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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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52
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Khadria A. Tools to measure membrane potential of neurons. Biomed J 2022; 45:749-762. [DOI: 10.1016/j.bj.2022.05.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 05/08/2022] [Accepted: 05/29/2022] [Indexed: 12/31/2022] Open
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Swanson JL, Chin PS, Romero JM, Srivastava S, Ortiz-Guzman J, Hunt PJ, Arenkiel BR. Advancements in the Quest to Map, Monitor, and Manipulate Neural Circuitry. Front Neural Circuits 2022; 16:886302. [PMID: 35719420 PMCID: PMC9204427 DOI: 10.3389/fncir.2022.886302] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/27/2022] [Indexed: 01/27/2023] Open
Abstract
Neural circuits and the cells that comprise them represent the functional units of the brain. Circuits relay and process sensory information, maintain homeostasis, drive behaviors, and facilitate cognitive functions such as learning and memory. Creating a functionally-precise map of the mammalian brain requires anatomically tracing neural circuits, monitoring their activity patterns, and manipulating their activity to infer function. Advancements in cell-type-specific genetic tools allow interrogation of neural circuits with increased precision. This review provides a broad overview of recombination-based and activity-driven genetic targeting approaches, contemporary viral tracing strategies, electrophysiological recording methods, newly developed calcium, and voltage indicators, and neurotransmitter/neuropeptide biosensors currently being used to investigate circuit architecture and function. Finally, it discusses methods for acute or chronic manipulation of neural activity, including genetically-targeted cellular ablation, optogenetics, chemogenetics, and over-expression of ion channels. With this ever-evolving genetic toolbox, scientists are continuing to probe neural circuits with increasing resolution, elucidating the structure and function of the incredibly complex mammalian brain.
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Affiliation(s)
- Jessica L. Swanson
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, United States
| | - Pey-Shyuan Chin
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, United States
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, United States
| | - Juan M. Romero
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, United States
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, United States
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, United States
| | - Snigdha Srivastava
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, United States
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, United States
| | - Joshua Ortiz-Guzman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, United States
| | - Patrick J. Hunt
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, United States
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, United States
| | - Benjamin R. Arenkiel
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, United States
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, United States
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, United States
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54
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Beck C, Gong Y. Engineering rhodopsins' activation spectra using a FRET-based approach. Biophys J 2022; 121:1765-1776. [PMID: 35331688 PMCID: PMC9117881 DOI: 10.1016/j.bpj.2022.03.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 12/01/2021] [Accepted: 03/18/2022] [Indexed: 11/16/2022] Open
Abstract
In the past decade, optogenetics has become a nearly ubiquitous tool in neuroscience because it enables researchers to manipulate neural activity with high temporal resolution and genetic specificity. Rational engineering of optogenetic tools has produced channelrhodopsins with a wide range of kinetics and photocurrent magnitude. Genome mining for previously unidentified species of rhodopsin has uncovered optogenetic tools with diverse spectral sensitivities. However, rational engineering of a rhodopsin has thus far been unable to re-engineer spectral sensitivity while preserving full photocurrent. Here, we developed and characterized ChroME-mTFP, a rhodopsin-fluorescent protein fusion that drives photocurrent through Förster resonance energy transfer (FRET). This FRET-opsin mechanism artificially broadened the activation spectrum of the blue-green-light-activated rhodopsin ChroME by approximately 50 nm, driving higher photocurrent at blue-shifted excitation wavelengths without sacrificing kinetics. The excitation spectra's increase at short wavelengths enabled us to optogenetically excite neurons at lower excitation powers with shorter wavelengths of light. Increasing this rhodopsin's sensitivity to shorter, bluer wavelengths pushes it toward dual-channel, crosstalk-free optogenetic stimulation and imaging with green-light-activated sensors. However, this iteration of FRET-opsin suffers from some imaging-light-induced photocurrent crosstalk from green or yellow light due to maintained, low-efficiency excitation at longer wavelengths.
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Affiliation(s)
- Connor Beck
- Department of Biomedical Engineering, Duke University, Durham, North Carolina.
| | - Yiyang Gong
- Department of Biomedical Engineering, Duke University, Durham, North Carolina.
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55
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Kramer RH, Miller EW, Abdelfattah A, Baker B. Fluorescent Reporters for Sensing Membrane Potential: Tools for Bioelectricity. Bioelectricity 2022. [DOI: 10.1089/bioe.2022.0017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Richard H. Kramer
- Department of Molecular & Cell Biology and Helen Wills Neuroscience Institute, University of California, Berkeley, California, USA
| | - Evan W. Miller
- Departments of Chemistry and Molecular & Cell Biology and Helen Wills Neuroscience Institute, University of California, Berkeley, California, USA
| | - Ahmed Abdelfattah
- Department of Neuroscience, Brown University, Providence, Rhode Island, USA
| | - Bradley Baker
- Brain Science Institute, Korea Institute of Science and Technology, Seoul, South Korea
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56
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Yiangou L, Blanch-Asensio A, de Korte T, Miller DC, van Meer BJ, Mol MPH, van den Brink L, Brandão KO, Mummery CL, Davis RP. Optogenetic reporters delivered as mRNA facilitate repeatable action potential and calcium handling assessment in human iPSC-derived cardiomyocytes. Stem Cells 2022; 40:655-668. [PMID: 35429386 PMCID: PMC9332902 DOI: 10.1093/stmcls/sxac029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Accepted: 04/05/2022] [Indexed: 11/15/2022]
Abstract
Abstract
Electrical activity and intracellular Ca 2+ transients are key features of cardiomyocytes. They can be measured using organic voltage- and Ca 2+-sensitive dyes but their photostability and phototoxicity means they are unsuitable for long-term measurements. Here, we investigated whether genetically-encoded voltage and Ca 2+ indicators (GEVIs and GECIs) delivered as modified mRNA (modRNA) into human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) would be accurate alternatives allowing measurements over long periods. These indicators were detected in hiPSC-CMs for up to 7 days after transfection and did not affect responses to proarrhythmic compounds. Furthermore, using the GEVI ASAP2f we observed action potential prolongation in long QT syndrome models, while the GECI jRCaMP1b facilitated the repeated evaluation of Ca 2+ handling responses for various tyrosine kinase inhibitors. This study demonstrated that modRNAs encoding optogenetic constructs report cardiac physiology in hiPSC-CMs without toxicity or the need for stable integration, illustrating their value as alternatives to organic dyes or other gene delivery methods for expressing transgenes.
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Affiliation(s)
- Loukia Yiangou
- Department of Anatomy and Embryology, Leiden University Medical Center, The Netherlands
| | - Albert Blanch-Asensio
- Department of Anatomy and Embryology, Leiden University Medical Center, The Netherlands
| | - Tessa de Korte
- Department of Anatomy and Embryology, Leiden University Medical Center, The Netherlands
| | - Duncan C Miller
- Department of Anatomy and Embryology, Leiden University Medical Center, The Netherlands
- Present Max Delbrück Center for Molecular Medicine (MDC), Berlin, Berlin, Germany
| | - Berend J van Meer
- Department of Anatomy and Embryology, Leiden University Medical Center, The Netherlands
| | - Mervyn P H Mol
- Department of Anatomy and Embryology, Leiden University Medical Center, The Netherlands
| | - Lettine van den Brink
- Department of Anatomy and Embryology, Leiden University Medical Center, The Netherlands
| | - Karina O Brandão
- Department of Anatomy and Embryology, Leiden University Medical Center, The Netherlands
| | - Christine L Mummery
- Department of Anatomy and Embryology, Leiden University Medical Center, The Netherlands
- Department of Applied Stem Cell Technologies, University of Twente, Enschede, The Netherlands
| | - Richard P Davis
- Department of Anatomy and Embryology, Leiden University Medical Center, The Netherlands
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57
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Gong Y, Tian Y, Baker C. A fully water coupled oblique light-sheet microscope. Sci Rep 2022; 12:5940. [PMID: 35396532 PMCID: PMC8993908 DOI: 10.1038/s41598-022-09975-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 03/31/2022] [Indexed: 11/25/2022] Open
Abstract
Recently developed descanned versions of the oblique light-sheet microscope promise to enable high-frame rate volumetric imaging in a variety of convenient preparations. The efficiency of these microscopes depends on the implementation of the objective coupling that turns the intermediate imaging plane. In this work, we developed a fully immersed coupling strategy between the middle and end objectives of the oblique light-sheet microscope to enable facile alignment and high efficiency coupling. Our design outperformed conventional designs that used only air objectives in resolution and light-collection power. We further demonstrated our design’s ability to capture large fields-of-view when paired with a camera with built-in electronic binning. We simultaneously imaged the forebrain and hindbrain of larval zebrafish and found clusters of activity localized to each region of the brain.
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Affiliation(s)
- Yiyang Gong
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA.
| | - Yuqi Tian
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Casey Baker
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
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58
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Böhm UL, Kimura Y, Kawashima T, Ahrens MB, Higashijima SI, Engert F, Cohen AE. Voltage imaging identifies spinal circuits that modulate locomotor adaptation in zebrafish. Neuron 2022; 110:1211-1222.e4. [PMID: 35104451 PMCID: PMC8989672 DOI: 10.1016/j.neuron.2022.01.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 11/17/2021] [Accepted: 01/04/2022] [Indexed: 12/20/2022]
Abstract
Motor systems must continuously adapt their output to maintain a desired trajectory. While the spinal circuits underlying rhythmic locomotion are well described, little is known about how the network modulates its output strength. A major challenge has been the difficulty of recording from spinal neurons during behavior. Here, we use voltage imaging to map the membrane potential of large populations of glutamatergic neurons throughout the spinal cord of the larval zebrafish during fictive swimming in a virtual environment. We characterized a previously undescribed subpopulation of tonic-spiking ventral V3 neurons whose spike rate correlated with swimming strength and bout length. Optogenetic activation of V3 neurons led to stronger swimming and longer bouts but did not affect tail beat frequency. Genetic ablation of V3 neurons led to reduced locomotor adaptation. The power of voltage imaging allowed us to identify V3 neurons as a critical driver of locomotor adaptation in zebrafish.
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Affiliation(s)
- Urs L Böhm
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Yukiko Kimura
- National Institutes of Natural Sciences, Okazaki Institute for Integrative Bioscience, National Institute for Physiological Sciences, Okazaki, Aichi 444-8787, Japan
| | - Takashi Kawashima
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Misha B Ahrens
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Shin-Ichi Higashijima
- National Institutes of Natural Sciences, Okazaki Institute for Integrative Bioscience, National Institute for Physiological Sciences, Okazaki, Aichi 444-8787, Japan
| | - Florian Engert
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Adam E Cohen
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Department of Physics, Harvard University, Cambridge, MA 02138, USA.
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59
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Bando Y, Ishibashi M, Yamagishi S, Fukuda A, Sato K. Orchestration of Ion Channels and Transporters in Neocortical Development and Neurological Disorders. Front Neurosci 2022; 16:827284. [PMID: 35237124 PMCID: PMC8884360 DOI: 10.3389/fnins.2022.827284] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 01/24/2022] [Indexed: 12/17/2022] Open
Abstract
Electrical activity plays crucial roles in neural circuit formation and remodeling. During neocortical development, neurons are generated in the ventricular zone, migrate to their correct position, elongate dendrites and axons, and form synapses. In this review, we summarize the functions of ion channels and transporters in neocortical development. Next, we discuss links between neurological disorders caused by dysfunction of ion channels (channelopathies) and neocortical development. Finally, we introduce emerging optical techniques with potential applications in physiological studies of neocortical development and the pathophysiology of channelopathies.
