1
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Subramanian N, Leong LM, Salemi Mokri Boukani P, Storace DA. Recent odor experience selectively modulates olfactory sensitivity across the glomerular output in the mouse olfactory bulb. Chem Senses 2025; 50:bjae045. [PMID: 39786438 PMCID: PMC11753175 DOI: 10.1093/chemse/bjae045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Indexed: 01/12/2025] Open
Abstract
Although animals can reliably locate and recognize odorants embedded in complex environments, the neural circuits for accomplishing these tasks remain incompletely understood. Adaptation is likely to be important as it could allow neurons in a brain area to adjust to the broader sensory environment. Adaptive processes must be flexible enough to allow the brain to make dynamic adjustments, while maintaining sufficient stability so that organisms do not forget important olfactory associations. Processing within the mouse olfactory bulb is likely involved in generating adaptation, although there are conflicting models of how it transforms the glomerular output of the mouse olfactory bulb. Here we performed 2-photon Ca2+ imaging from mitral/tufted glomeruli in awake mice to determine the time course of recovery from adaptation, and whether it acts broadly or selectively across the glomerular population. Individual glomerular responses, as well as the overall population odor representation were similar across imaging sessions. However, odor-concentration pairings presented with interstimulus intervals upwards of 30-s evoked heterogeneous adaptation that was concentration-dependent. We demonstrate that this form of adaptation is unrelated to variations in respiration, and olfactory receptor neuron glomerular measurements indicate that it is unlikely to be inherited from the periphery. Our results indicate that the olfactory bulb output can reliably transmit stable odor representations, but recent odor experiences can selectively shape neural responsiveness for upwards of 30 seconds. We propose that neural circuits that allow for non-uniform adaptation across mitral/tufted glomeruli could be important for making dynamic adjustments in complex odor environments.
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Affiliation(s)
- Narayan Subramanian
- Department of Biological Science, Florida State University, Tallahassee, FL, United States
| | - Lee Min Leong
- Department of Biological Science, Florida State University, Tallahassee, FL, United States
| | - Paria Salemi Mokri Boukani
- Department of Biological Science, Florida State University, Tallahassee, FL, United States
- Program in Neuroscience, Florida State University, Tallahassee, FL, United States
| | - Douglas A Storace
- Department of Biological Science, Florida State University, Tallahassee, FL, United States
- Program in Neuroscience, Florida State University, Tallahassee, FL, United States
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, United States
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2
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Nguyen TN, Shalaby RA, Lee E, Kim SS, Ro Kim Y, Kim S, Je HS, Kwon HS, Chung E. Ultrafast optical imaging techniques for exploring rapid neuronal dynamics. NEUROPHOTONICS 2025; 12:S14608. [PMID: 40017464 PMCID: PMC11867703 DOI: 10.1117/1.nph.12.s1.s14608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2024] [Revised: 01/20/2025] [Accepted: 01/27/2025] [Indexed: 03/01/2025]
Abstract
Optical neuroimaging has significantly advanced our understanding of brain function, particularly through techniques such as two-photon microscopy, which captures three-dimensional brain structures with sub-cellular resolution. However, traditional methods struggle to record fast, complex neuronal interactions in real time, which are crucial for understanding brain networks and developing treatments for neurological diseases such as Alzheimer's, Parkinson's, and chronic pain. Recent advancements in ultrafast imaging technologies, including kilohertz two-photon microscopy, light field microscopy, and event-based imaging, are pushing the boundaries of temporal resolution in neuroimaging. These techniques enable the capture of rapid neural events with unprecedented speed and detail. This review examines the principles, applications, and limitations of these technologies, highlighting their potential to revolutionize neuroimaging and improve the diagnose and treatment of neurological disorders. Despite challenges such as photodamage risks and spatial resolution trade-offs, integrating these approaches promises to enhance our understanding of brain function and drive future breakthroughs in neuroscience and medicine. Continued interdisciplinary collaboration is essential to fully leverage these innovations for advancements in both basic and clinical neuroscience.
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Affiliation(s)
- Tien Nhat Nguyen
- Gwangju Institute of Science and Technology, Department of Biomedical Science and Engineering, Gwangju, Republic of Korea
| | - Reham A. Shalaby
- Gwangju Institute of Science and Technology, Department of Biomedical Science and Engineering, Gwangju, Republic of Korea
| | - Eunbin Lee
- Gwangju Institute of Science and Technology, Department of Biomedical Science and Engineering, Gwangju, Republic of Korea
| | - Sang Seong Kim
- Gwangju Institute of Science and Technology, Department of Biomedical Science and Engineering, Gwangju, Republic of Korea
| | - Young Ro Kim
- Massachusetts General Hospital, Athinoula A. Martinos Center for Biomedical Imaging, Charlestown, Massachusetts United States
- Harvard Medical School, Department of Radiology, Boston, Massachusetts, United States
| | - Seonghoon Kim
- Tsinghua University, Institute for Brain and Cognitive Sciences, Beijing, China
- Hangzhou Zhuoxi Institute of Brain and Intelligence, Hangzhou, China
| | - Hyunsoo Shawn Je
- Duke-NUS Medical School, Program in Neuroscience and Behavioral Disorders, Singapore
| | - Hyuk-Sang Kwon
- Gwangju Institute of Science and Technology, Department of Biomedical Science and Engineering, Gwangju, Republic of Korea
| | - Euiheon Chung
- Gwangju Institute of Science and Technology, Department of Biomedical Science and Engineering, Gwangju, Republic of Korea
- Gwangju Institute of Science and Technology, AI Graduate School, Gwangju, Republic of Korea
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3
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Subramanian N, Leong LM, Boukani PSM, Storace DA. Recent odor experience selectively modulates olfactory sensitivity across the glomerular output in the mouse olfactory bulb. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.21.604478. [PMID: 39386559 PMCID: PMC11463640 DOI: 10.1101/2024.07.21.604478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/12/2024]
Abstract
Although animals can reliably locate and recognize odorants embedded in complex environments, the neural circuits for accomplishing these tasks remain incompletely understood. Adaptation is likely to be important as it could allow neurons in a brain area to adjust to the broader sensory environment. Adaptive processes must be flexible enough to allow the brain to make dynamic adjustments, while maintaining sufficient stability so that organisms do not forget important olfactory associations. Processing within the mouse olfactory bulb is likely involved in generating adaptation, although there are conflicting models of how it transforms the glomerular output of the mouse olfactory bulb. Here we performed 2-photon Ca2+ imaging from mitral/tufted glomeruli in awake mice to determine the time course of recovery from adaptation, and whether it acts broadly or selectively across the glomerular population. Individual glomerular responses, as well as the overall population odor representation was similar across imaging sessions. However, odor-concentration pairings presented with interstimulus intervals upwards of 30-s evoked heterogeneous adaptation that was concentration-dependent. We demonstrate that this form of adaptation is unrelated to variations in respiration, and olfactory receptor neuron glomerular measurements indicate that it is unlikely to be inherited from the periphery. Our results indicate that the olfactory bulb output can reliably transmit stable odor representations, but recent odor experiences can selectively shape neural responsiveness for upwards of 30 seconds. We propose that neural circuits that allow for non-uniform adaptation across mitral/tufted glomerular could be important for making dynamic adjustments in complex odor environments.
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Affiliation(s)
| | - Lee Min Leong
- Department of Biological Science, Florida State University, Tallahassee, FL
| | - Paria Salemi Mokri Boukani
- Department of Biological Science, Florida State University, Tallahassee, FL
- Program in Neuroscience, Florida State University, Tallahassee, FL
| | - Douglas A. Storace
- Department of Biological Science, Florida State University, Tallahassee, FL
- Program in Neuroscience, Florida State University, Tallahassee, FL
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL
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4
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Fitzpatrick MJ, Krizan J, Hsiang JC, Shen N, Kerschensteiner D. A pupillary contrast response in mice and humans: Neural mechanisms and visual functions. Neuron 2024; 112:2404-2422.e9. [PMID: 38697114 PMCID: PMC11257825 DOI: 10.1016/j.neuron.2024.04.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 12/21/2023] [Accepted: 04/10/2024] [Indexed: 05/04/2024]
Abstract
In the pupillary light response (PLR), increases in ambient light constrict the pupil to dampen increases in retinal illuminance. Here, we report that the pupillary reflex arc implements a second input-output transformation; it senses temporal contrast to enhance spatial contrast in the retinal image and increase visual acuity. The pupillary contrast response (PCoR) is driven by rod photoreceptors via type 6 bipolar cells and M1 ganglion cells. Temporal contrast is transformed into sustained pupil constriction by the M1's conversion of excitatory input into spike output. Computational modeling explains how the PCoR shapes retinal images. Pupil constriction improves acuity in gaze stabilization and predation in mice. Humans exhibit a PCoR with similar tuning properties to mice, which interacts with eye movements to optimize the statistics of the visual input for retinal encoding. Thus, we uncover a conserved component of active vision, its cell-type-specific pathway, computational mechanisms, and optical and behavioral significance.
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Affiliation(s)
- Michael J Fitzpatrick
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; Graduate Program in Neuroscience, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; Medical Scientist Training Program, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - Jenna Krizan
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; Graduate Program in Neuroscience, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - Jen-Chun Hsiang
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - Ning Shen
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - Daniel Kerschensteiner
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; Department of Neuroscience, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; Department of Biomedical Engineering, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA.
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5
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Leong LM, Storace DA. Imaging different cell populations in the mouse olfactory bulb using the genetically encoded voltage indicator ArcLight. NEUROPHOTONICS 2024; 11:033402. [PMID: 38288247 PMCID: PMC10823906 DOI: 10.1117/1.nph.11.3.033402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 11/30/2023] [Accepted: 12/14/2023] [Indexed: 01/31/2024]
Abstract
Genetically encoded voltage indicators (GEVIs) are protein-based optical sensors that allow for measurements from genetically defined populations of neurons. Although in vivo imaging in the mammalian brain with early generation GEVIs was difficult due to poor membrane expression and low signal-to-noise ratio, newer and more sensitive GEVIs have begun to make them useful for answering fundamental questions in neuroscience. We discuss principles of imaging using GEVIs and genetically encoded calcium indicators, both useful tools for in vivo imaging of neuronal activity, and review some of the recent mechanistic advances that have led to GEVI improvements. We provide an overview of the mouse olfactory bulb (OB) and discuss recent studies using the GEVI ArcLight to study different cell types within the bulb using both widefield and two-photon microscopy. Specific emphasis is placed on using GEVIs to begin to study the principles of concentration coding in the OB, how to interpret the optical signals from population measurements in the in vivo brain, and future developments that will push the field forward.
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Affiliation(s)
- Lee Min Leong
- Florida State University, Department of Biological Science, Tallahassee, Florida, United States
| | - Douglas A. Storace
- Florida State University, Department of Biological Science, Tallahassee, Florida, United States
- Florida State University, Program in Neuroscience, Tallahassee, Florida, United States
- Florida State University, Institute of Molecular Biophysics, Tallahassee, Florida, United States
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6
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Hara Y, Ichiraku A, Matsuda T, Sakane A, Sasaki T, Nagai T, Horikawa K. High-affinity tuning of single fluorescent protein-type indicators by flexible linker length optimization in topology mutant. Commun Biol 2024; 7:705. [PMID: 38851844 PMCID: PMC11162441 DOI: 10.1038/s42003-024-06394-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 05/29/2024] [Indexed: 06/10/2024] Open
Abstract
Genetically encoded Ca2+ indicators (GECIs) are versatile for live imaging of cellular activities. Besides the brightness and dynamic range of signal change of GECIs, Ca2+ affinity is another critical parameter for successful Ca2+ imaging, as the concentration range of Ca2+ dynamics differs from low nanomolar to sub-millimolar depending on the celltype and organism. However, ultrahigh-affinity GECIs, particularly the single fluorescent protein (1FP)-type, are lacking. Here, we report a simple strategy that increases Ca2+ affinity through the linker length optimization in topology mutants of existing 1FP-type GECIs. The resulting ultrahigh-affinity GECIs, CaMPARI-nano, BGECO-nano, and RCaMP-nano (Kd = 17-25 nM), enable unique biological applications, including the detection of low nanomolar Ca2+ dynamics, highlighting active signaling cells, and multi-functional imaging with other second messengers. The linker length optimization in topology mutants could be applied to other 1FP-type indicators of glutamate and potassium, rendering it a widely applicable technique for modulating indicator affinity.
