1
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Chacko AN, Miller ADC, Dhanabalan KM, Mukherjee A. Exploring the potential of water channels for developing genetically encoded reporters and biosensors for diffusion-weighted MRI. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2024; 365:107743. [PMID: 39053029 DOI: 10.1016/j.jmr.2024.107743] [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: 12/30/2023] [Revised: 07/02/2024] [Accepted: 07/17/2024] [Indexed: 07/27/2024]
Abstract
Genetically encoded reporters for magnetic resonance imaging (MRI) offer a valuable technology for making molecular-scale measurements of biological processes within living organisms with high anatomical resolution and whole-organ coverage without relying on ionizing radiation. However, most MRI reporters rely on synthetic contrast agents, typically paramagnetic metals and metal complexes, which often need to be supplemented exogenously to create optimal contrast. To eliminate the need for synthetic contrast agents, we previously introduced aquaporin-1, a mammalian water channel, as a new reporter gene for the fully autonomous detection of genetically labeled cells using diffusion-weighted MRI. In this study, we aimed to expand the toolbox of diffusion-based genetic reporters by modulating aquaporin membrane trafficking and harnessing the evolutionary diversity of water channels across species. We identified a number of new water channels that functioned as diffusion-weighted reporter genes. In addition, we show that loss-of-function variants of yeast and human aquaporins can be leveraged to design first-in-class diffusion-based sensors for detecting the activity of a model protease within living cells.
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Affiliation(s)
- Asish N Chacko
- Department of Chemistry, University of California, Santa Barbara, CA 93106-5080, USA
| | - Austin D C Miller
- Biomolecular Science and Engineering Graduate Program, University of California, Santa Barbara, CA 93106-5080, USA
| | - Kaamini M Dhanabalan
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106-5080, USA
| | - Arnab Mukherjee
- Department of Chemistry, University of California, Santa Barbara, CA 93106-5080, USA; Biomolecular Science and Engineering Graduate Program, University of California, Santa Barbara, CA 93106-5080, USA; Department of Chemical Engineering, University of California, Santa Barbara, CA 93106-5080, USA; Department of Bioengineering, University of California, Santa Barbara, CA 93106-5080, USA.
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2
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Chacko AN, Miller AD, Dhanabalan KM, Mukherjee A. Exploring the potential of water channels for developing MRI reporters and sensors without the need for exogenous contrast agents. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.21.576580. [PMID: 38328035 PMCID: PMC10849501 DOI: 10.1101/2024.01.21.576580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Genetically encoded reporters for magnetic resonance imaging (MRI) offer a valuable technology for making molecular-scale measurements of biological processes within living organisms with high anatomical resolution and whole-organ coverage without relying on ionizing radiation. However, most MRI reporters rely on contrast agents, typically paramagnetic metals and metal complexes, which often need to be supplemented exogenously to create optimal contrast. To eliminate the need for contrast agents, we previously introduced aquaporin-1, a mammalian water channel, as a new reporter gene for the fully autonomous detection of genetically labeled cells using diffusion-weighted MRI. In this study, we aimed to expand the toolbox of diffusion-based genetic reporters by modulating aquaporin membrane trafficking and harnessing the evolutionary diversity of water channels across species. We identified a number of new water channels that functioned as diffusion-weighted reporter genes. In addition, we show that loss-of-function variants of yeast and human aquaporins can be leveraged to design first-in-class diffusion-based sensors for detecting the activity of a model protease within living cells.
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Affiliation(s)
| | | | | | - Arnab Mukherjee
- Department of Chemistry
- Biomolecular Science and Engineering Graduate Program
- Department of Chemical Engineering
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3
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Evans SW, Shi DQ, Chavarha M, Plitt MH, Taxidis J, Madruga B, Fan JL, Hwang FJ, van Keulen SC, Suomivuori CM, Pang MM, Su S, Lee S, Hao YA, Zhang G, Jiang D, Pradhan L, Roth RH, Liu Y, Dorian CC, Reese AL, Negrean A, Losonczy A, Makinson CD, Wang S, Clandinin TR, Dror RO, Ding JB, Ji N, Golshani P, Giocomo LM, Bi GQ, Lin MZ. A positively tuned voltage indicator for extended electrical recordings in the brain. Nat Methods 2023; 20:1104-1113. [PMID: 37429962 PMCID: PMC10627146 DOI: 10.1038/s41592-023-01913-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 05/15/2023] [Indexed: 07/12/2023]
Abstract
Genetically encoded voltage indicators (GEVIs) enable optical recording of electrical signals in the brain, providing subthreshold sensitivity and temporal resolution not possible with calcium indicators. However, one- and two-photon voltage imaging over prolonged periods with the same GEVI has not yet been demonstrated. Here, we report engineering of ASAP family GEVIs to enhance photostability by inversion of the fluorescence-voltage relationship. Two of the resulting GEVIs, ASAP4b and ASAP4e, respond to 100-mV depolarizations with ≥180% fluorescence increases, compared with the 50% fluorescence decrease of the parental ASAP3. With standard microscopy equipment, ASAP4e enables single-trial detection of spikes in mice over the course of minutes. Unlike GEVIs previously used for one-photon voltage recordings, ASAP4b and ASAP4e also perform well under two-photon illumination. By imaging voltage and calcium simultaneously, we show that ASAP4b and ASAP4e can identify place cells and detect voltage spikes with better temporal resolution than commonly used calcium indicators. Thus, ASAP4b and ASAP4e extend the capabilities of voltage imaging to standard one- and two-photon microscopes while improving the duration of voltage recordings.
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Affiliation(s)
- S Wenceslao Evans
- Department of Neurobiology, Stanford University Medical Center, Stanford, CA, USA
| | - Dong-Qing Shi
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Mariya Chavarha
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Mark H Plitt
- Department of Neurobiology, Stanford University Medical Center, Stanford, CA, USA
| | - Jiannis Taxidis
- Department of Neurology, UCLA David Geffen School of Medicine, Los Angeles, CA, USA
- Program in Neurosciences & Mental Health, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada
- Program in Neurosciences & Mental Health, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada
| | - Blake Madruga
- Department of Neurology, UCLA David Geffen School of Medicine, Los Angeles, CA, USA
| | - Jiang Lan Fan
- UC Berkeley/UCSF Joint Program in Bioengineering, University of California Berkeley, Berkeley, CA, USA
| | - Fuu-Jiun Hwang
- Department of Neurosurgery, Stanford University Medical Center, Stanford, CA, USA
| | - Siri C van Keulen
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | | | - Michelle M Pang
- Department of Neurobiology, Stanford University Medical Center, Stanford, CA, USA
| | - Sharon Su
- Department of Neurobiology, Stanford University Medical Center, Stanford, CA, USA
| | - Sungmoo Lee
- Department of Neurobiology, Stanford University Medical Center, Stanford, CA, USA
| | - Yukun A Hao
- Department of Neurobiology, Stanford University Medical Center, Stanford, CA, USA
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Guofeng Zhang
- Department of Neurobiology, Stanford University Medical Center, Stanford, CA, USA
| | - Dongyun Jiang
- Department of Neurobiology, Stanford University Medical Center, Stanford, CA, USA
| | - Lagnajeet Pradhan
- Department of Neurobiology, Stanford University Medical Center, Stanford, CA, USA
| | - Richard H Roth
- Department of Neurosurgery, Stanford University Medical Center, Stanford, CA, USA
| | - Yu Liu
- Department of Neurosurgery, Stanford University Medical Center, Stanford, CA, USA
- Department of Ophthalmology, Stanford University Medical Center, Stanford, CA, USA
| | - Conor C Dorian
- Department of Neurology, UCLA David Geffen School of Medicine, Los Angeles, CA, USA
| | - Austin L Reese
- Institute for Genomic Medicine, Columbia University, New York, NY, USA
| | - Adrian Negrean
- Department of Neuroscience, Columbia University, New York, NY, USA
| | - Attila Losonczy
- Department of Neuroscience, Columbia University, New York, NY, USA
- Mortimer B. Zuckerman Mind Brain Behavior Institute, New York, NY, USA
- Kavli Institute for Brain Science, New York, NY, USA
| | - Christopher D Makinson
- Institute for Genomic Medicine, Columbia University, New York, NY, USA
- Department of Neurology, Columbia University, New York, NY, USA
| | - Sui Wang
- Department of Ophthalmology, Stanford University Medical Center, Stanford, CA, USA
| | - Thomas R Clandinin
- Department of Neurobiology, Stanford University Medical Center, Stanford, CA, USA
| | - Ron O Dror
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, USA
| | - Jun B Ding
- Department of Neurosurgery, Stanford University Medical Center, Stanford, CA, USA
- Department of Neurology and Neurological Sciences, Stanford University Medical Center, Stanford, CA, USA
| | - Na Ji
- Program in Neurosciences & Mental Health, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
- Department of Physics, University of California Berkeley, Berkeley, CA, USA
- Helen Wills Neuroscience Institute, University of California Berkeley, Berkeley, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Peyman Golshani
- Department of Neurology, UCLA David Geffen School of Medicine, Los Angeles, CA, USA
- Semel Institute for Neuroscience and Human Behavior, UCLA David Geffen School of Medicine, Los Angeles, CA, USA
| | - Lisa M Giocomo
- Department of Neurobiology, Stanford University Medical Center, Stanford, CA, USA
| | - Guo-Qiang Bi
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Interdisciplinary Center for Brain Information, Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Michael Z Lin
- Department of Neurobiology, Stanford University Medical Center, Stanford, CA, USA.
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
- Department of Chemical and Systems Biology, Stanford University, Stanford, USA.
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4
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Platisa J, Ye X, Ahrens AM, Liu C, Chen IA, Davison IG, Tian L, Pieribone VA, Chen JL. High-speed low-light in vivo two-photon voltage imaging of large neuronal populations. Nat Methods 2023; 20:1095-1103. [PMID: 36973547 PMCID: PMC10894646 DOI: 10.1038/s41592-023-01820-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 02/16/2023] [Indexed: 03/29/2023]
Abstract
Monitoring spiking activity across large neuronal populations at behaviorally relevant timescales is critical for understanding neural circuit function. Unlike calcium imaging, voltage imaging requires kilohertz sampling rates that reduce fluorescence detection to near shot-noise levels. High-photon flux excitation can overcome photon-limited shot noise, but photobleaching and photodamage restrict the number and duration of simultaneously imaged neurons. We investigated an alternative approach aimed at low two-photon flux, which is voltage imaging below the shot-noise limit. This framework involved developing positive-going voltage indicators with improved spike detection (SpikeyGi and SpikeyGi2); a two-photon microscope ('SMURF') for kilohertz frame rate imaging across a 0.4 mm × 0.4 mm field of view; and a self-supervised denoising algorithm (DeepVID) for inferring fluorescence from shot-noise-limited signals. Through these combined advances, we achieved simultaneous high-speed deep-tissue imaging of more than 100 densely labeled neurons over 1 hour in awake behaving mice. This demonstrates a scalable approach for voltage imaging across increasing neuronal populations.
