1
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Bonney SK, Nielson CD, Sosa MJ, Bonnar O, Shih AY. Capillary regression leads to sustained local hypoperfusion by inducing constriction of upstream transitional vessels. Proc Natl Acad Sci U S A 2024; 121:e2321021121. [PMID: 39236241 DOI: 10.1073/pnas.2321021121] [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: 12/01/2023] [Accepted: 08/07/2024] [Indexed: 09/07/2024] Open
Abstract
In the brain, a microvascular sensory web coordinates oxygen delivery to regions of neuronal activity. This involves a dense network of capillaries that send conductive signals upstream to feeding arterioles to promote vasodilation and blood flow. Although this process is critical to the metabolic supply of healthy brain tissue, it may also be a point of vulnerability in disease. Deterioration of capillary networks is a feature of many neurological disorders and injuries and how this web is engaged during vascular damage remains unknown. We performed in vivo two-photon microscopy on young adult mural cell reporter mice and induced focal capillary injuries using precise two-photon laser irradiation of single capillaries. We found that ~59% of the injuries resulted in regression of the capillary segment 7 to 14 d following injury, and the remaining repaired to reestablish blood flow within 7 d. Injuries that resulted in capillary regression induced sustained vasoconstriction in the upstream arteriole-capillary transition (ACT) zone at least 21 days postinjury in both awake and anesthetized mice. The degree of vasomotor dynamics was chronically attenuated in the ACT zone consequently reducing blood flow in the ACT zone and in secondary, uninjured downstream capillaries. These findings demonstrate how focal capillary injury and regression can impair the microvascular sensory web and contribute to cerebral hypoperfusion.
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Affiliation(s)
- Stephanie K Bonney
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98101
| | - Cara D Nielson
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98101
- Graduate Program in Neuroscience, University of Washington, Seattle, WA 98195
| | - Maria J Sosa
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98101
| | - Orla Bonnar
- MassGeneral Institute for Neurodegenerative Disease, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02129
| | - Andy Y Shih
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98101
- Department of Pediatrics, University of Washington, Seattle, WA 98195
- Department of Bioengineering, University of Washington, Seattle, WA 98195
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2
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Barykina NV, Carey EM, Oliinyk OS, Nimmerjahn A, Verkhusha VV. Destabilized near-infrared fluorescent nanobodies enable background-free targeting of GFP-based biosensors for imaging and manipulation. Nat Commun 2024; 15:7788. [PMID: 39242569 PMCID: PMC11379940 DOI: 10.1038/s41467-024-51857-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 08/19/2024] [Indexed: 09/09/2024] Open
Abstract
Near-infrared (NIR) probes are highly sought after as fluorescent tags for multicolor cellular and in vivo imaging. Here we develop small NIR fluorescent nanobodies, termed NIR-FbLAG16 and NIR-FbLAG30, enabling background-free visualization of various GFP-derived probes and biosensors. We also design a red-shifted variant, NIR-Fb(718), to simultaneously target several antigens within the NIR spectral range. Leveraging the antigen-stabilizing property of the developed NIR-Fbs, we then create two modular systems for precise control of gene expression in GFP-labeled cells. Applying the NIR-Fbs in vivo, we target cells expressing GFP and the calcium biosensor GCaMP6 in the somatosensory cortex of transgenic mice. Simultaneously tracking calcium activity and the reference signal from NIR-FbLAGs bound to GCaMP6 enables ratiometric deep-brain in vivo imaging. Altogether, NIR-FbLAGs present a promising approach for imaging and manipulating various processes in live cells and behaving animals expressing GFP-based probes.
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Affiliation(s)
- Natalia V Barykina
- Department of Genetics, and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York, NY, 10461, USA
| | - Erin M Carey
- Waitt Advanced Biophotonics Center, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Olena S Oliinyk
- Medicum, Faculty of Medicine, University of Helsinki, Helsinki, 00290, Finland
| | - Axel Nimmerjahn
- Waitt Advanced Biophotonics Center, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Vladislav V Verkhusha
- Department of Genetics, and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York, NY, 10461, USA.
- Medicum, Faculty of Medicine, University of Helsinki, Helsinki, 00290, Finland.
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3
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Dong C, Gowrishankar R, Jin Y, He XJ, Gupta A, Wang H, Sayar-Atasoy N, Flores RJ, Mahe K, Tjahjono N, Liang R, Marley A, Or Mizuno G, Lo DK, Sun Q, Whistler JL, Li B, Gomes I, Von Zastrow M, Tejeda HA, Atasoy D, Devi LA, Bruchas MR, Banghart MR, Tian L. Unlocking opioid neuropeptide dynamics with genetically encoded biosensors. Nat Neurosci 2024; 27:1844-1857. [PMID: 39009835 PMCID: PMC11374718 DOI: 10.1038/s41593-024-01697-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 06/05/2024] [Indexed: 07/17/2024]
Abstract
Neuropeptides are ubiquitous in the nervous system. Research into neuropeptides has been limited by a lack of experimental tools that allow for the precise dissection of their complex and diverse dynamics in a circuit-specific manner. Opioid peptides modulate pain, reward and aversion and as such have high clinical relevance. To illuminate the spatiotemporal dynamics of endogenous opioid signaling in the brain, we developed a class of genetically encoded fluorescence sensors based on kappa, delta and mu opioid receptors: κLight, δLight and µLight, respectively. We characterized the pharmacological profiles of these sensors in mammalian cells and in dissociated neurons. We used κLight to identify electrical stimulation parameters that trigger endogenous opioid release and the spatiotemporal scale of dynorphin volume transmission in brain slices. Using in vivo fiber photometry in mice, we demonstrated the utility of these sensors in detecting optogenetically driven opioid release and observed differential opioid release dynamics in response to fearful and rewarding conditions.
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Affiliation(s)
- Chunyang Dong
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California Davis, Davis, CA, USA
| | - Raajaram Gowrishankar
- Center for the Neurobiology of Addiction, Pain, and Emotion, Departments of Anesthesiology and Pharmacology, University of Washington, Seattle, WA, USA
| | - Yihan Jin
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California Davis, Davis, CA, USA
| | - Xinyi Jenny He
- Department of Neurobiology, School of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Achla Gupta
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Huikun Wang
- Unit on Neuromodulation and Synaptic Integration, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
| | - Nilüfer Sayar-Atasoy
- Department of Neuroscience and Pharmacology, Iowa Neuroscience Institute, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Rodolfo J Flores
- Unit on Neuromodulation and Synaptic Integration, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
| | - Karan Mahe
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California Davis, Davis, CA, USA
| | - Nikki Tjahjono
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California Davis, Davis, CA, USA
| | - Ruqiang Liang
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California Davis, Davis, CA, USA
| | - Aaron Marley
- Department of Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Grace Or Mizuno
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California Davis, Davis, CA, USA
| | - Darren K Lo
- College of Biological Sciences, University of California Davis, Davis, CA, USA
| | - Qingtao Sun
- Cold Spring Harbor Laboratory, New York, NY, USA
| | | | - Bo Li
- Cold Spring Harbor Laboratory, New York, NY, USA
| | - Ivone Gomes
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Mark Von Zastrow
- Department of Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Hugo A Tejeda
- Unit on Neuromodulation and Synaptic Integration, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
| | - Deniz Atasoy
- Department of Neuroscience and Pharmacology, Iowa Neuroscience Institute, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Lakshmi A Devi
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Michael R Bruchas
- Center for the Neurobiology of Addiction, Pain, and Emotion, Departments of Anesthesiology and Pharmacology, University of Washington, Seattle, WA, USA.
| | - Matthew R Banghart
- Department of Neurobiology, School of Biological Sciences, University of California, San Diego, La Jolla, CA, USA.
| | - Lin Tian
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California Davis, Davis, CA, USA.
- Max Planck Florida Institute for Neuroscience, Jupiter, FL, USA.
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4
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Xu Z, Kunala K, Murphy P, Patak L, Puthussery T, McGregor J. Foveal Retinal Ganglion Cells Develop Altered Calcium Dynamics Weeks After Photoreceptor Ablation. OPHTHALMOLOGY SCIENCE 2024; 4:100520. [PMID: 38881601 PMCID: PMC11179405 DOI: 10.1016/j.xops.2024.100520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 02/28/2024] [Accepted: 03/14/2024] [Indexed: 06/18/2024]
Abstract
Purpose Physiological changes in retinal ganglion cells (RGCs) have been reported in rodent models of photoreceptor (PR) loss, but this has not been investigated in primates. By expressing both a calcium indicator (GCaMP6s) and an optogenetic actuator (ChrimsonR) in foveal RGCs of the macaque, we reactivated RGCs in vivo and assessed their response in the weeks and years after PR loss. Design We used an in vivo calcium imaging approach to record optogenetically evoked activity in deafferented RGCs in primate fovea. Cellular scale recordings were made longitudinally over a 10-week period after PR ablation and compared with responses from RGCs that had lost PR input >2 years prior. Participants Three eyes received PR ablation, the right eye of a male Macaca mulatta (M1), the left eye of a female Macaca fascicularis (M2), and the right eye of a male Macaca fascicularis (M3). Two animals were used for in vivo recording, 1 for histological assessment. Methods Cones were ablated with an ultrafast laser delivered through an adaptive optics scanning light ophthalmoscope (AOSLO). A 0.5 second pulse of 25 Hz 660 nm light optogenetically stimulated RGCs, and the resulting GCaMP fluorescence signal was recorded using an AOSLO. Measurements were repeated over 10 weeks immediately after PR ablation, at 2.3 years and in control RGCs. Main Outcome Measures The calcium rise time, decay constant, and sensitivity index of optogenetic-mediated RGC were derived from GCaMP fluorescence recordings from 221 RGCs (animal M1) and 218 RGCs (animal M2) in vivo. Results After PR ablation, the mean decay constant of the calcium response in RGCs decreased 1.5-fold (standard deviation 1.6 ± 0.5 seconds to 0.6 ± 0.3 seconds) over the 10-week observation period in subject 1 and 2.1-fold (standard deviation 2.5 ± 0.5 seconds to 1.2 ± 0.2 seconds) within 8 weeks in subject 2. Calcium rise time and sensitivity index were stable. Optogenetic reactivation remained possible 2.3 years after PR ablation. Conclusions Altered calcium dynamics developed in primate foveal RGCs in the weeks after PR ablation. The mean decay constant of optogenetic-mediated calcium responses decreased 1.5- to twofold. This is the first report of this phenomenon in primate retina and further work is required to understand the role these changes play in cell survival and activity. Financial Disclosures Proprietary or commercial disclosure may be found in the Footnotes and Disclosures at the end of this article.
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Affiliation(s)
- Zhengyang Xu
- Institute of Optics, University of Rochester, Rochester, New York
| | - Karteek Kunala
- Center for Visual Science, University of Rochester Medical Center, Rochester, New York
| | - Peter Murphy
- Institute of Optics, University of Rochester, Rochester, New York
| | - Laura Patak
- Herbert Wertheim School of Optometry & Vision Science, University of California Berkeley, Berkeley, California
- Vision Science Graduate Program, University of California Berkeley, Berkeley, California
| | - Teresa Puthussery
- Herbert Wertheim School of Optometry & Vision Science, University of California Berkeley, Berkeley, California
- Helen Wills Neuroscience Institute, University of California Berkeley, Berkeley, California
| | - Juliette McGregor
- Center for Visual Science, University of Rochester Medical Center, Rochester, New York
- Department of Ophthalmology, University of Rochester Medical Center, Rochester, New York
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5
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Xu C, Nedergaard M, Fowell DJ, Friedl P, Ji N. Multiphoton fluorescence microscopy for in vivo imaging. Cell 2024; 187:4458-4487. [PMID: 39178829 PMCID: PMC11373887 DOI: 10.1016/j.cell.2024.07.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 07/18/2024] [Accepted: 07/22/2024] [Indexed: 08/26/2024]
Abstract
Multiphoton fluorescence microscopy (MPFM) has been a game-changer for optical imaging, particularly for studying biological tissues deep within living organisms. MPFM overcomes the strong scattering of light in heterogeneous tissue by utilizing nonlinear excitation that confines fluorescence emission mostly to the microscope focal volume. This enables high-resolution imaging deep within intact tissue and has opened new avenues for structural and functional studies. MPFM has found widespread applications and has led to numerous scientific discoveries and insights into complex biological processes. Today, MPFM is an indispensable tool in many research communities. Its versatility and effectiveness make it a go-to technique for researchers investigating biological phenomena at the cellular and subcellular levels in their native environments. In this Review, the principles, implementations, capabilities, and limitations of MPFM are presented. Three application areas of MPFM, neuroscience, cancer biology, and immunology, are reviewed in detail and serve as examples for applying MPFM to biological research.
