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Luo Q, Zhang J, Huang M, Lin G, Tanaka M, Lepler S, Guan J, Siemann D, Tang X. Automatic Multi-functional Integration Program (AMFIP) towards all-optical mechano-electrophysiology interrogation. PLoS One 2022; 17:e0266098. [PMID: 35901062 PMCID: PMC9333221 DOI: 10.1371/journal.pone.0266098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 03/14/2022] [Indexed: 11/25/2022] Open
Abstract
Automatic operations of multi-functional and time-lapse live-cell imaging are necessary for the biomedical science community to study active, multi-faceted, and long-term biological phenomena. To achieve automatic control, most existing solutions often require the purchase of extra software programs and hardware that rely on the manufacturers’ own specifications. However, these software programs are usually non-user-programmable and unaffordable for many laboratories. To address this unmet need, we have developed a novel open-source software program, titled Automatic Multi-functional Integration Program (AMFIP), as a new Java-based and hardware-independent system that provides proven advantages over existing alternatives to the scientific community. Without extra hardware, AMFIP enables the functional synchronization of the μManager software platform, the Nikon NIS-Elements platform, and other 3rd party software to achieve automatic operations of most commercially available microscopy systems, including but not limited to those from Nikon. AMFIP provides a user-friendly and programmable graphical user interface (GUI), opening the door to expanding the customizability for myriad hardware and software systems according to user-specific experimental requirements and environments. To validate the intended purposes of developing AMFIP, we applied it to elucidate the question whether single cells, prior to their full spreading, can sense and respond to a soft solid substrate, and if so, how does the interaction depend on the cell spreading time and the stiffness of the substrate. Using a CRISPR/Cas9-engineered human epithelial Beas2B (B2B) cell line that expresses mNeonGreen2-tagged mechanosensitive Yes-associated protein (YAP), we show that single B2B cells develop distinct substrate-stiffness-dependent YAP expressions within 10 hours at most on the substrate, suggesting that cells are able to sense, distinguish, and respond to mechanical cues prior to the establishment of full cell spreading. In summary, AMFIP provides a reliable, open-source, and cost-free solution that has the validated long-term utility to satisfy the need of automatic imaging operations in the scientific community.
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Affiliation(s)
- Qin Luo
- Department of Electrical and Computer Engineering, Herbert Wertheim College of Engineering, University of Florida, Gainesville, Florida, United States of America
| | - Justin Zhang
- Department of Electrical and Computer Engineering, University of California, Santa Barbara, California, United States of America
| | - Miao Huang
- Department of Mechanical and Aerospace Engineering, Herbert Wertheim College of Engineering, UF, Gainesville, Florida, United States of America
| | - Gaoming Lin
- Department of Electrical and Computer Engineering, Herbert Wertheim College of Engineering, University of Florida, Gainesville, Florida, United States of America
| | - Mai Tanaka
- Department of Radiation Oncology, College of Medicine, University of Florida, Gainesville, Florida, United States of America
- UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Sharon Lepler
- Department of Radiation Oncology, College of Medicine, University of Florida, Gainesville, Florida, United States of America
- UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Juan Guan
- UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
- Department of Physics, College of Liberal Arts and Sciences, University of Florida, Gainesville, Florida, United States of America
- Department of Anatomy and Cell Biology, College of Medicine, University of Florida, Gainesville, Florida, United States of America
| | - Dietmar Siemann
- Department of Radiation Oncology, College of Medicine, University of Florida, Gainesville, Florida, United States of America
- UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Xin Tang
- Department of Mechanical and Aerospace Engineering, Herbert Wertheim College of Engineering, UF, Gainesville, Florida, United States of America
- UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
- * E-mail:
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de Grip WJ, Ganapathy S. Rhodopsins: An Excitingly Versatile Protein Species for Research, Development and Creative Engineering. Front Chem 2022; 10:879609. [PMID: 35815212 PMCID: PMC9257189 DOI: 10.3389/fchem.2022.879609] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 05/16/2022] [Indexed: 01/17/2023] Open
Abstract
The first member and eponym of the rhodopsin family was identified in the 1930s as the visual pigment of the rod photoreceptor cell in the animal retina. It was found to be a membrane protein, owing its photosensitivity to the presence of a covalently bound chromophoric group. This group, derived from vitamin A, was appropriately dubbed retinal. In the 1970s a microbial counterpart of this species was discovered in an archaeon, being a membrane protein also harbouring retinal as a chromophore, and named bacteriorhodopsin. Since their discovery a photogenic panorama unfolded, where up to date new members and subspecies with a variety of light-driven functionality have been added to this family. The animal branch, meanwhile categorized as type-2 rhodopsins, turned out to form a large subclass in the superfamily of G protein-coupled receptors and are essential to multiple elements of light-dependent animal sensory physiology. The microbial branch, the type-1 rhodopsins, largely function as light-driven ion pumps or channels, but also contain sensory-active and enzyme-sustaining subspecies. In this review we will follow the development of this exciting membrane protein panorama in a representative number of highlights and will present a prospect of their extraordinary future potential.