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Affiliation(s)
- Jelena Platisa
- Department of Cellular and Molecular Physiology, Yale University, New Haven, CT, USA
- The John B. Pierce Laboratory, New Haven, CT, USA
| | - Xin Ye
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
- Neurophotonics Center, Boston University, Boston, MA, USA
| | | | - Chang Liu
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | | | - Ian G Davison
- Neurophotonics Center, Boston University, Boston, MA, USA
- Department of Biology, Boston University, Boston, MA, USA
- Center for Systems Neuroscience, Boston University, Boston, MA, USA
| | - Lei Tian
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
- Neurophotonics Center, Boston University, Boston, MA, USA
- Department of Electrical and Computer Engineering, Boston University, Boston, MA, USA
| | - Vincent A Pieribone
- Department of Cellular and Molecular Physiology, Yale University, New Haven, CT, USA.
- The John B. Pierce Laboratory, New Haven, CT, USA.
- Department of Neuroscience, Yale University, New Haven, CT, USA.
| | - Jerry L Chen
- Department of Biomedical Engineering, Boston University, Boston, MA, USA.
- Neurophotonics Center, Boston University, Boston, MA, USA.
- Department of Biology, Boston University, Boston, MA, USA.
- Center for Systems Neuroscience, Boston University, Boston, MA, USA.
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5
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Weinstein JY, Martí-Gómez C, Lipsh-Sokolik R, Hoch SY, Liebermann D, Nevo R, Weissman H, Petrovich-Kopitman E, Margulies D, Ivankov D, McCandlish DM, Fleishman SJ. Designed active-site library reveals thousands of functional GFP variants. Nat Commun 2023; 14:2890. [PMID: 37210560 DOI: 10.1038/s41467-023-38099-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 04/13/2023] [Indexed: 05/22/2023] Open
Abstract
Mutations in a protein active site can lead to dramatic and useful changes in protein activity. The active site, however, is sensitive to mutations due to a high density of molecular interactions, substantially reducing the likelihood of obtaining functional multipoint mutants. We introduce an atomistic and machine-learning-based approach, called high-throughput Functional Libraries (htFuncLib), that designs a sequence space in which mutations form low-energy combinations that mitigate the risk of incompatible interactions. We apply htFuncLib to the GFP chromophore-binding pocket, and, using fluorescence readout, recover >16,000 unique designs encoding as many as eight active-site mutations. Many designs exhibit substantial and useful diversity in functional thermostability (up to 96 °C), fluorescence lifetime, and quantum yield. By eliminating incompatible active-site mutations, htFuncLib generates a large diversity of functional sequences. We envision that htFuncLib will be used in one-shot optimization of activity in enzymes, binders, and other proteins.
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Affiliation(s)
| | - Carlos Martí-Gómez
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Rosalie Lipsh-Sokolik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Shlomo Yakir Hoch
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Demian Liebermann
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Reinat Nevo
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Haim Weissman
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | | | - David Margulies
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Dmitry Ivankov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - David M McCandlish
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Sarel J Fleishman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel.
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6
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Silic MR, Zhang G. Bioelectricity in Developmental Patterning and Size Control: Evidence and Genetically Encoded Tools in the Zebrafish Model. Cells 2023; 12:cells12081148. [PMID: 37190057 DOI: 10.3390/cells12081148] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 04/03/2023] [Accepted: 04/10/2023] [Indexed: 05/17/2023] Open
Abstract
Developmental patterning is essential for regulating cellular events such as axial patterning, segmentation, tissue formation, and organ size determination during embryogenesis. Understanding the patterning mechanisms remains a central challenge and fundamental interest in developmental biology. Ion-channel-regulated bioelectric signals have emerged as a player of the patterning mechanism, which may interact with morphogens. Evidence from multiple model organisms reveals the roles of bioelectricity in embryonic development, regeneration, and cancers. The Zebrafish model is the second most used vertebrate model, next to the mouse model. The zebrafish model has great potential for elucidating the functions of bioelectricity due to many advantages such as external development, transparent early embryogenesis, and tractable genetics. Here, we review genetic evidence from zebrafish mutants with fin-size and pigment changes related to ion channels and bioelectricity. In addition, we review the cell membrane voltage reporting and chemogenetic tools that have already been used or have great potential to be implemented in zebrafish models. Finally, new perspectives and opportunities for bioelectricity research with zebrafish are discussed.
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Affiliation(s)
- Martin R Silic
- Department of Comparative Pathobiology, Purdue University, West Lafayette, IN 47907, USA
| | - GuangJun Zhang
- Department of Comparative Pathobiology, Purdue University, West Lafayette, IN 47907, USA
- Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
- Purdue Institute for Inflammation, Immunology and Infectious Diseases (PI4D), Purdue University, West Lafayette, IN 47907, USA
- Purdue Institute for Integrative Neuroscience, Purdue University, 625 Harrison Street, West Lafayette, IN 47907, USA
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7
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Jeyarajan S, Zhang IX, Arvan P, Lentz SI, Satin LS. Simultaneous Measurement of Changes in Mitochondrial and Endoplasmic Reticulum Free Calcium in Pancreatic Beta Cells. BIOSENSORS 2023; 13:382. [PMID: 36979594 PMCID: PMC10046164 DOI: 10.3390/bios13030382] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 02/28/2023] [Accepted: 03/08/2023] [Indexed: 05/28/2023]
Abstract
The free calcium (Ca2+) levels in pancreatic beta cell organelles have been the subject of many recent investigations. Under pathophysiological conditions, disturbances in these pools have been linked to altered intracellular communication and cellular dysfunction. To facilitate studies of subcellular Ca2+ signaling in beta cells and, particularly, signaling between the endoplasmic reticulum (ER) and mitochondria, we designed a novel dual Ca2+ sensor which we termed DS-1. DS-1 encodes two stoichiometrically fluorescent proteins within a single plasmid, G-CEPIA-er, targeted to the ER and R-CEPIA3-mt, targeted to mitochondria. Our goal was to simultaneously measure the ER and mitochondrial Ca2+ in cells in real time. The Kds of G-CEPIA-er and R-CEPIA3-mt for Ca2+ are 672 and 3.7 μM, respectively. Confocal imaging of insulin-secreting INS-1 832/13 expressing DS-1 confirmed that the green and red fluorophores correctly colocalized with organelle-specific fluorescent markers as predicted. Further, we tested whether DS-1 exhibited the functional properties expected by challenging an INS-1 cell to glucose concentrations or drugs having well-documented effects on the ER and mitochondrial Ca2+ handling. The data obtained were consistent with those seen using other single organelle targeted probes. These results taken together suggest that DS-1 is a promising new approach for investigating Ca2+ signaling within multiple organelles of the cell.
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Affiliation(s)
- Sivakumar Jeyarajan
- Department of Pharmacology, University of Michigan Medical School, Ann Arbor, MI 48105, USA; (S.J.)
| | - Irina X Zhang
- Department of Pharmacology, University of Michigan Medical School, Ann Arbor, MI 48105, USA; (S.J.)
| | - Peter Arvan
- Department of Internal Medicine, Division of Metabolism, Endocrinology & Diabetes, University of Michigan Medical School, Ann Arbor, MI 48105, USA
- Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48105, USA
| | - Stephen I. Lentz
- Department of Internal Medicine, Division of Metabolism, Endocrinology & Diabetes, University of Michigan Medical School, Ann Arbor, MI 48105, USA
| | - Leslie S. Satin
- Department of Pharmacology, University of Michigan Medical School, Ann Arbor, MI 48105, USA; (S.J.)
- Department of Internal Medicine, Division of Metabolism, Endocrinology & Diabetes, University of Michigan Medical School, Ann Arbor, MI 48105, USA
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8
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Kannan M, Vasan G, Haziza S, Huang C, Chrapkiewicz R, Luo J, Cardin JA, Schnitzer MJ, Pieribone VA. Dual-polarity voltage imaging of the concurrent dynamics of multiple neuron types. Science 2022; 378:eabm8797. [PMID: 36378956 PMCID: PMC9703638 DOI: 10.1126/science.abm8797] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Genetically encoded fluorescent voltage indicators are ideally suited to reveal the millisecond-scale interactions among and between targeted cell populations. However, current indicators lack the requisite sensitivity for in vivo multipopulation imaging. We describe next-generation green and red voltage sensors, Ace-mNeon2 and VARNAM2, and their reverse response-polarity variants pAce and pAceR. Our indicators enable 0.4- to 1-kilohertz voltage recordings from >50 spiking neurons per field of view in awake mice and ~30-minute continuous imaging in flies. Using dual-polarity multiplexed imaging, we uncovered brain state–dependent antagonism between neocortical somatostatin-expressing (SST
+
) and vasoactive intestinal peptide–expressing (VIP
+
) interneurons and contributions to hippocampal field potentials from cell ensembles with distinct axonal projections. By combining three mutually compatible indicators, we performed simultaneous triple-population imaging. These approaches will empower investigations of the dynamic interplay between neuronal subclasses at single-spike resolution.