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Affiliation(s)
- Chris Xu
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14850, USA
| | - Maiken Nedergaard
- Center for Translational Neuromedicine, Faculty of Health and Medical Sciences, University of Copenhagen, Nørre Alle 3B, 2200 Copenhagen, Denmark; University of Rochester Medical School, 601 Elmwood Avenue, Rochester, NY 14642, USA
| | - Deborah J Fowell
- Department of Microbiology & Immunology, Cornell University, Ithaca, NY 14853, USA
| | - Peter Friedl
- Department of Medical BioSciences, Radboud University Medical Centre, Geert Grooteplein 26-28, Nijmegen HB 6500, the Netherlands
| | - Na Ji
- Department of Neuroscience, Department of Physics, University of California Berkeley, Berkeley, CA 94720, USA.
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6
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Xu Q, Zheng Q, Cui X, Cleland A, Hincapie J, Raja SN, Dong X, Guan Y. Visualizing the modulation of neurokinin 1 receptor-positive neurons in the superficial dorsal horn by spinal cord stimulation in vivo. Pain 2024:00006396-990000000-00683. [PMID: 39140483 DOI: 10.1097/j.pain.0000000000003361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 06/25/2024] [Indexed: 08/15/2024]
Abstract
ABSTRACT Spinal cord stimulation (SCS) is an effective modality for pain treatment, yet its underlying mechanisms remain elusive. Neurokinin 1 receptor-positive (NK1R+) neurons in spinal lamina I play a pivotal role in pain transmission. To enhance our mechanistic understanding of SCS-induced analgesia, we investigated how different SCS paradigms modulate the activation of NK1R+ neurons, by developing NK1R-Cre;GCaMP6s transgenic mice and using in vivo calcium imaging of superficial NK1R+ neurons under anesthesia (1.5% isoflurane). Neurokinin 1 receptor-positive neurons in the lumbar spinal cord (L4-5) showed a greater activation by electrical test stimulation (TS, 3.0 mA, 1 Hz) at the hindpaw at 2 weeks after tibia-sparing nerve injury (SNI-t) than in naïve mice. Spinal cord stimulation was then delivered through a bipolar plate electrode placed epidurally at L1-2 level. The short-term 50-Hz high-intensity SCS (80% motor threshold [MoT], 10 minutes) induced robust and prolonged inhibition of NK1R+ neuronal responses to TS in both naïve and SNI-t mice. The 30-minute 50-Hz and 900-Hz SCS applied at moderate intensity (50% MoT) also significantly inhibited neuronal responses in SNI-t mice. However, at low intensity (20% MoT), the 30-minute 900-Hz SCS only induced persistent neuronal inhibition in naïve mice, but not in SNI-t mice. In conclusion, both 10-minute high-intensity SCS and 30-minute SCS at moderate intensity inhibit the activation of superficial NK1R+ neurons, potentially attenuating spinal nociceptive transmission. Furthermore, in vivo calcium imaging of NK1R+ neurons provides a new approach for exploring the spinal neuronal mechanisms of pain inhibition by neuromodulation pain therapies.
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Affiliation(s)
- Qian Xu
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University, School of Medicine, Baltimore, MD, United States
- Howard Hughes Medical Institute, Johns Hopkins University, School of Medicine, Baltimore, MD, United States
| | - Qin Zheng
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University, School of Medicine, Baltimore, MD, United States
| | - Xiang Cui
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University, School of Medicine, Baltimore, MD, United States
| | | | | | - Srinivasa N Raja
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University, School of Medicine, Baltimore, MD, United States
| | - Xinzhong Dong
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University, School of Medicine, Baltimore, MD, United States
- Howard Hughes Medical Institute, Johns Hopkins University, School of Medicine, Baltimore, MD, United States
- Department of Neurological Surgery, Johns Hopkins University, School of Medicine, Baltimore, MD, United States
| | - Yun Guan
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University, School of Medicine, Baltimore, MD, United States
- Department of Neurological Surgery, Johns Hopkins University, School of Medicine, Baltimore, MD, United States
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7
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Rutter GA, Gresch A, Delgadillo Silva L, Benninger RKP. Exploring pancreatic beta-cell subgroups and their connectivity. Nat Metab 2024:10.1038/s42255-024-01097-6. [PMID: 39117960 DOI: 10.1038/s42255-024-01097-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 07/05/2024] [Indexed: 08/10/2024]
Abstract
Functional pancreatic islet beta cells are essential to ensure glucose homeostasis across species from zebrafish to humans. These cells show significant heterogeneity, and emerging studies have revealed that connectivity across a hierarchical network is required for normal insulin release. Here, we discuss current thinking and areas of debate around intra-islet connectivity, cellular hierarchies and potential "controlling" beta-cell populations. We focus on methodologies, including comparisons of different cell preparations as well as in vitro and in vivo approaches to imaging and controlling the activity of human and rodent islet preparations. We also discuss the analytical approaches that can be applied to live-cell data to identify and study critical subgroups of cells with a disproportionate role in control Ca2+ dynamics and thus insulin secretion (such as "first responders", "leaders" and "hubs", as defined by Ca2+ responses to glucose stimulation). Possible mechanisms by which this hierarchy is achieved, its physiological relevance and how its loss may contribute to islet failure in diabetes mellitus are also considered. A glossary of terms and links to computational resources are provided.
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Affiliation(s)
- Guy A Rutter
- CHUM Research Center and Faculty of Medicine, University of Montréal, Montréal, QC, Canada.
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK.
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore.
| | - Anne Gresch
- Department of Bioengineering, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Luis Delgadillo Silva
- CHUM Research Center and Faculty of Medicine, University of Montréal, Montréal, QC, Canada
| | - Richard K P Benninger
- Department of Bioengineering, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
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8
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Patel R, Bryant AS, Castelletto ML, Walsh B, Akimori D, Hallem EA. The generation of stable transgenic lines in the human-infective nematode Strongyloides stercoralis. G3 (BETHESDA, MD.) 2024; 14:jkae122. [PMID: 38839055 PMCID: PMC11304987 DOI: 10.1093/g3journal/jkae122] [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: 03/22/2024] [Revised: 05/13/2024] [Accepted: 05/23/2024] [Indexed: 06/07/2024]
Abstract
The skin-penetrating gastrointestinal parasitic nematode Strongyloides stercoralis causes strongyloidiasis, which is a neglected tropical disease that is associated with severe chronic illness and fatalities. Unlike other human-infective nematodes, S. stercoralis cycles through a single free-living generation and thus serves as a genetically tractable model organism for understanding the mechanisms that enable parasitism. Techniques such as CRISPR/Cas9-mediated mutagenesis and transgenesis are now routinely performed in S. stercoralis by introducing exogenous DNA into free-living adults and then screening their F1 progeny for transgenic or mutant larvae. However, transgenesis in S. stercoralis has been severely hindered by the inability to establish stable transgenic lines that can be propagated for multiple generations through a host; to date, studies of transgenic S. stercoralis have been limited to heterogeneous populations of transgenic F1 larvae. Here, we develop an efficient pipeline for the generation of stable transgenic lines in S. stercoralis. We also show that this approach can be used to efficiently generate stable transgenic lines in the rat-infective nematode Strongyloides ratti. The ability to generate stable transgenic lines circumvents the limitations of working with heterogeneous F1 populations, such as variable transgene expression and the inability to generate transgenics of all life stages. Our transgenesis approach will enable novel lines of inquiry into parasite biology, such as transgene-based comparisons between free-living and parasitic generations.
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Affiliation(s)
- Ruhi Patel
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Astra S Bryant
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195, USA
| | - Michelle L Castelletto
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Breanna Walsh
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Molecular Biology Interdepartmental PhD Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Medical Scientist Training Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Damia Akimori
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Molecular Biology Interdepartmental PhD Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Elissa A Hallem
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
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9
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Zhang R, Anguiano M, Aarrestad IK, Lin S, Chandra J, Vadde SS, Olson DE, Kim CK. Rapid, biochemical tagging of cellular activity history in vivo. Nat Methods 2024:10.1038/s41592-024-02375-7. [PMID: 39103446 DOI: 10.1038/s41592-024-02375-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 06/21/2024] [Indexed: 08/07/2024]
Abstract
Intracellular calcium (Ca2+) is ubiquitous to cell signaling across biology. While existing fluorescent sensors and reporters can detect activated cells with elevated Ca2+ levels, these approaches require implants to deliver light to deep tissue, precluding their noninvasive use in freely behaving animals. Here we engineered an enzyme-catalyzed approach that rapidly and biochemically tags cells with elevated Ca2+ in vivo. Ca2+-activated split-TurboID (CaST) labels activated cells within 10 min with an exogenously delivered biotin molecule. The enzymatic signal increases with Ca2+ concentration and biotin labeling time, demonstrating that CaST is a time-gated integrator of total Ca2+ activity. Furthermore, the CaST readout can be performed immediately after activity labeling, in contrast to transcriptional reporters that require hours to produce signal. These capabilities allowed us to apply CaST to tag prefrontal cortex neurons activated by psilocybin, and to correlate the CaST signal with psilocybin-induced head-twitch responses in untethered mice.
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Affiliation(s)
- Run Zhang
- Biomedical Engineering Graduate Group, University of California, Davis, Davis, CA, USA
- Center for Neuroscience, University of California, Davis, Davis, CA, USA
| | - Maribel Anguiano
- Center for Neuroscience, University of California, Davis, Davis, CA, USA
- Neuroscience Graduate Group, University of California, Davis, Davis, CA, USA
| | - Isak K Aarrestad
- Center for Neuroscience, University of California, Davis, Davis, CA, USA
- Neuroscience Graduate Group, University of California, Davis, Davis, CA, USA
- Institute for Psychedelics and Neurotherapeutics, University of California, Davis, Davis, CA, USA
| | - Sophia Lin
- Center for Neuroscience, University of California, Davis, Davis, CA, USA
- Department of Neurology, University of California, Davis, Sacramento, CA, USA
| | - Joshua Chandra
- Center for Neuroscience, University of California, Davis, Davis, CA, USA
- Neuroscience Graduate Group, University of California, Davis, Davis, CA, USA
| | - Sruti S Vadde
- Center for Neuroscience, University of California, Davis, Davis, CA, USA
- Department of Neurology, University of California, Davis, Sacramento, CA, USA
| | - David E Olson
- Center for Neuroscience, University of California, Davis, Davis, CA, USA
- Institute for Psychedelics and Neurotherapeutics, University of California, Davis, Davis, CA, USA
- Department of Chemistry, University of California, Davis, Davis, CA, USA
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Sacramento, CA, USA
| | - Christina K Kim
- Center for Neuroscience, University of California, Davis, Davis, CA, USA.
- Institute for Psychedelics and Neurotherapeutics, University of California, Davis, Davis, CA, USA.
- Department of Neurology, University of California, Davis, Sacramento, CA, USA.