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Affiliation(s)
- Willem J. de Grip
- Leiden Institute of Chemistry, Department of Biophysical Organic Chemistry, Leiden University, Leiden, Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Srividya Ganapathy
- Department of Imaging Physics, Delft University of Technology, Netherlands
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Adam Y. All-optical electrophysiology in behaving animals. J Neurosci Methods 2021; 353:109101. [PMID: 33600851 DOI: 10.1016/j.jneumeth.2021.109101] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 01/13/2021] [Accepted: 02/09/2021] [Indexed: 12/28/2022]
Abstract
Technology for simultaneous control and readout of the membrane potential of multiple neurons in behaving animals at high spatio-temporal resolution will have a high impact on neuroscience research. Significant progress in the development of Genetically Encoded Voltage Indicators (GEVIs) now enables to optically record subthreshold and spiking activity from ensembles of cells in behaving animals. In some cases, the GEVIs were also combined with optogenetic actuators to enable 'all-optical' control and readout of membrane potential at cellular resolution. Here I describe the recent progress in GEVI development and discuss the various aspects necessary to perform a successful 'all-optical' electrophysiology experiment in behaving, head-fixed animals. These aspects include the voltage indicators, the optogenetic actuators, strategies for protein expression, optical hardware, and image processing software. Furthermore, I discuss various applications of the technology, highlighting its advantages over classic electrode-based techniques. I argue that GEVIs now transformed from a 'promising' technology to a practical tool that can be used to tackle fundamental questions in neuroscience.
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Affiliation(s)
- Yoav Adam
- Edmond and Lily Safra Center for Brain Science, The Hebrew University of Jerusalem, Jerusalem, Israel.
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Harris JM, Wang AYD, Boulanger-Weill J, Santoriello C, Foianini S, Lichtman JW, Zon LI, Arlotta P. Long-Range Optogenetic Control of Axon Guidance Overcomes Developmental Boundaries and Defects. Dev Cell 2020; 53:577-588.e7. [PMID: 32516597 PMCID: PMC7375170 DOI: 10.1016/j.devcel.2020.05.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 03/12/2020] [Accepted: 05/11/2020] [Indexed: 01/12/2023]
Abstract
Axons connect neurons together, establishing the wiring architecture of neuronal networks. Axonal connectivity is largely built during embryonic development through highly constrained processes of axon guidance, which have been extensively studied. However, the inability to control axon guidance, and thus neuronal network architecture, has limited investigation of how axonal connections influence subsequent development and function of neuronal networks. Here, we use zebrafish motor neurons expressing a photoactivatable Rac1 to co-opt endogenous growth cone guidance machinery to precisely and non-invasively direct axon growth using light. Axons can be guided over large distances, within complex environments of living organisms, overriding competing endogenous signals and redirecting axons across potent repulsive barriers to construct novel circuitry. Notably, genetic axon guidance defects can be rescued, restoring functional connectivity. These data demonstrate that intrinsic growth cone guidance machinery can be co-opted to non-invasively build new connectivity, allowing investigation of neural network dynamics in intact living organisms.