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Affiliation(s)
- Yuki Bando
- Department of Organ and Tissue Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Japan
- *Correspondence: Yuki Bando,
| | - Masaru Ishibashi
- Department of Neurophysiology, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Satoru Yamagishi
- Department of Organ and Tissue Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Atsuo Fukuda
- Department of Neurophysiology, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Kohji Sato
- Department of Organ and Tissue Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Japan
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60
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Optogenetics for Understanding and Treating Brain Injury: Advances in the Field and Future Prospects. Int J Mol Sci 2022; 23:ijms23031800. [PMID: 35163726 PMCID: PMC8836693 DOI: 10.3390/ijms23031800] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/21/2022] [Accepted: 02/03/2022] [Indexed: 02/07/2023] Open
Abstract
Optogenetics is emerging as an ideal method for controlling cellular activity. It overcomes some notable shortcomings of conventional methods in the elucidation of neural circuits, promotion of neuroregeneration, prevention of cell death and treatment of neurological disorders, although it is not without its own limitations. In this review, we narratively review the latest research on the improvement and existing challenges of optogenetics, with a particular focus on the field of brain injury, aiming at advancing optogenetics in the study of brain injury and collating the issues that remain. Finally, we review the most current examples of research, applying photostimulation in clinical treatment, and we explore the future prospects of these technologies.
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61
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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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62
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Yoo S, Mittelstein DR, Hurt RC, Lacroix J, Shapiro MG. Focused ultrasound excites cortical neurons via mechanosensitive calcium accumulation and ion channel amplification. Nat Commun 2022; 13:493. [PMID: 35078979 PMCID: PMC8789820 DOI: 10.1038/s41467-022-28040-1] [Citation(s) in RCA: 162] [Impact Index Per Article: 81.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 01/05/2022] [Indexed: 12/16/2022] Open
Abstract
Ultrasonic neuromodulation has the unique potential to provide non-invasive control of neural activity in deep brain regions with high spatial precision and without chemical or genetic modification. However, the biomolecular and cellular mechanisms by which focused ultrasound excites mammalian neurons have remained unclear, posing significant challenges for the use of this technology in research and potential clinical applications. Here, we show that focused ultrasound excites primary murine cortical neurons in culture through a primarily mechanical mechanism mediated by specific calcium-selective mechanosensitive ion channels. The activation of these channels results in a gradual build-up of calcium, which is amplified by calcium- and voltage-gated channels, generating a burst firing response. Cavitation, temperature changes, large-scale deformation, and synaptic transmission are not required for this excitation to occur. Pharmacological and genetic inhibition of specific ion channels leads to reduced responses to ultrasound, while over-expressing these channels results in stronger ultrasonic stimulation. These findings provide a mechanistic explanation for the effect of ultrasound on neurons to facilitate the further development of ultrasonic neuromodulation and sonogenetics as tools for neuroscience research.
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Affiliation(s)
- Sangjin Yoo
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - David R Mittelstein
- Division of Engineering and Applied Science, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Robert C Hurt
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Jerome Lacroix
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
- Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, CA, 91766, USA
| | - Mikhail G Shapiro
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA.
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63
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Yoon J, Shin M, Kim D, Lim J, Kim HW, Kang T, Choi JW. Bionanohybrid composed of metalloprotein/DNA/MoS 2/peptides to control the intracellular redox states of living cells and its applicability as a cell-based biomemory device. Biosens Bioelectron 2022; 196:113725. [PMID: 34678652 DOI: 10.1016/j.bios.2021.113725] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 10/17/2021] [Indexed: 12/13/2022]
Abstract
The development of cell-based bioelectronic devices largely depends on the direct control of intracellular redox states. However, most related studies have focused on the accurate measurement of electrical signals from living cells, whereas direct intracellular state control remains largely unexplored. Here, we developed a biocompatible transmembranal bionanohybrid structure composed of a recombinant metalloprotein, DNA, molybdenum disulfide nanoparticles (MoS2), and peptides to control intracellular redox states, which can be used as a cell-based biomemory device. Using the capacitance of MoS2 located inside the cell, the bionanohybrid controled the intracellular redox states of living cells by recording and extracting intracellular charges, which inturn was achieved by activating (writing) and deactivating (erasing) the cells. As a proof of concept, cell-based biomemory functions including writing, reading, and erasing were successfully demonstrated and confirmed via electrochemical methods and patch-clamp analyses, resulting in the development of the first in vitro cell-based biomemory device. This newly developed bionanohybrid provides a novel approach to control cellular redox states for cell-based bioelectronic applications, and can be applicable in a wide range of biological fields including bioelectronic medicine and intracellular redox status regulation.
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Affiliation(s)
- Jinho Yoon
- Department of Chemical & Biomolecular Engineering, Sogang University, 35 Baekbeom-Ro, Mapo-Gu, Seoul 04107, Republic of Korea
| | - Minkyu Shin
- Department of Chemical & Biomolecular Engineering, Sogang University, 35 Baekbeom-Ro, Mapo-Gu, Seoul 04107, Republic of Korea
| | - Dongyeon Kim
- Department of Chemical & Biomolecular Engineering, Sogang University, 35 Baekbeom-Ro, Mapo-Gu, Seoul 04107, Republic of Korea
| | - Joungpyo Lim
- Department of Chemical & Biomolecular Engineering, Sogang University, 35 Baekbeom-Ro, Mapo-Gu, Seoul 04107, Republic of Korea
| | - Hyun-Woong Kim
- Department of Chemical & Biomolecular Engineering, Sogang University, 35 Baekbeom-Ro, Mapo-Gu, Seoul 04107, Republic of Korea
| | - Taewook Kang
- Department of Chemical & Biomolecular Engineering, Sogang University, 35 Baekbeom-Ro, Mapo-Gu, Seoul 04107, Republic of Korea
| | - Jeong-Woo Choi
- Department of Chemical & Biomolecular Engineering, Sogang University, 35 Baekbeom-Ro, Mapo-Gu, Seoul 04107, Republic of Korea.
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64
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Kim TH, Schnitzer MJ. Fluorescence imaging of large-scale neural ensemble dynamics. Cell 2022; 185:9-41. [PMID: 34995519 PMCID: PMC8849612 DOI: 10.1016/j.cell.2021.12.007] [Citation(s) in RCA: 68] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 12/06/2021] [Accepted: 12/07/2021] [Indexed: 12/14/2022]
Abstract
Recent progress in fluorescence imaging allows neuroscientists to observe the dynamics of thousands of individual neurons, identified genetically or by their connectivity, across multiple brain areas and for extended durations in awake behaving mammals. We discuss advances in fluorescent indicators of neural activity, viral and genetic methods to express these indicators, chronic animal preparations for long-term imaging studies, and microscopes to monitor and manipulate the activity of large neural ensembles. Ca2+ imaging studies of neural activity can track brain area interactions and distributed information processing at cellular resolution. Across smaller spatial scales, high-speed voltage imaging reveals the distinctive spiking patterns and coding properties of targeted neuron types. Collectively, these innovations will propel studies of brain function and dovetail with ongoing neuroscience initiatives to identify new neuron types and develop widely applicable, non-human primate models. The optical toolkit's growing sophistication also suggests that "brain observatory" facilities would be useful open resources for future brain-imaging studies.
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Affiliation(s)
- Tony Hyun Kim
- James Clark Center for Biomedical Engineering & Sciences, Stanford University, Stanford, CA 94305, USA; CNC Program, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA.
| | - Mark J Schnitzer
- James Clark Center for Biomedical Engineering & Sciences, Stanford University, Stanford, CA 94305, USA; CNC Program, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA.
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65
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Abdelfattah AS, Ahuja S, Akkin T, Allu SR, Brake J, Boas DA, Buckley EM, Campbell RE, Chen AI, Cheng X, Čižmár T, Costantini I, De Vittorio M, Devor A, Doran PR, El Khatib M, Emiliani V, Fomin-Thunemann N, Fainman Y, Fernandez-Alfonso T, Ferri CGL, Gilad A, Han X, Harris A, Hillman EMC, Hochgeschwender U, Holt MG, Ji N, Kılıç K, Lake EMR, Li L, Li T, Mächler P, Miller EW, Mesquita RC, Nadella KMNS, Nägerl UV, Nasu Y, Nimmerjahn A, Ondráčková P, Pavone FS, Perez Campos C, Peterka DS, Pisano F, Pisanello F, Puppo F, Sabatini BL, Sadegh S, Sakadzic S, Shoham S, Shroff SN, Silver RA, Sims RR, Smith SL, Srinivasan VJ, Thunemann M, Tian L, Tian L, Troxler T, Valera A, Vaziri A, Vinogradov SA, Vitale F, Wang LV, Uhlířová H, Xu C, Yang C, Yang MH, Yellen G, Yizhar O, Zhao Y. Neurophotonic tools for microscopic measurements and manipulation: status report. NEUROPHOTONICS 2022; 9:013001. [PMID: 35493335 PMCID: PMC9047450 DOI: 10.1117/1.nph.9.s1.013001] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Neurophotonics was launched in 2014 coinciding with the launch of the BRAIN Initiative focused on development of technologies for advancement of neuroscience. For the last seven years, Neurophotonics' agenda has been well aligned with this focus on neurotechnologies featuring new optical methods and tools applicable to brain studies. While the BRAIN Initiative 2.0 is pivoting towards applications of these novel tools in the quest to understand the brain, this status report reviews an extensive and diverse toolkit of novel methods to explore brain function that have emerged from the BRAIN Initiative and related large-scale efforts for measurement and manipulation of brain structure and function. Here, we focus on neurophotonic tools mostly applicable to animal studies. A companion report, scheduled to appear later this year, will cover diffuse optical imaging methods applicable to noninvasive human studies. For each domain, we outline the current state-of-the-art of the respective technologies, identify the areas where innovation is needed, and provide an outlook for the future directions.