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10
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Sheng CQ, Wu SS, Cheng YK, Wu Y, Li YM. Comprehensive review of indicators and techniques for optical mapping of intracellular calcium ions. Cereb Cortex 2024; 34:bhae346. [PMID: 39191664 DOI: 10.1093/cercor/bhae346] [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: 05/01/2024] [Revised: 07/27/2024] [Accepted: 08/09/2024] [Indexed: 08/29/2024] Open
Abstract
Calcium ions (Ca2+) play crucial roles in almost every cellular process, making the detection of changes in intracellular Ca2+ essential to understanding cell function. The fluorescence indicator method has garnered widespread application due to its exceptional sensitivity, rapid analysis, cost-effectiveness, and user-friendly nature. It has successfully delineated the spatial and temporal dynamics of Ca2+ signaling across diverse cell types. However, it is vital to understand that different indicators have varying levels of accuracy, sensitivity, and stability, making choosing the right inspection method crucial. As optical detection technologies advance, they continually broaden the horizons of scientific inquiry. This primer offers a systematic synthesis of the current fluorescence indicators and optical imaging modalities utilized for the detection of intracellular Ca2+. It elucidates their practical applications and inherent limitations, serving as an essential reference for researchers seeking to identify the most suitable detection methodologies for their calcium-centric investigations.
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Affiliation(s)
- Chu-Qiao Sheng
- Department of Pediatric Intensive Care Unit, Children's Medical Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, No. 2699, Qianjin Street, Changchun, Jilin 130012, China
| | - Shuang-Shuang Wu
- Department of Pediatric Hematology, Children's Medical Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Yong-Kang Cheng
- Department of Pediatric Intensive Care Unit, Children's Medical Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Yao Wu
- Department of Pediatric Intensive Care Unit, Children's Medical Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Yu-Mei Li
- Department of Pediatric Intensive Care Unit, Children's Medical Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China
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11
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Jiang X, Dimitriou E, Grabe V, Sun R, Chang H, Zhang Y, Gershenzon J, Rybak J, Hansson BS, Sachse S. Ring-shaped odor coding in the antennal lobe of migratory locusts. Cell 2024; 187:3973-3991.e24. [PMID: 38897195 DOI: 10.1016/j.cell.2024.05.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 04/05/2024] [Accepted: 05/20/2024] [Indexed: 06/21/2024]
Abstract
The representation of odors in the locust antennal lobe with its >2,000 glomeruli has long remained a perplexing puzzle. We employed the CRISPR-Cas9 system to generate transgenic locusts expressing the genetically encoded calcium indicator GCaMP in olfactory sensory neurons. Using two-photon functional imaging, we mapped the spatial activation patterns representing a wide range of ecologically relevant odors across all six developmental stages. Our findings reveal a functionally ring-shaped organization of the antennal lobe composed of specific glomerular clusters. This configuration establishes an odor-specific chemotopic representation by encoding different chemical classes and ecologically distinct odors in the form of glomerular rings. The ring-shaped glomerular arrangement, which we confirm by selective targeting of OR70a-expressing sensory neurons, occurs throughout development, and the odor-coding pattern within the glomerular population is consistent across developmental stages. Mechanistically, this unconventional spatial olfactory code reflects the locust-specific and multiplexed glomerular innervation pattern of the antennal lobe.
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Affiliation(s)
- Xingcong Jiang
- Department of Evolutionary Neuroethology, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany; Research Group Olfactory Coding, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
| | - Eleftherios Dimitriou
- Department of Evolutionary Neuroethology, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
| | - Veit Grabe
- Microscopic Service Group, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
| | - Ruo Sun
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
| | - Hetan Chang
- Department of Evolutionary Neuroethology, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
| | - Yifu Zhang
- Department of Evolutionary Neuroethology, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
| | - Jonathan Gershenzon
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
| | - Jürgen Rybak
- Department of Evolutionary Neuroethology, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
| | - Bill S Hansson
- Department of Evolutionary Neuroethology, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany.
| | - Silke Sachse
- Research Group Olfactory Coding, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany.
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12
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Hu M, Feng X, Liu Q, Liu S, Huang F, Xu H. The ion channels of endomembranes. Physiol Rev 2024; 104:1335-1385. [PMID: 38451235 DOI: 10.1152/physrev.00025.2023] [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: 06/30/2023] [Revised: 02/20/2024] [Accepted: 02/25/2024] [Indexed: 03/08/2024] Open
Abstract
The endomembrane system consists of organellar membranes in the biosynthetic pathway [endoplasmic reticulum (ER), Golgi apparatus, and secretory vesicles] as well as those in the degradative pathway (early endosomes, macropinosomes, phagosomes, autophagosomes, late endosomes, and lysosomes). These endomembrane organelles/vesicles work together to synthesize, modify, package, transport, and degrade proteins, carbohydrates, and lipids, regulating the balance between cellular anabolism and catabolism. Large ion concentration gradients exist across endomembranes: Ca2+ gradients for most endomembrane organelles and H+ gradients for the acidic compartments. Ion (Na+, K+, H+, Ca2+, and Cl-) channels on the organellar membranes control ion flux in response to cellular cues, allowing rapid informational exchange between the cytosol and organelle lumen. Recent advances in organelle proteomics, organellar electrophysiology, and luminal and juxtaorganellar ion imaging have led to molecular identification and functional characterization of about two dozen endomembrane ion channels. For example, whereas IP3R1-3 channels mediate Ca2+ release from the ER in response to neurotransmitter and hormone stimulation, TRPML1-3 and TMEM175 channels mediate lysosomal Ca2+ and H+ release, respectively, in response to nutritional and trafficking cues. This review aims to summarize the current understanding of these endomembrane channels, with a focus on their subcellular localizations, ion permeation properties, gating mechanisms, cell biological functions, and disease relevance.
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Affiliation(s)
- Meiqin Hu
- Department of Neurology and Department of Cardiology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, People's Republic of China
- New Cornerstone Science Laboratory, Liangzhu Laboratory and School of Basic Medical Sciences, Zhejiang University, Hangzhou, People's Republic of China
| | - Xinghua Feng
- Department of Neurology and Department of Cardiology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, People's Republic of China
- New Cornerstone Science Laboratory, Liangzhu Laboratory and School of Basic Medical Sciences, Zhejiang University, Hangzhou, People's Republic of China
| | - Qiang Liu
- New Cornerstone Science Laboratory, Liangzhu Laboratory and School of Basic Medical Sciences, Zhejiang University, Hangzhou, People's Republic of China
| | - Siyu Liu
- New Cornerstone Science Laboratory, Liangzhu Laboratory and School of Basic Medical Sciences, Zhejiang University, Hangzhou, People's Republic of China
| | - Fangqian Huang
- New Cornerstone Science Laboratory, Liangzhu Laboratory and School of Basic Medical Sciences, Zhejiang University, Hangzhou, People's Republic of China
| | - Haoxing Xu
- Department of Neurology and Department of Cardiology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, People's Republic of China
- New Cornerstone Science Laboratory, Liangzhu Laboratory and School of Basic Medical Sciences, Zhejiang University, Hangzhou, People's Republic of China
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States
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13
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Gilad A. Wide-field imaging in behaving mice as a tool to study cognitive function. NEUROPHOTONICS 2024; 11:033404. [PMID: 38384657 PMCID: PMC10879934 DOI: 10.1117/1.nph.11.3.033404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 01/17/2024] [Accepted: 01/22/2024] [Indexed: 02/23/2024]
Abstract
Cognitive functions are mediated through coordinated and dynamic neuronal responses that involve many different areas across the brain. Therefore, it is of high interest to simultaneously record neuronal activity from as many brain areas as possible while the subject performs a cognitive behavioral task. One of the emerging tools to achieve a mesoscopic field of view is wide-field imaging of cortex-wide dynamics in mice. Wide-field imaging is cost-effective, user-friendly, and enables obtaining cortex-wide signals from mice performing complex and demanding cognitive tasks. Importantly, wide-field imaging offers an unbiased cortex-wide observation that sheds light on overlooked cortical regions and highlights parallel processing circuits. Recent wide-field imaging studies have shown that multi-area cortex-wide patterns, rather than just a single area, are involved in encoding cognitive functions. The optical properties of wide-field imaging enable imaging of different brain signals, such as layer-specific, inhibitory subtypes, or neuromodulation signals. Here, I review the main advantages of wide-field imaging in mice, review the recent literature, and discuss future directions of the field. It is expected that wide-field imaging in behaving mice will continue to gain popularity and aid in understanding the mesoscale dynamics underlying cognitive function.
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Affiliation(s)
- Ariel Gilad
- Hebrew University of Jerusalem, Institute for Medical Research Israel-Canada, Department of Medical Neurobiology, Faculty of Medicine, Jerusalem, Israel
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14
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Frei MS, Mehta S, Zhang J. Next-Generation Genetically Encoded Fluorescent Biosensors Illuminate Cell Signaling and Metabolism. Annu Rev Biophys 2024; 53:275-297. [PMID: 38346245 DOI: 10.1146/annurev-biophys-030722-021359] [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: 02/28/2024]
Abstract
Genetically encoded fluorescent biosensors have revolutionized the study of cell signaling and metabolism, as they allow for live-cell measurements with high spatiotemporal resolution. This success has spurred the development of tailor-made biosensors that enable the study of dynamic phenomena on different timescales and length scales. In this review, we discuss different approaches to enhancing and developing new biosensors. We summarize the technologies used to gain structural insights into biosensor design and comment on useful screening technologies. Furthermore, we give an overview of different applications where biosensors have led to key advances over recent years. Finally, we give our perspective on where future work is bound to make a large impact.
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Affiliation(s)
- Michelle S Frei
- Department of Pharmacology, University of California San Diego, La Jolla, California, USA; , ,
| | - Sohum Mehta
- Department of Pharmacology, University of California San Diego, La Jolla, California, USA; , ,
| | - Jin Zhang
- Department of Pharmacology, University of California San Diego, La Jolla, California, USA; , ,
- Shu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, California, USA
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, USA
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15
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Ito Y, Takano T. Recording calcium concentrations. Nat Chem Biol 2024; 20:805-806. [PMID: 38907109 DOI: 10.1038/s41589-024-01656-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/23/2024]
Affiliation(s)
- Yuki Ito
- Division of Molecular Systems for Brain Function, Institute for Advanced Study, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
- Division of Integrated Omics, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Tetsuya Takano
- Division of Molecular Systems for Brain Function, Institute for Advanced Study, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.
- Department of Neurophysiology, Keio University School of Medicine, Tokyo, Japan.
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Japan.
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16
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Sims RR, Bendifallah I, Grimm C, Lafirdeen ASM, Domínguez S, Chan CY, Lu X, Forget BC, St-Pierre F, Papagiakoumou E, Emiliani V. Scanless two-photon voltage imaging. Nat Commun 2024; 15:5095. [PMID: 38876987 PMCID: PMC11178882 DOI: 10.1038/s41467-024-49192-2] [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: 12/24/2022] [Accepted: 05/28/2024] [Indexed: 06/16/2024] Open
Abstract
Two-photon voltage imaging has long been heralded as a transformative approach capable of answering many long-standing questions in modern neuroscience. However, exploiting its full potential requires the development of novel imaging approaches well suited to the photophysical properties of genetically encoded voltage indicators. We demonstrate that parallel excitation approaches developed for scanless two-photon photostimulation enable high-SNR two-photon voltage imaging. We use whole-cell patch-clamp electrophysiology to perform a thorough characterization of scanless two-photon voltage imaging using three parallel illumination approaches and lasers with different repetition rates and wavelengths. We demonstrate voltage recordings of high-frequency spike trains and sub-threshold depolarizations from neurons expressing the soma-targeted genetically encoded voltage indicator JEDI-2P-Kv. Using a low repetition-rate laser, we perform multi-cell recordings from up to fifteen targets simultaneously. We co-express JEDI-2P-Kv and the channelrhodopsin ChroME-ST and capitalize on their overlapping two-photon absorption spectra to simultaneously evoke and image action potentials using a single laser source. We also demonstrate in vivo scanless two-photon imaging of multiple cells simultaneously up to 250 µm deep in the barrel cortex of head-fixed, anaesthetised mice.