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Affiliation(s)
- Yusuke Hara
- Department of Optical Imaging, Advanced Research Promotion Center, Tokushima University, 3-18-15 Kuramoto, Tokushima, Tokushima, 770-8503, Japan
| | - Aya Ichiraku
- Department of Optical Imaging, Advanced Research Promotion Center, Tokushima University, 3-18-15 Kuramoto, Tokushima, Tokushima, 770-8503, Japan
| | - Tomoki Matsuda
- Department of Biomolecular Science and Engineering, SANKEN, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka, 567-0047, Japan
| | - Ayuko Sakane
- Department of Biochemistry, Tokushima University Graduate School of Medicine, 3-18-15 Kuramoto, Tokushima, Tokushima, 770-8503, Japan
- Division of Interdisciplinary Researches for Medicine and Photonics, Institute of Post-LED Photonics (pLED), Tokushima University, 3-18-15 Kuramoto, Tokushima, Tokushima, 770-8503, Japan
| | - Takuya Sasaki
- Department of Biochemistry, Tokushima University Graduate School of Medicine, 3-18-15 Kuramoto, Tokushima, Tokushima, 770-8503, Japan
| | - Takeharu Nagai
- Department of Biomolecular Science and Engineering, SANKEN, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka, 567-0047, Japan
- Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Yamadaoka 2-1, Suita, Osaka, 565-0871, Japan
| | - Kazuki Horikawa
- Department of Optical Imaging, Advanced Research Promotion Center, Tokushima University, 3-18-15 Kuramoto, Tokushima, Tokushima, 770-8503, Japan.
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7
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Boto T, Tomchik SM. Functional Imaging of Learning-Induced Plasticity in the Central Nervous System with Genetically Encoded Reporters in Drosophila. Cold Spring Harb Protoc 2024; 2024:pdb.top107799. [PMID: 37197830 DOI: 10.1101/pdb.top107799] [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] [Indexed: 05/19/2023]
Abstract
Learning and memory allow animals to adjust their behavior based on the predictive value of their past experiences. Memories often exist in complex representations, spread across numerous cells and synapses in the brain. Studying relatively simple forms of memory provides insights into the fundamental processes that underlie multiple forms of memory. Associative learning occurs when an animal learns the relationship between two previously unrelated sensory stimuli, such as when a hungry animal learns that a particular odor is followed by a tasty reward. Drosophila is a particularly powerful model to study how this type of memory works. The fundamental principles are widely shared among animals, and there is a wide range of genetic tools available to study circuit function in flies. In addition, the olfactory structures that mediate associative learning in flies, such as the mushroom body and its associated neurons, are anatomically organized, relatively well-characterized, and readily accessible to imaging. Here, we review the olfactory anatomy and physiology of the olfactory system, describe how plasticity in the olfactory pathway mediates learning and memory, and explain the general principles underlying calcium imaging approaches.
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Affiliation(s)
- Tamara Boto
- Department of Physiology, Trinity College Dublin, Dublin 2, Ireland
- Trinity College Institute of Neuroscience, Trinity College Dublin, Dublin 2, Ireland
| | - Seth M Tomchik
- Neuroscience and Pharmacology, University of Iowa Carver College of Medicine, Iowa City, Iowa 52242, USA
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, Iowa 52242, USA
- Iowa Neuroscience Institute, University of Iowa Carver College of Medicine, Iowa City, Iowa 52242, USA
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8
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Pachetti M, Palandri A, de Castro Reis F, Recupero L, Ballerini L. Exploring Ca 2+ Dynamics in Myelinating Oligodendrocytes through rAAV-Mediated jGCaMP8s Expression in Developing Spinal Cord Organ Cultures. eNeuro 2024; 11:ENEURO.0540-23.2024. [PMID: 38744490 PMCID: PMC11151195 DOI: 10.1523/eneuro.0540-23.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 04/15/2024] [Accepted: 04/16/2024] [Indexed: 05/16/2024] Open
Abstract
Oligodendrocytes, the myelin-producing glial cells of the central nervous system (CNS), crucially contribute to myelination and circuit function. An increasing amount of evidence suggests that intracellular calcium (Ca2+) dynamics in oligodendrocytes mediates activity-dependent and activity-independent myelination. Unraveling how myelinating oligodendrocytes orchestrate and integrate Ca2+ signals, particularly in relation to axonal firing, is crucial for gaining insights into their role in the CNS development and function, both in health and disease. In this framework, we used the recombinant adeno-associated virus/Olig001 capsid variant to express the genetically encoded Ca2+ indicator jGCaMP8s, under the control of the myelin basic protein promoter. In our study, this tool exhibits excellent tropism and selectivity for myelinating and mature oligodendrocytes, and it allows monitoring Ca2+ activity in myelin-forming cells, both in isolated primary cultures and organotypic spinal cord explants. By live imaging of myelin Ca2+ events in oligodendrocytes within organ cultures, we observed a rapid decline in the amplitude and duration of Ca2+ events across different in vitro developmental stages. Active myelin sheath remodeling and growth are modulated at the level of myelin-axon interface through Ca2+ signaling, and, during early myelination in organ cultures, this phase is finely tuned by the firing of axon action potentials. In the later stages of myelination, Ca2+ events in mature oligodendrocytes no longer display such a modulation, underscoring the involvement of complex Ca2+ signaling in CNS myelination.
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Affiliation(s)
- Maria Pachetti
- Scuola Internazionale Superiore di Studi Avanzati, Trieste 34146, Italy
| | - Anabela Palandri
- Scuola Internazionale Superiore di Studi Avanzati, Trieste 34146, Italy
| | | | - Luca Recupero
- Scuola Internazionale Superiore di Studi Avanzati, Trieste 34146, Italy
| | - Laura Ballerini
- Scuola Internazionale Superiore di Studi Avanzati, Trieste 34146, Italy
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9
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Jensen GC, Janis MK, Nguyen HN, David OW, Zastrow ML. Fluorescent Protein-Based Sensors for Detecting Essential Metal Ions across the Tree of Life. ACS Sens 2024; 9:1622-1643. [PMID: 38587931 PMCID: PMC11073808 DOI: 10.1021/acssensors.3c02695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/10/2024]
Abstract
Genetically encoded fluorescent metal ion sensors are powerful tools for elucidating metal dynamics in living systems. Over the last 25 years since the first examples of genetically encoded fluorescent protein-based calcium indicators, this toolbox of probes has expanded to include other essential and non-essential metal ions. Collectively, these tools have illuminated fundamental aspects of metal homeostasis and trafficking that are crucial to fields ranging from neurobiology to human nutrition. Despite these advances, much of the application of metal ion sensors remains limited to mammalian cells and tissues and a limited number of essential metals. Applications beyond mammalian systems and in vivo applications in living organisms have primarily used genetically encoded calcium ion sensors. The aim of this Perspective is to provide, with the support of historical and recent literature, an updated and critical view of the design and use of fluorescent protein-based sensors for detecting essential metal ions in various organisms. We highlight the historical progress and achievements with calcium sensors and discuss more recent advances and opportunities for the detection of other essential metal ions. We also discuss outstanding challenges in the field and directions for future studies, including detecting a wider variety of metal ions, developing and implementing a broader spectral range of sensors for multiplexing experiments, and applying sensors to a wider range of single- and multi-species biological systems.
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Affiliation(s)
- Gary C Jensen
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Makena K Janis
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Hazel N Nguyen
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Ogonna W David
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Melissa L Zastrow
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
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10
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Zhang Y, Looger LL. Fast and sensitive GCaMP calcium indicators for neuronal imaging. J Physiol 2024; 602:1595-1604. [PMID: 36811153 DOI: 10.1113/jp283832] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Accepted: 02/15/2023] [Indexed: 02/24/2023] Open
Abstract
We review the principles of development and deployment of genetically encoded calcium indicators (GECIs) for the detection of neural activity. Our focus is on the popular GCaMP family of green GECIs, culminating in the recent release of the jGCaMP8 sensors, with dramatically improved kinetics relative to previous generations. We summarize the properties of GECIs in multiple colour channels (blue, cyan, green, yellow, red, far-red) and highlight areas for further improvement. With their low-millisecond rise-times, the jGCaMP8 indicators allow new classes of experiments following neural activity in time frames approaching the underlying computations.
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Affiliation(s)
- Yan Zhang
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Loren L Looger
- Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA, USA
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11
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Du X, Weng X, Lyu B, Zhao L, Wang H. Localized calcium transients in phragmoplast regulate cytokinesis of tobacco BY-2 cells. PLANT CELL REPORTS 2024; 43:97. [PMID: 38488911 DOI: 10.1007/s00299-024-03181-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Accepted: 02/22/2024] [Indexed: 03/17/2024]
Abstract
KEY MESSAGE Plants exhibit a unique pattern of cytosolic Ca2+ dynamics to correlate with microtubules to regulate cytokinesis, which significantly differs from those observed in animal and yeast cells. Calcium (Ca2+) transients mediated signaling is known to be essential in cytokinesis across eukaryotic cells. However, the detailed spatiotemporal dynamics of Ca2+ during plant cytokinesis remain largely unexplored. In this study, we employed GCaMP5, a genetically encoded Ca2+ sensor, to investigate cytokinetic Ca2+ transients during cytokinesis in Nicotiana tabacum Bright Yellow-2 (BY-2) cells. We validated the effectiveness of GCaMP5 to capture fluctuations in intracellular free Ca2+ in transgenic BY-2 cells. Our results reveal that Ca2+ dynamics during BY-2 cell cytokinesis are distinctly different from those observed in embryonic and yeast cells. It is characterized by an initial significant Ca2+ spike within the phragmoplast region. This spike is followed by a decrease in Ca2+ concentration at the onset of cytokinesis in phragmoplast, which then remains elevated in comparison to the cytosolic Ca2+ until the completion of cell plate formation. At the end of cytokinesis, Ca2+ becomes uniformly distributed in the cytosol. This pattern contrasts with the typical dual waves of Ca2+ spikes observed during cytokinesis in animal embryonic cells and fission yeasts. Furthermore, applications of pharmaceutical inhibitors for either Ca2+ or microtubules revealed a close correlation between Ca2+ transients and microtubule organization in the regulation of cytokinesis. Collectively, our findings highlight the unique dynamics and crucial role of Ca2+ transients during plant cell cytokinesis, and provides new insights into plant cell division mechanisms.
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Affiliation(s)
- Xiaojuan Du
- Department of Cell and Developmental Biology, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Xun Weng
- Department of Cell and Developmental Biology, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Binyang Lyu
- Department of Cell and Developmental Biology, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Lifeng Zhao
- Department of Cell and Developmental Biology, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Hao Wang
- Department of Cell and Developmental Biology, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China.
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12
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Félix R, Markov DA, Renninger SL, Tomás AR, Laborde A, Carey MR, Orger MB, Portugues R. Structural and Functional Organization of Visual Responses in the Inferior Olive of Larval Zebrafish. J Neurosci 2024; 44:e2352212023. [PMID: 38195508 PMCID: PMC10883660 DOI: 10.1523/jneurosci.2352-21.2023] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 11/22/2023] [Accepted: 12/01/2023] [Indexed: 01/11/2024] Open
Abstract
The olivo-cerebellar system plays an important role in vertebrate sensorimotor control. Here, we investigate sensory representations in the inferior olive (IO) of larval zebrafish and their spatial organization. Using single-cell labeling of genetically identified IO neurons, we find that they can be divided into at least two distinct groups based on their spatial location, dendritic morphology, and axonal projection patterns. In the same genetically targeted population, we recorded calcium activity in response to a set of visual stimuli using two-photon imaging. We found that most IO neurons showed direction-selective and binocular responses to visual stimuli and that the functional properties were spatially organized within the IO. Light-sheet functional imaging that allowed for simultaneous activity recordings at the soma and axonal level revealed tight coupling between functional properties, soma location, and axonal projection patterns of IO neurons. Taken together, our results suggest that anatomically defined classes of IO neurons correspond to distinct functional types, and that topographic connections between IO and cerebellum contribute to organization of the cerebellum into distinct functional zones.