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Affiliation(s)
- Ahmed S. Abdelfattah
- Brown University, Department of Neuroscience, Providence, Rhode Island, United States
| | - Sapna Ahuja
- University of Pennsylvania, Perelman School of Medicine, Department of Biochemistry and Biophysics, Philadelphia, Pennsylvania, United States
- University of Pennsylvania, School of Arts and Sciences, Department of Chemistry, Philadelphia, Pennsylvania, United States
| | - Taner Akkin
- University of Minnesota, Department of Biomedical Engineering, Minneapolis, Minnesota, United States
| | - Srinivasa Rao Allu
- University of Pennsylvania, Perelman School of Medicine, Department of Biochemistry and Biophysics, Philadelphia, Pennsylvania, United States
- University of Pennsylvania, School of Arts and Sciences, Department of Chemistry, Philadelphia, Pennsylvania, United States
| | - Joshua Brake
- Harvey Mudd College, Department of Engineering, Claremont, California, United States
| | - David A. Boas
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - Erin M. Buckley
- Georgia Institute of Technology and Emory University, Wallace H. Coulter Department of Biomedical Engineering, Atlanta, Georgia, United States
- Emory University, Department of Pediatrics, Atlanta, Georgia, United States
| | - Robert E. Campbell
- University of Tokyo, Department of Chemistry, Tokyo, Japan
- University of Alberta, Department of Chemistry, Edmonton, Alberta, Canada
| | - Anderson I. Chen
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - Xiaojun Cheng
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - Tomáš Čižmár
- Institute of Scientific Instruments of the Czech Academy of Sciences, Brno, Czech Republic
| | - Irene Costantini
- University of Florence, European Laboratory for Non-Linear Spectroscopy, Department of Biology, Florence, Italy
- National Institute of Optics, National Research Council, Rome, Italy
| | - Massimo De Vittorio
- Istituto Italiano di Tecnologia, Center for Biomolecular Nanotechnologies, Arnesano, Italy
| | - Anna Devor
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
- Massachusetts General Hospital, Harvard Medical School, Athinoula A. Martinos Center for Biomedical Imaging, Charlestown, Massachusetts, United States
| | - Patrick R. Doran
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - Mirna El Khatib
- University of Pennsylvania, Perelman School of Medicine, Department of Biochemistry and Biophysics, Philadelphia, Pennsylvania, United States
- University of Pennsylvania, School of Arts and Sciences, Department of Chemistry, Philadelphia, Pennsylvania, United States
| | | | - Natalie Fomin-Thunemann
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - Yeshaiahu Fainman
- University of California San Diego, Department of Electrical and Computer Engineering, La Jolla, California, United States
| | - Tomas Fernandez-Alfonso
- University College London, Department of Neuroscience, Physiology and Pharmacology, London, United Kingdom
| | - Christopher G. L. Ferri
- University of California San Diego, Departments of Neurosciences, La Jolla, California, United States
| | - Ariel Gilad
- The Hebrew University of Jerusalem, Institute for Medical Research Israel–Canada, Department of Medical Neurobiology, Faculty of Medicine, Jerusalem, Israel
| | - Xue Han
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - Andrew Harris
- Weizmann Institute of Science, Department of Brain Sciences, Rehovot, Israel
| | | | - Ute Hochgeschwender
- Central Michigan University, Department of Neuroscience, Mount Pleasant, Michigan, United States
| | - Matthew G. Holt
- University of Porto, Instituto de Investigação e Inovação em Saúde (i3S), Porto, Portugal
| | - Na Ji
- University of California Berkeley, Department of Physics, Berkeley, California, United States
| | - Kıvılcım Kılıç
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - Evelyn M. R. Lake
- Yale School of Medicine, Department of Radiology and Biomedical Imaging, New Haven, Connecticut, United States
| | - Lei Li
- California Institute of Technology, Andrew and Peggy Cherng Department of Medical Engineering, Department of Electrical Engineering, Pasadena, California, United States
| | - Tianqi Li
- University of Minnesota, Department of Biomedical Engineering, Minneapolis, Minnesota, United States
| | - Philipp Mächler
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - Evan W. Miller
- University of California Berkeley, Departments of Chemistry and Molecular & Cell Biology and Helen Wills Neuroscience Institute, Berkeley, California, United States
| | | | | | - U. Valentin Nägerl
- Interdisciplinary Institute for Neuroscience University of Bordeaux & CNRS, Bordeaux, France
| | - Yusuke Nasu
- University of Tokyo, Department of Chemistry, Tokyo, Japan
| | - Axel Nimmerjahn
- Salk Institute for Biological Studies, Waitt Advanced Biophotonics Center, La Jolla, California, United States
| | - Petra Ondráčková
- Institute of Scientific Instruments of the Czech Academy of Sciences, Brno, Czech Republic
| | - Francesco S. Pavone
- National Institute of Optics, National Research Council, Rome, Italy
- University of Florence, European Laboratory for Non-Linear Spectroscopy, Department of Physics, Florence, Italy
| | - Citlali Perez Campos
- Columbia University, Zuckerman Mind Brain Behavior Institute, New York, United States
| | - Darcy S. Peterka
- Columbia University, Zuckerman Mind Brain Behavior Institute, New York, United States
| | - Filippo Pisano
- Istituto Italiano di Tecnologia, Center for Biomolecular Nanotechnologies, Arnesano, Italy
| | - Ferruccio Pisanello
- Istituto Italiano di Tecnologia, Center for Biomolecular Nanotechnologies, Arnesano, Italy
| | - Francesca Puppo
- University of California San Diego, Departments of Neurosciences, La Jolla, California, United States
| | - Bernardo L. Sabatini
- Harvard Medical School, Howard Hughes Medical Institute, Department of Neurobiology, Boston, Massachusetts, United States
| | - Sanaz Sadegh
- University of California San Diego, Departments of Neurosciences, La Jolla, California, United States
| | - Sava Sakadzic
- Massachusetts General Hospital, Harvard Medical School, Athinoula A. Martinos Center for Biomedical Imaging, Charlestown, Massachusetts, United States
| | - Shy Shoham
- New York University Grossman School of Medicine, Tech4Health and Neuroscience Institutes, New York, New York, United States
| | - Sanaya N. Shroff
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - R. Angus Silver
- University College London, Department of Neuroscience, Physiology and Pharmacology, London, United Kingdom
| | - Ruth R. Sims
- Sorbonne University, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Spencer L. Smith
- University of California Santa Barbara, Department of Electrical and Computer Engineering, Santa Barbara, California, United States
| | - Vivek J. Srinivasan
- New York University Langone Health, Departments of Ophthalmology and Radiology, New York, New York, United States
| | - Martin Thunemann
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - Lei Tian
- Boston University, Departments of Electrical Engineering and Biomedical Engineering, Boston, Massachusetts, United States
| | - Lin Tian
- University of California Davis, Department of Biochemistry and Molecular Medicine, Davis, California, United States
| | - Thomas Troxler
- University of Pennsylvania, Perelman School of Medicine, Department of Biochemistry and Biophysics, Philadelphia, Pennsylvania, United States
- University of Pennsylvania, School of Arts and Sciences, Department of Chemistry, Philadelphia, Pennsylvania, United States
| | - Antoine Valera
- University College London, Department of Neuroscience, Physiology and Pharmacology, London, United Kingdom
| | - Alipasha Vaziri
- Rockefeller University, Laboratory of Neurotechnology and Biophysics, New York, New York, United States
- The Rockefeller University, The Kavli Neural Systems Institute, New York, New York, United States
| | - Sergei A. Vinogradov
- University of Pennsylvania, Perelman School of Medicine, Department of Biochemistry and Biophysics, Philadelphia, Pennsylvania, United States
- University of Pennsylvania, School of Arts and Sciences, Department of Chemistry, Philadelphia, Pennsylvania, United States
| | - Flavia Vitale
- Center for Neuroengineering and Therapeutics, Departments of Neurology, Bioengineering, Physical Medicine and Rehabilitation, Philadelphia, Pennsylvania, United States
| | - Lihong V. Wang
- California Institute of Technology, Andrew and Peggy Cherng Department of Medical Engineering, Department of Electrical Engineering, Pasadena, California, United States
| | - Hana Uhlířová
- Institute of Scientific Instruments of the Czech Academy of Sciences, Brno, Czech Republic
| | - Chris Xu
- Cornell University, School of Applied and Engineering Physics, Ithaca, New York, United States
| | - Changhuei Yang
- California Institute of Technology, Departments of Electrical Engineering, Bioengineering and Medical Engineering, Pasadena, California, United States
| | - Mu-Han Yang
- University of California San Diego, Department of Electrical and Computer Engineering, La Jolla, California, United States
| | - Gary Yellen
- Harvard Medical School, Department of Neurobiology, Boston, Massachusetts, United States
| | - Ofer Yizhar
- Weizmann Institute of Science, Department of Brain Sciences, Rehovot, Israel
| | - Yongxin Zhao
- Carnegie Mellon University, Department of Biological Sciences, Pittsburgh, Pennsylvania, United States
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Bando Y, Wenzel M, Yuste R. Simultaneous two-photon imaging of action potentials and subthreshold inputs in vivo. Nat Commun 2021; 12:7229. [PMID: 34893595 PMCID: PMC8664861 DOI: 10.1038/s41467-021-27444-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 11/18/2021] [Indexed: 11/09/2022] Open
Abstract
To better understand the input-output computations of neuronal populations, we developed ArcLight-ST, a genetically-encoded voltage indicator, to specifically measure subthreshold membrane potentials. We combined two-photon imaging of voltage and calcium, and successfully discriminated subthreshold inputs and spikes with cellular resolution in vivo. We demonstrate the utility of the method by mapping epileptic seizures progression through cortical circuits, revealing divergent sub- and suprathreshold dynamics within compartmentalized epileptic micronetworks. Two-photon, two-color imaging of calcium and voltage enables mapping of inputs and outputs in neuronal populations in living animals.
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Affiliation(s)
- Yuki Bando
- NeuroTechnology Center, Department of Biological Sciences, Columbia University, New York, NY, 10027, USA. .,Department of Organ and Tissue Anatomy, Hamamatsu University School of Medicine, Hamamatsu, 431-3192, Japan.
| | - Michael Wenzel
- NeuroTechnology Center, Department of Biological Sciences, Columbia University, New York, NY, 10027, USA.,Department of Epileptology, University of Bonn, 53127, Bonn, Germany
| | - Rafael Yuste
- NeuroTechnology Center, Department of Biological Sciences, Columbia University, New York, NY, 10027, USA
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67
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Bloxham W, Brinks D, Kheifets S, Cohen AE. Linearly polarized excitation enhances signals from fluorescent voltage indicators. Biophys J 2021; 120:5333-5342. [PMID: 34710379 DOI: 10.1016/j.bpj.2021.10.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 10/10/2021] [Accepted: 10/20/2021] [Indexed: 10/20/2022] Open
Abstract
Voltage imaging in cells requires high-speed recording of small fluorescent signals, often leading to low signal/noise ratios. Because voltage indicators are membrane bound, their orientations are partially constrained by the plane of the membrane. We explored whether tuning the linear polarization of excitation light could enhance voltage indicator fluorescence. We tested a panel of dye- and protein-based voltage indicators in mammalian cells. The dye BeRST1 showed a 73% increase in brightness between the least and most favorable polarizations. The protein-based reporter ASAP1 showed a 22% increase in brightness, and QuasAr3 showed a 14% increase in brightness. In very thin neurites expressing QuasAr3, improvements were anomalously large, with a 170% increase in brightness between polarization parallel versus perpendicular to the dendrite. Signal/noise ratios of optically recorded action potentials were increased by up to 50% in neurites expressing QuasAr3. These results demonstrate that polarization control can be a facile means to enhance signals from fluorescent voltage indicators, particularly in thin neurites or in high-background environments.
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Affiliation(s)
- William Bloxham
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts; Department of Physics, Harvard University, Cambridge, Massachusetts; Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Daan Brinks
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts; Department of Imaging Physics, Delft University of Technology, Delft, the Netherlands; Department of Molecular Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Simon Kheifets
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts
| | - Adam E Cohen
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts; Department of Physics, Harvard University, Cambridge, Massachusetts.