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Affiliation(s)
- Ruth R Sims
- Institut de la Vision, Sorbonne Université, INSERM, CNRS, Paris, France
| | - Imane Bendifallah
- Institut de la Vision, Sorbonne Université, INSERM, CNRS, Paris, France
| | - Christiane Grimm
- Institut de la Vision, Sorbonne Université, INSERM, CNRS, Paris, France
| | | | - Soledad Domínguez
- Institut de la Vision, Sorbonne Université, INSERM, CNRS, Paris, France
| | - Chung Yuen Chan
- Institut de la Vision, Sorbonne Université, INSERM, CNRS, Paris, France
| | - Xiaoyu Lu
- Systems, Synthetic, and Physical Biology Program, Rice University, Houston, TX, USA
| | - Benoît C Forget
- Institut de la Vision, Sorbonne Université, INSERM, CNRS, Paris, France
| | - François St-Pierre
- Systems, Synthetic, and Physical Biology Program, Rice University, Houston, TX, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
- Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
- Department of Electrical and Computer Engineering, Rice University, Houston, TX, USA
| | | | - Valentina Emiliani
- Institut de la Vision, Sorbonne Université, INSERM, CNRS, Paris, France.
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17
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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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18
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Omond SET, Lesku JA. Why study sleep in flatworms? J Comp Physiol B 2024; 194:233-239. [PMID: 36899149 PMCID: PMC11233290 DOI: 10.1007/s00360-023-01480-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 01/31/2023] [Accepted: 02/23/2023] [Indexed: 03/12/2023]
Abstract
The behaviors that characterize sleep have been observed across a broad range of different species. While much attention has been placed on vertebrates (mostly mammals and birds), the grand diversity of invertebrates has gone largely unexplored. Here, we introduce the intrigue and special value in the study of sleeping platyhelminth flatworms. Flatworms are closely related to annelids and mollusks, and yet are comparatively simple. They lack a circulatory system, respiratory system, endocrine glands, a coelom, and an anus. They retain a central and peripheral nervous system, various sensory systems, and an ability to learn. Flatworms sleep, like other animals, a state which is regulated by prior sleep/wake history and by the neurotransmitter GABA. Furthermore, they possess a remarkable ability to regenerate from a mere fragment of the original animal. The regenerative capabilities of flatworms make them a unique bilaterally symmetric animal to study a link between sleep and neurodevelopment. Lastly, the recent applications of tools for probing the flatworm genome, metabolism, and brain activity make their entrance into the field of sleep research all the more timely.
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Affiliation(s)
- Shauni E T Omond
- School of Agriculture, Biomedicine & Environment, La Trobe University, Melbourne, Australia.
| | - John A Lesku
- School of Agriculture, Biomedicine & Environment, La Trobe University, Melbourne, Australia.
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19
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Nassrallah WB, Cheng J, Mackay JP, Hogg PW, Raymond LA. Mechanisms of synapse-to-nucleus calcium signalling in striatal neurons and impairments in Huntington's disease. J Neurochem 2024. [PMID: 38770573 DOI: 10.1111/jnc.16132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 04/15/2024] [Accepted: 05/06/2024] [Indexed: 05/22/2024]
Abstract
Huntington's disease (HD) is a monogenic disorder with autosomal dominant inheritance. In HD patients, neurons in the striatum and cortex degenerate, leading to motor, psychiatric and cognitive disorders. Dysregulated synaptic function and calcium handling are common in many neurodegenerative diseases, including HD. N-methyl-D-aspartate (NMDA) receptor function is enhanced in HD at extrasynaptic sites, altering the balance of calcium-dependent neuronal survival versus death signalling pathways. Endoplasmic reticulum (ER) calcium handling is also abnormal in HD. The ER, which is continuous with the nuclear envelope, is purportedly involved in nuclear calcium signalling; based on this, we hypothesised that nuclear calcium signalling is altered in HD. We explored this hypothesis with calcium imaging techniques, including simultaneous epifluorescent imaging of cytosolic and nuclear calcium using jRCaMP1b and GCaMP3 sensors, respectively, in striatal spiny projection neurons in cortical-striatal co-cultures from the YAC128 mouse model of HD. Our data show contributions from a variety of calcium channels to nuclear calcium signalling. NMDA receptors (NMDARs) play an essential role in initiating action potential-dependent calcium signalling to the nucleus, and ryanodine receptors (RyR) contribute to both cytosolic and nuclear calcium signals. Unlike previous reports in glutamatergic hippocampal and cortical neurons, we found that in GABAergic striatal neurons, L-type voltage-gated calcium channels (CaV) contribute to cytosolic, but not nuclear calcium signalling. Calcium imaging also suggests impairments in nuclear calcium signalling in HD striatal neurons, where spontaneous action potential-dependent calcium transients in the nucleus were smaller in YAC128 striatal neurons compared to those of wild-type (WT). Our results elucidate mechanisms involved in action potential-dependent nuclear calcium signalling in GABAergic striatal neurons, and have revealed a clear deficit in this signalling in HD.
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Affiliation(s)
- Wissam B Nassrallah
- Graduate Program in Neuroscience, University of British Columbia, Vancouver, British Columbia, Canada
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Psychiatry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Judy Cheng
- Graduate Program in Neuroscience, University of British Columbia, Vancouver, British Columbia, Canada
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Psychiatry, University of British Columbia, Vancouver, British Columbia, Canada
| | - James P Mackay
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Psychiatry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Peter W Hogg
- Graduate Program in Neuroscience, University of British Columbia, Vancouver, British Columbia, Canada
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Lynn A Raymond
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Psychiatry, University of British Columbia, Vancouver, British Columbia, Canada
- Division of Neurology, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
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20
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Wu Y, Jensen N, Rossner MJ, Wehr MC. Exploiting Cell-Based Assays to Accelerate Drug Development for G Protein-Coupled Receptors. Int J Mol Sci 2024; 25:5474. [PMID: 38791511 PMCID: PMC11121687 DOI: 10.3390/ijms25105474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 05/10/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024] Open
Abstract
G protein-coupled receptors (GPCRs) are relevant targets for health and disease as they regulate various aspects of metabolism, proliferation, differentiation, and immune pathways. They are implicated in several disease areas, including cancer, diabetes, cardiovascular diseases, and mental disorders. It is worth noting that about a third of all marketed drugs target GPCRs, making them prime pharmacological targets for drug discovery. Numerous functional assays have been developed to assess GPCR activity and GPCR signaling in living cells. Here, we review the current literature of genetically encoded cell-based assays to measure GPCR activation and downstream signaling at different hierarchical levels of signaling, from the receptor to transcription, via transducers, effectors, and second messengers. Singleplex assay formats provide one data point per experimental condition. Typical examples are bioluminescence resonance energy transfer (BRET) assays and protease cleavage assays (e.g., Tango or split TEV). By contrast, multiplex assay formats allow for the parallel measurement of multiple receptors and pathways and typically use molecular barcodes as transcriptional reporters in barcoded assays. This enables the efficient identification of desired on-target and on-pathway effects as well as detrimental off-target and off-pathway effects. Multiplex assays are anticipated to accelerate drug discovery for GPCRs as they provide a comprehensive and broad identification of compound effects.
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Affiliation(s)
- Yuxin Wu
- Research Group Cell Signalling, Department of Psychiatry and Psychotherapy, LMU University Hospital, LMU Munich, Nussbaumstr. 7, 80336 Munich, Germany
- Systasy Bioscience GmbH, Balanstr. 6, 81669 Munich, Germany
| | - Niels Jensen
- Systasy Bioscience GmbH, Balanstr. 6, 81669 Munich, Germany
- Section of Molecular Neurobiology, Department of Psychiatry and Psychotherapy, LMU University Hospital, LMU Munich, Nussbaumstr. 7, 80336 Munich, Germany
| | - Moritz J. Rossner
- Systasy Bioscience GmbH, Balanstr. 6, 81669 Munich, Germany
- Section of Molecular Neurobiology, Department of Psychiatry and Psychotherapy, LMU University Hospital, LMU Munich, Nussbaumstr. 7, 80336 Munich, Germany
| | - Michael C. Wehr
- Research Group Cell Signalling, Department of Psychiatry and Psychotherapy, LMU University Hospital, LMU Munich, Nussbaumstr. 7, 80336 Munich, Germany
- Systasy Bioscience GmbH, Balanstr. 6, 81669 Munich, Germany
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21
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Zhang R, Anguiano M, Aarrestad IK, Lin S, Chandra J, Vadde SS, Olson DE, Kim CK. Rapid, biochemical tagging of cellular activity history in vivo. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.06.556431. [PMID: 38798353 PMCID: PMC11118534 DOI: 10.1101/2023.09.06.556431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Intracellular calcium (Ca2+) is ubiquitous to cell signaling across all biology. While existing fluorescent sensors and reporters can detect activated cells with elevated Ca2+ levels, these approaches require implants to deliver light to deep tissue, precluding their noninvasive use in freely-behaving animals. Here we engineered an enzyme-catalyzed approach that rapidly and biochemically tags cells with elevated Ca2+ in vivo. Ca2+-activated Split-TurboID (CaST) labels activated cells within 10 minutes with an exogenously-delivered biotin molecule. The enzymatic signal increases with Ca2+ concentration and biotin labeling time, demonstrating that CaST is a time-gated integrator of total Ca2+ activity. Furthermore, the CaST read-out can be performed immediately after activity labeling, in contrast to transcriptional reporters that require hours to produce signal. These capabilities allowed us to apply CaST to tag prefrontal cortex neurons activated by psilocybin, and to correlate the CaST signal with psilocybin-induced head-twitch responses in untethered mice.
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Affiliation(s)
- Run Zhang
- Biomedical Engineering Graduate Group, University of California, Davis, Davis, CA 95616
- Center for Neuroscience, University of California, Davis, Davis, CA 95618
| | - Maribel Anguiano
- Center for Neuroscience, University of California, Davis, Davis, CA 95618
- Neuroscience Graduate Group, University of California, Davis, Davis, CA 95618
| | - Isak K. Aarrestad
- Center for Neuroscience, University of California, Davis, Davis, CA 95618
- Neuroscience Graduate Group, University of California, Davis, Davis, CA 95618
- Institute for Psychedelics and Neurotherapeutics, University of California, Davis, Davis, CA 95616
| | - Sophia Lin
- Center for Neuroscience, University of California, Davis, Davis, CA 95618
- Department of Neurology, University of California, Davis, Sacramento, CA 95817
| | - Joshua Chandra
- Center for Neuroscience, University of California, Davis, Davis, CA 95618
- Neuroscience Graduate Group, University of California, Davis, Davis, CA 95618
| | - Sruti S. Vadde
- Center for Neuroscience, University of California, Davis, Davis, CA 95618
- Department of Neurology, University of California, Davis, Sacramento, CA 95817
| | - David E. Olson
- Center for Neuroscience, University of California, Davis, Davis, CA 95618
- Institute for Psychedelics and Neurotherapeutics, University of California, Davis, Davis, CA 95616
- Department of Chemistry, University of California, Davis, Davis, CA 95616
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Sacramento, CA 95817
| | - Christina K. Kim
- Center for Neuroscience, University of California, Davis, Davis, CA 95618
- Institute for Psychedelics and Neurotherapeutics, University of California, Davis, Davis, CA 95616
- Department of Neurology, University of California, Davis, Sacramento, CA 95817
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22
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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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23
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Li L, Zhang B, Zhao W, Sheng D, Yin L, Sheng X, Yao D. Multimodal Technologies for Closed-Loop Neural Modulation and Sensing. Adv Healthc Mater 2024:e2303289. [PMID: 38640468 DOI: 10.1002/adhm.202303289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 03/11/2024] [Indexed: 04/21/2024]
Abstract
Existing methods for studying neural circuits and treating neurological disorders are typically based on physical and chemical cues to manipulate and record neural activities. These approaches often involve predefined, rigid, and unchangeable signal patterns, which cannot be adjusted in real time according to the patient's condition or neural activities. With the continuous development of neural interfaces, conducting in vivo research on adaptive and modifiable treatments for neurological diseases and neural circuits is now possible. In this review, current and potential integration of various modalities to achieve precise, closed-loop modulation, and sensing in neural systems are summarized. Advanced materials, devices, or systems that generate or detect electrical, magnetic, optical, acoustic, or chemical signals are highlighted and utilized to interact with neural cells, tissues, and networks for closed-loop interrogation. Further, the significance of developing closed-loop techniques for diagnostics and treatment of neurological disorders such as epilepsy, depression, rehabilitation of spinal cord injury patients, and exploration of brain neural circuit functionality is elaborated.