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Affiliation(s)
- James M. Harris
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, MA 02115, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02138, USA
| | - Andy Yu-Der Wang
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,Current Address: Tufts University School of Medicine, Boston, MA 02115, USA
| | - Jonathan Boulanger-Weill
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Cristina Santoriello
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,Stem Cell Program and Division of Hematology/Oncology, Children’s Hospital and Dana Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Medical School, Harvard Stem Cell Institute, Stem Cell and Regenerative Biology Department, Harvard University, Boston, MA 02115, USA
| | - Stephan Foianini
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Jeff W. Lichtman
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,Center for Brain Science, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Leonard I. Zon
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,Stem Cell Program and Division of Hematology/Oncology, Children’s Hospital and Dana Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Medical School, Harvard Stem Cell Institute, Stem Cell and Regenerative Biology Department, Harvard University, Boston, MA 02115, USA
| | - Paola Arlotta
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02138, USA.,Lead contact. Correspondence:
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Toward Decoding Bioelectric Events in Xenopus Embryogenesis: New Methodology for Tracking Interplay Between Calcium and Resting Potentials In Vivo. J Mol Biol 2019; 432:605-620. [PMID: 31711960 DOI: 10.1016/j.jmb.2019.10.029] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 10/07/2019] [Accepted: 10/15/2019] [Indexed: 12/16/2022]
Abstract
Although chemical signaling during embryogenesis is readily addressed by a plethora of available techniques, the developmental functions of ionic signaling are still poorly understood. It is increasingly realized that bioelectric events in nonneural cells are critical for pattern regulation, but their study has been hampered by difficulties in monitoring and manipulating them in vivo. Recent developments in visualizing electrical signaling dynamics in the field of neuroscience have facilitated functional experiments that reveal instructive developmental bioelectric signals. However, there is a pressing need for additional tools to explore time-dependent ionic signaling to understand complex endogenous dynamics. Here, we present methodological advances, including 4D imaging and data analysis, for improved tracking of calcium flux in the Xenopus laevis embryo, lowering the barrier for in vivo physiology work in this important model system. Using these techniques, we investigated the relationship between bioelectric ion channel activity and calcium, finding that cell hyperpolarization and depolarization both induce persistent static elevation of cytoplasmic calcium levels that fade over developmental time. These calcium changes correlate with increased cell mobility in early embryos and abnormal craniofacial morphology in later embryos. We thus highlight membrane potential modulation as a tractable tool for modulation of signaling cascades that rely on calcium as a transduction mechanism. The methods we describe facilitate the study of important novel aspects of developmental physiology, are extendable to numerous classes of existing and forthcoming fluorescent physiological reporters, and establish highly accessible, inexpensive protocols for their investigation.
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Stahlberg MA, Ramakrishnan C, Willig KI, Boyden ES, Deisseroth K, Dean C. Investigating the feasibility of channelrhodopsin variants for nanoscale optogenetics. NEUROPHOTONICS 2019; 6:015007. [PMID: 30854405 PMCID: PMC6393647 DOI: 10.1117/1.nph.6.1.015007] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 02/05/2019] [Indexed: 06/09/2023]
Abstract
Optogenetics has revolutionized the study of circuit function in the brain, by allowing activation of specific ensembles of neurons by light. However, this technique has not yet been exploited extensively at the subcellular level. Here, we test the feasibility of a focal stimulation approach using stimulated emission depletion/reversible saturable optical fluorescence transitions-like illumination, whereby switchable light-gated channels are focally activated by a laser beam of one wavelength and deactivated by an overlapping donut-shaped beam of a different wavelength, confining activation to a center focal region. This method requires that activated channelrhodopsins are inactivated by overlapping illumination of a distinct wavelength and that photocurrents are large enough to be detected at the nanoscale. In tests of current optogenetic tools, we found that ChR2 C128A/H134R/T159C and CoChR C108S and C108S/D136A-activated with 405-nm light and inactivated by coillumination with 594-nm light-and C1V1 E122T/C167S-activated by 561-nm light and inactivated by 405-nm light-were most promising in terms of highest photocurrents and efficient inactivation with coillumination. Although further engineering of step-function channelrhodopsin variants with higher photoconductances will be required to employ this approach at the nanoscale, our findings provide a framework to guide future development of this technique.