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Affiliation(s)
- Madhuvanthi Kannan
- The John B. Pierce Laboratory, New Haven, CT 06519, USA
- Department of Cellular and Molecular Physiology, Yale University, New Haven, CT 06520, USA
| | - Ganesh Vasan
- The John B. Pierce Laboratory, New Haven, CT 06519, USA
- Department of Cellular and Molecular Physiology, Yale University, New Haven, CT 06520, USA
| | - Simon Haziza
- James H. Clark Center, Stanford University, Stanford, CA 94305, USA
- CNC Program, Stanford University, Stanford, CA 94305, USA
| | - Cheng Huang
- James H. Clark Center, Stanford University, Stanford, CA 94305, USA
| | - Radosław Chrapkiewicz
- James H. Clark Center, Stanford University, Stanford, CA 94305, USA
- CNC Program, Stanford University, Stanford, CA 94305, USA
| | - Junjie Luo
- James H. Clark Center, Stanford University, Stanford, CA 94305, USA
- CNC Program, Stanford University, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Jessica A. Cardin
- Department of Neuroscience, Yale University, New Haven, CT 06520, USA
- Kavli Institute of Neuroscience, Yale University, New Haven, CT 06520, USA
- Wu Tsai Institute, Yale University, New Haven, CT 06520, USA
| | - Mark J. Schnitzer
- James H. Clark Center, Stanford University, Stanford, CA 94305, USA
- CNC Program, Stanford University, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Vincent A. Pieribone
- The John B. Pierce Laboratory, New Haven, CT 06519, USA
- Department of Cellular and Molecular Physiology, Yale University, New Haven, CT 06520, USA
- Department of Neuroscience, Yale University, New Haven, CT 06520, USA
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9
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Wide-Field Calcium Imaging of Neuronal Network Dynamics In Vivo. BIOLOGY 2022; 11:biology11111601. [PMID: 36358302 PMCID: PMC9687960 DOI: 10.3390/biology11111601] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/28/2022] [Accepted: 10/31/2022] [Indexed: 11/06/2022]
Abstract
A central tenet of neuroscience is that sensory, motor, and cognitive behaviors are generated by the communications and interactions among neurons, distributed within and across anatomically and functionally distinct brain regions. Therefore, to decipher how the brain plans, learns, and executes behaviors requires characterizing neuronal activity at multiple spatial and temporal scales. This includes simultaneously recording neuronal dynamics at the mesoscale level to understand the interactions among brain regions during different behavioral and brain states. Wide-field Ca2+ imaging, which uses single photon excitation and improved genetically encoded Ca2+ indicators, allows for simultaneous recordings of large brain areas and is proving to be a powerful tool to study neuronal activity at the mesoscopic scale in behaving animals. This review details the techniques used for wide-field Ca2+ imaging and the various approaches employed for the analyses of the rich neuronal-behavioral data sets obtained. Also discussed is how wide-field Ca2+ imaging is providing novel insights into both normal and altered neural processing in disease. Finally, we examine the limitations of the approach and new developments in wide-field Ca2+ imaging that are bringing new capabilities to this important technique for investigating large-scale neuronal dynamics.
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10
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Liu Z, Lu X, Villette V, Gou Y, Colbert KL, Lai S, Guan S, Land MA, Lee J, Assefa T, Zollinger DR, Korympidou MM, Vlasits AL, Pang MM, Su S, Cai C, Froudarakis E, Zhou N, Patel SS, Smith CL, Ayon A, Bizouard P, Bradley J, Franke K, Clandinin TR, Giovannucci A, Tolias AS, Reimer J, Dieudonné S, St-Pierre F. Sustained deep-tissue voltage recording using a fast indicator evolved for two-photon microscopy. Cell 2022; 185:3408-3425.e29. [PMID: 35985322 PMCID: PMC9563101 DOI: 10.1016/j.cell.2022.07.013] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 04/13/2022] [Accepted: 07/18/2022] [Indexed: 11/23/2022]
Abstract
Genetically encoded voltage indicators are emerging tools for monitoring voltage dynamics with cell-type specificity. However, current indicators enable a narrow range of applications due to poor performance under two-photon microscopy, a method of choice for deep-tissue recording. To improve indicators, we developed a multiparameter high-throughput platform to optimize voltage indicators for two-photon microscopy. Using this system, we identified JEDI-2P, an indicator that is faster, brighter, and more sensitive and photostable than its predecessors. We demonstrate that JEDI-2P can report light-evoked responses in axonal termini of Drosophila interneurons and the dendrites and somata of amacrine cells of isolated mouse retina. JEDI-2P can also optically record the voltage dynamics of individual cortical neurons in awake behaving mice for more than 30 min using both resonant-scanning and ULoVE random-access microscopy. Finally, ULoVE recording of JEDI-2P can robustly detect spikes at depths exceeding 400 μm and report voltage correlations in pairs of neurons.
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Affiliation(s)
- Zhuohe Liu
- Department of Electrical and Computer Engineering, Rice University, Houston, TX 77005, USA
| | - Xiaoyu Lu
- Systems, Synthetic, and Physical Biology Program, Rice University, Houston, TX 77005, USA
| | - Vincent Villette
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Research University, Paris 75005, France
| | - Yueyang Gou
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kevin L Colbert
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shujuan Lai
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sihui Guan
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Michelle A Land
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jihwan Lee
- Systems, Synthetic, and Physical Biology Program, Rice University, Houston, TX 77005, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Tensae Assefa
- Department of Bioengineering, Rice University, Houston, TX 77005, USA
| | - Daniel R Zollinger
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Maria M Korympidou
- Institute for Ophthalmic Research, University of Tübingen, Tübingen, Baden-Württemberg 72076, Germany; Center for Integrative Neuroscience, University of Tübingen, Tübingen, Baden-Württemberg 72076, Germany; Bernstein Center for Computational Neuroscience, University of Tübingen, Tübingen, Baden-Württemberg, 72076, Germany
| | - Anna L Vlasits
- Institute for Ophthalmic Research, University of Tübingen, Tübingen, Baden-Württemberg 72076, Germany; Center for Integrative Neuroscience, University of Tübingen, Tübingen, Baden-Württemberg 72076, Germany
| | - Michelle M Pang
- Department of Neurobiology, Stanford University, Stanford, CA 94305, USA
| | - Sharon Su
- Department of Neurobiology, Stanford University, Stanford, CA 94305, USA
| | - Changjia Cai
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, NC 27599, USA
| | - Emmanouil Froudarakis
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, Heraklion 70013, Greece
| | - Na Zhou
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Saumil S Patel
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Cameron L Smith
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Center for Neuroscience and Artificial Intelligence, Baylor College of Medicine, Houston, TX 77030, USA
| | - Annick Ayon
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Research University, Paris 75005, France
| | - Pierre Bizouard
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Research University, Paris 75005, France
| | - Jonathan Bradley
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Research University, Paris 75005, France
| | - Katrin Franke
- Institute for Ophthalmic Research, University of Tübingen, Tübingen, Baden-Württemberg 72076, Germany; Center for Integrative Neuroscience, University of Tübingen, Tübingen, Baden-Württemberg 72076, Germany; Bernstein Center for Computational Neuroscience, University of Tübingen, Tübingen, Baden-Württemberg, 72076, Germany
| | - Thomas R Clandinin
- Department of Neurobiology, Stanford University, Stanford, CA 94305, USA
| | - Andrea Giovannucci
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, NC 27599, USA; UNC Neuroscience Center, Chapel Hill, NC 27599, USA
| | - Andreas S Tolias
- Department of Electrical and Computer Engineering, Rice University, Houston, TX 77005, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Center for Neuroscience and Artificial Intelligence, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jacob Reimer
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Center for Neuroscience and Artificial Intelligence, Baylor College of Medicine, Houston, TX 77030, USA
| | - Stéphane Dieudonné
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Research University, Paris 75005, France
| | - François St-Pierre
- Department of Electrical and Computer Engineering, Rice University, Houston, TX 77005, USA; Systems, Synthetic, and Physical Biology Program, Rice University, Houston, TX 77005, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA.
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11
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Lee S, Kang BE, Song YK, Baker BJ. A trafficking motif alters GEVI activity implicating persistent protein interactions at the membrane. BIOPHYSICAL REPORTS 2022; 2:100047. [PMID: 36425771 PMCID: PMC9680705 DOI: 10.1016/j.bpr.2022.100047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 02/18/2022] [Indexed: 11/30/2022]
Abstract
Efficient plasma-membrane expression is critical for genetically encoded voltage indicators (GEVIs). To improve the plasma-membrane expression, we introduced multiple combinations of plasma-membrane trafficking motifs at different positions to members of the Bongwoori family of GEVIs. An improvement from 20% to 27% in the ΔF/F/100 mV depolarization of the plasma membrane was observed when a Golgi transport motif was inserted near the N-terminus in conjunction with an endoplasmic reticulum release motif near the C-terminus of the protein. Unfortunately, this variant was also slower. The weighted tau on of the variant (25 ms) was more than double the original construct (11 ms). The weighted tau off was >20 ms compared with 10 ms for the original GEVI. The voltage range of the GEVI was also shifted to more negative potentials. Insertion of spacer amino acids between the fluorescent-protein domain and the endoplasmic reticulum release motif at the C-terminus rescued the speed of both the tau on and tau off while restoring the voltage range and maintaining the improved voltage-dependent optical signal. These results suggest that while trafficking motifs do improve plasma-membrane expression, they may also mediate persistent associations that affect the functioning of the protein.
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12
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Voltage imaging in the olfactory bulb using transgenic mouse lines expressing the genetically encoded voltage indicator ArcLight. Sci Rep 2022; 12:1875. [PMID: 35115567 PMCID: PMC8813909 DOI: 10.1038/s41598-021-04482-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 12/09/2021] [Indexed: 01/06/2023] Open
Abstract
Genetically encoded voltage indicators (GEVIs) allow optical recordings of membrane potential changes in defined cell populations. Transgenic reporter animals that facilitate precise and repeatable targeting with high expression levels would further the use of GEVIs in the in vivo mammalian brain. However, the literature on developing and applying transgenic mouse lines as vehicles for GEVI expression is limited. Here we report the first in vivo experiments using a transgenic reporter mouse for the GEVI ArcLight, which utilizes a Cre/tTA dependent expression system (TIGRE 1.0). We developed two mouse lines with ArcLight expression restricted to either olfactory receptor neurons, or a subpopulation of interneurons located in the granule and glomerular layers in the olfactory bulb. The ArcLight expression in these lines was sufficient for in vivo imaging of odorant responses in single trials using epifluorescence and 2-photon imaging. The voltage responses were odor-specific and concentration-dependent, which supported earlier studies about perceptual transformations carried out by the bulb that used calcium sensors of neural activity. This study demonstrates that the ArcLight transgenic line is a flexible genetic tool that can be used to record the neuronal electrical activity of different cell types with a signal-to-noise ratio that is comparable to previous reports using viral transduction.