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Affiliation(s)
- Lizhu Li
- Sichuan Provincial Key Laboratory for Human Disease Gene Study and the Center for Medical Genetics, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 611731, China
| | - Bozhen Zhang
- School of Materials Science and Engineering, The Key Laboratory of Advanced Materials of Ministry of Education, State Key Laboratory of New Ceramics and Fine Processing, Laboratory of Flexible Electronics Technology, Tsinghua University, Beijing, 100084, China
| | - Wenxin Zhao
- Department of Electronic Engineering, Beijing National Research Center for Information Science and Technology, Institute for Precision Medicine, Laboratory of Flexible Electronics Technology, IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing, 100084, China
| | - David Sheng
- Department of Electronic Engineering, Beijing National Research Center for Information Science and Technology, Institute for Precision Medicine, Laboratory of Flexible Electronics Technology, IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing, 100084, China
| | - Lan Yin
- School of Materials Science and Engineering, The Key Laboratory of Advanced Materials of Ministry of Education, State Key Laboratory of New Ceramics and Fine Processing, Laboratory of Flexible Electronics Technology, Tsinghua University, Beijing, 100084, China
| | - Xing Sheng
- Department of Electronic Engineering, Beijing National Research Center for Information Science and Technology, Institute for Precision Medicine, Laboratory of Flexible Electronics Technology, IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing, 100084, China
| | - Dezhong Yao
- Sichuan Provincial Key Laboratory for Human Disease Gene Study and the Center for Medical Genetics, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 611731, China
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24
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Xu S, Xiao X, Manshaii F, Chen J. Injectable Fluorescent Neural Interfaces for Cell-Specific Stimulating and Imaging. NANO LETTERS 2024. [PMID: 38606614 DOI: 10.1021/acs.nanolett.4c00815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/13/2024]
Abstract
Building on current explorations in chronic optical neural interfaces, it is essential to address the risk of photothermal damage in traditional optogenetics. By focusing on calcium fluorescence for imaging rather than stimulation, injectable fluorescent neural interfaces significantly minimize photothermal damage and improve the accuracy of neuronal imaging. Key advancements including the use of injectable microelectronics for targeted electrical stimulation and their integration with cell-specific genetically encoded calcium indicators have been discussed. These injectable electronics that allow for post-treatment retrieval offer a minimally invasive solution, enhancing both usability and reliability. Furthermore, the integration of genetically encoded fluorescent calcium indicators with injectable bioelectronics enables precise neuronal recording and imaging of individual neurons. This shift not only minimizes risks such as photothermal conversion but also boosts safety, specificity, and effectiveness of neural imaging. Embracing these advancements represents a significant leap forward in biomedical engineering and neuroscience, paving the way for advanced brain-machine interfaces.
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Affiliation(s)
- Shumao Xu
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Xiao Xiao
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Farid Manshaii
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Jun Chen
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, California 90095, United States
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25
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Shen Q, Hasegawa K, Oelerich N, Prakken A, Tersch LW, Wang J, Reichhardt F, Tersch A, Choo JC, Timmers T, Hofmann K, Parker JE, Chai J, Maekawa T. Cytoplasmic calcium influx mediated by plant MLKLs confers TNL-triggered immunity. Cell Host Microbe 2024; 32:453-465.e6. [PMID: 38513655 DOI: 10.1016/j.chom.2024.02.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 01/29/2024] [Accepted: 02/28/2024] [Indexed: 03/23/2024]
Abstract
The plant homolog of vertebrate necroptosis inducer mixed-lineage kinase domain-like (MLKL) contributes to downstream steps in Toll-interleukin-1 receptor domain NLR (TNL)-receptor-triggered immunity. Here, we show that Arabidopsis MLKL1 (AtMLKL1) clusters into puncta at the plasma membrane upon TNL activation and that this sub-cellular reorganization is dependent on the TNL signal transducer, EDS1. We find that AtMLKLs confer TNL-triggered immunity in parallel with RPW8-type HeLo-domain-containing NLRs (RNLs) and that the AtMLKL N-terminal HeLo domain is indispensable for both immunity and clustering. We show that the AtMLKL HeLo domain mediates cytoplasmic Ca2+ ([Ca2+]cyt) influx in plant and human cells, and AtMLKLs are responsible for sustained [Ca2+]cyt influx during TNL-triggered, but not CNL-triggered, immunity. Our study reveals parallel immune signaling functions of plant MLKLs and RNLs as mediators of [Ca2+]cyt influx and a potentially common role of the HeLo domain fold in the Ca2+-signal relay of diverse organisms.
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Affiliation(s)
- Qiaochu Shen
- Institute for Plant Sciences, University of Cologne, 50674 Cologne, NRW, Germany
| | - Keiichi Hasegawa
- Institute for Biochemistry, University of Cologne, 50674 Cologne, NRW, Germany
| | - Nicole Oelerich
- Institute for Genetics, University of Cologne, 50674 Cologne, NRW, Germany
| | - Anna Prakken
- Institute for Plant Sciences, University of Cologne, 50674 Cologne, NRW, Germany
| | - Lea Weiler Tersch
- Institute for Plant Sciences, University of Cologne, 50674 Cologne, NRW, Germany
| | - Junli Wang
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, NRW, Germany
| | - Frowin Reichhardt
- Institute for Plant Sciences, University of Cologne, 50674 Cologne, NRW, Germany
| | - Alexandra Tersch
- Institute for Plant Sciences, University of Cologne, 50674 Cologne, NRW, Germany
| | - Je Cuan Choo
- Institute for Plant Sciences, University of Cologne, 50674 Cologne, NRW, Germany
| | - Ton Timmers
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, NRW, Germany
| | - Kay Hofmann
- Institute for Genetics, University of Cologne, 50674 Cologne, NRW, Germany
| | - Jane E Parker
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, NRW, Germany; Cluster of Excellence on Plant Sciences (CEPLAS), Cologne, NRW, Germany
| | - Jijie Chai
- Institute for Biochemistry, University of Cologne, 50674 Cologne, NRW, Germany; Max Planck Institute for Plant Breeding Research, 50829 Cologne, NRW, Germany; Cluster of Excellence on Plant Sciences (CEPLAS), Cologne, NRW, Germany
| | - Takaki Maekawa
- Institute for Plant Sciences, University of Cologne, 50674 Cologne, NRW, Germany; Cluster of Excellence on Plant Sciences (CEPLAS), Cologne, NRW, Germany.
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26
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Varma A, Udupa S, Sengupta M, Ghosh PK, Thirumalai V. A machine-learning tool to identify bistable states from calcium imaging data. J Physiol 2024; 602:1243-1271. [PMID: 38482722 DOI: 10.1113/jp284373] [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: 01/13/2023] [Accepted: 02/09/2024] [Indexed: 04/04/2024] Open
Abstract
Mapping neuronal activation using calcium imaging in vivo during behavioural tasks has advanced our understanding of nervous system function. In almost all of these studies, calcium imaging is used to infer spike probabilities because action potentials activate voltage-gated calcium channels and increase intracellular calcium levels. However, neurons not only fire action potentials, but also convey information via intrinsic dynamics such as by generating bistable membrane potential states. Although a number of tools for spike inference have been developed and are currently being used, no tool exists for converting calcium imaging signals to maps of cellular state in bistable neurons. Purkinje neurons in the larval zebrafish cerebellum exhibit membrane potential bistability, firing either tonically or in bursts. Several studies have implicated the role of a population code in cerebellar function, with bistability adding an extra layer of complexity to this code. In the present study, we develop a tool, CaMLSort, which uses convolutional recurrent neural networks to classify calcium imaging traces as arising from either tonic or bursting cells. We validate this classifier using a number of different methods and find that it performs well on simulated event rasters as well as real biological data that it had not previously seen. Moreover, we find that CaMLsort generalizes to other bistable neurons, such as dopaminergic neurons in the ventral tegmental area of mice. Thus, this tool offers a new way of analysing calcium imaging data from bistable neurons to understand how they participate in network computation and natural behaviours. KEY POINTS: Calcium imaging, compriising the gold standard of inferring neuronal activity, does not report cellular state in neurons that are bistable, such as Purkinje neurons in the cerebellum of larval zebrafish. We model the relationship between Purkinje neuron electrical activity and its corresponding calcium signal to compile a dataset of state-labelled simulated calcium signals. We apply machine-learning methods to this dataset to develop a tool that can classify the state of a Purkinje neuron using only its calcium signal, which works well on real data even though it was trained only on simulated data. CaMLsort (Calcium imaging and Machine Learning based tool to sort intracellular state) also generalizes well to bistable neurons in a different brain region (ventral tegmental area) in a different model organism (mouse). This tool can facilitate our understanding of how these neurons carry out their functions in a circuit.
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Affiliation(s)
- Aalok Varma
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
| | - Sathvik Udupa
- Department of Electrical Engineering, Indian Institute of Science, Bangalore, India
| | - Mohini Sengupta
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
| | - Prasanta Kumar Ghosh
- Department of Electrical Engineering, Indian Institute of Science, Bangalore, India
| | - Vatsala Thirumalai
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
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27
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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: 10] [Impact Index Per Article: 10.0] [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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28
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Vareberg AD, Bok I, Eizadi J, Ren X, Hai A. Inference of network connectivity from temporally binned spike trains. J Neurosci Methods 2024; 404:110073. [PMID: 38309313 PMCID: PMC10949361 DOI: 10.1016/j.jneumeth.2024.110073] [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: 10/03/2023] [Revised: 01/19/2024] [Accepted: 01/30/2024] [Indexed: 02/05/2024]
Abstract
BACKGROUND Processing neural activity to reconstruct network connectivity is a central focus of neuroscience, yet the spatiotemporal requisites of biological nervous systems are challenging for current neuronal sensing modalities. Consequently, methods that leverage limited data to successfully infer synaptic connections, predict activity at single unit resolution, and decipher their effect on whole systems, can uncover critical information about neural processing. Despite the emergence of powerful methods for inferring connectivity, network reconstruction based on temporally subsampled data remains insufficiently unexplored. NEW METHOD We infer synaptic weights by processing firing rates within variable time bins for a heterogeneous feed-forward network of excitatory, inhibitory, and unconnected units. We assess classification and optimize model parameters for postsynaptic spike train reconstruction. We test our method on a physiological network of leaky integrate-and-fire neurons displaying bursting patterns and assess prediction of postsynaptic activity from microelectrode array data. RESULTS Results reveal parameters for improved prediction and performance and suggest that lower resolution data and limited access to neurons can be preferred. COMPARISON WITH EXISTING METHOD(S) Recent computational methods demonstrate highly improved reconstruction of connectivity from networks of parallel spike trains by considering spike lag, time-varying firing rates, and other underlying dynamics. However, these methods insufficiently explore temporal subsampling representative of novel data types. CONCLUSIONS We provide a framework for reverse engineering neural networks from data with limited temporal quality, describing optimal parameters for each bin size, which can be further improved using non-linear methods and applied to more complicated readouts and connectivity distributions in multiple brain circuits.