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Affiliation(s)
- Markus A. Stahlberg
- European Neuroscience Institute, Trans-Synaptic Signaling Group, Goettingen, Germany
| | - Charu Ramakrishnan
- Stanford University, Howard Hughes Medical Institute, Department of Bioengineering, Department of Psychiatry, CNC Program, Stanford, California, United States
| | - Katrin I. Willig
- University Medical Center, Center for Nanoscale Microscopy and Molecular Physiology of the Brain, Goettingen, Germany
| | - Edward S. Boyden
- MIT Media Lab and McGovern Institute, Departments of Brain and Cognitive Science and Biological Engineering, Cambridge, Massachusetts, United States
| | - Karl Deisseroth
- Stanford University, Howard Hughes Medical Institute, Department of Bioengineering, Department of Psychiatry, CNC Program, Stanford, California, United States
| | - Camin Dean
- European Neuroscience Institute, Trans-Synaptic Signaling Group, Goettingen, Germany
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Dunkel P, Petit M, Dhimane H, Blanchard-Desce M, Ogden D, Dalko PI. Quinoline-Derived Two-Photon-Sensitive Octupolar Probes. ChemistryOpen 2017; 6:660-667. [PMID: 29046861 PMCID: PMC5641908 DOI: 10.1002/open.201700097] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Indexed: 01/05/2023] Open
Abstract
A systematic study on quinoline‐derived light sensitive probes, having third‐order rotational symmetry is presented. The electronically linked octupolar structures show considerably improved linear and nonlinear photophysical properties under one‐ and two‐photon irradiation conditions compared to the corresponding monomers. Photolysis of the three acetate derivatives shows strong structure dependency: whereas irradiation of the 6‐ and 7‐aminoquinoline derivatives resulted in fast intramolecular cyclization and only trace amounts of fragmentation products, the 8‐aminoquinoline derivative afforded clean and selective photolysis, with a sequential release of their acetate groups (δu[730]=0.67 GM).
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Affiliation(s)
- Petra Dunkel
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques Université Paris Descartes 45, rue des Saints-Pères 75270 Paris Cedex 06 France
| | - Morgane Petit
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques Université Paris Descartes 45, rue des Saints-Pères 75270 Paris Cedex 06 France
| | - Hamid Dhimane
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques Université Paris Descartes 45, rue des Saints-Pères 75270 Paris Cedex 06 France
| | - Mireille Blanchard-Desce
- Université de Bordeaux ISM (CNRS UMR5255) Bâtiment A12, 351, Cours de la Libération 33405 Talence Cedex France
| | - David Ogden
- Laboratoire de Physiologie Cérébrale Université Paris Descartes 45, rue des Saints-Pères 75270 Paris Cedex 06 France
| | - Peter I Dalko
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques Université Paris Descartes 45, rue des Saints-Pères 75270 Paris Cedex 06 France
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Dagnew R, Lin YY, Agatep J, Cheng M, Jann A, Quach V, Monroe M, Singh G, Minasyan A, Hakimian J, Kee T, Cushman J, Walwyn W. CerebraLux: a low-cost, open-source, wireless probe for optogenetic stimulation. NEUROPHOTONICS 2017; 4:045001. [PMID: 29057282 PMCID: PMC5635269 DOI: 10.1117/1.nph.4.4.045001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 08/30/2017] [Indexed: 06/07/2023]
Abstract
The use of optogenetics to activate or inhibit neurons is an important toolbox for neuroscientists. Several optogenetic devices are in use. These range from wired systems where the optoprobe is physically connected to the light source by a tether, to wireless systems that are remotely controlled. There are advantages and disadvantages of both; the wired systems are lightweight but limit movement due to the tether, and wireless systems allow unrestricted movement but may be heavier than wired systems. Both systems can be expensive to install and use. We have developed a low cost, wireless optogenetic probe, CerebraLux, built from off-the-shelf components. CerebraLux consists of two separable units; an optical component consisting of the baseplate holding the fiber-optic in place and an electronic component consisting of a light-emitting diode, custom-printed circuit board, an infrared receiver, microcontroller, and a rechargeable, lightweight lithium polymer battery. The optical component (0.5 g) is mounted on the head permanently, whereas the electronic component (2.3 g) is removable and is applied for each experiment. We describe the device, provide all designs and specifications, the methods to manufacture and use the device in vivo, and demonstrate feasibility in a mouse behavioral paradigm.