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68
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Ortiz G, Liu P, Deal PE, Nensel AK, Martinez KN, Shamardani K, Adesnik H, Miller EW. A silicon-rhodamine chemical-genetic hybrid for far red voltage imaging from defined neurons in brain slice. RSC Chem Biol 2021; 2:1594-1599. [PMID: 34977574 PMCID: PMC8637932 DOI: 10.1039/d1cb00156f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 09/27/2021] [Indexed: 02/06/2023] Open
Abstract
We describe the design, synthesis, and application of voltage-sensitive silicon rhodamines. Based on the Berkeley Red Sensor of Transmembrane potential, or BeRST, scaffold, the new dyes possess an isomeric molecular wire for improved alignment in the plasma membrane and 2′ carboxylic acids for ready functionalization. The new isoBeRST dyes have a voltage sensitivity of 24% ΔF/F per 100 mV. Combined with a flexible polyethyleneglycol (PEG) linker and a chloroalkane HaloTag ligand, isoBeRST dyes enable voltage imaging from genetically defined cells and neurons and provide improved labeling over previous, rhodamine-based hybrid strategies. isoBeRST-Halo hybrid indicators achieve single-trial voltage imaging of membrane potential dynamics from cultured hippocampal neurons or cortical neurons in brain slices. With far-red/near infrared excitation and emission, turn-on response to action potentials, and effective cell labeling in thick tissue, the new isoBeRST-Halo derivatives provide an important complement to voltage imaging in neurobiology. Small-molecule enzyme hybrids pair a far-red voltage-sensitive fluorophore with a cell-surface expressed HaloTag enzyme via a flexible linker to enable voltage imaging from genetically defined neurons in culture and brain slice.![]()
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Affiliation(s)
- Gloria Ortiz
- Department of Chemistry, University of California Berkeley California 94720-1460 USA
| | - Pei Liu
- Department of Chemistry, University of California Berkeley California 94720-1460 USA
| | - Parker E Deal
- Department of Chemistry, University of California Berkeley California 94720-1460 USA
| | - Ashley K Nensel
- Department of Chemistry, University of California Berkeley California 94720-1460 USA
| | - Kayli N Martinez
- Department of Chemistry, University of California Berkeley California 94720-1460 USA
| | - Kiarash Shamardani
- Department of Molecular & Cell Biology, University of California Berkeley California 94720-1460 USA
| | - Hillel Adesnik
- Department of Molecular & Cell Biology, University of California Berkeley California 94720-1460 USA.,Helen Wills Neuroscience Institute, University of California Berkeley California 94720-1460 USA
| | - Evan W Miller
- Department of Chemistry, University of California Berkeley California 94720-1460 USA .,Department of Molecular & Cell Biology, University of California Berkeley California 94720-1460 USA.,Helen Wills Neuroscience Institute, University of California Berkeley California 94720-1460 USA
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69
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Penzkofer A, Silapetere A, Hegemann P. Photocycle dynamics of the Archaerhodopsin 3 based fluorescent voltage sensor Archon2. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2021; 225:112331. [PMID: 34688164 DOI: 10.1016/j.jphotobiol.2021.112331] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 09/21/2021] [Accepted: 10/05/2021] [Indexed: 11/28/2022]
Abstract
The retinal photocycle dynamics of the fluorescent voltage sensor Archon2 in pH 8 Tris buffer was studied. Archon2 is a mutant of Archaerhodopsin 3 (Arch) from Halorubrum sodomense obtained by a robotic multidimensional directed evolution approach (Archon2 = Arch T56P-P60S-T80P-D95H-T99S-T116I-F161V-T183I-L197I-A225C). The samples were photo-excited to the first absorption band of the protonated retinal Schiff base (PRSB) Ret_586 (absorption maximum at λmax = 586 nm, excitation wavelengths λexc = 590 nm and 632.8 nm). The photocycle dynamics were studied by recording absorption spectra during light exposure and after light exposure. Ret_586 photoisomerized to Ret_535 (main component) and Ret_485 (minor component). Ret_535 backward photoisomerized to Ret_586 in light-adapted state (named Ret_586la) and partly deprotonated to neutral retinal Schiff base (RSB) Ret_372 in light adapted state (named Ret_372la, same isomer form as Ret_535). After excitation light switch-off Ret_372la recovered to Ret_372 in dark-adapted state (Ret_372da) which slowly re-protonated to Ret_535, and Ret_535 slowly isomerized back to Ret_586 in dark-adapted state (Ret_586da). Photocycle schemes and reaction coordinate diagrams are developed and photocycle parameters are determined.
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Affiliation(s)
- Alfons Penzkofer
- Fakultät für Physik, Universität Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany.
| | - Arita Silapetere
- Experimentelle Biophysik, Institut für Biologie, Humboldt Universität zu Berlin, Invalidenstraße 42, D-10115 Berlin, Germany
| | - Peter Hegemann
- Experimentelle Biophysik, Institut für Biologie, Humboldt Universität zu Berlin, Invalidenstraße 42, D-10115 Berlin, Germany
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70
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Xiao S, Lowet E, Gritton HJ, Fabris P, Wang Y, Sherman J, Mount RA, Tseng HA, Man HY, Straub C, Piatkevich KD, Boyden ES, Mertz J, Han X. Large-scale voltage imaging in behaving mice using targeted illumination. iScience 2021; 24:103263. [PMID: 34761183 PMCID: PMC8567393 DOI: 10.1016/j.isci.2021.103263] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 08/30/2021] [Accepted: 10/11/2021] [Indexed: 11/26/2022] Open
Abstract
Recent improvements in genetically encoded voltage indicators enabled optical imaging of action potentials and subthreshold transmembrane voltage in vivo. To perform high-speed voltage imaging of many neurons simultaneously over a large anatomical area, widefield microscopy remains an essential tool. However, the lack of optical sectioning makes widefield microscopy prone to background cross-contamination. We implemented a digital-micromirror-device-based targeted illumination strategy to restrict illumination to the cells of interest and quantified the resulting improvement both theoretically and experimentally with SomArchon expressing neurons. We found that targeted illumination increased SomArchon signal contrast, decreased photobleaching, and reduced background cross-contamination. With the use of a high-speed, large-area sCMOS camera, we routinely imaged tens of spiking neurons simultaneously over minutes in behaving mice. Thus, the targeted illumination strategy described here offers a simple solution for widefield voltage imaging of many neurons over a large field of view in behaving animals.
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Affiliation(s)
- Sheng Xiao
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - Eric Lowet
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - Howard J. Gritton
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
- Department of Comparative Biosciences, University of Illinois, Urbana, IL 61802, USA
| | - Pierre Fabris
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - Yangyang Wang
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - Jack Sherman
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - Rebecca A. Mount
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - Hua-an Tseng
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - Heng-Ye Man
- Department of Biology, Boston University, Boston, MA 02215, USA
| | - Christoph Straub
- Department of Biomedical Sciences, College of Osteopathic Medicine, University of New England, Biddeford, ME 04005, USA
| | - Kiryl D. Piatkevich
- School of Life Sciences, Westlake University, Westlake Laboratory of Life Sciences and Biomedicine, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Edward S. Boyden
- MIT McGovern Institute for Brain Research, MIT, Cambridge, MA 02139, USA
- Howard Hughes Medical Institute, MIT, Cambridge, MA 02139, USA
| | - Jerome Mertz
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - Xue Han
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
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71
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Kirk MJ, Benlian BR, Han Y, Gold A, Ravi A, Deal PE, Molina RS, Drobizhev M, Dickman D, Scott K, Miller EW. Voltage Imaging in Drosophila Using a Hybrid Chemical-Genetic Rhodamine Voltage Reporter. Front Neurosci 2021; 15:754027. [PMID: 34867164 PMCID: PMC8637050 DOI: 10.3389/fnins.2021.754027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 10/15/2021] [Indexed: 12/03/2022] Open
Abstract
We combine a chemically-synthesized, voltage-sensitive fluorophore with a genetically encoded, self-labeling enzyme to enable voltage imaging in Drosophila melanogaster. Previously, we showed that a rhodamine voltage reporter (RhoVR) combined with the HaloTag self-labeling enzyme could be used to monitor membrane potential changes from mammalian neurons in culture and brain slice. Here, we apply this hybrid RhoVR-Halo approach in vivo to achieve selective neuron labeling in intact fly brains. We generate a Drosophila UAS-HaloTag reporter line in which the HaloTag enzyme is expressed on the surface of cells. We validate the voltage sensitivity of this new construct in cell culture before driving expression of HaloTag in specific brain neurons in flies. We show that selective labeling of synapses, cells, and brain regions can be achieved with RhoVR-Halo in either larval neuromuscular junction (NMJ) or in whole adult brains. Finally, we validate the voltage sensitivity of RhoVR-Halo in fly tissue via dual-electrode/imaging at the NMJ, show the efficacy of this approach for measuring synaptic excitatory post-synaptic potentials (EPSPs) in muscle cells, and perform voltage imaging of carbachol-evoked depolarization and osmolarity-evoked hyperpolarization in projection neurons and in interoceptive subesophageal zone neurons in fly brain explants following in vivo labeling. We envision the turn-on response to depolarizations, fast response kinetics, and two-photon compatibility of chemical indicators, coupled with the cellular and synaptic specificity of genetically-encoded enzymes, will make RhoVR-Halo a powerful complement to neurobiological imaging in Drosophila.
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Affiliation(s)
- Molly J. Kirk
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Brittany R. Benlian
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Yifu Han
- Department of Neurobiology, University of Southern California, Los Angeles, CA, United States
| | - Arya Gold
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, United States
| | - Ashvin Ravi
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, United States
| | - Parker E. Deal
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, United States
| | - Rosana S. Molina
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, United States
| | - Mikhail Drobizhev
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, United States
| | - Dion Dickman
- Department of Neurobiology, University of Southern California, Los Angeles, CA, United States
| | - Kristin Scott
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States
- Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA, United States
| | - Evan W. Miller
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, United States
- Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA, United States
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72
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Vollmer KM, Doncheck EM, Grant RI, Winston KT, Romanova EV, Bowen CW, Siegler PN, Green LM, Bobadilla AC, Trujillo-Pisanty I, Kalivas PW, Otis JM. A Novel Assay Allowing Drug Self-Administration, Extinction, and Reinstatement Testing in Head-Restrained Mice. Front Behav Neurosci 2021; 15:744715. [PMID: 34776891 PMCID: PMC8585999 DOI: 10.3389/fnbeh.2021.744715] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 09/30/2021] [Indexed: 01/15/2023] Open
Abstract
Multiphoton microscopy is one of several new technologies providing unprecedented insight into the activity dynamics and function of neural circuits. Unfortunately, some of these technologies require experimentation in head-restrained animals, limiting the behavioral repertoire that can be integrated and studied. This issue is especially evident in drug addiction research, as no laboratories have coupled multiphoton microscopy with simultaneous intravenous drug self-administration, a behavioral paradigm that has predictive validity for treatment outcomes and abuse liability. Here, we describe a new experimental assay wherein head-restrained mice will press an active lever, but not inactive lever, for intravenous delivery of heroin or cocaine. Similar to freely moving animals, we find that lever pressing is suppressed through daily extinction training and subsequently reinstated through the presentation of relapse-provoking triggers (drug-associative cues, the drug itself, and stressors). Finally, we show that head-restrained mice will show similar patterns of behavior for oral delivery of a sucrose reward, a common control used for drug self-administration experiments. Overall, these data demonstrate the feasibility of combining drug self-administration experiments with technologies that require head-restraint, such as multiphoton imaging. The assay described could be replicated by interested labs with readily available materials to aid in identifying the neural underpinnings of substance use disorder.
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Affiliation(s)
- Kelsey M Vollmer
- Department of Neuroscience, Medical University of South Carolina, Charleston, SC, United States
| | - Elizabeth M Doncheck
- Department of Neuroscience, Medical University of South Carolina, Charleston, SC, United States
| | - Roger I Grant
- Department of Neuroscience, Medical University of South Carolina, Charleston, SC, United States
| | - Kion T Winston
- Department of Neuroscience, Medical University of South Carolina, Charleston, SC, United States
| | - Elizaveta V Romanova
- Department of Neuroscience, Medical University of South Carolina, Charleston, SC, United States
| | - Christopher W Bowen
- Department of Neuroscience, Medical University of South Carolina, Charleston, SC, United States
| | - Preston N Siegler
- Department of Neuroscience, Medical University of South Carolina, Charleston, SC, United States
| | - Lisa M Green
- Department of Neuroscience, Medical University of South Carolina, Charleston, SC, United States
| | | | | | - Peter W Kalivas
- Department of Neuroscience, Medical University of South Carolina, Charleston, SC, United States
| | - James M Otis
- Department of Neuroscience, Medical University of South Carolina, Charleston, SC, United States.,Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, United States
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73
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Abstract
Rhodopsins are photoreceptive membrane proteins consisting of a common heptahelical transmembrane architecture that contains a retinal chromophore. Rhodopsin was first discovered in the animal retina in 1876, but a different type of rhodopsin, bacteriorhodopsin, was reported to be present in the cell membrane of an extreme halophilic archaeon, Halobacterium salinarum, 95 years later. Although these findings were made by physiological observation of pigmented tissue and cell bodies, recent progress in genomic and metagenomic analyses has revealed that there are more than 10,000 microbial rhodopsins and 9000 animal rhodopsins with large diversity and tremendous new functionality. In this Cell Science at a Glance article and accompanying poster, we provide an overview of the diversity of functions, structures, color discrimination mechanisms and optogenetic applications of these two rhodopsin families, and will also highlight the third distinctive rhodopsin family, heliorhodopsin.