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Affiliation(s)
- Adam D Vareberg
- Department of Biomedical Engineering, University of Wisconsin-Madison, United States; Wisconsin Institute for Translational Neuroengineering (WITNe), University of Wisconsin-Madison, United States
| | - Ilhan Bok
- Department of Electrical and Computer Engineering, University of Wisconsin-Madison, United States; Wisconsin Institute for Translational Neuroengineering (WITNe), University of Wisconsin-Madison, United States
| | - Jenna Eizadi
- Department of Biomedical Engineering, University of Wisconsin-Madison, United States; Wisconsin Institute for Translational Neuroengineering (WITNe), University of Wisconsin-Madison, United States
| | - Xiaoxuan Ren
- Department of Electrical and Computer Engineering, University of Wisconsin-Madison, United States
| | - Aviad Hai
- Department of Biomedical Engineering, University of Wisconsin-Madison, United States; Department of Electrical and Computer Engineering, University of Wisconsin-Madison, United States; Wisconsin Institute for Translational Neuroengineering (WITNe), University of Wisconsin-Madison, United States.
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29
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Zhao Y, Wan J, Li Y. Genetically encoded sensors for in vivo detection of neurochemicals relevant to depression. J Neurochem 2024. [PMID: 38468468 DOI: 10.1111/jnc.16046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 12/03/2023] [Accepted: 12/29/2023] [Indexed: 03/13/2024]
Abstract
Depressive disorders are a common and debilitating form of mental illness with significant impacts on individuals and society. Despite the high prevalence, the underlying causes and mechanisms of depressive disorders are still poorly understood. Neurochemical systems, including serotonin, norepinephrine, and dopamine, have been implicated in the development and perpetuation of depressive symptoms. Current treatments for depression target these neuromodulator systems, but there is a need for a better understanding of their role in order to develop more effective treatments. Monitoring neurochemical dynamics during depressive symptoms is crucial for gaining a better a understanding of their involvement in depressive disorders. Genetically encoded sensors have emerged recently that offer high spatial-temporal resolution and the ability to monitor neurochemical dynamics in real time. This review explores the neurochemical systems involved in depression and discusses the applications and limitations of current monitoring tools for neurochemical dynamics. It also highlights the potential of genetically encoded sensors for better characterizing neurochemical dynamics in depression-related behaviors. Furthermore, potential improvements to current sensors are discussed in order to meet the requirements of depression research.
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Affiliation(s)
- Yulin Zhao
- State Key Laboratory of Membrane Biology, School of Life Sciences, Peking University, Beijing, China
- PKU-IDG/McGovern Institute for Brain Research, Beijing, China
| | - Jinxia Wan
- State Key Laboratory of Membrane Biology, School of Life Sciences, Peking University, Beijing, China
- PKU-IDG/McGovern Institute for Brain Research, Beijing, China
| | - Yulong Li
- State Key Laboratory of Membrane Biology, School of Life Sciences, Peking University, Beijing, China
- PKU-IDG/McGovern Institute for Brain Research, Beijing, China
- National Biomedical Imaging Center, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Chinese Institute for Brain Research, Beijing, China
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30
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Zachry JE, Kutlu MG, Yoon HJ, Leonard MZ, Chevée M, Patel DD, Gaidici A, Kondev V, Thibeault KC, Bethi R, Tat J, Melugin PR, Isiktas AU, Joffe ME, Cai DJ, Conn PJ, Grueter BA, Calipari ES. D1 and D2 medium spiny neurons in the nucleus accumbens core have distinct and valence-independent roles in learning. Neuron 2024; 112:835-849.e7. [PMID: 38134921 PMCID: PMC10939818 DOI: 10.1016/j.neuron.2023.11.023] [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: 12/20/2022] [Revised: 10/03/2023] [Accepted: 11/22/2023] [Indexed: 12/24/2023]
Abstract
At the core of value-based learning is the nucleus accumbens (NAc). D1- and D2-receptor-containing medium spiny neurons (MSNs) in the NAc core are hypothesized to have opposing valence-based roles in behavior. Using optical imaging and manipulation approaches in mice, we show that neither D1 nor D2 MSNs signal valence. D1 MSN responses were evoked by stimuli regardless of valence or contingency. D2 MSNs were evoked by both cues and outcomes, were dynamically changed with learning, and tracked valence-free prediction error at the population and individual neuron level. Finally, D2 MSN responses to cues were necessary for associative learning. Thus, D1 and D2 MSNs work in tandem, rather than in opposition, by signaling specific properties of stimuli to control learning.
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Affiliation(s)
- Jennifer E Zachry
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA; Vanderbilt Center for Addiction Research, Vanderbilt University, Nashville, TN 37232, USA
| | - Munir Gunes Kutlu
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA; Vanderbilt Center for Addiction Research, Vanderbilt University, Nashville, TN 37232, USA
| | - Hye Jean Yoon
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA; Vanderbilt Center for Addiction Research, Vanderbilt University, Nashville, TN 37232, USA
| | - Michael Z Leonard
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA; Vanderbilt Center for Addiction Research, Vanderbilt University, Nashville, TN 37232, USA
| | - Maxime Chevée
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA; Vanderbilt Center for Addiction Research, Vanderbilt University, Nashville, TN 37232, USA
| | - Dev D Patel
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA; Vanderbilt Center for Addiction Research, Vanderbilt University, Nashville, TN 37232, USA
| | - Anthony Gaidici
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA; Vanderbilt Center for Addiction Research, Vanderbilt University, Nashville, TN 37232, USA
| | - Veronika Kondev
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA; Vanderbilt Center for Addiction Research, Vanderbilt University, Nashville, TN 37232, USA
| | - Kimberly C Thibeault
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA; Vanderbilt Center for Addiction Research, Vanderbilt University, Nashville, TN 37232, USA
| | - Rishik Bethi
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA; Vanderbilt Center for Addiction Research, Vanderbilt University, Nashville, TN 37232, USA
| | - Jennifer Tat
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA; Vanderbilt Center for Addiction Research, Vanderbilt University, Nashville, TN 37232, USA
| | - Patrick R Melugin
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA; Vanderbilt Center for Addiction Research, Vanderbilt University, Nashville, TN 37232, USA
| | - Atagun U Isiktas
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA; Vanderbilt Center for Addiction Research, Vanderbilt University, Nashville, TN 37232, USA; Department of Neuroscience, Yale University, New Haven, CT 06520, USA
| | - Max E Joffe
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA; Vanderbilt Center for Addiction Research, Vanderbilt University, Nashville, TN 37232, USA; Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Denise J Cai
- Nash Family Department of Neuroscience, Icahn School of Medicine, Mount Sinai, New York, NY 10029, USA
| | - P Jeffrey Conn
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA; Vanderbilt Center for Addiction Research, Vanderbilt University, Nashville, TN 37232, USA
| | - Brad A Grueter
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA; Vanderbilt Center for Addiction Research, Vanderbilt University, Nashville, TN 37232, USA; Department of Anesthesiology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Erin S Calipari
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA; Vanderbilt Center for Addiction Research, Vanderbilt University, Nashville, TN 37232, USA.
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31
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Lacin ME, Yildirim M. Applications of multiphoton microscopy in imaging cerebral and retinal organoids. Front Neurosci 2024; 18:1360482. [PMID: 38505776 PMCID: PMC10948410 DOI: 10.3389/fnins.2024.1360482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Accepted: 02/21/2024] [Indexed: 03/21/2024] Open
Abstract
Cerebral organoids, self-organizing structures with increased cellular diversity and longevity, have addressed shortcomings in mimicking human brain complexity and architecture. However, imaging intact organoids poses challenges due to size, cellular density, and light-scattering properties. Traditional one-photon microscopy faces limitations in resolution and contrast, especially for deep regions. Here, we first discuss the fundamentals of multiphoton microscopy (MPM) as a promising alternative, leveraging non-linear fluorophore excitation and longer wavelengths for improved imaging of live cerebral organoids. Then, we review recent applications of MPM in studying morphogenesis and differentiation, emphasizing its potential for overcoming limitations associated with other imaging techniques. Furthermore, our paper underscores the crucial role of cerebral organoids in providing insights into human-specific neurodevelopmental processes and neurological disorders, addressing the scarcity of human brain tissue for translational neuroscience. Ultimately, we envision using multimodal multiphoton microscopy for longitudinal imaging of intact cerebral organoids, propelling advancements in our understanding of neurodevelopment and related disorders.
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Affiliation(s)
| | - Murat Yildirim
- Department of Neurosciences, Cleveland Clinic Lerner Research Institute, Cleveland, OH, United States
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32
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Dana H. Accelerating protein sensor optimization with machine learning. NATURE COMPUTATIONAL SCIENCE 2024; 4:165-166. [PMID: 38532136 DOI: 10.1038/s43588-024-00612-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/28/2024]
Affiliation(s)
- Hod Dana
- Department of Neurosciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA.
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.
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33
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Fenelon KD, Krause J, Koromila T. Opticool: Cutting-edge transgenic optical tools. PLoS Genet 2024; 20:e1011208. [PMID: 38517915 PMCID: PMC10959397 DOI: 10.1371/journal.pgen.1011208] [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: 03/24/2024] Open
Abstract
Only a few short decades have passed since the sequencing of GFP, yet the modern repertoire of transgenically encoded optical tools implies an exponential proliferation of ever improving constructions to interrogate the subcellular environment. A myriad of tags for labeling proteins, RNA, or DNA have arisen in the last few decades, facilitating unprecedented visualization of subcellular components and processes. Development of a broad array of modern genetically encoded sensors allows real-time, in vivo detection of molecule levels, pH, forces, enzyme activity, and other subcellular and extracellular phenomena in ever expanding contexts. Optogenetic, genetically encoded optically controlled manipulation systems have gained traction in the biological research community and facilitate single-cell, real-time modulation of protein function in vivo in ever broadening, novel applications. While this field continues to explosively expand, references are needed to assist scientists seeking to use and improve these transgenic devices in new and exciting ways to interrogate development and disease. In this review, we endeavor to highlight the state and trajectory of the field of in vivo transgenic optical tools.
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Affiliation(s)
- Kelli D. Fenelon
- Department of Biology, University of Texas at Arlington, Arlington, Texas, United States of America
| | - Julia Krause
- Department of Biology, University of Texas at Arlington, Arlington, Texas, United States of America
| | - Theodora Koromila
- Department of Biology, University of Texas at Arlington, Arlington, Texas, United States of America
- School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
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34
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Wait SJ, Expòsit M, Lin S, Rappleye M, Lee JD, Colby SA, Torp L, Asencio A, Smith A, Regnier M, Moussavi-Harami F, Baker D, Kim CK, Berndt A. Machine learning-guided engineering of genetically encoded fluorescent calcium indicators. NATURE COMPUTATIONAL SCIENCE 2024; 4:224-236. [PMID: 38532137 DOI: 10.1038/s43588-024-00611-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 02/15/2024] [Indexed: 03/28/2024]
Abstract
Here we used machine learning to engineer genetically encoded fluorescent indicators, protein-based sensors critical for real-time monitoring of biological activity. We used machine learning to predict the outcomes of sensor mutagenesis by analyzing established libraries that link sensor sequences to functions. Using the GCaMP calcium indicator as a scaffold, we developed an ensemble of three regression models trained on experimentally derived GCaMP mutation libraries. The trained ensemble performed an in silico functional screen on 1,423 novel, uncharacterized GCaMP variants. As a result, we identified the ensemble-derived GCaMP (eGCaMP) variants, eGCaMP and eGCaMP+, which achieve both faster kinetics and larger ∆F/F0 responses upon stimulation than previously published fast variants. Furthermore, we identified a combinatorial mutation with extraordinary dynamic range, eGCaMP2+, which outperforms the tested sixth-, seventh- and eighth-generation GCaMPs. These findings demonstrate the value of machine learning as a tool to facilitate the efficient engineering of proteins for desired biophysical characteristics.