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Affiliation(s)
- Rita Félix
- Champalimaud Research, Champalimaud Centre for the Unknown, Lisbon 1400-038, Portugal
| | - Daniil A Markov
- Max Planck Institute of Neurobiology, Sensorimotor Control Research Group, 82152 Martinsried, Germany
| | - Sabine L Renninger
- Champalimaud Research, Champalimaud Centre for the Unknown, Lisbon 1400-038, Portugal
| | - Ana Raquel Tomás
- Champalimaud Research, Champalimaud Centre for the Unknown, Lisbon 1400-038, Portugal
| | - Alexandre Laborde
- Champalimaud Research, Champalimaud Centre for the Unknown, Lisbon 1400-038, Portugal
| | - Megan R Carey
- Champalimaud Research, Champalimaud Centre for the Unknown, Lisbon 1400-038, Portugal
| | - Michael B Orger
- Champalimaud Research, Champalimaud Centre for the Unknown, Lisbon 1400-038, Portugal
| | - Ruben Portugues
- Max Planck Institute of Neurobiology, Sensorimotor Control Research Group, 82152 Martinsried, Germany
- Institute of Neuroscience, Technical University of Munich, 80802 Munich, Germany
- Munich Cluster of Systems Neurology (SyNergy), 81377 Munich, Germany
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13
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Sekhon H, Ha JH, Presti MF, Procopio SB, Jarvis AR, Mirsky PO, John AM, Loh SN. Adaptable, turn-on maturation (ATOM) fluorescent biosensors for multiplexed detection in cells. Nat Methods 2023; 20:1920-1929. [PMID: 37945909 PMCID: PMC11080272 DOI: 10.1038/s41592-023-02065-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 10/04/2023] [Indexed: 11/12/2023]
Abstract
A grand challenge in biosensor design is to develop a single-molecule, fluorescent protein-based platform that can be easily adapted to recognize targets of choice. Here, we created a family of adaptable, turn-on maturation (ATOM) biosensors consisting of a monobody (circularly permuted at one of two positions) or a nanobody (circularly permuted at one of three positions) inserted into a fluorescent protein at one of three surface loops. Multiplexed imaging of live human cells coexpressing cyan, yellow and red ATOM sensors detected biosensor targets that were specifically localized to various subcellular compartments. Fluorescence activation involved ligand-dependent chromophore maturation with turn-on ratios of up to 62-fold in cells and 100-fold in vitro. Endoplasmic reticulum- and mitochondria-localized ATOM sensors detected ligands that were targeted to those organelles. The ATOM design was validated with three monobodies and one nanobody inserted into distinct fluorescent proteins, suggesting that customized ATOM sensors can be generated quickly.
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Affiliation(s)
- Harsimranjit Sekhon
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Jeung-Hoi Ha
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Maria F Presti
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Spencer B Procopio
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Ava R Jarvis
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Paige O Mirsky
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Anna M John
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Stewart N Loh
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA.
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14
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Davis LC, Morgan AJ, Galione A. Optical profiling of autonomous Ca 2+ nanodomains generated by lysosomal TPC2 and TRPML1. Cell Calcium 2023; 116:102801. [PMID: 37742482 DOI: 10.1016/j.ceca.2023.102801] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 08/30/2023] [Accepted: 09/17/2023] [Indexed: 09/26/2023]
Abstract
Multiple families of Ca2+-permeable channels co-exist on lysosomal Ca2+ stores but how each family couples to its own unique downstream physiology is unclear. We have therefore investigated the Ca2+-signalling architecture underpinning different channels on the same vesicle that drive separate pathways, using phagocytosis as a physiological stimulus. Lysosomal Ca2+-channels are a major Ca2+ source driving particle uptake in macrophages, but different channels drive different aspects of Fc-receptor-mediated phagocytosis: TPC2 couples to dynamin activation, whilst TRPML1 couples to lysosomal exocytosis. We hypothesised that they are driven by discrete local plumes of Ca2+ around open channels (Ca2+ nanodomains). To test this, we optimized Ca2+-nanodomain recordings by screening panels of genetically encoded Ca2+ indicators (GECIs) fused to TPC2 to monitor the [Ca2+] next to the channel. Signal calibration accounting for the distance of the GECI from the channel mouth reveals that, during phagocytosis, TPC2 generates local Ca2+ nanodomains around itself of up to 42 µM, nearly a hundred-fold greater than the global cytosolic [Ca2+] rise. We further show that TPC2 and TRPML1, though on the same lysosomes, generate autonomous Ca2+ nanodomains of high [Ca2+] that are largely insulated from one another, a platform allowing their discrete Ca2+-decoding to promote unique respective physiologies.
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Affiliation(s)
- Lianne C Davis
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3QT, UK
| | - Anthony J Morgan
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3QT, UK
| | - Antony Galione
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3QT, UK.
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15
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Chen J, Gish CM, Fransen JW, Salazar-Gatzimas E, Clark DA, Borghuis BG. Direct comparison reveals algorithmic similarities in fly and mouse visual motion detection. iScience 2023; 26:107928. [PMID: 37810236 PMCID: PMC10550730 DOI: 10.1016/j.isci.2023.107928] [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: 06/27/2023] [Revised: 08/07/2023] [Accepted: 09/12/2023] [Indexed: 10/10/2023] Open
Abstract
Evolution has equipped vertebrates and invertebrates with neural circuits that selectively encode visual motion. While similarities in the computations performed by these circuits in mouse and fruit fly have been noted, direct experimental comparisons have been lacking. Because molecular mechanisms and neuronal morphology in the two species are distinct, we directly compared motion encoding in these two species at the algorithmic level, using matched stimuli and focusing on a pair of analogous neurons, the mouse ON starburst amacrine cell (ON SAC) and Drosophila T4 neurons. We find that the cells share similar spatiotemporal receptive field structures, sensitivity to spatiotemporal correlations, and tuning to sinusoidal drifting gratings, but differ in their responses to apparent motion stimuli. Both neuron types showed a response to summed sinusoids that deviates from models for motion processing in these cells, underscoring the similarities in their processing and identifying response features that remain to be explained.
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Affiliation(s)
- Juyue Chen
- Interdepartmental Neurosciences Program, Yale University, New Haven, CT 06511, USA
| | - Caitlin M Gish
- Department of Physics, Yale University, New Haven, CT 06511, USA
| | - James W Fransen
- Department of Anatomical Sciences and Neurobiology, University of Louisville, Louisville, KY 40202, USA
| | | | - Damon A Clark
- Interdepartmental Neurosciences Program, Yale University, New Haven, CT 06511, USA
- Department of Physics, Yale University, New Haven, CT 06511, USA
- Department of Molecular, Cellular, Developmental Biology, Yale University, New Haven, CT 06511, USA
- Department of Neuroscience, Yale University, New Haven, CT 06511, USA
| | - Bart G Borghuis
- Department of Anatomical Sciences and Neurobiology, University of Louisville, Louisville, KY 40202, USA
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16
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Yaganoglu S, Kalyviotis K, Vagena-Pantoula C, Jülich D, Gaub BM, Welling M, Lopes T, Lachowski D, Tang SS, Del Rio Hernandez A, Salem V, Müller DJ, Holley SA, Vermot J, Shi J, Helassa N, Török K, Pantazis P. Highly specific and non-invasive imaging of Piezo1-dependent activity across scales using GenEPi. Nat Commun 2023; 14:4352. [PMID: 37468521 PMCID: PMC10356793 DOI: 10.1038/s41467-023-40134-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 07/11/2023] [Indexed: 07/21/2023] Open
Abstract
Mechanosensing is a ubiquitous process to translate external mechanical stimuli into biological responses. Piezo1 ion channels are directly gated by mechanical forces and play an essential role in cellular mechanotransduction. However, readouts of Piezo1 activity are mainly examined by invasive or indirect techniques, such as electrophysiological analyses and cytosolic calcium imaging. Here, we introduce GenEPi, a genetically-encoded fluorescent reporter for non-invasive optical monitoring of Piezo1-dependent activity. We demonstrate that GenEPi has high spatiotemporal resolution for Piezo1-dependent stimuli from the single-cell level to that of the entire organism. GenEPi reveals transient, local mechanical stimuli in the plasma membrane of single cells, resolves repetitive contraction-triggered stimulation of beating cardiomyocytes within microtissues, and allows for robust and reliable monitoring of Piezo1-dependent activity in vivo. GenEPi will enable non-invasive optical monitoring of Piezo1 activity in mechanochemical feedback loops during development, homeostatic regulation, and disease.
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Affiliation(s)
- Sine Yaganoglu
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich, Basel, Switzerland
| | | | | | - Dörthe Jülich
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Benjamin M Gaub
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich, Basel, Switzerland
| | - Maaike Welling
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich, Basel, Switzerland
- Department of Bioengineering, Imperial College London, London, UK
| | - Tatiana Lopes
- Section of Investigative Medicine, Department of Metabolism, Digestion, and Reproduction, Imperial College London, London, UK
| | | | - See Swee Tang
- Department of Bioengineering, Imperial College London, London, UK
| | | | - Victoria Salem
- Department of Bioengineering, Imperial College London, London, UK
| | - Daniel J Müller
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich, Basel, Switzerland
| | - Scott A Holley
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Julien Vermot
- Department of Bioengineering, Imperial College London, London, UK
| | - Jian Shi
- Leeds Institute of Cardiovascular and Metabolic Medicine, LIGHT Laboratories, University of Leeds, Leeds, UK
| | - Nordine Helassa
- Molecular and Clinical Sciences Research Institute, St. George's, University of London, London, UK
- Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Katalin Török
- Molecular and Clinical Sciences Research Institute, St. George's, University of London, London, UK
| | - Periklis Pantazis
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich, Basel, Switzerland.
- Department of Bioengineering, Imperial College London, London, UK.
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17
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Abstract
Our ability to understand the function of the nervous system is dependent upon defining the connections of its constituent neurons. Development of methods to define connections within neural networks has always been a growth industry in the neurosciences. Transneuronal spread of neurotropic viruses currently represents the best means of defining synaptic connections within neural networks. The method exploits the ability of viruses to invade neurons, replicate, and spread through the intimate synaptic connections that enable communication among neurons. Since the method was first introduced in the 1970s, it has benefited from an increased understanding of the virus life cycle, the function of viral genomes, and the ability to manipulate the viral genome in support of directional spread of virus and the expression of transgenes. In this article, we review these advances in viral tracing technology and the ways in which they may be applied for functional dissection of neural networks. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Retrograde infection of CNS circuits by peripheral injection of virus Basic Protocol 2: Transneuronal analysis by intracerebral injection Alternate Protocol 1: Transneuronal analysis with multiple recombinant strains Alternate Protocol 2: Conditional replication and spread of PRV Alternate Protocol 3: Conditional reporters of PRV infection and spread Alternate Protocol 4: Reporters of neural activity in polysynaptic circuits Support Protocol 1: Growing and titering a PRV viral stock Support Protocol 2: Immunohistochemical processing and detection Support Protocol 3: Dual-immunofluorescence localization.
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Affiliation(s)
- Esteban A Engel
- Princeton Neuroscience Institute, Princeton University, Princeton, New Jersey
- Current address: Spark Therapeutics, Philadelphia, PA, 19104
| | - J Patrick Card
- Department of Neuroscience, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Lynn W Enquist
- Department of Molecular Biology, Princeton University, Princeton, New Jersey
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18
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Sekhon H, Ha JH, Presti MF, Procopio SB, Mirsky PO, John AM, Loh SN. Adaptable, Turn-On Monobody (ATOM) Fluorescent Biosensors for Multiplexed Detection in Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.28.534597. [PMID: 37034669 PMCID: PMC10081266 DOI: 10.1101/2023.03.28.534597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
A grand challenge in biosensor design is to develop a single molecule, fluorescent protein-based platform that can be easily adapted to recognize targets of choice. Conceptually, this can be achieved by fusing a small, antibody-like binding domain to a fluorescent protein in such a way that target binding activates fluorescence. Although this design is simple to envision, its execution is not obvious. Here, we created a family of adaptable, turn-on monobody (ATOM) biosensors consisting of a monobody, circularly permuted at one of two positions, inserted into a fluorescent protein at one of three surface loops. Multiplexed imaging of live human cells co-expressing cyan, yellow, and red ATOM sensors detected the biosensor targets (WDR5, SH2, and hRAS proteins) that were localized to the nucleus, cytoplasm, and plasma membrane, respectively, with high specificity. ER- and mitochondria-localized ATOM sensors also detected ligands that were targeted to those organelles. Fluorescence activation involved ligand-dependent chromophore maturation with fluorescence turn-on ratios of >20-fold in cells and up to 100-fold in vitro . The sensing mechanism was validated with three arbitrarily chosen monobodies inserted into jellyfish as well as anemone lineages of fluorescent proteins, suggesting that ATOM sensors with different binding specificities and additional colors can be generated relatively quickly.