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13
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Liu S, Lin C, Xu Y, Luo H, Peng L, Zeng X, Zheng H, Chen PR, Zou P. A far-red hybrid voltage indicator enabled by bioorthogonal engineering of rhodopsin on live neurons. Nat Chem 2021; 13:472-479. [PMID: 33859392 DOI: 10.1038/s41557-021-00641-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 01/15/2021] [Indexed: 01/24/2023]
Abstract
Membrane potential is a key aspect of cellular signalling and is dynamically regulated by an array of ion-selective pumps and channels. Fluorescent voltage indicators enable non-invasive optical recording of the cellular membrane potential with high spatial resolution. Here, we report a palette of bright and sensitive hybrid voltage indicators (HVIs) with fluorescence intensities sensitive to changes in membrane potential via electrochromic Förster resonance energy transfer. Enzyme-mediated site-specific incorporation of a probe, followed by an inverse-electron-demand Diels-Alder cycloaddition, was used to create enhanced voltage-sensing rhodopsins with hybrid dye-protein architectures. The most sensitive indicator, HVI-Cy3, displays high voltage sensitivity (-39% ΔF/F0 per 100 mV) and millisecond response kinetics, enabling optical recording of action potentials at a sampling rate of 400 Hz over 10 min across a large neuronal population. The far-red indicator HVI-Cy5 could be paired with optogenetic actuators and green/red-emitting fluorescent indicators, allowing an all-optical investigation of neuronal electrophysiology.
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Affiliation(s)
- Shuzhang Liu
- College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education, Peking University, Beijing, China
| | - Chang Lin
- College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education, Peking University, Beijing, China
| | - Yongxian Xu
- College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education, Peking University, Beijing, China.,School of Life Sciences, Tsinghua University, Beijing, China
| | - Huixin Luo
- College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education, Peking University, Beijing, China
| | - Luxin Peng
- College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education, Peking University, Beijing, China
| | - Xiangmei Zeng
- College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education, Peking University, Beijing, China
| | - Huangtao Zheng
- College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education, Peking University, Beijing, China
| | - Peng R Chen
- College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education, Peking University, Beijing, China. .,Peking-Tsinghua Center for Life Sciences, Beijing, China.
| | - Peng Zou
- College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education, Peking University, Beijing, China. .,Peking-Tsinghua Center for Life Sciences, Beijing, China. .,PKU-IDG/McGovern Institute for Brain Research, Beijing, China. .,Chinese Institute for Brain Research (CIBR), Beijing, China.
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14
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Leong LM, Kang BE, Baker BJ. Improving the flexibility of genetically encoded voltage indicators via intermolecular FRET. Biophys J 2021; 120:1927-1941. [PMID: 33744262 PMCID: PMC8204331 DOI: 10.1016/j.bpj.2021.03.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 02/25/2021] [Accepted: 03/10/2021] [Indexed: 11/16/2022] Open
Abstract
A new family of genetically encoded voltage indicators (GEVIs) has been developed based on intermolecular Förster resonance energy transfer (FRET). To test the hypothesis that the GEVI ArcLight functions via interactions between the fluorescent protein (FP) domains of neighboring probes, the FP of ArcLight was replaced with either a FRET donor or acceptor FP. We discovered relatively large FRET signals only when cells were cotransfected with both the FRET donor and acceptor GEVIs. Using a cyan fluorescent protein donor and an RFP acceptor, we were able to observe a voltage-dependent signal with an emission peak separated by over 200 nm from the excitation wavelength. The intermolecular FRET strategy also works for rhodopsin-based probes, potentially improving their flexibility as well. Separating the FRET pair into two distinct proteins has important advantages over intramolecular FRET constructs. The signals are larger because the voltage-induced conformational change moves two FPs independently. The expression of the FRET donor and acceptor can also be restricted independently, enabling greater cell type specificity as well as refined subcellular voltage reporting.
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Affiliation(s)
- Lee Min Leong
- Brain Science Institute, Korea Institute of Science and Technology, Seongbuk-gu, 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
- Brain Science Institute, Korea Institute of Science and Technology, Seongbuk-gu, Seoul, Republic of Korea
| | - Bradley J Baker
- Brain Science Institute, Korea Institute of Science and Technology, Seongbuk-gu, 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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15
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Mechanism of ArcLight derived GEVIs involves electrostatic interactions that can affect proton wires. Biophys J 2021; 120:1916-1926. [PMID: 33744263 PMCID: PMC8204334 DOI: 10.1016/j.bpj.2021.03.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 02/28/2021] [Accepted: 03/10/2021] [Indexed: 11/24/2022] Open
Abstract
The genetically encoded voltage indicators ArcLight and its derivatives mediate voltage-dependent optical signals by intermolecular, electrostatic interactions between neighboring fluorescent proteins (FPs). A random mutagenesis event placed a negative charge on the exterior of the FP, resulting in a greater than 10-fold improvement of the voltage-dependent optical signal. Repositioning this negative charge on the exterior of the FP reversed the polarity of voltage-dependent optical signals, suggesting the presence of “hot spots” capable of interacting with the negative charge on a neighboring FP, thereby changing the fluorescent output. To explore the potential effect on the chromophore state, voltage-clamp fluorometry was performed with alternating excitation at 390 nm followed by excitation at 470 nm, resulting in several mutants exhibiting voltage-dependent, ratiometric optical signals of opposing polarities. However, the kinetics, voltage ranges, and optimal FP fusion sites were different depending on the wavelength of excitation. These results suggest that the FP has external, electrostatic pathways capable of quenching fluorescence that are wavelength specific. One mutation to the FP (E222H) showed a voltage-dependent increase in fluorescence when excited at 390 nm, indicating the ability to affect the proton wire from the protonated chromophore to the H222 position. ArcLight-derived sensors may therefore offer a novel way to map how conditions external to the β-can structure can affect the fluorescence of the chromophore and transiently affect those pathways via conformational changes mediated by manipulating membrane potential.
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16
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Tsutsui H, Mizutani N, Okamura Y. Engineering voltage sensing phosphatase (VSP). Methods Enzymol 2021; 654:85-114. [PMID: 34120726 DOI: 10.1016/bs.mie.2021.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Voltage sensing phosphatase (VSP), consists of a voltage sensor domain (VSD) like that found in voltage-gated ion channels and a phosphoinositide (PIP) phosphatase region exhibiting remarkable structural similarity to a tumor suppressor enzyme, PTEN. Membrane depolarization activates the enzyme activity through tight coupling between the VSD and enzyme region. The VSD of VSP has a unique nature; it is a self-contained module that can be transferred to other proteins, conferring voltage sensitivity. Thanks to this nature, numerous versions of gene-encoded voltage indicators (GEVIs) have been developed through combination of a fluorescent protein with the VSD of VSP. In addition, VSP itself can also serve as a tool to alter PIP levels in cells. Cellular levels of PIPs, PI(4,5)P2 in particular, can be acutely and transiently reduced using a simple voltage protocol after heterologous expression of VSP. Recent progress in our understanding of the molecular structure and mechanisms underlying VSP facilitates optimization of its molecular properties for its use as a molecular tool.
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Affiliation(s)
- Hidekazu Tsutsui
- School of Materials Science, Japan Advanced Institute of Science and Technology (JAIST), Nomi, Ishikawa, Japan.
| | - Natsuki Mizutani
- Graduate School of Medicine, Japan Advanced Institute of Science and Technology (JAIST), Osaka University, Suita, Osaka, Japan
| | - Yasushi Okamura
- Graduate School of Medicine, Japan Advanced Institute of Science and Technology (JAIST), Osaka University, Suita, Osaka, Japan.
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17
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Monakhov MV, Matlashov ME, Colavita M, Song C, Shcherbakova DM, Antic SD, Verkhusha VV, Knöpfel T. Screening and Cellular Characterization of Genetically Encoded Voltage Indicators Based on Near-Infrared Fluorescent Proteins. ACS Chem Neurosci 2020; 11:3523-3531. [PMID: 33063984 DOI: 10.1021/acschemneuro.0c00046] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
We developed genetically encoded voltage indicators using a transmembrane voltage-sensing domain and bright near-infrared fluorescent proteins derived from bacterial phytochromes. These new voltage indicators are excited by 640 nm light and emission is measured at 670 nm, allowing imaging in the near-infrared tissue transparency window. The spectral properties of our new indicators permit seamless voltage imaging with simultaneous blue-green light optogenetic actuator activation as well as simultaneous voltage-calcium imaging when paired with green calcium indicators. Iterative optimizations led to a fluorescent probe, here termed nirButterfly, which reliably reports neuronal activities including subthreshold membrane potential depolarization and hyperpolarization as well as spontaneous spiking or electrically- and optogenetically evoked action potentials. This enables largely improved all-optical causal interrogations of physiology.
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Affiliation(s)
- Mikhail V Monakhov
- Institute for Systems Genomics, Stem Cell Institute, Department of Neuroscience, UConn Health, Farmington, Connecticut 06030, United States
- Department of Anatomy and Structural Biology and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Mikhail E Matlashov
- Department of Anatomy and Structural Biology and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Michelangelo Colavita
- Laboratory for Neuronal Circuit Dynamics, Imperial College London, London W12 0NN, U.K
| | - Chenchen Song
- Laboratory for Neuronal Circuit Dynamics, Imperial College London, London W12 0NN, U.K
| | - Daria M Shcherbakova
- Department of Anatomy and Structural Biology and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Srdjan D Antic
- Institute for Systems Genomics, Stem Cell Institute, Department of Neuroscience, UConn Health, Farmington, Connecticut 06030, United States
| | - Vladislav V Verkhusha
- Department of Anatomy and Structural Biology and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Thomas Knöpfel
- Laboratory for Neuronal Circuit Dynamics, Imperial College London, London W12 0NN, U.K
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18
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Zhou X, Mehta S, Zhang J. Genetically Encodable Fluorescent and Bioluminescent Biosensors Light Up Signaling Networks. Trends Biochem Sci 2020; 45:889-905. [PMID: 32660810 PMCID: PMC7502535 DOI: 10.1016/j.tibs.2020.06.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Revised: 05/25/2020] [Accepted: 06/01/2020] [Indexed: 12/12/2022]
Abstract
Cell signaling networks are intricately regulated in time and space to determine the responses and fates of cells to different cues. Genetically encodable fluorescent and bioluminescent biosensors enable the direct visualization of these spatiotemporal signaling dynamics within the native biological context, and have therefore become powerful molecular tools whose unique benefits are being used to address challenging biological questions. We first review the basis of biosensor design and remark on recent technologies that are accelerating biosensor development. We then discuss a few of the latest advances in the development and application of genetically encodable fluorescent and bioluminescent biosensors that have led to scientific or technological breakthroughs.
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Affiliation(s)
- Xin Zhou
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA
| | - Sohum Mehta
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA
| | - Jin Zhang
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA.