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Affiliation(s)
- Sarah J Wait
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA, USA
- Institute of Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Marc Expòsit
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Sophia Lin
- Center for Neuroscience, University of California, Davis, Davis, CA, USA
- Department of Neurology, University of California, Davis, Davis, CA, USA
| | - Michael Rappleye
- Institute of Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Institute of Pharmacology and Toxicology, University of Zürich, Zurich, Switzerland
| | - Justin Daho Lee
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA, USA
- Institute of Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Samuel A Colby
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA, USA
| | - Lily Torp
- Institute of Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Anthony Asencio
- Institute of Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Annette Smith
- Institute of Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Michael Regnier
- Institute of Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Farid Moussavi-Harami
- Institute of Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
- Division of Cardiology, University of Washington, Seattle, WA, USA
| | - David Baker
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Christina K Kim
- Center for Neuroscience, University of California, Davis, Davis, CA, USA
- Department of Neurology, University of California, Davis, Davis, CA, USA
| | - Andre Berndt
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA, USA.
- Institute of Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA.
- Department of Bioengineering, University of Washington, Seattle, WA, USA.
- Center for Neurobiology of Addiction, Pain, and Emotion, University of Washington, Seattle, WA, USA.
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Zheng L, Yu Y, Zheng Y, Wang Y, Wu N, Jiang C, Zhao H, Niu D. Long small RNA76113 targets CYCLIC NUCLEOTIDE-GATED ION CHANNEL 5 to repress disease resistance in rice. PLANT PHYSIOLOGY 2024; 194:1889-1905. [PMID: 37949839 PMCID: PMC10904327 DOI: 10.1093/plphys/kiad599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 10/17/2023] [Accepted: 10/17/2023] [Indexed: 11/12/2023]
Abstract
Small RNAs are widely involved in plant immune responses. However, the role of long small RNAs (25 to 40 nt) in monocot plant disease resistance is largely unknown. Here, we identified a long small RNA (lsiR76113) from rice (Oryza sativa) that is downregulated by Magnaporthe oryzae infection and targets a gene encoding CYCLIC NUCLEOTIDE-GATED CHANNEL 5 (CNGC5). The cngc5 mutant lines were more susceptible to M. oryzae than the wild type, while knocking down lsiR76113 in transgenic rice plants promoted pathogen resistance. A protoplast transient expression assay showed that OsCNGC5 promotes Ca2+ influx. These results demonstrate that OsCNGC5 enhances rice resistance to rice blast by increasing the cytosolic Ca2+ concentration. Importantly, exogenous Ca2+ application enhanced rice M. oryzae resistance by affecting reactive oxygen species (ROS) production. Moreover, cngc5 mutants attenuated the PAMP-triggered immunity response, including chitin-induced and flg22-induced ROS bursts and protein phosphorylation in the mitogen-activated protein kinase cascade, indicating that OsCNGC5 is essential for PAMP-induced calcium signaling in rice. Taken together, these results suggest that lsiR76113-mediated regulation of Ca2+ influx is important for PTI responses and disease resistance in rice.
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Affiliation(s)
- Liyu Zheng
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing 210095, China
- State Key Laboratory of Biological Interactions and Crop Health, Nanjing Agricultural University, Nanjing 210095, China
| | - Yiyang Yu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing 210095, China
- State Key Laboratory of Biological Interactions and Crop Health, Nanjing Agricultural University, Nanjing 210095, China
| | - Ying Zheng
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing 210095, China
- State Key Laboratory of Biological Interactions and Crop Health, Nanjing Agricultural University, Nanjing 210095, China
| | - Yaxin Wang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing 210095, China
- State Key Laboratory of Biological Interactions and Crop Health, Nanjing Agricultural University, Nanjing 210095, China
| | - Na Wu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing 210095, China
- State Key Laboratory of Biological Interactions and Crop Health, Nanjing Agricultural University, Nanjing 210095, China
| | - Chunhao Jiang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing 210095, China
- State Key Laboratory of Biological Interactions and Crop Health, Nanjing Agricultural University, Nanjing 210095, China
| | - Hongwei Zhao
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing 210095, China
- State Key Laboratory of Biological Interactions and Crop Health, Nanjing Agricultural University, Nanjing 210095, China
| | - Dongdong Niu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing 210095, China
- State Key Laboratory of Biological Interactions and Crop Health, Nanjing Agricultural University, Nanjing 210095, China
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Li R, Xu Y, Wen X, Chen YH, Wang PZ, Zhao JL, Wu PP, Wu JJ, Liu H, Huang JH, Li SJ, Wu ZX. GCY-20 signaling controls suppression of Caenorhabditis elegans egg laying by moderate cold. Cell Rep 2024; 43:113708. [PMID: 38294902 DOI: 10.1016/j.celrep.2024.113708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 10/19/2023] [Accepted: 01/11/2024] [Indexed: 02/02/2024] Open
Abstract
Organisms sensing environmental cues and internal states and integrating the sensory information to control fecundity are essential for survival and proliferation. The present study finds that a moderate cold temperature of 11°C reduces egg laying in Caenorhabditis elegans. ASEL and AWC neurons sense the cold via GCY-20 signaling and act antagonistically on egg laying through the ASEL and AWC/AIA/HSN circuits. Upon cold stimulation, ASEL and AWC release glutamate to activate and inhibit AIA interneurons by acting on highly and lowly sensitive ionotropic GLR-2 and GLC-3 receptors, respectively. AIA inhibits HSN motor neuron activity via acetylcholinergic ACR-14 receptor signaling and suppresses egg laying. Thus, ASEL and AWC initiate and reduce the cold suppression of egg laying. ASEL's action on AIA and egg laying dominates AWC's action. The biased opposite actions of these neurons on egg laying provide animals with a precise adaptation of reproductive behavior to environmental temperatures.
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Affiliation(s)
- Rong Li
- Key Laboratory of Molecular Biophysics of Ministry of Education, Institute of Biophysics and Biochemistry, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Yu Xu
- Key Laboratory of Molecular Biophysics of Ministry of Education, Institute of Biophysics and Biochemistry, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Xin Wen
- College of Life Science, Henan Agricultural University, Zhengzhou, Henan, China
| | - Yuan-Hua Chen
- Key Laboratory of Molecular Biophysics of Ministry of Education, Institute of Biophysics and Biochemistry, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Ping-Zhou Wang
- Key Laboratory of Molecular Biophysics of Ministry of Education, Institute of Biophysics and Biochemistry, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Jia-Lu Zhao
- Key Laboratory of Molecular Biophysics of Ministry of Education, Institute of Biophysics and Biochemistry, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Piao-Ping Wu
- Key Laboratory of Molecular Biophysics of Ministry of Education, Institute of Biophysics and Biochemistry, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Jing-Jing Wu
- Key Laboratory of Molecular Biophysics of Ministry of Education, Institute of Biophysics and Biochemistry, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Hui Liu
- Key Laboratory of Molecular Biophysics of Ministry of Education, Institute of Biophysics and Biochemistry, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Jia-Hao Huang
- Key Laboratory of Molecular Biophysics of Ministry of Education, Institute of Biophysics and Biochemistry, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Si-Jia Li
- Key Laboratory of Molecular Biophysics of Ministry of Education, Institute of Biophysics and Biochemistry, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Zheng-Xing Wu
- Key Laboratory of Molecular Biophysics of Ministry of Education, Institute of Biophysics and Biochemistry, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.
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Xu Z, Kunala K, Murphy P, Patak L, Puthussery T, McGregor J. Foveal RGCs develop altered calcium dynamics weeks after photoreceptor ablation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.30.542908. [PMID: 37398439 PMCID: PMC10312553 DOI: 10.1101/2023.05.30.542908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Objective or purpose Physiological changes in retinal ganglion cells (RGCs) have been reported in rodent models of photoreceptor (PR) loss but this has not been investigated in primates. By expressing both a calcium indicator (GCaMP6s) and an optogenetic actuator (ChrimsonR) in foveal RGCs of the macaque, we reactivated RGCs in vivo and assessed their response in the weeks and years following PR loss. Design We used an in vivo calcium imaging approach to record optogenetically evoked activity in deafferented RGCs in primate fovea. Cellular scale recordings were made longitudinally over a 10 week period following photoreceptor ablation and compared to responses from RGCs that had lost photoreceptor input more than two years prior. Participants Three eyes received photoreceptor ablation, OD of a male Macaca mulatta (M1), OS of a female Macaca fascicularis (M2) and OD of a male Macaca fascicularis (M3). Two animals were used for in vivo recording, one for histological assessment. Methods Cones were ablated with an ultrafast laser delivered through an adaptive optics scanning light ophthalmoscope (AOSLO). A 0.5 s pulse of 25Hz 660nm light optogenetically stimulated RGCs, and the resulting GCaMP fluorescence signal was recorded using AOSLO. Measurements were repeated over 10 weeks immediately after PR ablation, at 2.3 years and in control RGCs. Main Outcome measures The calcium rise time, decay constant and sensitivity index of optogenetic mediated RGC were derived from GCaMP fluorescence recordings from 221 RGCs (Animal M1) and 218 RGCs (Animal M2) in vivo. Results Following photoreceptor ablation, the mean decay constant of the calcium response in RGCs decreased 1.5 fold (1.6±0.5 s to 0.6±0.3 s SD) over the 10 week observation period in subject 1 and 2.1 fold (2.5±0.5 s to 1.2±0.2 s SD) within 8 weeks in subject 2. Calcium rise time and sensitivity index were stable. Optogenetic reactivation remained possible 2.3 years after PR ablation. Conclusions Altered calcium dynamics developed in primate foveal RGCs in the weeks after photoreceptor ablation. The mean decay constant of optogenetic mediated calcium responses decreased 1.5 - 2-fold. This is the first report of this phenomenon in primate retina and further work is required to understand the role these changes play in cell survival and activity.