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19
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Zhang Y, Rózsa M, Liang Y, Bushey D, Wei Z, Zheng J, Reep D, Broussard GJ, Tsang A, Tsegaye G, Narayan S, Obara CJ, Lim JX, Patel R, Zhang R, Ahrens MB, Turner GC, Wang SSH, Korff WL, Schreiter ER, Svoboda K, Hasseman JP, Kolb I, Looger LL. Fast and sensitive GCaMP calcium indicators for imaging neural populations. Nature 2023; 615:884-891. [PMID: 36922596 PMCID: PMC10060165 DOI: 10.1038/s41586-023-05828-9] [Citation(s) in RCA: 313] [Impact Index Per Article: 156.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 02/10/2023] [Indexed: 03/17/2023]
Abstract
Calcium imaging with protein-based indicators1,2 is widely used to follow neural activity in intact nervous systems, but current protein sensors report neural activity at timescales much slower than electrical signalling and are limited by trade-offs between sensitivity and kinetics. Here we used large-scale screening and structure-guided mutagenesis to develop and optimize several fast and sensitive GCaMP-type indicators3-8. The resulting 'jGCaMP8' sensors, based on the calcium-binding protein calmodulin and a fragment of endothelial nitric oxide synthase, have ultra-fast kinetics (half-rise times of 2 ms) and the highest sensitivity for neural activity reported for a protein-based calcium sensor. jGCaMP8 sensors will allow tracking of large populations of neurons on timescales relevant to neural computation.
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Affiliation(s)
- Yan Zhang
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Márton Rózsa
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Allen Institute for Neural Dynamics, Seattle, WA, USA
| | - Yajie Liang
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Genetically Encoded Neural Indicator and Effector (GENIE) Project, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Department of Diagnostic Radiology and Nuclear Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Daniel Bushey
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Ziqiang Wei
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Jihong Zheng
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Genetically Encoded Neural Indicator and Effector (GENIE) Project, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Daniel Reep
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Genetically Encoded Neural Indicator and Effector (GENIE) Project, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | | | - Arthur Tsang
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Genetically Encoded Neural Indicator and Effector (GENIE) Project, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Getahun Tsegaye
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Genetically Encoded Neural Indicator and Effector (GENIE) Project, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Sujatha Narayan
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Allen Institute for Neural Dynamics, Seattle, WA, USA
| | | | - Jing-Xuan Lim
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Ronak Patel
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Rongwei Zhang
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Misha B Ahrens
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Glenn C Turner
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.
- Genetically Encoded Neural Indicator and Effector (GENIE) Project, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.
| | - Samuel S-H Wang
- Neuroscience Institute, Princeton University, Princeton, NJ, USA.
| | - Wyatt L Korff
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Genetically Encoded Neural Indicator and Effector (GENIE) Project, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Eric R Schreiter
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Genetically Encoded Neural Indicator and Effector (GENIE) Project, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Karel Svoboda
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.
- Allen Institute for Neural Dynamics, Seattle, WA, USA.
- Genetically Encoded Neural Indicator and Effector (GENIE) Project, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.
| | - Jeremy P Hasseman
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.
- Genetically Encoded Neural Indicator and Effector (GENIE) Project, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.
| | - Ilya Kolb
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Genetically Encoded Neural Indicator and Effector (GENIE) Project, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Loren L Looger
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.
- Genetically Encoded Neural Indicator and Effector (GENIE) Project, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA.
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20
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Abstract
The genetically encoded fluorescent sensors convert chemical and physical signals into light. They are powerful tools for the visualisation of physiological processes in living cells and freely moving animals. The fluorescent protein is the reporter module of a genetically encoded biosensor. In this study, we first review the history of the fluorescent protein in full emission spectra on a structural basis. Then, we discuss the design of the genetically encoded biosensor. Finally, we briefly review several major types of genetically encoded biosensors that are currently widely used based on their design and molecular targets, which may be useful for the future design of fluorescent biosensors.
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Affiliation(s)
- Minji Wang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, No. 3663 Zhong Shan Road North, Shanghai, 200062, China
| | - Yifan Da
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, No. 3663 Zhong Shan Road North, Shanghai, 200062, China
| | - Yang Tian
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, No. 3663 Zhong Shan Road North, Shanghai, 200062, China
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21
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Aoki I, Shiota M, Tsukada Y, Nakano S, Mori I. cGMP dynamics that underlies thermosensation in temperature-sensing neuron regulates thermotaxis behavior in C. elegans. PLoS One 2022; 17:e0278343. [PMID: 36472979 PMCID: PMC9725164 DOI: 10.1371/journal.pone.0278343] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 11/08/2022] [Indexed: 12/12/2022] Open
Abstract
Living organisms including bacteria, plants and animals sense ambient temperature so that they can avoid noxious temperature or adapt to new environmental temperature. A nematode C. elegans can sense innocuous temperature, and navigate themselves towards memorize past cultivation temperature (Tc) of their preference. For this thermotaxis, AFD thermosensory neuron is pivotal, which stereotypically responds to warming by increasing intracellular Ca2+ level in a manner dependent on the remembered past Tc. We aimed to reveal how AFD encodes the information of temperature into neural activities. cGMP synthesis in AFD is crucial for thermosensation in AFD and thermotaxis behavior. Here we characterized the dynamic change of cGMP level in AFD by imaging animals expressing a fluorescence resonance energy transfer (FRET)-based cGMP probe specifically in AFD and found that cGMP dynamically responded to both warming and cooling in a manner dependent on past Tc. Moreover, we characterized mutant animals that lack guanylyl cyclases (GCYs) or phosphodiesterases (PDEs), which synthesize and hydrolyze cGMP, respectively, and uncovered how GCYs and PDEs contribute to cGMP and Ca2+ dynamics in AFD and to thermotaxis behavior.
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Affiliation(s)
- Ichiro Aoki
- Group of Molecular Neurobiology, Neuroscience Institute, Graduate School of Science, Nagoya University, Nagoya, Japan
- Department of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Makoto Shiota
- Department of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Yuki Tsukada
- Group of Molecular Neurobiology, Neuroscience Institute, Graduate School of Science, Nagoya University, Nagoya, Japan
- Department of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Shunji Nakano
- Group of Molecular Neurobiology, Neuroscience Institute, Graduate School of Science, Nagoya University, Nagoya, Japan
- Department of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Ikue Mori
- Group of Molecular Neurobiology, Neuroscience Institute, Graduate School of Science, Nagoya University, Nagoya, Japan
- Department of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
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22
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Human cancer cells generate spontaneous calcium transients and intercellular waves that modulate tumor growth. Biomaterials 2022; 290:121823. [DOI: 10.1016/j.biomaterials.2022.121823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 09/24/2022] [Indexed: 11/02/2022]
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23
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Carattino MD, Ruiz WG, Apodaca G. Ex Vivo Analysis of Mechanically Activated Ca2+ Transients in Urothelial Cells. J Vis Exp 2022:10.3791/64532. [PMID: 36279534 PMCID: PMC10069332 DOI: 10.3791/64532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Mechanically activated ion channels are biological transducers that convert mechanical stimuli such as stretch or shear forces into electrical and biochemical signals. In mammals, mechanically activated channels are essential for the detection of external and internal stimuli in processes as diverse as touch sensation, hearing, red blood cell volume regulation, basal blood pressure regulation, and the sensation of urinary bladder fullness. While the function of mechanically activated ion channels has been extensively studied in the in vitro setting using the patch-clamp technique, assessing their function in their native environment remains a difficult task, often because of limited access to the sites of expression of these channels (e.g., afferent terminals, Merkel cells, baroreceptors, and kidney tubules) or difficulties applying the patch-clamp technique (e.g., the apical surfaces of urothelial umbrella cells). This protocol describes a procedure to assess mechanically evoked Ca2+ transients using the fluorescent sensor GCaMP5G in an ex vivo urothelial preparation, a technique that could be readily adapted for the study of mechanically evoked Ca2+ events in other native tissue preparations.
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Affiliation(s)
- Marcelo D Carattino
- Renal-Electrolyte Division, Department of Medicine, University of Pittsburgh; Department of Cell Biology, University of Pittsburgh;
| | - Wily G Ruiz
- Renal-Electrolyte Division, Department of Medicine, University of Pittsburgh
| | - Gerard Apodaca
- Renal-Electrolyte Division, Department of Medicine, University of Pittsburgh; Department of Cell Biology, University of Pittsburgh
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24
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Chen Z, Zhou Q, Deán‐Ben XL, Gezginer I, Ni R, Reiss M, Shoham S, Razansky D. Multimodal Noninvasive Functional Neurophotonic Imaging of Murine Brain-Wide Sensory Responses. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2105588. [PMID: 35798308 PMCID: PMC9404388 DOI: 10.1002/advs.202105588] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 05/09/2022] [Indexed: 05/28/2023]
Abstract
Modern optical neuroimaging approaches are expanding the ability to elucidate complex brain function. Diverse imaging contrasts enable direct observation of neural activity with functional sensors along with the induced hemodynamic responses. To date, decoupling the complex interplay of neurovascular coupling and dynamical physiological states has remained challenging when employing single-modality functional neuroimaging readings. A hybrid fluorescence optoacoustic tomography platform combined with a custom data processing pipeline based on statistical parametric mapping is devised, attaining the first noninvasive observation of simultaneous calcium and hemodynamic activation patterns using optical contrasts. Correlated changes in the oxy- and deoxygenated hemoglobin, total hemoglobin, oxygen saturation, and rapid GCaMP6f fluorescence signals are observed in response to peripheral sensory stimulation. While the concurrent epifluorescence serves to corroborate and complement the functional optoacoustic observations, the latter further aids in decoupling the rapid calcium responses from the slowly varying background in the fluorescence recordings mediated by hemodynamic changes. The hybrid imaging platform expands the capabilities of conventional neuroimaging methods to provide more comprehensive functional readings for studying neurovascular and neurometabolic coupling mechanisms and related diseases.