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19
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Liu Y, Lu Y, Chen G, Wang Q. Recent Progress of Hybrid Optical Probes for Neural Membrane Potential Imaging. Biotechnol J 2020; 15:e2000086. [PMID: 32662937 DOI: 10.1002/biot.202000086] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 07/04/2020] [Indexed: 12/17/2022]
Abstract
The neural membrane potential of nerve cells is the basis of neural activity production, which controls advanced brain activities such as memory, emotion, and learning. In the past decades, optical voltage indicator has emerged as a promising tool to decode neural activities with high-fidelity and excellent spatiotemporal resolution. In particular, the hybrid optical probes can combine the advantageous photophysical properties of different components such as voltage-sensitive molecules, highly fluorescent fluorophores, membrane-targeting tags, and optogenetic materials, thus showing numerous advantages in improving the photoluminescence intensity, voltage sensitivity, photostability, and cell specificity of probes. In this review, the current state-of-the-art hybrid probes are highlighted, that are designed by using fluorescent proteins, organic dyes, and fluorescent nanoprobes as the fluorophores, respectively. Then, the design strategies, voltage-sensing mechanisms and the in vitro and in vivo neural activity imaging applications of the hybrid probes are summarized. Finally, based on the current achievements of voltage imaging studies, the challenges and prospects for design and application of hybrid optical probes in the future are presented.
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Affiliation(s)
- Yongyang Liu
- School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, Hefei, 230026, China.,CAS Key Laboratory of Nano-Bio Interface, Suzhou Key Laboratory of Functional Molecular Imaging Technology, Division of Nanobiomedicine and i-Lab, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215123, China
| | - Yaxin Lu
- School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, Hefei, 230026, China.,CAS Key Laboratory of Nano-Bio Interface, Suzhou Key Laboratory of Functional Molecular Imaging Technology, Division of Nanobiomedicine and i-Lab, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215123, China
| | - Guangcun Chen
- School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, Hefei, 230026, China.,CAS Key Laboratory of Nano-Bio Interface, Suzhou Key Laboratory of Functional Molecular Imaging Technology, Division of Nanobiomedicine and i-Lab, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215123, China
| | - Qiangbin Wang
- School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, Hefei, 230026, China.,CAS Key Laboratory of Nano-Bio Interface, Suzhou Key Laboratory of Functional Molecular Imaging Technology, Division of Nanobiomedicine and i-Lab, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215123, China.,College of Materials Sciences and Opto-Electronic Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
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20
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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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21
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Rhee JK, Leong LM, Mukim MSI, Kang BE, Lee S, Bilbao-Broch L, Baker BJ. Biophysical Parameters of GEVIs: Considerations for Imaging Voltage. Biophys J 2020; 119:1-8. [PMID: 32521239 PMCID: PMC7335909 DOI: 10.1016/j.bpj.2020.05.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 04/17/2020] [Accepted: 05/20/2020] [Indexed: 11/29/2022] Open
Abstract
Genetically encoded voltage indicators (GEVIs) continue to evolve, resulting in many different probes with varying strengths and weaknesses. Developers of new GEVIs tend to highlight their positive features. A recent article from an independent laboratory has compared the signal/noise ratios of a number of GEVIs. Such a comparison can be helpful to investigators eager to try to image the voltage of excitable cells. In this perspective, we will present examples of how the biophysical features of GEVIs affect the imaging of excitable cells in an effort to assist researchers when considering probes for their specific needs.
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Affiliation(s)
- Jun Kyu Rhee
- Center for Functional Connectomics, Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, Republic of Korea; Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology (UST), Seoul, Republic of Korea
| | - Lee Min Leong
- Center for Functional Connectomics, Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, Republic of Korea; Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology (UST), Seoul, Republic of Korea
| | - Md Sofequl Islam Mukim
- Center for Functional Connectomics, Brain Science Institute, Korea Institute of Science and Technology (KIST), 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
- Center for Functional Connectomics, Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, Republic of Korea
| | - Sungmoo Lee
- Center for Functional Connectomics, Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, Republic of Korea
| | - Laura Bilbao-Broch
- Center for Functional Connectomics, Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, Republic of Korea; Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology (UST), Seoul, Republic of Korea
| | - Bradley J Baker
- Center for Functional Connectomics, Brain Science Institute, Korea Institute of Science and Technology (KIST), 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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22
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Villette V, Chavarha M, Dimov IK, Bradley J, Pradhan L, Mathieu B, Evans SW, Chamberland S, Shi D, Yang R, Kim BB, Ayon A, Jalil A, St-Pierre F, Schnitzer MJ, Bi G, Toth K, Ding J, Dieudonné S, Lin MZ. Ultrafast Two-Photon Imaging of a High-Gain Voltage Indicator in Awake Behaving Mice. Cell 2020; 179:1590-1608.e23. [PMID: 31835034 DOI: 10.1016/j.cell.2019.11.004] [Citation(s) in RCA: 196] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 07/08/2019] [Accepted: 10/31/2019] [Indexed: 10/25/2022]
Abstract
Optical interrogation of voltage in deep brain locations with cellular resolution would be immensely useful for understanding how neuronal circuits process information. Here, we report ASAP3, a genetically encoded voltage indicator with 51% fluorescence modulation by physiological voltages, submillisecond activation kinetics, and full responsivity under two-photon excitation. We also introduce an ultrafast local volume excitation (ULoVE) method for kilohertz-rate two-photon sampling in vivo with increased stability and sensitivity. Combining a soma-targeted ASAP3 variant and ULoVE, we show single-trial tracking of spikes and subthreshold events for minutes in deep locations, with subcellular resolution and with repeated sampling over days. In the visual cortex, we use soma-targeted ASAP3 to illustrate cell-type-dependent subthreshold modulation by locomotion. Thus, ASAP3 and ULoVE enable high-speed optical recording of electrical activity in genetically defined neurons at deep locations during awake behavior.
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Affiliation(s)
- Vincent Villette
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Research University, Paris 75005, France
| | - Mariya Chavarha
- Department of Neurobiology, Stanford University, Stanford, CA 94305, USA; Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Ivan K Dimov
- Department of Neurobiology, Stanford University, Stanford, CA 94305, USA; CNC Program, Stanford University, Stanford, CA 94305, USA
| | - Jonathan Bradley
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Research University, Paris 75005, France
| | - Lagnajeet Pradhan
- Department of Neurobiology, Stanford University, Stanford, CA 94305, USA; CNC Program, Stanford University, Stanford, CA 94305, USA
| | - Benjamin Mathieu
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Research University, Paris 75005, France
| | - Stephen W Evans
- Department of Neurobiology, Stanford University, Stanford, CA 94305, USA
| | - Simon Chamberland
- Department of Psychiatry and Neuroscience, CERVO Brain Research Centre, Université Laval, Quebec City, QC G1J 2G3, Canada
| | - Dongqing Shi
- Department of Neurobiology, Stanford University, Stanford, CA 94305, USA; School of Life Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Renzhi Yang
- Department of Neurosurgery, Stanford University, Stanford, CA 94305, USA; Biology PhD Program, Stanford University, Stanford, CA 94305, USA
| | - Benjamin B Kim
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Annick Ayon
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Research University, Paris 75005, France
| | - Abdelali Jalil
- Université de Paris, SPPIN - Saints-Pères Paris Institute for the Neurosciences, CNRS, Paris F-75006, France
| | - François St-Pierre
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mark J Schnitzer
- CNC Program, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Guoqiang Bi
- School of Life Sciences, University of Science and Technology of China, Hefei 230026, China; CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai 20031, China
| | - Katalin Toth
- Department of Psychiatry and Neuroscience, CERVO Brain Research Centre, Université Laval, Quebec City, QC G1J 2G3, Canada
| | - Jun Ding
- Department of Neurosurgery, Stanford University, Stanford, CA 94305, USA
| | - Stéphane Dieudonné
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Research University, Paris 75005, France.
| | - Michael Z Lin
- Department of Neurobiology, Stanford University, Stanford, CA 94305, USA; Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
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23
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Lee S, Song YK, Baker BJ. Engineering Photoactivatability in Genetically Encoded Voltage and pH Indicators. Front Cell Neurosci 2019; 13:482. [PMID: 31736711 PMCID: PMC6828978 DOI: 10.3389/fncel.2019.00482] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 10/10/2019] [Indexed: 11/13/2022] Open
Abstract
Genetically-encoded indicators of neuronal activity enable the labeling of a genetically defined population of neurons to optically monitor their activities. However, researchers often find difficulties in identifying relevant signals from excessive background fluorescence. A photoactivatable version of a genetically encoded calcium indicator, sPA-GCaMP6f is a good example of circumventing such an obstacle by limiting the fluorescence to a region of interest defined by the user. Here, we apply this strategy to genetically encoded voltage (GEVI) and pH (GEPI) indicators. Three photoactivatable GEVI candidates were considered. The first one used a circularly-permuted fluorescent protein, the second design involved a Förster resonance energy transfer (FRET) pair, and the third approach employed a pH-sensitive variant of GFP, ecliptic pHluorin. The candidate with a variant of ecliptic pHluorin exhibited photoactivation and a voltage-dependent fluorescence change. This effort also yielded a pH-sensitive photoactivatable GFP that varies its brightness in response to intracellular pH changes.