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Affiliation(s)
- Takashi Nagata
- The Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8581, Japan.,PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Keiichi Inoue
- The Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8581, Japan
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74
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Lin PY, Hwang SPL, Lee CH, Chen BC. Two-photon scanned light sheet fluorescence microscopy with axicon imaging for fast volumetric imaging. JOURNAL OF BIOMEDICAL OPTICS 2021; 26:JBO-210219RR. [PMID: 34796706 PMCID: PMC8601431 DOI: 10.1117/1.jbo.26.11.116503] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 11/01/2021] [Indexed: 05/31/2023]
Abstract
SIGNIFICANCE Two-photon microscopy has become the standard platform for deep-tissue fluorescence imaging. However, the use of point scanning in conventional two-photon microscopy limits the speed of volumetric image acquisition. AIM To obtain fast and deep volumetric images, we combine two-photon light sheet fluorescence microscopy (2p-LSFM) and axicon imaging that yields an extended depth of field (DOF) in 2p-LSFM. APPROACH Axicon imaging is achieved by imposing an axicon lens in the detection part of LSFM. RESULTS The DOF with axicon imaging is extended more than 20-fold over that of a conventional imaging lens, liberating the synchronized scanning in LSFM. We captured images of dynamic beating hearts and red blood cells in zebrafish larvae at volume acquisition rates up to 30 Hz. CONCLUSIONS We demonstrate the fast three-dimensional imaging capability of 2p-LSFM with axicon imaging by recording the rapid dynamics of physiological processes.
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Affiliation(s)
- Po-Yen Lin
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Sheng-Ping L. Hwang
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Chi-Hon Lee
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Bi-Chang Chen
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
- Research Center for Applied Sciences, Academia Sinica, Taipei, Taiwan
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75
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Bringing together the best of chemistry and biology: hybrid indicators for imaging neuronal membrane potential. J Neurosci Methods 2021; 363:109348. [PMID: 34480955 DOI: 10.1016/j.jneumeth.2021.109348] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 08/27/2021] [Accepted: 08/30/2021] [Indexed: 12/15/2022]
Abstract
Membrane potential is an indispensable biophysical signal in neurobiology. Imaging neuronal electrical signals with fluorescent indicators allows for non-invasive recording at high spatial resolution. Over the past decades, both genetically encoded voltage indicators (GEVIs) and organic voltage sensing dyes (OVSDs) have been developed to achieve imaging membrane potential dynamics in cultured neurons and in vivo. More recently, hybrid voltage indicators have gained increasing attention due to their superior fluorescent quantum yield and photostability as compared to conventional GEVIs. In this mini-review, we summarize the design, characterization and biological applications of hybrid voltage indicators, and discuss future improvements.
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76
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Narcisse D, Mustafi SM, Carlson M, Batabyal S, Kim S, Wright W, Kumar Mohanty S. Bioluminescent Multi-Characteristic Opsin for Simultaneous Optical Stimulation and Continuous Monitoring of Cortical Activities. Front Cell Neurosci 2021; 15:750663. [PMID: 34759801 PMCID: PMC8573050 DOI: 10.3389/fncel.2021.750663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 09/20/2021] [Indexed: 12/02/2022] Open
Abstract
Stimulation and continuous monitoring of neural activities at cellular resolution are required for the understanding of the sensory processing of stimuli and development of effective neuromodulation therapies. We present bioluminescence multi-characteristic opsin (bMCOII), a hybrid optogenetic actuator, and a bioluminescence Ca2+ sensor for excitation-free, continuous monitoring of neural activities in the visual cortex, with high spatiotemporal resolution. An exceptionally low intensity (10 μW/mm2) of light could elicit neural activation that could be detected by Ca2+ bioluminescence imaging. An uninterrupted (>14 h) recording of visually evoked neural activities in the cortex of mice enabled the determination of strength of sensory activation. Furthermore, an artificial intelligence-based neural activation parameter transformed Ca2+ bioluminescence signals to network activity patterns. During continuous Ca2+-bioluminescence recordings, visual cortical activity peaked at the seventh to eighth hour of anesthesia, coinciding with circadian rhythm. For both direct optogenetic stimulation in cortical slices and visually evoked activities in the visual cortex, we observed secondary delayed Ca2+-bioluminescence responses, suggesting the involvement of neuron-astrocyte-neuron pathway. Our approach will enable the development of a modular and scalable interface system capable of serving a multiplicity of applications to modulate and monitor large-scale activities in the brain.
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77
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Somogyi A, Wolf E. Increased Signal Delays and Unaltered Synaptic Input Pattern Recognition in Layer III Neocortical Pyramidal Neurons of the rTg4510 Mouse Model of Tauopathy: A Computer Simulation Study With Passive Membrane. Front Neurosci 2021; 15:721773. [PMID: 34733131 PMCID: PMC8558261 DOI: 10.3389/fnins.2021.721773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 09/22/2021] [Indexed: 11/13/2022] Open
Abstract
Abnormal tau proteins are involved in pathology of many neurodegenerative disorders. Transgenic rTg4510 mice express high levels of human tau protein with P301L mutation linked to chromosome 17 that has been associated with frontotemporal dementia with parkinsonism. By 9 months of age, these mice recapitulate key features of human tauopathies, including presence of hyperphosphorylated tau and neurofibrillary tangles (NFTs) in brain tissue, atrophy and loss of neurons and synapses, and hyperexcitability of neurons, as well as cognitive deficiencies. We investigated effects of such human mutant tau protein on neuronal membrane, subthreshold dendritic signaling, and synaptic input pattern recognition/discrimination in layer III frontal transgenic (TG) pyramidal neurons of 9-month-old rTg4510 mice and compared these characteristics to those of wild-type (WT) pyramidal neurons from age-matched control mice. Passive segmental cable models of WT and TG neurons were set up in the NEURON simulator by using three-dimensionally reconstructed morphology and electrophysiological data of these cells. Our computer simulations predict leakage resistance and capacitance of neuronal membrane to be unaffected by the mutant tau protein. Computer models of TG neurons showed only modest alterations in distance dependence of somatopetal voltage and current transfers along dendrites and in rise times and half-widths of somatic Excitatory Postsynaptic Potential (EPSPs) relative to WT control. In contrast, a consistent and statistically significant slowdown was detected in the speed of simulated subthreshold dendritic signal propagation in all regions of the dendritic surface of mutant neurons. Predictors of synaptic input pattern recognition/discrimination remained unaltered in model TG neurons. This suggests that tau pathology is primarily associated with failures/loss in synaptic connections rather than with altered intraneuronal synaptic integration in neurons of affected networks.
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Affiliation(s)
- Attila Somogyi
- Department of Anatomy, Histology and Embryology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
- Department of Emergency Medicine, University of Debrecen, Debrecen, Hungary
| | - Ervin Wolf
- Department of Anatomy, Histology and Embryology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
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78
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Zhou Y, Ding M, Nagel G, Konrad KR, Gao S. Advances and prospects of rhodopsin-based optogenetics in plant research. PLANT PHYSIOLOGY 2021; 187:572-589. [PMID: 35237820 PMCID: PMC8491038 DOI: 10.1093/plphys/kiab338] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 07/05/2021] [Indexed: 05/20/2023]
Abstract
Microbial rhodopsins have advanced optogenetics since the discovery of channelrhodopsins almost two decades ago. During this time an abundance of microbial rhodopsins has been discovered, engineered, and improved for studies in neuroscience and other animal research fields. Optogenetic applications in plant research, however, lagged largely behind. Starting with light-regulated gene expression, optogenetics has slowly expanded into plant research. The recently established all-trans retinal production in plants now enables the use of many microbial opsins, bringing extra opportunities to plant research. In this review, we summarize the recent advances of rhodopsin-based plant optogenetics and provide a perspective for future use, combined with fluorescent sensors to monitor physiological parameters.
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Affiliation(s)
- Yang Zhou
- Institute of Physiology, Department of Neurophysiology, Biocenter, University of Wuerzburg, Wuerzburg 97070, Germany
| | - Meiqi Ding
- Institute for Molecular Plant Physiology and Biophysics, Julius-von-Sachs-Institute, Biocenter, University of Wuerzburg, Wuerzburg 97082, Germany
| | - Georg Nagel
- Institute of Physiology, Department of Neurophysiology, Biocenter, University of Wuerzburg, Wuerzburg 97070, Germany
| | - Kai R. Konrad
- Institute for Molecular Plant Physiology and Biophysics, Julius-von-Sachs-Institute, Biocenter, University of Wuerzburg, Wuerzburg 97082, Germany
| | - Shiqiang Gao
- Institute of Physiology, Department of Neurophysiology, Biocenter, University of Wuerzburg, Wuerzburg 97070, Germany
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79
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Shcherbakova DM. Near-infrared and far-red genetically encoded indicators of neuronal activity. J Neurosci Methods 2021; 362:109314. [PMID: 34375713 PMCID: PMC8403644 DOI: 10.1016/j.jneumeth.2021.109314] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 06/15/2021] [Accepted: 08/05/2021] [Indexed: 12/18/2022]
Abstract
Genetically encoded fluorescent indicators of neuronal activity are ultimately developed to dissect functions of neuronal ensembles during behavior in living animals. Recent development of near-infrared shifted calcium and voltage indicators moved us closer to this goal and enabled crosstalk-free combination with blue light-controlled optogenetic tools for all-optical control and readout. Here I discuss designs of recent near-infrared and far-red calcium and voltage indicators, compare their properties and performance, and overview their applications to spectral multiplexing and in vivo imaging. I also provide perspectives for further development.
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Affiliation(s)
- Daria M Shcherbakova
- Department of Anatomy and Structural Biology and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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80
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Luciani A, Denley MCS, Govers LP, Sorrentino V, Froese DS. Mitochondrial disease, mitophagy, and cellular distress in methylmalonic acidemia. Cell Mol Life Sci 2021; 78:6851-6867. [PMID: 34524466 PMCID: PMC8558192 DOI: 10.1007/s00018-021-03934-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 08/18/2021] [Accepted: 08/30/2021] [Indexed: 01/09/2023]
Abstract
Mitochondria—the intracellular powerhouse in which nutrients are converted into energy in the form of ATP or heat—are highly dynamic, double-membraned organelles that harness a plethora of cellular functions that sustain energy metabolism and homeostasis. Exciting new discoveries now indicate that the maintenance of this ever changing and functionally pleiotropic organelle is particularly relevant in terminally differentiated cells that are highly dependent on aerobic metabolism. Given the central role in maintaining metabolic and physiological homeostasis, dysregulation of the mitochondrial network might therefore confer a potentially devastating vulnerability to high-energy requiring cell types, contributing to a broad variety of hereditary and acquired diseases. In this Review, we highlight the biological functions of mitochondria-localized enzymes from the perspective of understanding—and potentially reversing—the pathophysiology of inherited disorders affecting the homeostasis of the mitochondrial network and cellular metabolism. Using methylmalonic acidemia as a paradigm of complex mitochondrial dysfunction, we discuss how mitochondrial directed-signaling circuitries govern the homeostasis and physiology of specialized cell types and how these may be disturbed in disease. This Review also provides a critical analysis of affected tissues, potential molecular mechanisms, and novel cellular and animal models of methylmalonic acidemia which are being used to develop new therapeutic options for this disease. These insights might ultimately lead to new therapeutics, not only for methylmalonic acidemia, but also for other currently intractable mitochondrial diseases, potentially transforming our ability to regulate homeostasis and health.
