- China
| | - Chunbao Du
- School of Natural and Applied Science
- Northwestern Polytechnical University
- Xi'an 710072
- China
| | - Renyuan Song
- School of Natural and Applied Science
- Northwestern Polytechnical University
- Xi'an 710072
- China
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27
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Abstract
The new GWAS from the Schizophrenia Working Group of the Psychiatric Genomics Consortium (2014) clearly validates a genetic approach to understanding schizophrenia. The challenge now remains to track down the contributing genes and to develop appropriate models to elucidate the biological effects of the contributing variants.
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Affiliation(s)
- Anna C Need
- Division of Brain Sciences, Department of Medicine, Imperial College London, London, UK.
| | - David B Goldstein
- Center for Human Genome Variation, Duke University Medical School, Durham, NC 27708, USA.
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28
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One gene, many neuropsychiatric disorders: lessons from Mendelian diseases. Nat Neurosci 2014; 17:773-81. [PMID: 24866043 DOI: 10.1038/nn.3713] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 03/31/2014] [Indexed: 12/14/2022]
Abstract
Recent human genetic studies have consistently shown that mutations in the same gene or same genomic region can increase the risk of a broad range of complex neuropsychiatric disorders. Despite the steadily increasing number of examples of such nonspecific effects on risk, the underlying biological causes remain mysterious. Here we investigate the phenomenon of such nonspecific risk by identifying Mendelian disease genes that are associated with multiple diseases and explore what is known about the underlying mechanisms in these more 'simple' examples. Our analyses make clear that there are a variety of mechanisms at work, emphasizing how challenging it will be to elucidate the causes of nonspecific risk in complex disease. Ultimately, we conclude that functional approaches will be critical for explaining the causes of nonspecific risk factors discovered by human genetic studies of neuropsychiatric disorders.
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29
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Abstract
Any bilayer lipid membrane can support a membrane voltage. The combination of optical perturbation and optical readout of membrane voltage opens the door to studies of electrophysiology in a huge variety of systems previously inaccessible to electrode-based measurements. Yet, the application of optogenetic electrophysiology requires careful reconsideration of the fundamentals of bioelectricity. Rules of thumb appropriate for neuroscience and cardiology may not apply in systems with dramatically different sizes, lipid compositions, charge carriers, or protein machinery. Optogenetic tools are not electrodes; thus, optical and electrode-based measurements have different quirks. Here we review the fundamental aspects of bioelectricity with the aim of laying a conceptual framework for all-optical electrophysiology.
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Affiliation(s)
- Adam E Cohen
- Department of Chemistry and Chemical Biology and
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30
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Pederson T. Repeated TALEs: visualizing DNA sequence localization and chromosome dynamics in live cells. Nucleus 2014; 5:28-31. [PMID: 24637394 PMCID: PMC4028351 DOI: 10.4161/nucl.28143] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Three recent papers, published just weeks apart, describe the use of fluorescent TALEs to tag specific DNA sequences in live cells and, in one case, also in fixed cells, the latter with potential clinical applications.
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Affiliation(s)
- Thoru Pederson
- Program in Cell and Developmental Dynamics; Department of Biochemistry and Molecular Pharmacology; University of Massachusetts Medical School; Worcester, MA USA
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