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Affiliation(s)
- Sungmoo Lee
- Center for Functional Connectomics, Brain Science Institute, Korea Institute of Science and Technology, Seoul, South Korea
| | - Yoon-Kyu Song
- Program in Nano Science and Technology, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, South Korea.,Advanced Institutes of Convergence Technology, Suwon, South Korea
| | - Bradley J Baker
- Center for Functional Connectomics, Brain Science Institute, Korea Institute of Science and Technology, Seoul, South Korea.,Division of Bio-Medical Science and Technology, KIST School, University of Science and Technology (UST), Seoul, South Korea
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24
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Sun YH, Kao HKJ, Chang CW, Merleev A, Overton JL, Pretto D, Yechikov S, Maverakis E, Chiamvimonvat N, Chan JW, Lieu DK. Human induced pluripotent stem cell line with genetically encoded fluorescent voltage indicator generated via CRISPR for action potential assessment post-cardiogenesis. Stem Cells 2019; 38:90-101. [PMID: 31566285 DOI: 10.1002/stem.3085] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 08/08/2019] [Indexed: 12/22/2022]
Abstract
Genetically encoded fluorescent voltage indicators, such as ArcLight, have been used to report action potentials (APs) in human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs). However, the ArcLight expression, in all cases, relied on a high number of lentiviral vector-mediated random genome integrations (8-12 copy/cell), raising concerns such as gene disruption and alteration of global and local gene expression, as well as loss or silencing of reporter genes after differentiation. Here, we report the use of clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 nuclease technique to develop a hiPSC line stably expressing ArcLight from the AAVS1 safe harbor locus. The hiPSC line retained proliferative ability with a growth rate similar to its parental strain. Optical recording with conventional epifluorescence microscopy allowed the detection of APs as early as 21 days postdifferentiation, and could be repeatedly monitored for at least 5 months. Moreover, quantification and analysis of the APs of ArcLight-CMs identified two distinctive subtypes: a group with high frequency of spontaneous APs of small amplitudes that were pacemaker-like CMs and a group with low frequency of automaticity and large amplitudes that resembled the working CMs. Compared with FluoVolt voltage-sensitive dye, although dimmer, the ArcLight reporter exhibited better optical performance in terms of phototoxicity and photostability with comparable sensitivities and signal-to-noise ratios. The hiPSC line with targeted ArcLight engineering design represents a useful tool for studying cardiac development or hiPSC-derived cardiac disease models and drug testing.
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Affiliation(s)
- Yao-Hui Sun
- Department of Internal Medicine, Division of Cardiovascular Medicine, University of California, Davis, Davis, California.,Institute for Regenerative Cures and Stem Cell Program, University of California Davis Health Systems, Sacramento, California
| | - Hillary K J Kao
- Department of Internal Medicine, Division of Cardiovascular Medicine, University of California, Davis, Davis, California.,Institute for Regenerative Cures and Stem Cell Program, University of California Davis Health Systems, Sacramento, California
| | - Che-Wei Chang
- Department of Pathology and Laboratory Medicine, University of California, Davis, Sacramento, California
| | - Alexander Merleev
- Department of Dermatology, University of California, Davis, Davis, California
| | - James L Overton
- Department of Internal Medicine, Division of Cardiovascular Medicine, University of California, Davis, Davis, California.,Institute for Regenerative Cures and Stem Cell Program, University of California Davis Health Systems, Sacramento, California.,Bridges to Stem Cell Research Program, California State University, Sacramento, Sacramento, California
| | - Dalyir Pretto
- Department of Internal Medicine, Division of Cardiovascular Medicine, University of California, Davis, Davis, California.,Institute for Regenerative Cures and Stem Cell Program, University of California Davis Health Systems, Sacramento, California
| | - Sergey Yechikov
- Department of Internal Medicine, Division of Cardiovascular Medicine, University of California, Davis, Davis, California.,Institute for Regenerative Cures and Stem Cell Program, University of California Davis Health Systems, Sacramento, California
| | - Emanual Maverakis
- Department of Dermatology, University of California, Davis, Davis, California
| | - Nipavan Chiamvimonvat
- Department of Internal Medicine, Division of Cardiovascular Medicine, University of California, Davis, Davis, California.,Department of Veterans Affairs, Northern California Health Care System, Mather, California
| | - James W Chan
- Department of Pathology and Laboratory Medicine, University of California, Davis, Sacramento, California
| | - Deborah K Lieu
- Department of Internal Medicine, Division of Cardiovascular Medicine, University of California, Davis, Davis, California.,Institute for Regenerative Cures and Stem Cell Program, University of California Davis Health Systems, Sacramento, California
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25
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Abstract
As a "holy grail" of neuroscience, optical imaging of membrane potential could enable high resolution measurements of spiking and synaptic activity in neuronal populations. This has been partly achieved using organic voltage-sensitive dyes in vitro, or in invertebrate preparations yet unspecific staining has prevented single-cell resolution measurements from mammalian preparations in vivo. The development of genetically encoded voltage indicators (GEVIs) and chemogenetic sensors has enabled targeting voltage indicators to plasma membranes and selective neuronal populations. Here, we review recent advances in the design and use of genetic voltage indicators and discuss advantages and disadvantages of three classes of them. Although genetic voltage indicators could revolutionize neuroscience, there are still significant challenges, particularly two-photon performance. To overcome them may require cross-disciplinary collaborations, team effort, and sustained support by large-scale research initiatives.
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Affiliation(s)
- Yuki Bando
- Neurotechnology Center, Department Biological Sciences, Columbia University, 550 W 120th Street, New York, NY, 10027, USA
- Present address: Department Organ and Tissue Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka, 431-3192, Japan
| | - Christiane Grimm
- Neurotechnology Center, Department Biological Sciences, Columbia University, 550 W 120th Street, New York, NY, 10027, USA
| | - Victor H Cornejo
- Neurotechnology Center, Department Biological Sciences, Columbia University, 550 W 120th Street, New York, NY, 10027, USA
| | - Rafael Yuste
- Neurotechnology Center, Department Biological Sciences, Columbia University, 550 W 120th Street, New York, NY, 10027, USA.
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26
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Kost LA, Ivanova VO, Balaban PM, Lukyanov KA, Nikitin ES, Bogdanov AM. Red Fluorescent Genetically Encoded Voltage Indicators with Millisecond Responsiveness. SENSORS (BASEL, SWITZERLAND) 2019; 19:E2982. [PMID: 31284557 PMCID: PMC6651345 DOI: 10.3390/s19132982] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 07/02/2019] [Accepted: 07/04/2019] [Indexed: 01/09/2023]
Abstract
Genetically encoded fluorescent indicators typically consist of the sensitive and reporter protein domains connected with the amino acid linkers. The final performance of a particular indicator may depend on the linker length and composition as strong as it depends on the both domains nature. Here we aimed to optimize interdomain linkers in VSD-FR189-188-a recently described red fluorescent protein-based voltage indicator. We have tested 13 shortened linker versions and monitored the dynamic range, response speed and polarity of the corresponding voltage indicator variants. While the new indicators didn't show a contrast enhancement, some of them carrying very short interdomain linkers responded 25-fold faster than the parental VSD-FR189-188. Also we found the critical linker length at which fluorescence response to voltage shift changes its polarity from negative to positive slope. Our observations thus make an important contribution to the designing principles of the fluorescent protein-derived voltage indicators.
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Affiliation(s)
- Liubov A Kost
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
| | - Violetta O Ivanova
- Institute of Higher Nervous Activity and Neurophysiology, Moscow 117485, Russia
| | - Pavel M Balaban
- Institute of Higher Nervous Activity and Neurophysiology, Moscow 117485, Russia
| | - Konstantin A Lukyanov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Evgeny S Nikitin
- Institute of Higher Nervous Activity and Neurophysiology, Moscow 117485, Russia
| | - Alexey M Bogdanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia.
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27
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Oh J, Lee C, Kaang BK. Imaging and analysis of genetically encoded calcium indicators linking neural circuits and behaviors. THE KOREAN JOURNAL OF PHYSIOLOGY & PHARMACOLOGY : OFFICIAL JOURNAL OF THE KOREAN PHYSIOLOGICAL SOCIETY AND THE KOREAN SOCIETY OF PHARMACOLOGY 2019; 23:237-249. [PMID: 31297008 PMCID: PMC6609268 DOI: 10.4196/kjpp.2019.23.4.237] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 05/29/2019] [Accepted: 05/29/2019] [Indexed: 12/21/2022]
Abstract
Confirming the direct link between neural circuit activity and animal behavior has been a principal aim of neuroscience. The genetically encoded calcium indicator (GECI), which binds to calcium ions and emits fluorescence visualizing intracellular calcium concentration, enables detection of in vivo neuronal firing activity. Various GECIs have been developed and can be chosen for diverse purposes. These GECI-based signals can be acquired by several tools including two-photon microscopy and microendoscopy for precise or wide imaging at cellular to synaptic levels. In addition, the images from GECI signals can be analyzed with open source codes including constrained non-negative matrix factorization for endoscopy data (CNMF_E) and miniscope 1-photon-based calcium imaging signal extraction pipeline (MIN1PIPE), and considering parameters of the imaged brain regions (e.g., diameter or shape of soma or the resolution of recorded images), the real-time activity of each cell can be acquired and linked with animal behaviors. As a result, GECI signal analysis can be a powerful tool for revealing the functions of neuronal circuits related to specific behaviors.
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Affiliation(s)
- Jihae Oh
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Chiwoo Lee
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Bong-Kiun Kaang
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
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28
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Pu J, Disare M, Dickinson BC. Evolution of C-Terminal Modification Tolerance in Full-Length and Split T7 RNA Polymerase Biosensors. Chembiochem 2019; 20:1547-1553. [PMID: 30694596 DOI: 10.1002/cbic.201800707] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Revised: 01/27/2019] [Indexed: 01/23/2023]
Abstract
T7 RNA polymerase (RNAP) is a powerful protein scaffold for the construction of synthetic biology tools and biosensors. However, both T7 RNAP and its split variants are intolerant to C-terminal modifications or fusions, thus placing a key limitation on their engineering and deployment. Here, we use rapid continuous-evolution approaches to evolve both full-length and split T7 RNAP variants that tolerate modified C termini and fusions to entire other proteins. Moreover, we show that the evolved split C-terminal RNAP variants can function as small-molecule biosensors, even in the context of large C-terminal fusions. This work provides a panel of modified RNAP variants with robust activity and tolerance to C-terminal fusions, and provides insights into the biophysical requirements of the C-terminal carboxylic acid functional group of T7 RNAP.
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Affiliation(s)
- Jinyue Pu
- Department of Chemistry, The University of Chicago, 929 E. 57th Street, Chicago, IL, 60637, USA
| | - Michael Disare
- Department of Chemistry, The University of Chicago, 929 E. 57th Street, Chicago, IL, 60637, USA
| | - Bryan C Dickinson
- Department of Chemistry, The University of Chicago, 929 E. 57th Street, Chicago, IL, 60637, USA
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29
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Anderson HE, Weir RFF. On the development of optical peripheral nerve interfaces. Neural Regen Res 2019; 14:425-436. [PMID: 30539808 PMCID: PMC6334609 DOI: 10.4103/1673-5374.245461] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Accepted: 09/19/2018] [Indexed: 11/04/2022] Open
Abstract
Limb loss and spinal cord injury are two debilitating conditions that continue to grow in prevalence. Prosthetic limbs and limb reanimation present two ways of providing affected individuals with means to interact in the world. These techniques are both dependent on a robust interface with the peripheral nerve. Current methods for interfacing with the peripheral nerve tend to suffer from low specificity, high latency and insufficient robustness for a chronic implant. An optical peripheral nerve interface may solve some of these problems by decreasing invasiveness and providing single axon specificity. In order to implement such an interface three elements are required: (1) a transducer capable of translating light into a neural stimulus or translating neural activity into changes in fluorescence, (2) a means for delivering said transducer and (3) a microscope for providing the stimulus light and detecting the fluorescence change. There are continued improvements in both genetically encoded calcium and voltage indicators as well as new optogenetic actuators for stimulation. Similarly, improvements in specificity of viral vectors continue to improve expression in the axons of the peripheral nerve. Our work has recently shown that it is possible to virally transduce axons of the peripheral nerve for recording from small fibers. The improvements of these components make an optical peripheral nerve interface a rapidly approaching alternative to current methods.