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Affiliation(s)
- Robel Dagnew
- University of California, Department of Bioengineering, Los Angeles, California, United States
| | - Yin-Ying Lin
- University of California, Department of Bioengineering, Los Angeles, California, United States
| | - Jerikko Agatep
- University of California, Department of Bioengineering, Los Angeles, California, United States
| | - Michael Cheng
- University of California, Department of Bioengineering, Los Angeles, California, United States
| | - Andrew Jann
- University of California, Department of Bioengineering, Los Angeles, California, United States
| | - Viola Quach
- University of California, Department of Bioengineering, Los Angeles, California, United States
| | - Michelle Monroe
- University of California, Department of Bioengineering, Los Angeles, California, United States
| | - Ganeev Singh
- University of California, David Geffen School of Medicine, Department of Psychiatry and Biobehavioral Sciences, Los Angeles, California, United States
| | - Ani Minasyan
- University of California, David Geffen School of Medicine, Department of Psychiatry and Biobehavioral Sciences, Los Angeles, California, United States
| | - Joshua Hakimian
- University of California, David Geffen School of Medicine, Department of Psychiatry and Biobehavioral Sciences, Los Angeles, California, United States
| | - Theodore Kee
- University of California, Department of Bioengineering, Los Angeles, California, United States
| | - Jesse Cushman
- University of California, Department of Psychology, Los Angeles, California, United States
| | - Wendy Walwyn
- University of California, David Geffen School of Medicine, Department of Psychiatry and Biobehavioral Sciences, Los Angeles, California, United States
- University of California, Brain Research Institute, Los Angeles, California, United States
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9
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Xu Y, Zou P, Cohen AE. Voltage imaging with genetically encoded indicators. Curr Opin Chem Biol 2017; 39:1-10. [PMID: 28460291 PMCID: PMC5581692 DOI: 10.1016/j.cbpa.2017.04.005] [Citation(s) in RCA: 121] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 04/03/2017] [Accepted: 04/07/2017] [Indexed: 02/06/2023]
Abstract
Membrane voltages are ubiquitous throughout cell biology. Voltage is most commonly associated with excitable cells such as neurons and cardiomyocytes, although many other cell types and organelles also support electrical signaling. Voltage imaging in vivo would offer unique capabilities in reporting the spatial pattern and temporal dynamics of electrical signaling at the cellular and circuit levels. Voltage is not directly visible, and so a longstanding challenge has been to develop genetically encoded fluorescent voltage indicator proteins. Recent advances have led to a profusion of new voltage indicators, based on different scaffolds and with different tradeoffs between voltage sensitivity, speed, brightness, and spectrum. In this review, we describe recent advances in design and applications of genetically-encoded voltage indicators (GEVIs). We also highlight the protein engineering strategies employed to improve the dynamic range and kinetics of GEVIs and opportunities for future advances.
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Affiliation(s)
- Yongxian Xu
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, PKU-IDG/McGovern Institute for Brain Research, Peking University, Beijing 100871, China
| | - Peng Zou
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, PKU-IDG/McGovern Institute for Brain Research, Peking University, Beijing 100871, China.
| | - Adam E Cohen
- Departments of Chemistry and Chemical Biology and of Physics, Harvard University, Cambridge, MA 02138, USA; Howard Hughes Medical Institute.
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