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Affiliation(s)
- Alessandro Luciani
- Mechanisms of Inherited Kidney Diseases Group, Institute of Physiology, University of Zurich, 8032, Zurich, Switzerland.
| | - Matthew C S Denley
- Division of Metabolism and Children's Research Center, University Children's Hospital Zurich, University of Zurich, 8032, Zurich, Switzerland
| | - Larissa P Govers
- Mechanisms of Inherited Kidney Diseases Group, Institute of Physiology, University of Zurich, 8032, Zurich, Switzerland
| | - Vincenzo Sorrentino
- Department of Musculo-Skeletal Health, Nestlé Institute of Health Sciences, Nestlé Research, 1015, Lausanne, Switzerland.
| | - D Sean Froese
- Division of Metabolism and Children's Research Center, University Children's Hospital Zurich, University of Zurich, 8032, Zurich, Switzerland.
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81
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Zhang XM, Yokoyama T, Sakamoto M. Imaging Voltage with Microbial Rhodopsins. Front Mol Biosci 2021; 8:738829. [PMID: 34513932 PMCID: PMC8423911 DOI: 10.3389/fmolb.2021.738829] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 08/11/2021] [Indexed: 12/15/2022] Open
Abstract
Membrane potential is the critical parameter that reflects the excitability of a neuron, and it is usually measured by electrophysiological recordings with electrodes. However, this is an invasive approach that is constrained by the problems of lacking spatial resolution and genetic specificity. Recently, the development of a variety of fluorescent probes has made it possible to measure the activity of individual cells with high spatiotemporal resolution. The adaptation of this technique to image electrical activity in neurons has become an informative method to study neural circuits. Genetically encoded voltage indicators (GEVIs) can be used with superior performance to accurately target specific genetic populations and reveal neuronal dynamics on a millisecond scale. Microbial rhodopsins are commonly used as optogenetic actuators to manipulate neuronal activities and to explore the circuit mechanisms of brain function, but they also can be used as fluorescent voltage indicators. In this review, we summarize recent advances in the design and the application of rhodopsin-based GEVIs.
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Affiliation(s)
- Xiao Min Zhang
- Department of Pathophysiology, Guangdong Provincial Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Tatsushi Yokoyama
- Department of Optical Neural and Molecular Physiology, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Masayuki Sakamoto
- Department of Optical Neural and Molecular Physiology, Graduate School of Biostudies, Kyoto University, Kyoto, Japan.,Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency, Kyoto, Japan
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82
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Hiyoshi K, Shiraishi A, Fukuda N, Tsuda S. In vivo wide-field voltage imaging in zebrafish with voltage-sensitive dye and genetically encoded voltage indicator. Dev Growth Differ 2021; 63:417-428. [PMID: 34411280 DOI: 10.1111/dgd.12744] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 07/01/2021] [Accepted: 07/04/2021] [Indexed: 11/28/2022]
Abstract
The brain consists of neural circuits, which are assemblies of various neuron types. For understanding how the brain works, it is essential to identify the functions of each type of neuron and neuronal circuits. Recent advances in our understanding of brain function and its development have been achieved using light to detect neuronal activity. Optical measurement of membrane potentials through voltage imaging is a desirable approach, enabling fast, direct, and simultaneous detection of membrane potentials in a population of neurons. Its high speed and directness can help detect synaptic and action potentials and hyperpolarization, which encode critical information for brain function. Here, we describe in vivo voltage imaging procedures that we have recently established using zebrafish, a powerful animal model in developmental biology and neuroscience. By applying two types of voltage sensors, voltage-sensitive dyes (VSDs, Di-4-ANEPPS) and genetically encoded voltage indicators (GEVIs, ASAP1), spatiotemporal dynamics of voltage signals can be detected in the whole cerebellum and spinal cord in awake fish at single-cell and neuronal population levels. Combining this method with other approaches, such as optogenetics, behavioral analysis, and electrophysiology would facilitate a deeper understanding of the network dynamics of the brain circuitry and its development.
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Affiliation(s)
- Kanae Hiyoshi
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Saitama City, Japan
| | - Asuka Shiraishi
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Saitama City, Japan
| | - Narumi Fukuda
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Saitama City, Japan
| | - Sachiko Tsuda
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Saitama City, Japan.,Integrative Research Center for Life Sciences and Biotechnology, Saitama University, Saitama City, Japan
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83
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Lai QTK, Yip GGK, Wu J, Wong JSJ, Lo MCK, Lee KCM, Le TTHD, So HKH, Ji N, Tsia KK. High-speed laser-scanning biological microscopy using FACED. Nat Protoc 2021; 16:4227-4264. [PMID: 34341580 DOI: 10.1038/s41596-021-00576-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 05/25/2021] [Indexed: 12/28/2022]
Abstract
Laser scanning is used in advanced biological microscopy to deliver superior imaging contrast, resolution and sensitivity. However, it is challenging to scale up the scanning speed required for interrogating a large and heterogeneous population of biological specimens or capturing highly dynamic biological processes at high spatiotemporal resolution. Bypassing the speed limitation of traditional mechanical methods, free-space angular-chirp-enhanced delay (FACED) is an all-optical, passive and reconfigurable laser-scanning approach that has been successfully applied in different microscopy modalities at an ultrafast line-scan rate of 1-80 MHz. Optimal FACED imaging performance requires optimized experimental design and implementation to enable specific high-speed applications. In this protocol, we aim to disseminate information allowing FACED to be applied to a broader range of imaging modalities. We provide (i) a comprehensive guide and design specifications for the FACED hardware; (ii) step-by-step optical implementations of the FACED module including the key custom components; and (iii) the overall image acquisition and reconstruction pipeline. We illustrate two practical imaging configurations: multimodal FACED imaging flow cytometry (bright-field, fluorescence and second-harmonic generation) and kHz 2D two-photon fluorescence microscopy. Users with basic experience in optical microscope operation and software engineering should be able to complete the setup of the FACED imaging hardware and software in ~2-3 months.
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Affiliation(s)
- Queenie T K Lai
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Hong Kong, China
| | - Gwinky G K Yip
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Hong Kong, China
| | - Jianglai Wu
- Department of Physics, University of California, Berkeley, Berkeley, CA, USA.,Chinese Institute for Brain Research, Beijing, China
| | - Justin S J Wong
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Hong Kong, China
| | - Michelle C K Lo
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Hong Kong, China
| | - Kelvin C M Lee
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Hong Kong, China
| | - Tony T H D Le
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Hong Kong, China
| | - Hayden K H So
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Hong Kong, China
| | - Na Ji
- Department of Physics, University of California, Berkeley, Berkeley, CA, USA. .,Department of Molecular and Cell Biology, 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.
| | - Kevin K Tsia
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Hong Kong, China. .,Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin New Town, Hong Kong.
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84
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Miranda C, Howell MR, Lusk JF, Marschall E, Eshima J, Anderson T, Smith BS. Automated microscope-independent fluorescence-guided micropipette. BIOMEDICAL OPTICS EXPRESS 2021; 12:4689-4699. [PMID: 34513218 PMCID: PMC8407805 DOI: 10.1364/boe.431372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 06/23/2021] [Accepted: 06/24/2021] [Indexed: 06/13/2023]
Abstract
Glass micropipette electrodes are commonly used to provide high resolution recordings of neurons. Although it is the gold standard for single cell recordings, it is highly dependent on the skill of the electrophysiologist. Here, we demonstrate a method of guiding micropipette electrodes to neurons by collecting fluorescence at the aperture, using an intra-electrode tapered optical fiber. The use of a tapered fiber for excitation and collection of fluorescence at the micropipette tip couples the feedback mechanism directly to the distance between the target and electrode. In this study, intra-electrode tapered optical fibers provide a targeted robotic approach to labeled neurons that is independent of microscopy.
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Affiliation(s)
- Christopher Miranda
- Arizona State University, School of Biological and Health Systems Engineering, Tempe, AZ 85210, USA
| | - Madeleine R. Howell
- Arizona State University, School of Biological and Health Systems Engineering, Tempe, AZ 85210, USA
| | - Joel F. Lusk
- Arizona State University, School of Biological and Health Systems Engineering, Tempe, AZ 85210, USA
| | - Ethan Marschall
- Arizona State University, School of Biological and Health Systems Engineering, Tempe, AZ 85210, USA
| | - Jarrett Eshima
- Arizona State University, School of Biological and Health Systems Engineering, Tempe, AZ 85210, USA
| | - Trent Anderson
- University of Arizona, College of Medicine – Phoenix, Phoenix, AZ 85004, USA
| | - Barbara S. Smith
- Arizona State University, School of Biological and Health Systems Engineering, Tempe, AZ 85210, USA
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85
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Retrograde Transgene Expression via Neuron-Specific Lentiviral Vector Depends on Both Species and Input Projections. Viruses 2021; 13:v13071387. [PMID: 34372593 PMCID: PMC8310113 DOI: 10.3390/v13071387] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/12/2021] [Accepted: 07/14/2021] [Indexed: 12/22/2022] Open
Abstract
For achieving retrograde gene transfer, we have so far developed two types of lentiviral vectors pseudotyped with fusion envelope glycoprotein, termed HiRet vector and NeuRet vector, consisting of distinct combinations of rabies virus and vesicular stomatitis virus glycoproteins. In the present study, we compared the patterns of retrograde transgene expression for the HiRet vs. NeuRet vectors by testing the cortical input system. These vectors were injected into the motor cortex in rats, marmosets, and macaques, and the distributions of retrograde labels were investigated in the cortex and thalamus. Our histological analysis revealed that the NeuRet vector generally exhibits a higher efficiency of retrograde gene transfer than the HiRet vector, though its capacity of retrograde transgene expression in the macaque brain is unexpectedly low, especially in terms of the intracortical connections, as compared to the rat and marmoset brains. It was also demonstrated that the NeuRet but not the HiRet vector displays sufficiently high neuron specificity and causes no marked inflammatory/immune responses at the vector injection sites in the primate (marmoset and macaque) brains. The present results indicate that the retrograde transgene efficiency of the NeuRet vector varies depending not only on the species but also on the input projections.
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86
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Wagner MJ, Savall J, Hernandez O, Mel G, Inan H, Rumyantsev O, Lecoq J, Kim TH, Li JZ, Ramakrishnan C, Deisseroth K, Luo L, Ganguli S, Schnitzer MJ. A neural circuit state change underlying skilled movements. Cell 2021; 184:3731-3747.e21. [PMID: 34214470 PMCID: PMC8844704 DOI: 10.1016/j.cell.2021.06.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 05/09/2021] [Accepted: 06/01/2021] [Indexed: 11/21/2022]
Abstract
In motor neuroscience, state changes are hypothesized to time-lock neural assemblies coordinating complex movements, but evidence for this remains slender. We tested whether a discrete change from more autonomous to coherent spiking underlies skilled movement by imaging cerebellar Purkinje neuron complex spikes in mice making targeted forelimb-reaches. As mice learned the task, millimeter-scale spatiotemporally coherent spiking emerged ipsilateral to the reaching forelimb, and consistent neural synchronization became predictive of kinematic stereotypy. Before reach onset, spiking switched from more disordered to internally time-locked concerted spiking and silence. Optogenetic manipulations of cerebellar feedback to the inferior olive bi-directionally modulated neural synchronization and reaching direction. A simple model explained the reorganization of spiking during reaching as reflecting a discrete bifurcation in olivary network dynamics. These findings argue that to prepare learned movements, olivo-cerebellar circuits enter a self-regulated, synchronized state promoting motor coordination. State changes facilitating behavioral transitions may generalize across neural systems.