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Affiliation(s)
- Hans E. Anderson
- Department of Bioengineering, University of Colorado Denver | Anschutz Medical Campus, Aurora, CO, USA
| | - Richard F. ff. Weir
- Department of Bioengineering, University of Colorado Denver | Anschutz Medical Campus, Aurora, CO, USA
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30
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Kannan M, Vasan G, Pieribone VA. Optimizing Strategies for Developing Genetically Encoded Voltage Indicators. Front Cell Neurosci 2019; 13:53. [PMID: 30863283 PMCID: PMC6399427 DOI: 10.3389/fncel.2019.00053] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 02/04/2019] [Indexed: 01/23/2023] Open
Abstract
Genetically encoded optical indicators of neuronal activity enable unambiguous recordings of input-output activity patterns from identified cells in intact circuits. Among them, genetically encoded voltage indicators (GEVIs) offer additional advantages over calcium indicators as they are direct sensors of membrane potential and can adeptly report subthreshold events and hyperpolarization. Here, we outline the major GEVI designs and give an account of properties that need to be carefully optimized during indicator engineering. While designing the ideal GEVI, one should keep in mind aspects such as membrane localization, signal size, signal-to-noise ratio, kinetics and voltage dependence of optical responses. Using ArcLight and derivatives as prototypes, we delineate how a probe should be optimized for the former properties and developed along other areas in a need-based manner. Finally, we present an overview of the GEVI engineering process and lend an insight into their discovery, delivery and diagnosis.
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Affiliation(s)
- Madhuvanthi Kannan
- The John B. Pierce Laboratory, New Haven, CT, United States.,Department of Cellular and Molecular Physiology, Yale School of Medicine, Yale University, New Haven, CT, United States
| | - Ganesh Vasan
- The John B. Pierce Laboratory, New Haven, CT, United States.,Department of Cellular and Molecular Physiology, Yale School of Medicine, Yale University, New Haven, CT, United States
| | - Vincent A Pieribone
- The John B. Pierce Laboratory, New Haven, CT, United States.,Department of Cellular and Molecular Physiology, Yale School of Medicine, Yale University, New Haven, CT, United States.,Department of Neuroscience, Yale School of Medicine, Yale University, New Haven, CT, United States
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31
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Greenwald EC, Mehta S, Zhang J. Genetically Encoded Fluorescent Biosensors Illuminate the Spatiotemporal Regulation of Signaling Networks. Chem Rev 2018; 118:11707-11794. [PMID: 30550275 PMCID: PMC7462118 DOI: 10.1021/acs.chemrev.8b00333] [Citation(s) in RCA: 302] [Impact Index Per Article: 50.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cellular signaling networks are the foundation which determines the fate and function of cells as they respond to various cues and stimuli. The discovery of fluorescent proteins over 25 years ago enabled the development of a diverse array of genetically encodable fluorescent biosensors that are capable of measuring the spatiotemporal dynamics of signal transduction pathways in live cells. In an effort to encapsulate the breadth over which fluorescent biosensors have expanded, we endeavored to assemble a comprehensive list of published engineered biosensors, and we discuss many of the molecular designs utilized in their development. Then, we review how the high temporal and spatial resolution afforded by fluorescent biosensors has aided our understanding of the spatiotemporal regulation of signaling networks at the cellular and subcellular level. Finally, we highlight some emerging areas of research in both biosensor design and applications that are on the forefront of biosensor development.
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Affiliation(s)
- Eric C Greenwald
- University of California , San Diego, 9500 Gilman Drive, BRFII , La Jolla , CA 92093-0702 , United States
| | - Sohum Mehta
- University of California , San Diego, 9500 Gilman Drive, BRFII , La Jolla , CA 92093-0702 , United States
| | - Jin Zhang
- University of California , San Diego, 9500 Gilman Drive, BRFII , La Jolla , CA 92093-0702 , United States
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32
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Nakajima R, Baker BJ. Mapping of excitatory and inhibitory postsynaptic potentials of neuronal populations in hippocampal slices using the GEVI, ArcLight. JOURNAL OF PHYSICS D: APPLIED PHYSICS 2018; 51:504003. [PMID: 30739956 PMCID: PMC6366634 DOI: 10.1088/1361-6463/aae2e3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
To understand the circuitry of the brain, it is essential to clarify the functional connectivity among distinct neuronal populations. For this purpose, neuronal activity imaging using genetically-encoded calcium sensors such as GCaMP has been a powerful approach due to its cell-type specificity. However, calcium (Ca2+) is an indirect measure of neuronal activity. A more direct approach would be to use genetically encoded voltage indicators (GEVIs) to observe subthreshold, synaptic activities. The GEVI, ArcLight, which exhibits large fluorescence transients in response to voltage, was expressed in excitatory neurons of the mouse CA1 hippocampus. Fluorescent signals in response to the electrical stimulation of the Schaffer collateral axons were observed in brain slice preparations. ArcLight was able to map both excitatory and inhibitory inputs projected to excitatory neurons. In contrast, the Ca2+ signal detected by GCaMP6f, was only associated with excitatory inputs. ArcLight and similar voltage sensing probes are also becoming powerful paradigms for functional connectivity mapping of brain circuitry.
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Affiliation(s)
- Ryuichi Nakajima
- Center for Functional Connectomics, Korea Institute of Science and Technology, Seongbuk-gu, Seoul, 136-791, Republic of Korea
| | - Bradley J. Baker
- Center for Functional Connectomics, Korea Institute of Science and Technology, Seongbuk-gu, Seoul, 136-791, Republic of Korea
- Department of Neuroscience, University of Science and Technology, Daejeon, Republic of Korea
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33
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Kannan M, Vasan G, Huang C, Haziza S, Li JZ, Inan H, Schnitzer MJ, Pieribone VA. Fast, in vivo voltage imaging using a red fluorescent indicator. Nat Methods 2018; 15:1108-1116. [PMID: 30420685 PMCID: PMC6516062 DOI: 10.1038/s41592-018-0188-7] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 09/25/2018] [Indexed: 11/09/2022]
Abstract
Genetically encoded voltage indicators (GEVIs) are emerging optical tools for acquiring brain-wide cell-type-specific functional data at unparalleled temporal resolution. To broaden the application of GEVIs in high-speed multispectral imaging, we used a high-throughput strategy to develop voltage-activated red neuronal activity monitor (VARNAM), a fusion of the fast Acetabularia opsin and the bright red fluorophore mRuby3. Imageable under the modest illumination intensities required by bright green probes (<50 mW mm-2), VARNAM is readily usable in vivo. VARNAM can be combined with blue-shifted optical tools to enable cell-type-specific all-optical electrophysiology and dual-color spike imaging in acute brain slices and live Drosophila. With enhanced sensitivity to subthreshold voltages, VARNAM resolves postsynaptic potentials in slices and cortical and hippocampal rhythms in freely behaving mice. Together, VARNAM lends a new hue to the optical toolbox, opening the door to high-speed in vivo multispectral functional imaging.
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Affiliation(s)
- Madhuvanthi Kannan
- The John B. Pierce Laboratory, New Haven, CT, USA
- Department of Cellular and Molecular Physiology, Yale University, New Haven, CT, USA
- Department of Neuroscience, Yale University, New Haven, CT, USA
| | - Ganesh Vasan
- The John B. Pierce Laboratory, New Haven, CT, USA
- Department of Cellular and Molecular Physiology, Yale University, New Haven, CT, USA
- Department of Neuroscience, Yale University, New Haven, CT, USA
| | - Cheng Huang
- James H. Clark Center, Stanford University, Stanford, CA, USA
| | - Simon Haziza
- James H. Clark Center, Stanford University, Stanford, CA, USA
| | - Jin Zhong Li
- James H. Clark Center, Stanford University, Stanford, CA, USA
- CNC Program, Stanford University, Stanford, CA, USA
| | - Hakan Inan
- James H. Clark Center, Stanford University, Stanford, CA, USA
| | - Mark J Schnitzer
- James H. Clark Center, Stanford University, Stanford, CA, USA
- CNC Program, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Vincent A Pieribone
- The John B. Pierce Laboratory, New Haven, CT, USA.
- Department of Cellular and Molecular Physiology, Yale University, New Haven, CT, USA.
- Department of Neuroscience, Yale University, New Haven, CT, USA.
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34
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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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35
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Abstract
Understanding how activity patterns in specific neural circuits coordinate an animal’s behavior remains a key area of neuroscience research. Genetic tools and a brain of tractable complexity make Drosophila a premier model organism for these studies. Here, we review the wealth of reagents available to map and manipulate neuronal activity with light.
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36
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Mathews J, Levin M. The body electric 2.0: recent advances in developmental bioelectricity for regenerative and synthetic bioengineering. Curr Opin Biotechnol 2018; 52:134-144. [PMID: 29684787 PMCID: PMC10464502 DOI: 10.1016/j.copbio.2018.03.008] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 03/23/2018] [Indexed: 12/18/2022]
Abstract
Breakthroughs in biomedicine and synthetic bioengineering require predictive, rational control over anatomical structure and function. Recent successes in manipulating cellular and molecular hardware have not been matched by progress in understanding the patterning software implemented during embryogenesis and regeneration. A fundamental capability gap is driving desired changes in growth and form to address birth defects and traumatic injury. Here we review new tools, results, and conceptual advances in an exciting emerging field: endogenous non-neural bioelectric signaling, which enables cellular collectives to make global decisions and implement large-scale pattern homeostasis. Spatially distributed electric circuits regulate gene expression, organ morphogenesis, and body-wide axial patterning. Developmental bioelectricity facilitates the interface to organ-level modular control points that direct patterning in vivo. Cracking the bioelectric code will enable transformative progress in bioengineering and regenerative medicine.