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Affiliation(s)
- Zhenyue Chen
- Institute for Biomedical Engineering and Institute of Pharmacology and ToxicologyFaculty of MedicineUniversity of ZurichZurich8057Switzerland
- Institute for Biomedical EngineeringDepartment of Information Technology and Electrical EngineeringETH ZurichZurich8092Switzerland
| | - Quanyu Zhou
- Institute for Biomedical Engineering and Institute of Pharmacology and ToxicologyFaculty of MedicineUniversity of ZurichZurich8057Switzerland
- Institute for Biomedical EngineeringDepartment of Information Technology and Electrical EngineeringETH ZurichZurich8092Switzerland
| | - Xosé Luís Deán‐Ben
- Institute for Biomedical Engineering and Institute of Pharmacology and ToxicologyFaculty of MedicineUniversity of ZurichZurich8057Switzerland
- Institute for Biomedical EngineeringDepartment of Information Technology and Electrical EngineeringETH ZurichZurich8092Switzerland
| | - Irmak Gezginer
- Institute for Biomedical Engineering and Institute of Pharmacology and ToxicologyFaculty of MedicineUniversity of ZurichZurich8057Switzerland
- Institute for Biomedical EngineeringDepartment of Information Technology and Electrical EngineeringETH ZurichZurich8092Switzerland
| | - Ruiqing Ni
- Institute for Biomedical Engineering and Institute of Pharmacology and ToxicologyFaculty of MedicineUniversity of ZurichZurich8057Switzerland
- Institute for Biomedical EngineeringDepartment of Information Technology and Electrical EngineeringETH ZurichZurich8092Switzerland
| | - Michael Reiss
- Institute for Biomedical Engineering and Institute of Pharmacology and ToxicologyFaculty of MedicineUniversity of ZurichZurich8057Switzerland
- Institute for Biomedical EngineeringDepartment of Information Technology and Electrical EngineeringETH ZurichZurich8092Switzerland
| | - Shy Shoham
- Department of Ophthalmology and Tech4Health and Neuroscience InstitutesNYU Langone HealthNew York10016USA
| | - Daniel Razansky
- Institute for Biomedical Engineering and Institute of Pharmacology and ToxicologyFaculty of MedicineUniversity of ZurichZurich8057Switzerland
- Institute for Biomedical EngineeringDepartment of Information Technology and Electrical EngineeringETH ZurichZurich8092Switzerland
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25
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Rabbitt RD, Holman HA. ATP and ACh Evoked Calcium Transients in the Neonatal Mouse Cochlear and Vestibular Sensory Epithelia. Front Neurosci 2021; 15:710076. [PMID: 34566562 PMCID: PMC8455828 DOI: 10.3389/fnins.2021.710076] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 08/18/2021] [Indexed: 12/02/2022] Open
Abstract
Hair cells in the mammalian inner ear sensory epithelia are surrounded by supporting cells which are essential for function of cochlear and vestibular systems. In mice, support cells exhibit spontaneous intracellular Ca2+ transients in both auditory and vestibular organs during the first postnatal week before the onset of hearing. We recorded long lasting (>200 ms) Ca2+ transients in cochlear and vestibular support cells in neonatal mice using the genetic calcium indicator GCaMP5. Both cochlear and vestibular support cells exhibited spontaneous intracellular Ca2+ transients (GCaMP5 ΔF/F), in some cases propagating as waves from the apical (endolymph facing) to the basolateral surface with a speed of ∼25 μm per second, consistent with inositol trisphosphate dependent calcium induced calcium release (CICR). Acetylcholine evoked Ca2+ transients were observed in both inner border cells in the cochlea and vestibular support cells, with a larger change in GCaMP5 fluorescence in the vestibular support cells. Adenosine triphosphate evoked robust Ca2+ transients predominantly in the cochlear support cells that included Hensen’s cells, Deiters’ cells, inner hair cells, inner phalangeal cells and inner border cells. A Ca2+ event initiated in one inner border cells propagated in some instances longitudinally to neighboring inner border cells with an intercellular speed of ∼2 μm per second, and decayed after propagating along ∼3 cells. Similar intercellular propagation was not observed in the radial direction from inner border cell to inner sulcus cells, and was not observed between adjacent vestibular support cells.
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Affiliation(s)
- Richard D Rabbitt
- Department of Biomedical Engineering, University of Utah, Salt Lake City, UT, United States.,Graduate Program in Neuroscience, University of Utah, Salt Lake City, UT, United States.,Department of Otolaryngology-Head and Neck Surgery, University of Utah, Salt Lake City, UT, United States
| | - Holly A Holman
- Department of Biomedical Engineering, University of Utah, Salt Lake City, UT, United States
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26
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Bogetti AT, Presti MF, Loh SN, Chong LT. The Next Frontier for Designing Switchable Proteins: Rational Enhancement of Kinetics. J Phys Chem B 2021; 125:9069-9077. [PMID: 34324338 PMCID: PMC8826494 DOI: 10.1021/acs.jpcb.1c04082] [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] [Indexed: 11/28/2022]
Abstract
Designing proteins that can switch between active (ON) and inactive (OFF) conformations in response to signals such as ligand binding and incident light has been a tantalizing endeavor in protein engineering for over a decade. While such designs have yielded novel biosensors, therapeutic agents, and smart biomaterials, the response times (times for switching ON and OFF) of many switches have been too slow to be of practical use. Among the defining properties of such switches, the kinetics of switching has been the most challenging to optimize. This is largely due to the difficulty of characterizing the structures of transient states, which are required for manipulating the height of the effective free energy barrier between the ON and OFF states. We share our perspective of the most promising new experimental and computational strategies over the past several years for tackling this next frontier for designing switchable proteins.
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Affiliation(s)
- Anthony T Bogetti
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Maria F Presti
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, New York 13210, United States
| | - Stewart N Loh
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, New York 13210, United States
| | - Lillian T Chong
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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27
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Song A, Gauthier JL, Pillow JW, Tank DW, Charles AS. Neural anatomy and optical microscopy (NAOMi) simulation for evaluating calcium imaging methods. J Neurosci Methods 2021; 358:109173. [PMID: 33839190 PMCID: PMC8217135 DOI: 10.1016/j.jneumeth.2021.109173] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 03/21/2021] [Accepted: 03/24/2021] [Indexed: 11/20/2022]
Abstract
BACKGROUND The past decade has seen a multitude of new in vivo functional imaging methodologies. However, the lack of ground-truth comparisons or evaluation metrics makes the large-scale, systematic validation vital to the continued development and use of optical microscopy impossible. NEW-METHOD We provide a new framework for evaluating two-photon microscopy methods via in silico Neural Anatomy and Optical Microscopy (NAOMi) simulation. Our computationally efficient model generates large anatomical volumes of mouse cortex, simulates neural activity, and incorporates optical propagation and scanning to create realistic calcium imaging datasets. RESULTS We verify NAOMi simulations against in vivo two-photon recordings from mouse cortex. We leverage this in silico ground truth to directly compare different segmentation algorithms and optical designs. We find modern segmentation algorithms extract strong neural time-courses comparable to estimation using oracle spatial information, but with an increase in the false positive rate. Comparison between optical setups demonstrate improved resilience to motion artifacts in sparsely labeled samples using Bessel beams, increased signal-to-noise ratio and cell-count using low numerical aperture Gaussian beams and nuclear GCaMP, and more uniform spatial sampling with temporal focusing versus multi-plane imaging. COMPARISON WITH EXISTING METHODS NAOMi is a first-of-its kind framework for assessing optical imaging modalities. Existing methods are either anatomical simulations or do not address functional imaging. Thus there is no competing method for simulating realistic functional optical microscopy data. CONCLUSIONS By leveraging the rich accumulated knowledge of neural anatomy and optical physics, we provide a powerful new tool to assess and develop important methods in neural imaging.
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Affiliation(s)
- Alexander Song
- Princeton Neuroscience Institute, Princeton University, Princeton, 08540 NJ, USA; Department of Physics, Princeton University, Princeton, 08540 NJ, USA
| | - Jeff L Gauthier
- Princeton Neuroscience Institute, Princeton University, Princeton, 08540 NJ, USA
| | - Jonathan W Pillow
- Princeton Neuroscience Institute, Princeton University, Princeton, 08540 NJ, USA; Department of Psychology, Princeton University, Princeton, 08540 NJ, USA
| | - David W Tank
- Princeton Neuroscience Institute, Princeton University, Princeton, 08540 NJ, USA; Bezos Center for Neural Circuit Dynamics, Princeton University, Princeton, 08540 NJ, USA; Department of Molecular Biology, Princeton University, Princeton, 08540 NJ, USA
| | - Adam S Charles
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, 21218, MD, USA; Mathematical Institute for Data Science, Johns Hopkins University, Baltimore, 21218, MD, USA; Center for Imaging Science, Johns Hopkins University, Baltimore, 21218, MD, USA; Kavli Neuroscience Discovery Institute, Johns Hopkins University, Baltimore, 21218, MD, USA
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28
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Yook JS, Kim J, Kim J. Convergence Circuit Mapping: Genetic Approaches From Structure to Function. Front Syst Neurosci 2021; 15:688673. [PMID: 34234652 PMCID: PMC8255632 DOI: 10.3389/fnsys.2021.688673] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 05/28/2021] [Indexed: 12/22/2022] Open
Abstract
Understanding the complex neural circuits that underpin brain function and behavior has been a long-standing goal of neuroscience. Yet this is no small feat considering the interconnectedness of neurons and other cell types, both within and across brain regions. In this review, we describe recent advances in mouse molecular genetic engineering that can be used to integrate information on brain activity and structure at regional, cellular, and subcellular levels. The convergence of structural inputs can be mapped throughout the brain in a cell type-specific manner by antero- and retrograde viral systems expressing various fluorescent proteins and genetic switches. Furthermore, neural activity can be manipulated using opto- and chemo-genetic tools to interrogate the functional significance of this input convergence. Monitoring neuronal activity is obtained with precise spatiotemporal resolution using genetically encoded sensors for calcium changes and specific neurotransmitters. Combining these genetically engineered mapping tools is a compelling approach for unraveling the structural and functional brain architecture of complex behaviors and malfunctioned states of neurological disorders.
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Affiliation(s)
- Jang Soo Yook
- Center for Functional Connectomics, Korea Institute of Science and Technology (KIST), Seoul, South Korea
| | - Jihyun Kim
- Center for Functional Connectomics, Korea Institute of Science and Technology (KIST), Seoul, South Korea.,Department of Integrated Biomedical and Life Sciences, Graduate School, Korea University, Seoul, South Korea
| | - Jinhyun Kim
- Center for Functional Connectomics, Korea Institute of Science and Technology (KIST), Seoul, South Korea.,Department of Integrated Biomedical and Life Sciences, Graduate School, Korea University, Seoul, South Korea
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29
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Post MR, Sulzer D. The chemical tools for imaging dopamine release. Cell Chem Biol 2021; 28:748-764. [PMID: 33894160 PMCID: PMC8532025 DOI: 10.1016/j.chembiol.2021.04.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 02/23/2021] [Accepted: 04/06/2021] [Indexed: 02/07/2023]
Abstract
Dopamine is a modulatory neurotransmitter involved in learning, motor functions, and reward. Many neuropsychiatric disorders, including Parkinson's disease, autism, and schizophrenia, are associated with imbalances or dysfunction in the dopaminergic system. Yet, our understanding of these pervasive public health issues is limited by our ability to effectively image dopamine in humans, which has long been a goal for chemists and neuroscientists. The last two decades have witnessed the development of many molecules used to trace dopamine. We review the small molecules, nanoparticles, and protein sensors used with fluorescent microscopy/photometry, MRI, and PET that shape dopamine research today. None of these tools observe dopamine itself, but instead harness the biology of the dopamine system-its synthetic and metabolic pathways, synaptic vesicle cycle, and receptors-in elegant ways. Their advantages and weaknesses are covered here, along with recent examples and the chemistry and biology that allow them to function.
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Affiliation(s)
- Michael R Post
- Department of Psychiatry, Columbia University Medical Center, New York, NY, USA; Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY, USA.
| | - David Sulzer
- Departments of Psychiatry, Neurology, and Pharmacology, Columbia University Medical Center, New York, NY, USA; Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY, USA.
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30
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Ren C, Komiyama T. Characterizing Cortex-Wide Dynamics with Wide-Field Calcium Imaging. J Neurosci 2021; 41:4160-4168. [PMID: 33893217 PMCID: PMC8143209 DOI: 10.1523/jneurosci.3003-20.2021] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 03/26/2021] [Accepted: 03/30/2021] [Indexed: 12/27/2022] Open
Abstract
The brain functions through coordinated activity among distributed regions. Wide-field calcium imaging, combined with improved genetically encoded calcium indicators, allows sufficient signal-to-noise ratio and spatiotemporal resolution to afford a unique opportunity to capture cortex-wide dynamics on a moment-by-moment basis in behaving animals. Recent applications of this approach have been uncovering cortical dynamics at unprecedented scales during various cognitive processes, ranging from relatively simple sensorimotor integration to more complex decision-making tasks. In this review, we will highlight recent scientific advances enabled by wide-field calcium imaging in behaving mice. We then summarize several technical considerations and future opportunities for wide-field imaging to uncover large-scale circuit dynamics.
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Affiliation(s)
- Chi Ren
- Neurobiology Section, Center for Neural Circuits and Behavior, Department of Neurosciences, and Halıcıoğlu Data Science Institute, University of California San Diego, La Jolla, California 92093
| | - Takaki Komiyama
- Neurobiology Section, Center for Neural Circuits and Behavior, Department of Neurosciences, and Halıcıoğlu Data Science Institute, University of California San Diego, La Jolla, California 92093
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31
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Bi X, Beck C, Gong Y. Genetically Encoded Fluorescent Indicators for Imaging Brain Chemistry. BIOSENSORS 2021; 11:116. [PMID: 33920418 PMCID: PMC8069469 DOI: 10.3390/bios11040116] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/06/2021] [Accepted: 04/09/2021] [Indexed: 12/17/2022]
Abstract
Genetically encoded fluorescent indicators, combined with optical imaging, enable the detection of physiologically or behaviorally relevant neural activity with high spatiotemporal resolution. Recent developments in protein engineering and screening strategies have improved the dynamic range, kinetics, and spectral properties of genetically encoded fluorescence indicators of brain chemistry. Such indicators have detected neurotransmitter and calcium dynamics with high signal-to-noise ratio at multiple temporal and spatial scales in vitro and in vivo. This review summarizes the current trends in these genetically encoded fluorescent indicators of neurotransmitters and calcium, focusing on their key metrics and in vivo applications.