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Affiliation(s)
- Mark J Wagner
- Neurosciences Program, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA; CNC Program, Stanford University, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA.
| | - Joan Savall
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA; CNC Program, Stanford University, Stanford, CA 94305, USA
| | | | - Gabriel Mel
- Neurosciences Program, Stanford University, Stanford, CA 94305, USA
| | - Hakan Inan
- CNC Program, Stanford University, Stanford, CA 94305, USA; Department of Electrical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Oleg Rumyantsev
- CNC Program, Stanford University, Stanford, CA 94305, USA; Department of Applied Physics, Stanford University, Stanford, CA 94305, USA
| | - Jérôme Lecoq
- CNC Program, Stanford University, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Tony Hyun Kim
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA; CNC Program, Stanford University, Stanford, CA 94305, USA; Department of Electrical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Jin Zhong Li
- CNC Program, Stanford University, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Charu Ramakrishnan
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA; Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Karl Deisseroth
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA; Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Liqun Luo
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Surya Ganguli
- Department of Applied Physics, Stanford University, Stanford, CA 94305, USA
| | - Mark J Schnitzer
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA; CNC Program, Stanford University, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA; Department of Applied Physics, Stanford University, Stanford, CA 94305, USA.
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87
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Gonzalez Sabater V, Rigby M, Burrone J. Voltage-Gated Potassium Channels Ensure Action Potential Shape Fidelity in Distal Axons. J Neurosci 2021; 41:5372-5385. [PMID: 34001627 PMCID: PMC8221596 DOI: 10.1523/jneurosci.2765-20.2021] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 03/29/2021] [Accepted: 04/01/2021] [Indexed: 11/21/2022] Open
Abstract
The initiation and propagation of the action potential (AP) along an axon allows neurons to convey information rapidly and across distant sites. Although AP properties have typically been characterized at the soma and proximal axon, knowledge of the propagation of APs toward distal axonal domains of mammalian CNS neurons remains limited. We used genetically encoded voltage indicators (GEVIs) to image APs with submillisecond temporal resolution simultaneously at different locations along the long axons of dissociated hippocampal neurons from rat embryos of either sex. We found that APs became sharper and showed remarkable fidelity as they traveled toward distal axons, even during a high-frequency train. Blocking voltage-gated potassium channels (Kv) with 4-AP resulted in an increase in AP width in all compartments, which was stronger at distal locations and exacerbated during AP trains. We conclude that the higher levels of Kv channel activity in distal axons serve to sustain AP fidelity, conveying a reliable digital signal to presynaptic boutons.SIGNIFICANCE STATEMENT The AP represents the electrical signal carried along axons toward distant presynaptic boutons where it culminates in the release of neurotransmitters. The nonlinearities involved in this process are such that small changes in AP shape can result in large changes in neurotransmitter release. Since axons are remarkably long structures, any distortions that APs suffer along the way have the potential to translate into a significant modulation of synaptic transmission, particularly in distal domains. To avoid these issues, distal axons have ensured that signals are kept remarkably constant and insensitive to modulation during a train, despite the long distances traveled. Here, we uncover the mechanisms that allow distal axonal domains to provide a reliable and faithful digital signal to presynaptic terminals.
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Affiliation(s)
- Victoria Gonzalez Sabater
- MRC Centre for Neurodevelopmental Disorders, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London SE1 1UL, United Kingdom
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London SE1 1UL, United Kingdom
| | - Mark Rigby
- MRC Centre for Neurodevelopmental Disorders, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London SE1 1UL, United Kingdom
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London SE1 1UL, United Kingdom
| | - Juan Burrone
- MRC Centre for Neurodevelopmental Disorders, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London SE1 1UL, United Kingdom
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London SE1 1UL, United Kingdom
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88
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Abstract
The measurement of ion concentrations and fluxes inside living cells is key to understanding cellular physiology. Fluorescent indicators that can infiltrate and provide intel on the cellular environment are critical tools for biological research. Developing these molecular informants began with the seminal work of Racker and colleagues ( Biochemistry (1979) 18, 2210), who demonstrated the passive loading of fluorescein in living cells to measure changes in intracellular pH. This work continues, employing a mix of old and new tradecraft to create innovative agents for monitoring ions inside living systems.
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Affiliation(s)
- Luke D Lavis
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia 20147, United States
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89
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Li JH, Fan LF, Zhao DJ, Zhou Q, Yao JP, Wang ZY, Huang L. Plant electrical signals: A multidisciplinary challenge. JOURNAL OF PLANT PHYSIOLOGY 2021; 261:153418. [PMID: 33887526 DOI: 10.1016/j.jplph.2021.153418] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 04/06/2021] [Accepted: 04/06/2021] [Indexed: 05/15/2023]
Abstract
Plant electrical signals, an early event in the plant-stimulus interaction, rapidly transmit information generated by the stimulus to other organs, and even the whole plant, to promote the corresponding response and trigger a regulatory cascade. In recent years, many promising state-of-the-art technologies applicable to study plant electrophysiology have emerged. Research focused on expression of genes associated with electrical signals has also proliferated. We propose that it is appropriate for plant electrical signals to be considered in the form of a "plant electrophysiological phenotype". This review synthesizes research on plant electrical signals from a novel, interdisciplinary perspective, which is needed to improve the efficient aggregation and use of plant electrical signal data and to expedite interpretation of plant electrical signals.
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Affiliation(s)
- Jin-Hai Li
- College of Information and Electrical Engineering, China Agricultural University, Beijing, 100083, China; Key Laboratory of Modern Precision Agriculture System Integration Research, Ministry of Education, Beijing, 100083, China
| | - Li-Feng Fan
- College of Information and Electrical Engineering, China Agricultural University, Beijing, 100083, China; Key Laboratory of Modern Precision Agriculture System Integration Research, Ministry of Education, Beijing, 100083, China
| | - Dong-Jie Zhao
- Institute for Future (IFF), Qingdao University, Qingdao, 266071, China
| | - Qiao Zhou
- College of Information and Electrical Engineering, China Agricultural University, Beijing, 100083, China; Key Laboratory of Agricultural Information Acquisition Technology, Ministry of Agriculture, Beijing, 100083, China
| | - Jie-Peng Yao
- College of Information and Electrical Engineering, China Agricultural University, Beijing, 100083, China; Key Laboratory of Agricultural Information Acquisition Technology, Ministry of Agriculture, Beijing, 100083, China
| | - Zhong-Yi Wang
- College of Information and Electrical Engineering, China Agricultural University, Beijing, 100083, China; Key Laboratory of Modern Precision Agriculture System Integration Research, Ministry of Education, Beijing, 100083, China; Key Laboratory of Agricultural Information Acquisition Technology, Ministry of Agriculture, Beijing, 100083, China.
| | - Lan Huang
- College of Information and Electrical Engineering, China Agricultural University, Beijing, 100083, China; Key Laboratory of Agricultural Information Acquisition Technology, Ministry of Agriculture, Beijing, 100083, China.
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90
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Yu H, Ying W, Li G, Lin X, Jiang D, Chen G, Chen S, Sun X, Xu Y, Ye J, Zhuo C. Exploring concomitant neuroimaging and genetic alterations in patients with and patients without auditory verbal hallucinations: A pilot study and mini review. J Int Med Res 2021; 48:300060519884856. [PMID: 32696690 PMCID: PMC7376300 DOI: 10.1177/0300060519884856] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Objective To explore concomitant neuroimaging and genetic alterations in patients with
schizophrenia with or without auditory verbal hallucinations (AVHs), and to
discuss the use of pattern recognition techniques in the development of an
objective index that may improve diagnostic accuracy and treatment outcomes
for schizophrenia. Methods The pilot study included patients with schizophrenia with AVHs (SCH-AVH
group) and without AVHs (SCH-no AVH group). High throughput sequencing (HTS)
was performed to explore RNA networks. Global functional connectivity
density (gFCD) analysis was performed to assess functional connectivity (FC)
alterations of the default mode network (DMN). Quantitative long noncoding
(lnc) RNA and mRNA expression data were related to peak T values of gFCDs
using Pearson’s correlation coefficient analysis. Results Compared with the SCH-no AVH group (n = 5), patients in the
SCH-AVH group (n = 5) exhibited differences in RNA
expression in RNA networks that were related to AVH severity, and displayed
alterations in FC (reflected by gFCD differences) within the DMN (posterior
cingulate and dorsal-medial prefrontal cortex), and in the right parietal
lobe, left occipital lobe, and left temporal lobe. Peak lncRNA expression
values were significantly related to peak gFCD T values within the DMN. Conclusion Among patients with schizophrenia, there are concomitant FC and genetic
expression alterations associated with AVHs. Data from pattern recognition
studies may inform the development of an objective index aimed at improving
early diagnostic accuracy and treatment planning for patients with
schizophrenia with and without AVHs.
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Affiliation(s)
- Haiping Yu
- Department of Psychiatric-Neuro-Imaging-Genetics Laboratory, Wenzhou Seventh People's Hospital, Wenzhou, Zhejiang, China
| | - Wang Ying
- Psychiatric Neuroimaging-Genetic and Comorbidity Laboratory, Tianjin Mental Health Centre, Tianjin Anding Hospital, Tianjin, China
| | - Gang Li
- Department of Psychiatry, Tianshui Third Hospital, Gansu, China
| | - Xiaodong Lin
- Department of Psychiatric-Neuro-Imaging-Genetics Laboratory, Wenzhou Seventh People's Hospital, Wenzhou, Zhejiang, China
| | - Deguo Jiang
- Department of Psychiatric-Neuro-Imaging-Genetics Laboratory, Wenzhou Seventh People's Hospital, Wenzhou, Zhejiang, China
| | - Guangdong Chen
- Department of Psychiatric-Neuro-Imaging-Genetics Laboratory, Wenzhou Seventh People's Hospital, Wenzhou, Zhejiang, China
| | - Suling Chen
- Department of Psychiatric-Neuro-Imaging-Genetics Laboratory, Wenzhou Seventh People's Hospital, Wenzhou, Zhejiang, China
| | - Xiuhai Sun
- Department of Neurology, Zoucheng People's Hospital, Jining Medical University Affiliated Zoucheng Hospital, Shandong, China
| | - Yong Xu
- Department of Psychiatry, The First Hospital of Shanxi Medical University, Shanxi, China
| | - Jiaen Ye
- Department of Psychiatric-Neuro-Imaging-Genetics Laboratory, Wenzhou Seventh People's Hospital, Wenzhou, Zhejiang, China
| | - Chuanjun Zhuo
- Department of Psychiatric-Neuro-Imaging-Genetics Laboratory, Wenzhou Seventh People's Hospital, Wenzhou, Zhejiang, China.,Psychiatric Neuroimaging-Genetic and Comorbidity Laboratory, Tianjin Mental Health Centre, Tianjin Anding Hospital, Tianjin, China.,Department of Psychiatry, Tianjin Fourth Centre Hospital, Tianjin, China.,Department of Psychiatric-Neuro-Imaging-Genetics Laboratory, School of Mental Health of Jining Medical University, Jining, Shandong, China
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91
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Walker AS, Raliski BK, Karbasi K, Zhang P, Sanders K, Miller EW. Optical Spike Detection and Connectivity Analysis With a Far-Red Voltage-Sensitive Fluorophore Reveals Changes to Network Connectivity in Development and Disease. Front Neurosci 2021; 15:643859. [PMID: 34054405 PMCID: PMC8155641 DOI: 10.3389/fnins.2021.643859] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 03/10/2021] [Indexed: 12/14/2022] Open
Abstract
The ability to optically record dynamics of neuronal membrane potential promises to revolutionize our understanding of neurobiology. In this study, we show that the far-red voltage sensitive fluorophore, Berkeley Red Sensor of Transmembrane potential-1, or BeRST 1, can be used to monitor neuronal membrane potential changes across dozens of neurons at a sampling rate of 500 Hz. Notably, voltage imaging with BeRST 1 can be implemented with affordable, commercially available illumination sources, optics, and detectors. BeRST 1 is well-tolerated in cultures of rat hippocampal neurons and provides exceptional optical recording fidelity, as judged by dual fluorescence imaging and patch-clamp electrophysiology. We developed a semi-automated spike-picking program to reduce user bias when calling action potentials and used this in conjunction with BeRST 1 to develop an optical spike and connectivity analysis (OSCA) for high-throughput dissection of neuronal activity dynamics. The high temporal resolution of BeRST 1 enables dissection of firing rate changes in response to acute, pharmacological interventions with commonly used inhibitors like gabazine and picrotoxin. Over longer periods of time, BeRST 1 also tracks chronic perturbations to neurons exposed to amyloid beta 1-42 (Aβ 1-42), revealing modest changes to spiking frequency but profound changes to overall network connectivity. Finally, we use OSCA to track changes in neuronal connectivity during maturation in culture, providing a functional readout of network assembly. We envision that use of BeRST 1 and OSCA described here will be of use to the broad neuroscience community.