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Affiliation(s)
- Juanita Mathews
- Biology Department, and Allen Discovery Center at Tufts University, Medford, MA 02155, United States
| | - Michael Levin
- Biology Department, and Allen Discovery Center at Tufts University, Medford, MA 02155, United States.
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37
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Hossain MN, Suzuki K, Iwano M, Matsuda T, Nagai T. Bioluminescent Low-Affinity Ca 2+ Indicator for ER with Multicolor Calcium Imaging in Single Living Cells. ACS Chem Biol 2018; 13:1862-1871. [PMID: 29494125 DOI: 10.1021/acschembio.7b01014] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The sarco/endoplasmic reticulum (SR/ER) is the foremost intercellular Ca2+ store (at submillimolar concentrations), playing a crucial role in controlling intracellular Ca2+ levels. For the investigation of SR/ER Ca2+ dynamics in cells, fluorescent protein-based genetically encoded calcium indicators (GECIs) with low Ca2+ affinity have been used. Recently, bioluminescent protein-based GECIs with high brightness have been reported to counter the constraints of fluorescence imaging, such as phototoxicity. However, their Ca2+ affinity is high and limited for imaging in the cytosol, nucleus, or mitochondria. In this study, we developed a novel cyan color, low-affinity ( Kd = 110 μM) intensiometric bioluminescent GECI, which enables monitoring of the Ca2+ dynamics in the ER of HeLa cells and the SR of C2C12-derived myotubes. To facilitate the broad concentration range of Ca2+ in cellular organelles, we additionally developed an intermediate affinity ( Kd = 18 μM), orange color, and bioluminescent GECI, which enables monitoring of Ca2+ dynamics in the mitochondria of HeLa cells. With these indicators, in conjunction with an existing high-affinity, green, bioluminescent GECI, we succeeded in multicolor bioluminescent Ca2+ imaging in three distinct organelles (nuclei, mitochondria, and ER) simultaneously. The multicolor, live, bioluminescent Ca2+ imaging demonstrated here can be used to stably reveal the ER Ca2+ homeostasis and cooperative Ca2+ regulation among organelles. This will lead to the further understanding of Ca2+-related physiological functions and pathophysiological mechanisms.
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Affiliation(s)
- Md Nadim Hossain
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita 565-0871, Japan
| | - Kazushi Suzuki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita 565-0871, Japan
| | - Megumi Iwano
- Department of Biomolecular Science and Engineering, The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan
| | - Tomoki Matsuda
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita 565-0871, Japan
- Department of Biomolecular Science and Engineering, The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan
| | - Takeharu Nagai
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita 565-0871, Japan
- Department of Biomolecular Science and Engineering, The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan
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38
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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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39
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Platisa J, Pieribone VA. Genetically encoded fluorescent voltage indicators: are we there yet? Curr Opin Neurobiol 2018; 50:146-153. [PMID: 29501950 PMCID: PMC5984684 DOI: 10.1016/j.conb.2018.02.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 01/04/2018] [Accepted: 02/14/2018] [Indexed: 12/12/2022]
Abstract
In order to understand how brain activity produces adaptive behavior we need large-scale, high-resolution recordings of neuronal activity. Fluorescent genetically encoded voltage indicators (GEVIs) offer the potential for these recordings to be performed chronically from targeted cells in a minimally invasive manner. As the number of GEVIs successfully tested for in vivo use grows, so has the number of open questions regarding the improvements that would facilitate broad adoption of this technology that surpasses mere 'proof of principle' studies. Our aim in this review is not to provide a status check of the current state of the field, as excellent publications covering this topic already exist. Here, we discuss specific questions regarding GEVI development and application that we think are crucial in achieving this goal.
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Affiliation(s)
- Jelena Platisa
- The John B. Pierce Laboratory, Inc., New Haven, CT 06519, United States; Department of Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, CT 06510, United States.
| | - Vincent A Pieribone
- The John B. Pierce Laboratory, Inc., New Haven, CT 06519, United States; Department of Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, CT 06510, United States; Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06510, United States
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40
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41
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Abstract
Fluorescent protein-based biosensors are indispensable molecular tools for life science research. The invention and development of high-fidelity biosensors for a particular molecule or molecular event often catalyze important scientific breakthroughs. Understanding the structural and functional organization of brain activities remain a subject for which optical sensors are in desperate need and of growing interest. Here, we review genetically encoded fluorescent sensors for imaging neuronal activities with a focus on the design principles and optimizations of various sensors. New bioluminescent sensors useful for deep-tissue imaging are also discussed. By highlighting the protein engineering efforts and experimental applications of these sensors, we can consequently analyze factors influencing their performance. Finally, we remark on how future developments can fill technological gaps and lead to new discoveries.
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Affiliation(s)
- Zhijie Chen
- California Institute for Quantitative Biosciences, QB3, University of California, Berkeley, CA 94720, USA
| | - Tan M. Truong
- Center for Membrane and Cell Physiology, and Biomedical Sciences (BIMS) Graduate Program, University of Virginia, Charlottesville, VA 22908, USA
| | - Hui-wang Ai
- Center for Membrane and Cell Physiology, and Biomedical Sciences (BIMS) Graduate Program, University of Virginia, Charlottesville, VA 22908, USA
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
- Correspondence:
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42
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Voltage and Calcium Imaging of Brain Activity. Biophys J 2017; 113:2160-2167. [PMID: 29102396 DOI: 10.1016/j.bpj.2017.09.040] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 09/14/2017] [Accepted: 09/21/2017] [Indexed: 01/02/2023] Open
Abstract
Sensors for imaging brain activity have been under development for almost 50 years. The development of some of these tools is relatively mature, whereas qualitative improvements of others are needed and are actively pursued. In particular, genetically encoded voltage indicators are just now starting to be used to answer neurobiological questions and, at the same time, more than 10 laboratories are working to improve them. In this Biophysical Perspective, we attempt to discuss the present state of the art and indicate areas of active development.
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Jung A, Rajakumar D, Yoon BJ, Baker BJ. Modulating the Voltage-sensitivity of a Genetically Encoded Voltage Indicator. Exp Neurobiol 2017; 26:241-251. [PMID: 29093633 PMCID: PMC5661057 DOI: 10.5607/en.2017.26.5.241] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 08/19/2017] [Accepted: 09/24/2017] [Indexed: 11/19/2022] Open
Abstract
Saturation mutagenesis was performed on a single position in the voltage-sensing domain (VSD) of a genetically encoded voltage indicator (GEVI). The VSD consists of four transmembrane helixes designated S1-S4. The V220 position located near the plasma membrane/extracellular interface had previously been shown to affect the voltage range of the optical signal. Introduction of polar amino acids at this position reduced the voltage-dependent optical signal of the GEVI. Negatively charged amino acids slightly reduced the optical signal by 33 percent while positively charge amino acids at this position reduced the optical signal by 80%. Surprisingly, the range of V220D was similar to that of V220K with shifted optical responses towards negative potentials. In contrast, the V220E mutant mirrored the responses of the V220R mutation suggesting that the length of the side chain plays in role in determining the voltage range of the GEVI. Charged mutations at the 219 position all behaved similarly slightly shifting the optical response to more negative potentials. Charged mutations to the 221 position behaved erratically suggesting interactions with the plasma membrane and/or other amino acids in the VSD. Introduction of bulky amino acids at the V220 position increased the range of the optical response to include hyperpolarizing signals. Combining The V220W mutant with the R217Q mutation resulted in a probe that reduced the depolarizing signal and enhanced the hyperpolarizing signal which may lead to GEVIs that only report neuronal inhibition.
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Affiliation(s)
- Arong Jung
- The Center for Functional Connectomics, Korea Institute of Science and Technology, Seoul, Korea.,College of Life Sciences and Biotechnology, Korea University, Seoul, Korea
| | - Dhanarajan Rajakumar
- The Center for Functional Connectomics, Korea Institute of Science and Technology, Seoul, Korea
| | - Bong-June Yoon
- College of Life Sciences and Biotechnology, Korea University, Seoul, Korea
| | - Bradley J Baker
- The Center for Functional Connectomics, Korea Institute of Science and Technology, Seoul, Korea.,Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology (UST), Seoul, Korea
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44
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Abstract
Optical methods for interrogating membrane potential changes in neurons promise to revolutionize our ability to dissect the activity of individual cells embedded in neural circuits underlying behavior and sensation. A number of voltage imaging strategies have emerged in the past few years. This Perspective discusses developments in both small-molecule and genetically encoded fluorescent indicators of membrane potential. We survey recent advances in small-molecule fluorescent indicators that rely on photoinduced electron transfer to sense voltage as well as refinements of voltage-sensitive fluorescent proteins and new opsin-based strategies for monitoring voltage changes. We compare the requirements of fluorescent voltage indicators to those for more canonical Ca2+ sensing as a way to illuminate the particular challenges associated with voltage imaging.
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Affiliation(s)
- Rishikesh U. Kulkarni
- Department of Chemistry, Department of Molecular and Cell Biology, and Helen Wills Neuroscience Institute, University of California, Berkeley, California 94720, United States
| | - Evan W. Miller
- Department of Chemistry, Department of Molecular and Cell Biology, and Helen Wills Neuroscience Institute, University of California, Berkeley, California 94720, United States
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45
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Improving a genetically encoded voltage indicator by modifying the cytoplasmic charge composition. Sci Rep 2017; 7:8286. [PMID: 28811673 PMCID: PMC5557843 DOI: 10.1038/s41598-017-08731-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 07/14/2017] [Indexed: 11/08/2022] Open
Abstract
An improved genetically encoded voltage indicator (GEVI) was achieved by altering the charge composition of the region linking the voltage-sensing domain of the GEVI to a pH-sensitive fluorescent protein. Negatively charged linker segments reduced the voltage-dependent optical signal while positively charged linkers increased the signal size. Arginine scanning mutagenesis of the linker region improved the signal size of the GEVI, Bongwoori, yielding fluorescent signals as high as 20% ΔF/F during the firing of action potentials. The speed of this new sensor was also capable of optically resolving action potentials firing at 65 Hz. This large signal size enabled individual pixels to become surrogate electrodes. Plotting the highest correlated pixels based only on fluorescence changes reproduced the image of the neuron exhibiting activity. Furthermore, the use of a pH-sensitive fluorescent protein facilitated the detection of the acidification of the neuron during the firing of action potentials.
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