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Affiliation(s)
| | | | - Yiyang Gong
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA; (X.B.); (C.B.)
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32
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Adelizzi B, Gielen V, Le Saux T, Dedecker P, Jullien L. Quantitative Model for Reversibly Photoswitchable Sensors. ACS Sens 2021; 6:1157-1165. [PMID: 33565309 PMCID: PMC8008439 DOI: 10.1021/acssensors.0c02414] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 01/21/2021] [Indexed: 12/11/2022]
Abstract
Composed of a reversibly photoswitchable unit allosterically linked to a sensing module, reversibly photoswitchable sensors (rs-sensors) represent a new and attractive strategy to quantitatively read-out analyte concentrations. However, their kinetic response to illumination is complex, and much attention is required from the design to the application steps. Here, we exploit a generic kinetic model of rs-sensors which enables us to point to key thermokinetic parameters, such as dissociation constants and kinetic rates for exchange toward the analyte, and cross-sections for photoswitching. The application of the model allows to evaluate the robustness of the analyzed parameters and to introduce a methodology for their reliable use. Model and methodology have been experimentally tested on a newly reported calcium sensor based on a reversibly photoswitchable green fluorescent protein allosterically linked to a calcium-sensing module integrating calmodulin and an RS20 peptide.
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Affiliation(s)
- Beatrice Adelizzi
- PASTEUR,
Département de Chimie, École
Normale Supérieure, PSL University, Sorbonne Université,
CNRS, 24, rue Lhomond, Paris 75005, France
| | - Vincent Gielen
- Laboratory
for Nanobiology, Department of Chemistry, KU Leuven, Celestijnenlaan
200G, Heverlee 3001, Belgium
| | - Thomas Le Saux
- PASTEUR,
Département de Chimie, École
Normale Supérieure, PSL University, Sorbonne Université,
CNRS, 24, rue Lhomond, Paris 75005, France
| | - Peter Dedecker
- Laboratory
for Nanobiology, Department of Chemistry, KU Leuven, Celestijnenlaan
200G, Heverlee 3001, Belgium
| | - Ludovic Jullien
- PASTEUR,
Département de Chimie, École
Normale Supérieure, PSL University, Sorbonne Université,
CNRS, 24, rue Lhomond, Paris 75005, France
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33
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Li ES, Saha MS. Optimizing Calcium Detection Methods in Animal Systems: A Sandbox for Synthetic Biology. Biomolecules 2021; 11:343. [PMID: 33668387 PMCID: PMC7996158 DOI: 10.3390/biom11030343] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/19/2021] [Accepted: 02/21/2021] [Indexed: 12/16/2022] Open
Abstract
Since the 1970s, the emergence and expansion of novel methods for calcium ion (Ca2+) detection have found diverse applications in vitro and in vivo across a series of model animal systems. Matched with advances in fluorescence imaging techniques, the improvements in the functional range and stability of various calcium indicators have significantly enhanced more accurate study of intracellular Ca2+ dynamics and its effects on cell signaling, growth, differentiation, and regulation. Nonetheless, the current limitations broadly presented by organic calcium dyes, genetically encoded calcium indicators, and calcium-responsive nanoparticles suggest a potential path toward more rapid optimization by taking advantage of a synthetic biology approach. This engineering-oriented discipline applies principles of modularity and standardization to redesign and interrogate endogenous biological systems. This review will elucidate how novel synthetic biology technologies constructed for eukaryotic systems can offer a promising toolkit for interfacing with calcium signaling and overcoming barriers in order to accelerate the process of Ca2+ detection optimization.
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Affiliation(s)
| | - Margaret S. Saha
- Department of Biology, College of William and Mary, Williamsburg, VA 23185, USA;
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34
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Transcriptional readout of neuronal activity via an engineered Ca 2+-activated protease. Proc Natl Acad Sci U S A 2020; 117:33186-33196. [PMID: 33323488 DOI: 10.1073/pnas.2006521117] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Molecular integrators, in contrast to real-time indicators, convert transient cellular events into stable signals that can be exploited for imaging, selection, molecular characterization, or cellular manipulation. Many integrators, however, are designed as complex multicomponent circuits that have limited robustness, especially at high, low, or nonstoichiometric protein expression levels. Here, we report a simplified design of the calcium and light dual integrator FLARE. Single-chain FLARE (scFLARE) is a single polypeptide chain that incorporates a transcription factor, a LOV domain-caged protease cleavage site, and a calcium-activated TEV protease that we designed through structure-guided mutagenesis and screening. We show that scFLARE has greater dynamic range and robustness than first-generation FLARE and can be used in culture as well as in vivo to record patterns of neuronal activation with 10-min temporal resolution.
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35
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Roberts RE, Vervliet T, Bultynck G, Parys JB, Hallett MB. EPIC3, a novel Ca 2+ indicator located at the cell cortex and in microridges, detects high Ca 2+ subdomains during Ca 2+ influx and phagocytosis. Cell Calcium 2020; 92:102291. [PMID: 33099169 DOI: 10.1016/j.ceca.2020.102291] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 09/11/2020] [Accepted: 09/17/2020] [Indexed: 11/15/2022]
Abstract
The construction of a low affinity Ca2+-probe that locates to the cell cortex and cell surface wrinkles, is described called. EPIC3 (ezrin-protein indicator of Ca2+). The novel probe is a fusion of CEPIA3 with ezrin, and is used in combination with a Ca2+-insensitive probe, ezrin-mCherry, both of which locate at the cell cortex. EPIC3 was used to monitor the effect of Ca2+ influx on intra-wrinkle Ca2+ in the macrophage cell line, RAW 264.7. During experimentally-induced Ca2+influx, EPIC3 reported Ca2+ concentrations at the cell cortex in the region of 30-50 μM, with peak locations towards the tips of wrinkles reaching 80 μM. These concentrations were associated with cleavage of ezrin (a substrate for the Ca2+ activated protease calpain-1) and released the C-terminal fluors. The cortical Ca2+ levels, restricted to near the site of phagocytic cup formation and pseudopodia extension during phagocytosis also reached high levels (50-80 μM) during phagocytosis. As phagocytosis was completed, hotspots of Ca2+ near the phagosome were also observed.
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Affiliation(s)
- Rhiannon E Roberts
- Neutrophil Signalling Group, Cardiff University Medical School, Cardiff, CF14 4XN, UK
| | - Tim Vervliet
- KU Leuven, Laboratory for Molecular and Cellular Signaling, Department of Cellular and Molecular Medicine, Leuven, Belgium
| | - Geert Bultynck
- KU Leuven, Laboratory for Molecular and Cellular Signaling, Department of Cellular and Molecular Medicine, Leuven, Belgium
| | - Jan B Parys
- KU Leuven, Laboratory for Molecular and Cellular Signaling, Department of Cellular and Molecular Medicine, Leuven, Belgium
| | - Maurice B Hallett
- Neutrophil Signalling Group, Cardiff University Medical School, Cardiff, CF14 4XN, UK.
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36
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Sakaki KDR, Podgorski K, Dellazizzo Toth TA, Coleman P, Haas K. Comprehensive Imaging of Sensory-Evoked Activity of Entire Neurons Within the Awake Developing Brain Using Ultrafast AOD-Based Random-Access Two-Photon Microscopy. Front Neural Circuits 2020; 14:33. [PMID: 32612514 PMCID: PMC7308460 DOI: 10.3389/fncir.2020.00033] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 05/07/2020] [Indexed: 11/18/2022] Open
Abstract
Determining how neurons transform synaptic input and encode information in action potential (AP) firing output is required for understanding dendritic integration, neural transforms and encoding. Limitations in the speed of imaging 3D volumes of brain encompassing complex dendritic arbors in vivo using conventional galvanometer mirror-based laser-scanning microscopy has hampered fully capturing fluorescent sensors of activity throughout an individual neuron's entire complement of synaptic inputs and somatic APs. To address this problem, we have developed a two-photon microscope that achieves high-speed scanning by employing inertia-free acousto-optic deflectors (AODs) for laser beam positioning, enabling random-access sampling of hundreds to thousands of points-of-interest restricted to a predetermined neuronal structure, avoiding wasted scanning of surrounding extracellular tissue. This system is capable of comprehensive imaging of the activity of single neurons within the intact and awake vertebrate brain. Here, we demonstrate imaging of tectal neurons within the brains of albino Xenopus laevis tadpoles labeled using single-cell electroporation for expression of a red space-filling fluorophore to determine dendritic arbor morphology, and either the calcium sensor jGCaMP7s or the glutamate sensor iGluSnFR as indicators of neural activity. Using discrete, point-of-interest scanning we achieve sampling rates of 3 Hz for saturation sampling of entire arbors at 2 μm resolution, 6 Hz for sequentially sampling 3 volumes encompassing the dendritic arbor and soma, and 200–250 Hz for scanning individual planes through the dendritic arbor. This system allows investigations of sensory-evoked information input-output relationships of neurons within the intact and awake brain.
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Affiliation(s)
- Kelly D R Sakaki
- Department of Cellular and Physiological Sciences, Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC, Canada
| | | | - Tristan A Dellazizzo Toth
- Department of Cellular and Physiological Sciences, Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC, Canada
| | - Patrick Coleman
- Department of Cellular and Physiological Sciences, Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC, Canada
| | - Kurt Haas
- Department of Cellular and Physiological Sciences, Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC, Canada
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37
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Genetically encoded calcium indicators to probe complex brain circuit dynamics in vivo. Neurosci Res 2020; 169:2-8. [PMID: 32531233 DOI: 10.1016/j.neures.2020.05.013] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 05/13/2020] [Accepted: 05/27/2020] [Indexed: 12/28/2022]
Abstract
Over the past two decades, genetically encoded calcium indicators (GECIs) have been used extensively to report intracellular calcium (Ca2+) dynamics in order to readout neuronal and network activity in living tissue. Single wavelength GECIs, such as GCaMP, have been widely adapted due to advances in dynamic range, sensitivity, and kinetics. Additionally, recent efforts in protein engineering have expanded the GECI color palette to enable direct optical interrogation of more complex circuit dynamics. Here, I discuss the engineering, application, and future directions of the most recently developed GECIs for in vivo neuroscience research.
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38
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Edwards KA, Hoppa MB, Bosco G. The Photoconvertible Fluorescent Probe, CaMPARI, Labels Active Neurons in Freely-Moving Intact Adult Fruit Flies. Front Neural Circuits 2020; 14:22. [PMID: 32457580 PMCID: PMC7227398 DOI: 10.3389/fncir.2020.00022] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 04/14/2020] [Indexed: 01/27/2023] Open
Abstract
Linking neural circuitry to behavior by mapping active neurons in vivo is a challenge. Both genetically encoded calcium indicators (GECIs) and intermediate early genes (IEGs) have been used to pinpoint active neurons during a stimulus or behavior but have drawbacks such as limiting the movement of the organism, requiring a priori knowledge of the active region or having poor temporal resolution. Calcium-modulated photoactivatable ratiometric integrator (CaMPARI) was engineered to overcome these spatial-temporal challenges. CaMPARI is a photoconvertible protein that only converts from green to red fluorescence in the presence of high calcium concentration and 405 nm light. This allows the experimenter to precisely mark active neurons within defined temporal windows. The photoconversion can then be quantified by taking the ratio of the red fluorescence to the green. CaMPARI promises the ability to trace active neurons during a specific stimulus; however, CaMPARI's uses in adult Drosophila have been limited to photoconversion during fly immobilization. Here, we demonstrate a method that allows photoconversion of multiple freely-moving intact adult flies during a stimulus. Flies were placed in a dish with filter paper wet with acetic acid (pH = 2) or neutralized acetic acid (pH = 7) and exposed to photoconvertible light (60 mW) for 30 min (500 ms on, 200 ms off). Immediately following photoconversion, whole flies were fixed and imaged by confocal microscopy. The red:green ratio was quantified for the DC4 glomerulus, a bundle of neurons expressing Ir64a, an ionotropic receptor that senses acids in the Drosophila antennal lobe. Flies exposed to acetic acid showed 1.3-fold greater photoconversion than flies exposed to neutralized acetic acid. This finding was recapitulated using a more physiological stimulus of apple cider vinegar. These results indicate that CaMPARI can be used to label neurons in intact, freely-moving adult flies and will be useful for identifying the circuitry underlying complex behaviors.