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Affiliation(s)
- Alison S. Walker
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, United States
- Department of Molecular & Cell Biology, University of California, Berkeley, Berkeley, CA, United States
- Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA, United States
| | - Benjamin K. Raliski
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, United States
| | - Kaveh Karbasi
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, United States
| | - Patrick Zhang
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, United States
| | - Kate Sanders
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, United States
| | - Evan W. Miller
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, United States
- Department of Molecular & Cell Biology, University of California, Berkeley, Berkeley, CA, United States
- Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA, United States
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92
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Chien MP, Brinks D, Testa-Silva G, Tian H, Phil Brooks F, Adam Y, Bloxham B, Gmeiner B, Kheifets S, Cohen AE. Photoactivated voltage imaging in tissue with an archaerhodopsin-derived reporter. SCIENCE ADVANCES 2021; 7:7/19/eabe3216. [PMID: 33952514 PMCID: PMC8099184 DOI: 10.1126/sciadv.abe3216] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 03/15/2021] [Indexed: 05/19/2023]
Abstract
Photoactivated genetically encoded voltage indicators (GEVIs) have the potential to enable optically sectioned voltage imaging at the intersection of a photoactivation beam and an imaging beam. We developed a pooled high-throughput screen to identify archaerhodopsin mutants with enhanced photoactivation. After screening ~105 cells, we identified a novel GEVI, NovArch, whose one-photon near-infrared fluorescence is reversibly enhanced by weak one-photon blue or two-photon near-infrared excitation. Because the photoactivation leads to fluorescent signals catalytically rather than stoichiometrically, high fluorescence signals, optical sectioning, and high time resolution are achieved simultaneously at modest blue or two-photon laser power. We demonstrate applications of the combined molecular and optical tools to optical mapping of membrane voltage in distal dendrites in acute mouse brain slices and in spontaneously active neurons in vivo.
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Affiliation(s)
- Miao-Ping Chien
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
- Department of Molecular Genetics, Erasmus University Medical Center, Rotterdam, Netherlands
- Oncode Institute, Utrecht, Netherlands
| | - Daan Brinks
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
- Department of Molecular Genetics, Erasmus University Medical Center, Rotterdam, Netherlands
- Department of Imaging Physics, Delft University of Technology, Delft, Netherlands
| | - Guilherme Testa-Silva
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
- Howard Hughes Medical Institute, Cambridge, MA 02138, USA
| | - He Tian
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - F Phil Brooks
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Yoav Adam
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Blox Bloxham
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Benjamin Gmeiner
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Simon Kheifets
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Adam E Cohen
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.
- Howard Hughes Medical Institute, Cambridge, MA 02138, USA
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93
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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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94
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Chadney OMT, Blankvoort S, Grimstvedt JS, Utz A, Kentros CG. Multiplexing viral approaches to the study of the neuronal circuits. J Neurosci Methods 2021; 357:109142. [PMID: 33753126 DOI: 10.1016/j.jneumeth.2021.109142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 02/27/2021] [Accepted: 03/10/2021] [Indexed: 12/16/2022]
Abstract
Neural circuits are composed of multitudes of elaborately interconnected cell types. Understanding neural circuit function requires not only cell-specific knowledge of connectivity, but the ability to record and manipulate distinct cell types independently. Recent advances in viral vectors promise the requisite specificity to perform true "circuit-breaking" experiments. However, such new avenues of multiplexed, cell-specific investigation raise new technical issues: one must ensure that both the viral vectors and their transgene payloads do not overlap with each other in both an anatomical and a functional sense. This review describes benefits and issues regarding the use of viral vectors to analyse the function of neural circuits and provides a resource for the design and implementation of such multiplexing experiments.
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Affiliation(s)
- Oscar M T Chadney
- Kavli Institute for Systems Neuroscience and Centre for Neural Computation, NTNU, Trondheim, Norway.
| | - Stefan Blankvoort
- Kavli Institute for Systems Neuroscience and Centre for Neural Computation, NTNU, Trondheim, Norway
| | - Joachim S Grimstvedt
- Kavli Institute for Systems Neuroscience and Centre for Neural Computation, NTNU, Trondheim, Norway
| | - Annika Utz
- Kavli Institute for Systems Neuroscience and Centre for Neural Computation, NTNU, Trondheim, Norway
| | - Clifford G Kentros
- Kavli Institute for Systems Neuroscience and Centre for Neural Computation, NTNU, Trondheim, Norway.
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95
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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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96
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Fabrication of a Nanoplasmonic Chip to Enhance Neuron Membrane Potential Imaging by Metal-Enhanced Fluorescence Effect. BIOCHIP JOURNAL 2021. [DOI: 10.1007/s13206-021-00017-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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97
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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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98
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A dark quencher genetically encodable voltage indicator (dqGEVI) exhibits high fidelity and speed. Proc Natl Acad Sci U S A 2021; 118:2020235118. [PMID: 33531364 PMCID: PMC8017929 DOI: 10.1073/pnas.2020235118] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Voltage sensing with genetically expressed optical probes is highly desirable for large-scale recordings of neuronal activity and detection of localized voltage signals in single neurons. Here we describe a method for a two-component (hybrid) genetically encodable fluorescent voltage sensing in neurons. The approach uses a glycosylphosphatidylinositol-tagged fluorescent protein (enhanced green fluorescent protein) that ensures the fluorescence to be specifically confined to the outside of the plasma membrane and D3, a voltage-dependent quencher. Previous hybrid genetically encoded voltage sensing approaches relied on a single quenching molecule, dipycrilamine (DPA), which is toxic, increases membrane capacitance, interferes with neurotransmitters, and is explosive. Our method uses a nontoxic and nonexplosive compound that performs better than DPA in all aspects of fluorescent voltage sensing. Voltage sensing with genetically expressed optical probes is highly desirable for large-scale recordings of neuronal activity and detection of localized voltage signals in single neurons. Most genetically encodable voltage indicators (GEVI) have drawbacks including slow response, low fluorescence, or excessive bleaching. Here we present a dark quencher GEVI approach (dqGEVI) using a Förster resonance energy transfer pair between a fluorophore glycosylphosphatidylinositol–enhanced green fluorescent protein (GPI-eGFP) on the outer surface of the neuronal membrane and an azo-benzene dye quencher (D3) that rapidly moves in the membrane driven by voltage. In contrast to previous probes, the sensor has a single photon bleaching time constant of ∼40 min, has a high temporal resolution and fidelity for detecting action potential firing at 100 Hz, resolves membrane de- and hyperpolarizations of a few millivolts, and has negligible effects on passive membrane properties or synaptic events. The dqGEVI approach should be a valuable tool for optical recordings of subcellular or population membrane potential changes in nerve cells.
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99
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Daria VR, Castañares ML, Bachor HA. Spatio-temporal parameters for optical probing of neuronal activity. Biophys Rev 2021; 13:13-33. [PMID: 33747244 PMCID: PMC7930150 DOI: 10.1007/s12551-021-00780-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 01/01/2021] [Indexed: 12/28/2022] Open
Abstract
The challenge to understand the complex neuronal circuit functions in the mammalian brain has brought about a revolution in light-based neurotechnologies and optogenetic tools. However, while recent seminal works have shown excellent insights on the processing of basic functions such as sensory perception, memory, and navigation, understanding more complex brain functions is still unattainable with current technologies. We are just scratching the surface, both literally and figuratively. Yet, the path towards fully understanding the brain is not totally uncertain. Recent rapid technological advancements have allowed us to analyze the processing of signals within dendritic arborizations of single neurons and within neuronal circuits. Understanding the circuit dynamics in the brain requires a good appreciation of the spatial and temporal properties of neuronal activity. Here, we assess the spatio-temporal parameters of neuronal responses and match them with suitable light-based neurotechnologies as well as photochemical and optogenetic tools. We focus on the spatial range that includes dendrites and certain brain regions (e.g., cortex and hippocampus) that constitute neuronal circuits. We also review some temporal characteristics of some proteins and ion channels responsible for certain neuronal functions. With the aid of the photochemical and optogenetic markers, we can use light to visualize the circuit dynamics of a functioning brain. The challenge to understand how the brain works continue to excite scientists as research questions begin to link macroscopic and microscopic units of brain circuits.
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Affiliation(s)
- Vincent R. Daria
- Research School of Physics, The Australian National University, Canberra, Australia
- John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | | | - Hans-A. Bachor
- Research School of Physics, The Australian National University, Canberra, Australia
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Vanwalleghem G, Constantin L, Scott EK. Calcium Imaging and the Curse of Negativity. Front Neural Circuits 2021; 14:607391. [PMID: 33488363 PMCID: PMC7815594 DOI: 10.3389/fncir.2020.607391] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 12/02/2020] [Indexed: 12/17/2022] Open
Abstract
The imaging of neuronal activity using calcium indicators has become a staple of modern neuroscience. However, without ground truths, there is a real risk of missing a significant portion of the real responses. Here, we show that a common assumption, the non-negativity of the neuronal responses as detected by calcium indicators, biases all levels of the frequently used analytical methods for these data. From the extraction of meaningful fluorescence changes to spike inference and the analysis of inferred spikes, each step risks missing real responses because of the assumption of non-negativity. We first show that negative deviations from baseline can exist in calcium imaging of neuronal activity. Then, we use simulated data to test three popular algorithms for image analysis, CaImAn, suite2p, and CellSort, finding that suite2p may be the best suited to large datasets. We also tested the spike inference algorithms included in CaImAn, suite2p, and Cellsort, as well as the dedicated inference algorithms MLspike and CASCADE, and found each to have limitations in dealing with inhibited neurons. Among these spike inference algorithms, FOOPSI, from CaImAn, performed the best on inhibited neurons, but even this algorithm inferred spurious spikes upon the return of the fluorescence signal to baseline. As such, new approaches will be needed before spikes can be sensitively and accurately inferred from calcium data in inhibited neurons. We further suggest avoiding data analysis approaches that, by assuming non-negativity, ignore inhibited responses. Instead, we suggest a first exploratory step, using k-means or PCA for example, to detect whether meaningful negative deviations are present. Taking these steps will ensure that inhibition, as well as excitation, is detected in calcium imaging datasets.
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Affiliation(s)
- Gilles Vanwalleghem
- Neural Circuits and Behavior Laboratory, Queensland Brain Institute, The University of Queensland, St Lucia, QLD, Australia
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