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Affiliation(s)
- Katie A. Edwards
- Department of Molecular and Systems Biology, Geisel School of Medicine, Dartmouth College, Hanover, NH, United States
| | - Michael B. Hoppa
- Department of Biological Sciences, Dartmouth College, Hanover, NH, United States
| | - Giovanni Bosco
- Department of Molecular and Systems Biology, Geisel School of Medicine, Dartmouth College, Hanover, NH, United States
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39
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Cardenas-Diaz FL, Leavens KF, Kishore S, Osorio-Quintero C, Chen YJ, Stanger BZ, Wang P, French D, Gadue P. A Dual Reporter EndoC-βH1 Human β-Cell Line for Efficient Quantification of Calcium Flux and Insulin Secretion. Endocrinology 2020; 161:bqaa005. [PMID: 31960055 PMCID: PMC7028009 DOI: 10.1210/endocr/bqaa005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Revised: 01/07/2020] [Accepted: 01/20/2020] [Indexed: 02/07/2023]
Abstract
Human in vitro model systems of diabetes are critical to both study disease pathophysiology and offer a platform for drug testing. We have generated a set of tools in the human β-cell line EndoC-βH1 that allows the efficient and inexpensive characterization of β-cell physiology and phenotypes driven by disruption of candidate genes. First, we generated a dual reporter line that expresses a preproinsulin-luciferase fusion protein along with GCaMP6s. This reporter line allows the quantification of insulin secretion by measuring luciferase activity and calcium flux, a critical signaling step required for insulin secretion, via fluorescence microscopy. Using these tools, we demonstrate that the generation of the reporter human β-cell line was highly efficient and validated that luciferase activity could accurately reflect insulin secretion. Second, we used a lentiviral vector carrying the CRISPR-Cas9 system to generate candidate gene disruptions in the reporter line. We also show that we can achieve gene disruption in ~90% of cells using a CRISPR-Cas9 lentiviral system. As a proof of principle, we disrupt the β-cell master regulator, PDX1, and show that mutant EndoC-βH1 cells display impaired calcium responses and fail to secrete insulin when stimulated with high glucose. Furthermore, we show that PDX1 mutant EndoC-βH1 cells exhibit decreased expression of the β-cell-specific genes MAFA and NKX6.1 and increased GCG expression. The system presented here provides a platform to quickly and easily test β-cell functionality in wildtype and cells lacking a gene of interest.
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Affiliation(s)
- Fabian L Cardenas-Diaz
- Center for Cellular and Molecular Therapeutics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Karla F Leavens
- Division of Endocrinology and Diabetes, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Siddharth Kishore
- Center for Cellular and Molecular Therapeutics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
- Department of Cell and Molecular Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Catherine Osorio-Quintero
- Center for Cellular and Molecular Therapeutics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Yi-Ju Chen
- Department of Cell and Molecular Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Ben Z Stanger
- Department of Cell and Molecular Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Gastroenterology Division, Department of Medicine, Abramson Family Cancer Research Institute, University of Pennsylvania School of Medicine, Philadelphia
| | - Pei Wang
- Departments of Cell Systems and Anatomy, University of Texas Health Science Center at San Antonio, San Antonio, Texas
| | - Deborah French
- Center for Cellular and Molecular Therapeutics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Paul Gadue
- Center for Cellular and Molecular Therapeutics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
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40
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Chhabria K, Plant K, Bandmann O, Wilkinson RN, Martin C, Kugler E, Armitage PA, Santoscoy PL, Cunliffe VT, Huisken J, McGown A, Ramesh T, Chico TJ, Howarth C. The effect of hyperglycemia on neurovascular coupling and cerebrovascular patterning in zebrafish. J Cereb Blood Flow Metab 2020; 40:298-313. [PMID: 30398083 PMCID: PMC6985997 DOI: 10.1177/0271678x18810615] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Neurovascular coupling (through which local cerebral blood flow changes in response to neural activation are mediated) is impaired in many diseases including diabetes. Current preclinical rodent models of neurovascular coupling rely on invasive surgery and instrumentation, but transgenic zebrafish coupled with advances in imaging techniques allow non-invasive quantification of cerebrovascular anatomy, neural activation, and cerebral vessel haemodynamics. We therefore established a novel non-invasive, non-anaesthetised zebrafish larval model of neurovascular coupling, in which visual stimulus evokes neuronal activation in the optic tectum that is associated with a specific increase in red blood cell speed in tectal blood vessels. We applied this model to the examination of the effect of glucose exposure on cerebrovascular patterning and neurovascular coupling. We found that chronic exposure of zebrafish to glucose impaired tectal blood vessel patterning and neurovascular coupling. The nitric oxide donor sodium nitroprusside rescued all these adverse effects of glucose exposure on cerebrovascular patterning and function. Our results establish the first non-mammalian model of neurovascular coupling, offering the potential to perform more rapid genetic modifications and high-throughput screening than is currently possible using rodents. Furthermore, using this zebrafish model, we reveal a potential strategy to ameliorate the effects of hyperglycemia on cerebrovascular function.
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Affiliation(s)
- Karishma Chhabria
- Neuroimaging in Cardiovascular Disease (NICAD) Network, University of Sheffield, Sheffield, UK.,Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield Medical School, Sheffield, UK.,The Bateson Centre, University of Sheffield, Sheffield, UK
| | - Karen Plant
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield Medical School, Sheffield, UK.,The Bateson Centre, University of Sheffield, Sheffield, UK
| | - Oliver Bandmann
- The Bateson Centre, University of Sheffield, Sheffield, UK.,Department of Neuroscience, University of Sheffield Medical School, Sheffield, UK
| | - Robert N Wilkinson
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield Medical School, Sheffield, UK.,The Bateson Centre, University of Sheffield, Sheffield, UK
| | - Chris Martin
- Neuroimaging in Cardiovascular Disease (NICAD) Network, University of Sheffield, Sheffield, UK.,Department of Psychology, University of Sheffield, Sheffield, UK
| | - Elisabeth Kugler
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield Medical School, Sheffield, UK.,The Bateson Centre, University of Sheffield, Sheffield, UK
| | - Paul A Armitage
- Neuroimaging in Cardiovascular Disease (NICAD) Network, University of Sheffield, Sheffield, UK.,Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield Medical School, Sheffield, UK
| | - Paola Lm Santoscoy
- The Bateson Centre, University of Sheffield, Sheffield, UK.,Department of Biomedical Science, University of Sheffield, Sheffield, UK
| | - Vincent T Cunliffe
- The Bateson Centre, University of Sheffield, Sheffield, UK.,Department of Biomedical Science, University of Sheffield, Sheffield, UK
| | - Jan Huisken
- Morgridge Institute for Research, Madison, WI, USA
| | - Alexander McGown
- The Bateson Centre, University of Sheffield, Sheffield, UK.,Department of Neuroscience, University of Sheffield Medical School, Sheffield, UK
| | - Tennore Ramesh
- The Bateson Centre, University of Sheffield, Sheffield, UK.,Department of Neuroscience, University of Sheffield Medical School, Sheffield, UK
| | - Tim Ja Chico
- Neuroimaging in Cardiovascular Disease (NICAD) Network, University of Sheffield, Sheffield, UK.,Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield Medical School, Sheffield, UK.,The Bateson Centre, University of Sheffield, Sheffield, UK
| | - Clare Howarth
- Neuroimaging in Cardiovascular Disease (NICAD) Network, University of Sheffield, Sheffield, UK.,Department of Psychology, University of Sheffield, Sheffield, UK
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41
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Shen Y, Nasu Y, Shkolnikov I, Kim A, Campbell RE. Engineering genetically encoded fluorescent indicators for imaging of neuronal activity: Progress and prospects. Neurosci Res 2020; 152:3-14. [PMID: 31991206 DOI: 10.1016/j.neures.2020.01.011] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 01/10/2020] [Accepted: 01/12/2020] [Indexed: 12/31/2022]
Abstract
Genetically encoded fluorescent indicators have transformed the way neuroscientists record neuronal activities and interrogate the nervous system in vivo. In this review, we discuss recent advances and new additions to the toolkit of indicators for calcium ion entry, membrane voltage change, neurotransmitter release, and other neuronal molecular processes. We highlight new engineering approaches for indicator design and development, and identify key areas for future improvement. From molecular tool developers' perspective, we aim to provide practical information for neuroscientists to evaluate and choose the most appropriate indicators for enabling new insights into brain function.
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Affiliation(s)
- Yi Shen
- Department of Chemistry, University of Alberta, Canada
| | - Yusuke Nasu
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Japan
| | | | - Anna Kim
- Department of Chemistry, University of Alberta, Canada
| | - Robert E Campbell
- Department of Chemistry, University of Alberta, Canada; Department of Chemistry, Graduate School of Science, The University of Tokyo, Japan.
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42
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Hallett MB, Roberts RE, Dewitt S. Optical Methods for the Measurement and Manipulation of Cytosolic Calcium Signals in Neutrophils. Methods Mol Biol 2020; 2087:191-205. [PMID: 31728992 DOI: 10.1007/978-1-0716-0154-9_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The measurement and manipulation of cytosolic free Ca2+ of neutrophils is crucial for investigating the mechanisms within living neutrophils which generate Ca2+ signals and the cellular responses triggered by them. Optical methods for this are the most applicable for neutrophils, and are discussed here, especially the use of fluorescent indicators of Ca2+ and photoactivation of reagents involved in Ca2+ signaling. Both of these synthetic agents can be loaded into neutrophils as lipid-soluble esters or can be microinjected into the cell. In this chapter, we outline some of the techniques that have been used to monitor, visualize, and manipulate Ca2+ in neutrophils.
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Affiliation(s)
| | | | - Sharon Dewitt
- School of Medicine and School of Dentistry, Cardiff University, Cardiff, UK
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43
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Mano O, Creamer MS, Matulis CA, Salazar-Gatzimas E, Chen J, Zavatone-Veth JA, Clark DA. Using slow frame rate imaging to extract fast receptive fields. Nat Commun 2019; 10:4979. [PMID: 31672963 PMCID: PMC6823504 DOI: 10.1038/s41467-019-12974-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 10/11/2019] [Indexed: 11/09/2022] Open
Abstract
In functional imaging, large numbers of neurons are measured during sensory stimulation or behavior. This data can be used to map receptive fields that describe neural associations with stimuli or with behavior. The temporal resolution of these receptive fields has traditionally been limited by image acquisition rates. However, even when acquisitions scan slowly across a population of neurons, individual neurons may be measured at precisely known times. Here, we apply a method that leverages the timing of neural measurements to find receptive fields with temporal resolutions higher than the image acquisition rate. We use this temporal super-resolution method to resolve fast voltage and glutamate responses in visual neurons in Drosophila and to extract calcium receptive fields from cortical neurons in mammals. We provide code to easily apply this method to existing datasets. This method requires no specialized hardware and can be used with any optical indicator of neural activity.
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Affiliation(s)
- Omer Mano
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, 06511, USA
| | - Matthew S Creamer
- Interdepartmental Neuroscience Program, Yale University, New Haven, CT, 06511, USA
| | | | | | - Juyue Chen
- Interdepartmental Neuroscience Program, Yale University, New Haven, CT, 06511, USA
| | | | - Damon A Clark
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, 06511, USA.
- Interdepartmental Neuroscience Program, Yale University, New Haven, CT, 06511, USA.
- Department of Physics, Yale University, New Haven, CT, 06511, USA.
- Department of Neuroscience, Yale University, New Haven, CT, 06511, USA.
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44
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Storace DA, Cohen LB, Choi Y. Using Genetically Encoded Voltage Indicators (GEVIs) to Study the Input-Output Transformation of the Mammalian Olfactory Bulb. Front Cell Neurosci 2019; 13:342. [PMID: 31417362 PMCID: PMC6684792 DOI: 10.3389/fncel.2019.00342] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 07/11/2019] [Indexed: 12/19/2022] Open
Abstract
Genetically encoded voltage indicators (GEVIs) are fluorescent protein reporters of membrane potential. These tools can, in principle, be used to monitor the neural activity of genetically distinct cell types in the brain. Although introduced in 1997, they have been a challenge to use to study intact neural circuits due to a combination of small signal-to-noise ratio, slow kinetics, and poor membrane expression. New strategies have yielded novel GEVIs such as ArcLight, which have improved properties. Here, we compare the in vivo properties of ArcLight with Genetically Encoded Calcium Indicators (GECIs) in the mouse olfactory bulb. We show how voltage imaging can be combined with organic calcium sensitive dyes to measure the input-output transformation of the olfactory bulb. Finally, we demonstrate that ArcLight can be targeted to olfactory bulb interneurons. The olfactory bulb contributes substantially to the perception of the concentration invariance of odor recognition.
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Affiliation(s)
- Douglas A Storace
- Department of Biological Science, Florida State University, Tallahassee, FL, United States.,Department of Cellular and Molecular Physiology, Yale School of Medicine, Yale University, New Haven, CT, United States
| | - Lawrence B Cohen
- Department of Cellular and Molecular Physiology, Yale School of Medicine, Yale University, New Haven, CT, United States.,Center for Functional Connectomics, Korea Institute of Science and Technology, Seoul, South Korea
| | - Yunsook Choi
- Department of Cellular and Molecular Physiology, Yale School of Medicine, Yale University, New Haven, CT, United States.,Center for Functional Connectomics, Korea Institute of Science and Technology, Seoul, South Korea
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45
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Kerruth S, Coates C, Dürst CD, Oertner TG, Török K. The kinetic mechanisms of fast-decay red-fluorescent genetically encoded calcium indicators. J Biol Chem 2019; 294:3934-3946. [PMID: 30651353 PMCID: PMC6422079 DOI: 10.1074/jbc.ra118.004543] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 01/14/2019] [Indexed: 01/06/2023] Open
Abstract
Genetically encoded calcium indicators (GECIs) are useful reporters of cell-signaling, neuronal, and network activities. We have generated novel fast variants and investigated the kinetic mechanisms of two recently developed red-fluorescent GECIs (RGECIs), mApple-based jRGECO1a and mRuby-based jRCaMP1a. In the formation of fluorescent jRGECO1a and jRCaMP1a complexes, calcium binding is followed by rate-limiting isomerization. However, fluorescence decay of calcium-bound jRGECO1a follows a different pathway from its formation: dissociation of calcium occurs first, followed by the peptide, similarly to GCaMP-s. In contrast, fluorescence decay of calcium-bound jRCaMP1a occurs by the reversal of the on-pathway: peptide dissociation is followed by calcium. The mechanistic differences explain the generally slower off-kinetics of jRCaMP1a-type indicators compared with GCaMP-s and jRGECO1a-type GECI: the fluorescence decay rate of f-RCaMP1 was 21 s-1, compared with 109 s-1 for f-RGECO1 and f-RGECO2 (37 °C). Thus, the CaM-peptide interface is an important determinant of the kinetic responses of GECIs; however, the topology of the structural link to the fluorescent protein demonstrably affects the internal dynamics of the CaM-peptide complex. In the dendrites of hippocampal CA3 neurons, f-RGECO1 indicates calcium elevation in response to a 100 action potential train in a linear fashion, making the probe particularly useful for monitoring large-amplitude, fast signals, e.g. those in dendrites, muscle cells, and immune cells.
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Affiliation(s)
- Silke Kerruth
- From the Molecular and Clinical Sciences Research Institute, St. George's, University of London, London SW17 0RE, United Kingdom and
| | - Catherine Coates
- From the Molecular and Clinical Sciences Research Institute, St. George's, University of London, London SW17 0RE, United Kingdom and
| | - Céline D Dürst
- the Institute for Synaptic Physiology, Center for Molecular Neurobiology Hamburg, 20251 Hamburg, Germany
| | - Thomas G Oertner
- the Institute for Synaptic Physiology, Center for Molecular Neurobiology Hamburg, 20251 Hamburg, Germany
| | - Katalin Török
- From the Molecular and Clinical Sciences Research Institute, St. George's, University of London, London SW17 0RE, United Kingdom and
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46
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Anderson HE, Weir RFF. On the development of optical peripheral nerve interfaces. Neural Regen Res 2019; 14:425-436. [PMID: 30539808 PMCID: PMC6334609 DOI: 10.4103/1673-5374.245461] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Accepted: 09/19/2018] [Indexed: 11/04/2022] Open
Abstract
Limb loss and spinal cord injury are two debilitating conditions that continue to grow in prevalence. Prosthetic limbs and limb reanimation present two ways of providing affected individuals with means to interact in the world. These techniques are both dependent on a robust interface with the peripheral nerve. Current methods for interfacing with the peripheral nerve tend to suffer from low specificity, high latency and insufficient robustness for a chronic implant. An optical peripheral nerve interface may solve some of these problems by decreasing invasiveness and providing single axon specificity. In order to implement such an interface three elements are required: (1) a transducer capable of translating light into a neural stimulus or translating neural activity into changes in fluorescence, (2) a means for delivering said transducer and (3) a microscope for providing the stimulus light and detecting the fluorescence change. There are continued improvements in both genetically encoded calcium and voltage indicators as well as new optogenetic actuators for stimulation. Similarly, improvements in specificity of viral vectors continue to improve expression in the axons of the peripheral nerve. Our work has recently shown that it is possible to virally transduce axons of the peripheral nerve for recording from small fibers. The improvements of these components make an optical peripheral nerve interface a rapidly approaching alternative to current methods.
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Affiliation(s)
- Hans E. Anderson
- Department of Bioengineering, University of Colorado Denver | Anschutz Medical Campus, Aurora, CO, USA
| | - Richard F. ff. Weir
- Department of Bioengineering, University of Colorado Denver | Anschutz Medical Campus, Aurora, CO, USA
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47
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Advances in Engineering and Application of Optogenetic Indicators for Neuroscience. APPLIED SCIENCES-BASEL 2019. [DOI: 10.3390/app9030562] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Our ability to investigate the brain is limited by available technologies that can record biological processes in vivo with suitable spatiotemporal resolution. Advances in optogenetics now enable optical recording and perturbation of central physiological processes within the intact brains of model organisms. By monitoring key signaling molecules noninvasively, we can better appreciate how information is processed and integrated within intact circuits. In this review, we describe recent efforts engineering genetically-encoded fluorescence indicators to monitor neuronal activity. We summarize recent advances of sensors for calcium, potassium, voltage, and select neurotransmitters, focusing on their molecular design, properties, and current limitations. We also highlight impressive applications of these sensors in neuroscience research. We adopt the view that advances in sensor engineering will yield enduring insights on systems neuroscience. Neuroscientists are eager to adopt suitable tools for imaging neural activity in vivo, making this a golden age for engineering optogenetic indicators.
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48
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Siciliano CA, Tye KM. Leveraging calcium imaging to illuminate circuit dysfunction in addiction. Alcohol 2019; 74:47-63. [PMID: 30470589 PMCID: PMC7575247 DOI: 10.1016/j.alcohol.2018.05.013] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 05/08/2018] [Accepted: 05/28/2018] [Indexed: 12/28/2022]
Abstract
Alcohol and drug use can dysregulate neural circuit function to produce a wide range of neuropsychiatric disorders, including addiction. To understand the neural circuit computations that mediate behavior, and how substances of abuse may transform them, we must first be able to observe the activity of circuits. While many techniques have been utilized to measure activity in specific brain regions, these regions are made up of heterogeneous sub-populations, and assessing activity from neuronal populations of interest has been an ongoing challenge. To fully understand how neural circuits mediate addiction-related behavior, we must be able to reveal the cellular granularity within brain regions and circuits by overlaying functional information with the genetic and anatomical identity of the cells involved. The development of genetically encoded calcium indicators, which can be targeted to populations of interest, allows for in vivo visualization of calcium dynamics, a proxy for neuronal activity, thus providing an avenue for real-time assessment of activity in genetically and anatomically defined populations during behavior. Here, we highlight recent advances in calcium imaging technology, compare the current technology with other state-of-the-art approaches for in vivo monitoring of neural activity, and discuss the strengths, limitations, and practical concerns for observing neural circuit activity in preclinical addiction models.
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Affiliation(s)
- Cody A Siciliano
- The Picower Institute for Learning and Memory, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, United States.
| | - Kay M Tye
- The Picower Institute for Learning and Memory, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, United States; The Salk Institute for Biological Sciences, 10010 N Torrey Pines Road, La Jolla, CA 92037, United States.
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49
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Sakaki KDR, Coleman P, Toth TD, Guerrier C, Haas K. Automating Event-detection of Brain Neuron Synaptic Activity and Action Potential Firing in vivo using a Random-access Multiphoton Laser Scanning Microscope for Real-time Analysis. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2018; 2018:1-7. [PMID: 30440280 DOI: 10.1109/embc.2018.8512983] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Determining how a neuron computes requires an understanding of the complex spatiotemporal relationship between its input (e.g. synaptic input as a result of external stimuli) and action potential output. Recent advances in in vivo, laser-scanning multiphoton technology, known as random-access microscopy (RAM), can capture this relationship by imaging fluorescent light, emitted from calcium-sensitive biosensors responding to synaptic and action potential firing in a neuron's full dendritic arbor and cell body. Ideally, a continuous output of fluorescent intensities from the neuron would be converted to a binary output (`event', 'or no-event'). These binary events can be used to correlate temporal and spatial associations between the input and output. However, neurons contain hundreds-to-thousands of synapses on the dendritic arbors generating an enormous quantity of data composed of physiological signals, which vary greatly in shape and size. Thus, automating data-processing tasks is essential to support high-throughput analysis for real-time/post-processing operations and to improve operators' comprehension of the data used to decipher neuron computations. Here, we describe an automated software algorithm to detect brain neuron events in real-time using an acousto-optic, multiphoton, laser scanning RAM developed in our laboratory. The fluorescent light intensities, from a genetically encoded, calcium biosensor (GCAMP 6m), are measured by our RAM system and are input to our 'event-detector', which converts them to a binary output meant for real-time applications. We evaluate three algorithms for this purpose: exponentially weighted moving average, cumulative sum, and template matching; present each algorithm's performance; and discuss user-feasibility of each. We validated our system in vivo, using the visual circuit of the Xenopus laevis.
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50
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Automatic Cell Segmentation by Adaptive Thresholding (ACSAT) for Large-Scale Calcium Imaging Datasets. eNeuro 2018; 5:eN-MNT-0056-18. [PMID: 30221189 PMCID: PMC6135987 DOI: 10.1523/eneuro.0056-18.2018] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2018] [Revised: 08/16/2018] [Accepted: 08/23/2018] [Indexed: 02/04/2023] Open
Abstract
Advances in calcium imaging have made it possible to record from an increasingly larger number of neurons simultaneously. Neuroscientists can now routinely image hundreds to thousands of individual neurons. An emerging technical challenge that parallels the advancement in imaging a large number of individual neurons is the processing of correspondingly large datasets. One important step is the identification of individual neurons. Traditional methods rely mainly on manual or semimanual inspection, which cannot be scaled for processing large datasets. To address this challenge, we focused on developing an automated segmentation method, which we refer to as automated cell segmentation by adaptive thresholding (ACSAT). ACSAT works with a time-collapsed image and includes an iterative procedure that automatically calculates global and local threshold values during successive iterations based on the distribution of image pixel intensities. Thus, the algorithm is capable of handling variations in morphological details and in fluorescence intensities in different calcium imaging datasets. In this paper, we demonstrate the utility of ACSAT by testing it on 500 simulated datasets, two wide-field hippocampus datasets, a wide-field striatum dataset, a wide-field cell culture dataset, and a two-photon hippocampus dataset. For the simulated datasets with truth, ACSAT achieved >80% recall and precision when the signal-to-noise ratio was no less than ∼24 dB.
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