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Affiliation(s)
- Zhengyang Xu
- Institute of Optics, University of Rochester, Rochester, New York, UNITED STATES
| | - Karteek Kunala
- Center for Visual Science, University of Rochester Medical Center, Rochester, New York, UNITED STATES
| | - Peter Murphy
- Institute of Optics, University of Rochester, Rochester, New York, UNITED STATES
| | - Laura Patak
- Herbert Wertheim School of Optometry & Vision Science, University of California Berkeley, Berkeley, California, UNITED STATES
- Vision Science Graduate Program, University of California Berkeley, Berkeley, California, UNITED STATES
| | - Teresa Puthussery
- Herbert Wertheim School of Optometry & Vision Science, University of California Berkeley, Berkeley, California, UNITED STATES
- Helen Wills Neuroscience Institute, University of California Berkeley, Berkeley, California, UNITED STATES
| | - Juliette McGregor
- Center for Visual Science, University of Rochester Medical Center, Rochester, New York, UNITED STATES
- Department of Ophthalmology, University of Rochester Medical Center, Rochester, New York, UNITED STATES
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Stoyek MR, Doane SE, Dallaire SE, Long ZD, Ramia JM, Cassidy-Nolan DL, Poon KL, Brand T, Quinn TA. POPDC1 Variants Cause Atrioventricular Node Dysfunction and Arrhythmogenic Changes in Cardiac Electrophysiology and Intracellular Calcium Handling in Zebrafish. Genes (Basel) 2024; 15:280. [PMID: 38540339 PMCID: PMC10969970 DOI: 10.3390/genes15030280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 02/21/2024] [Accepted: 02/22/2024] [Indexed: 06/15/2024] Open
Abstract
Popeye domain-containing (POPDC) proteins selectively bind cAMP and mediate cellular responses to sympathetic nervous system (SNS) stimulation. The first discovered human genetic variant (POPDC1S201F) is associated with atrioventricular (AV) block, which is exacerbated by increased SNS activity. Zebrafish carrying the homologous mutation (popdc1S191F) display a similar phenotype to humans. To investigate the impact of POPDC1 dysfunction on cardiac electrophysiology and intracellular calcium handling, homozygous popdc1S191F and popdc1 knock-out (popdc1KO) zebrafish larvae and adult isolated popdc1S191F hearts were studied by functional fluorescent analysis. It was found that in popdc1S191F and popdc1KO larvae, heart rate (HR), AV delay, action potential (AP) and calcium transient (CaT) upstroke speed, and AP duration were less than in wild-type larvae, whereas CaT duration was greater. SNS stress by β-adrenergic receptor stimulation with isoproterenol increased HR, lengthened AV delay, slowed AP and CaT upstroke speed, and shortened AP and CaT duration, yet did not result in arrhythmias. In adult popdc1S191F zebrafish hearts, there was a higher incidence of AV block, slower AP upstroke speed, and longer AP duration compared to wild-type hearts, with no differences in CaT. SNS stress increased AV delay and led to further AV block in popdc1S191F hearts while decreasing AP and CaT duration. Overall, we have revealed that arrhythmogenic effects of POPDC1 dysfunction on cardiac electrophysiology and intracellular calcium handling in zebrafish are varied, but already present in early development, and that AV node dysfunction may underlie SNS-induced arrhythmogenesis associated with popdc1 mutation in adults.
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Affiliation(s)
- Matthew R. Stoyek
- Department of Physiology & Biophysics, Dalhousie University, Halifax, NS B3H 4R2, Canada; (M.R.S.); (S.E.D.); (S.E.D.); (Z.D.L.); (J.M.R.); (D.L.C.-N.)
| | - Sarah E. Doane
- Department of Physiology & Biophysics, Dalhousie University, Halifax, NS B3H 4R2, Canada; (M.R.S.); (S.E.D.); (S.E.D.); (Z.D.L.); (J.M.R.); (D.L.C.-N.)
| | - Shannon E. Dallaire
- Department of Physiology & Biophysics, Dalhousie University, Halifax, NS B3H 4R2, Canada; (M.R.S.); (S.E.D.); (S.E.D.); (Z.D.L.); (J.M.R.); (D.L.C.-N.)
| | - Zachary D. Long
- Department of Physiology & Biophysics, Dalhousie University, Halifax, NS B3H 4R2, Canada; (M.R.S.); (S.E.D.); (S.E.D.); (Z.D.L.); (J.M.R.); (D.L.C.-N.)
| | - Jessica M. Ramia
- Department of Physiology & Biophysics, Dalhousie University, Halifax, NS B3H 4R2, Canada; (M.R.S.); (S.E.D.); (S.E.D.); (Z.D.L.); (J.M.R.); (D.L.C.-N.)
| | - Donovan L. Cassidy-Nolan
- Department of Physiology & Biophysics, Dalhousie University, Halifax, NS B3H 4R2, Canada; (M.R.S.); (S.E.D.); (S.E.D.); (Z.D.L.); (J.M.R.); (D.L.C.-N.)
| | - Kar-Lai Poon
- National Heart & Lung Institute, Imperial College London, London W12 0NN, UK; (K.-L.P.); (T.B.)
| | - Thomas Brand
- National Heart & Lung Institute, Imperial College London, London W12 0NN, UK; (K.-L.P.); (T.B.)
| | - T. Alexander Quinn
- Department of Physiology & Biophysics, Dalhousie University, Halifax, NS B3H 4R2, Canada; (M.R.S.); (S.E.D.); (S.E.D.); (Z.D.L.); (J.M.R.); (D.L.C.-N.)
- School of Biomedical Engineering, Dalhousie University, Halifax, NS B3H 4R2, Canada
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Li Y, Cheng Z, Wang C, Lin J, Jiang H, Cui M. Geometric transformation adaptive optics (GTAO) for volumetric deep brain imaging through gradient-index lenses. Nat Commun 2024; 15:1031. [PMID: 38310087 PMCID: PMC10838304 DOI: 10.1038/s41467-024-45434-5] [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: 07/27/2023] [Accepted: 01/22/2024] [Indexed: 02/05/2024] Open
Abstract
The advance of genetic function indicators has enabled the observation of neuronal activities at single-cell resolutions. A major challenge for the applications on mammalian brains is the limited optical access depth. Currently, the method of choice to access deep brain structures is to insert miniature optical components. Among these validated miniature optics, the gradient-index (GRIN) lens has been widely employed for its compactness and simplicity. However, due to strong fourth-order astigmatism, GRIN lenses suffer from a small imaging field of view, which severely limits the measurement throughput and success rate. To overcome these challenges, we developed geometric transformation adaptive optics (GTAO), which enables adaptable achromatic large-volume correction through GRIN lenses. We demonstrate its major advances through in vivo structural and functional imaging of mouse brains. The results suggest that GTAO can serve as a versatile solution to enable large-volume recording of deep brain structures and activities through GRIN lenses.
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Affiliation(s)
- Yuting Li
- School of Electrical and Computer Engineering, Purdue University, West Lafayette, IN, 47907, USA
- Bindley Bioscience Center, Purdue University, West Lafayette, IN, 47907, USA
| | - Zongyue Cheng
- School of Electrical and Computer Engineering, Purdue University, West Lafayette, IN, 47907, USA
- Bindley Bioscience Center, Purdue University, West Lafayette, IN, 47907, USA
| | - Chenmao Wang
- School of Electrical and Computer Engineering, Purdue University, West Lafayette, IN, 47907, USA
- Bindley Bioscience Center, Purdue University, West Lafayette, IN, 47907, USA
| | - Jianian Lin
- School of Electrical and Computer Engineering, Purdue University, West Lafayette, IN, 47907, USA
- Bindley Bioscience Center, Purdue University, West Lafayette, IN, 47907, USA
| | - Hehai Jiang
- School of Electrical and Computer Engineering, Purdue University, West Lafayette, IN, 47907, USA
- Bindley Bioscience Center, Purdue University, West Lafayette, IN, 47907, USA
| | - Meng Cui
- School of Electrical and Computer Engineering, Purdue University, West Lafayette, IN, 47907, USA.
- Bindley Bioscience Center, Purdue University, West Lafayette, IN, 47907, USA.
- Department of Biology, Purdue University, West Lafayette, IN, 47907, USA.
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Cea Salazar VI, Perez MD, Robison AJ, Trainor BC. Impacts of sex differences on optogenetic, chemogenetic, and calcium-imaging tools. Curr Opin Neurobiol 2024; 84:102817. [PMID: 38042130 PMCID: PMC11374099 DOI: 10.1016/j.conb.2023.102817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/05/2023] [Accepted: 11/06/2023] [Indexed: 12/04/2023]
Abstract
Technical innovation in neuroscience introduced powerful tools for measuring and manipulating neuronal activity via optical, chemogenetic, and calcium-imaging tools. These tools were initially tested primarily in male animals but are now increasingly being used in females as well. In this review, we consider how these tools may work differently in males and females. For example, we review sex differences in the metabolism of chemogenetic ligands and their downstream signaling effects. Optical tools more directly alter depolarization or hyperpolarization of neurons, but biological sex and gonadal hormones modulate synaptic inputs and intrinsic excitability. We review studies demonstrating that optogenetic manipulations are sometimes consistent across the rodent estrous cycle but within certain circuits; manipulations can vary across the ovarian cycle. Finally, calcium-imaging methods utilize genetically encoded calcium indicators to measure neuronal activity. Testosterone and estradiol can directly modulate calcium influx, and we consider these implications for interpreting the results of calcium-imaging studies. Together, our findings suggest that these neuroscientific tools may sometimes work differently in males and females and that users should be aware of these differences when applying these methods.
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Affiliation(s)
| | - Melvin D Perez
- Department of Physiology, University of California, Davis, CA 95616, USA
| | - A J Robison
- Department of Psychology, University of California, Davis, CA 95616, USA
| | - Brian C Trainor
- Neuroscience Graduate Group, University of California, Davis, CA 95616, USA; Department of Physiology, Michigan State University, East Lansing, MI 48824, USA.
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Baker CM, Gong Y. A Semi-supervised Pipeline for Accurate Neuron Segmentation with Fewer Ground Truth Labels. eNeuro 2024; 11:ENEURO.0352-23.2024. [PMID: 38242690 PMCID: PMC10880440 DOI: 10.1523/eneuro.0352-23.2024] [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: 09/09/2023] [Revised: 12/21/2023] [Accepted: 01/04/2024] [Indexed: 01/21/2024] Open
Abstract
Recent advancements in two-photon calcium imaging have enabled scientists to record the activity of thousands of neurons with cellular resolution. This scope of data collection is crucial to understanding the next generation of neuroscience questions, but analyzing these large recordings requires automated methods for neuron segmentation. Supervised methods for neuron segmentation achieve state of-the-art accuracy and speed but currently require large amounts of manually generated ground truth training labels. We reduced the required number of training labels by designing a semi-supervised pipeline. Our pipeline used neural network ensembling to generate pseudolabels to train a single shallow U-Net. We tested our method on three publicly available datasets and compared our performance to three widely used segmentation methods. Our method outperformed other methods when trained on a small number of ground truth labels and could achieve state-of-the-art accuracy after training on approximately a quarter of the number of ground truth labels as supervised methods. When trained on many ground truth labels, our pipeline attained higher accuracy than that of state-of-the-art methods. Overall, our work will help researchers accurately process large neural recordings while minimizing the time and effort needed to generate manual labels.
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Affiliation(s)
- Casey M Baker
- Departments of Biomedical Engineering, Duke University, Durham, North Carolina 27701
| | - Yiyang Gong
- Departments of Biomedical Engineering, Duke University, Durham, North Carolina 27701
- Neurobiology, Duke University, Durham, North Carolina 27701
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Liu Y, Lin W, Liu J, Zhu H. Structural and temporal dynamics analysis of neural circuit from 2002 to 2022: A bibliometric analysis. Heliyon 2024; 10:e24649. [PMID: 38298625 PMCID: PMC10828061 DOI: 10.1016/j.heliyon.2024.e24649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 01/05/2024] [Accepted: 01/11/2024] [Indexed: 02/02/2024] Open
Abstract
Background In the pursuit of causal insights into neural circuit functionality, various interventions, including electrical, genetic, and pharmacological approaches, have been applied over recent decades. This study employs a comprehensive bibliometric perspective to explore the field of neural circuits. Methods Reviews and articles on neural circuits were obtained from the Web of Science Core Collection (WOSCC) database on Apr. 12, 2023. In this article, co-authorship analysis, co-occurrence analysis, citation analysis, bibliographic analysis, and co-citation analysis were used to clarify the authors, journals, institutions, countries, topics, and internal associations between them. Results More than 2000 organizations from 52 different countries published 3975 articles in the field of "neural circuit" were used to analysis. Luo liqun emerged as the most prolific author, and Deisseroth Karl garners the highest co-citations (3643). The Journal of Neuroscience leaded in publications, while Nature toped in citations. Chinese Academy of Science recorded the highest article count institutionally, with Stanford University ranking first with 14,350 citations. Since 2020, neurodynamic, anxiety-related mechanisms, and GABAergic neurons have gained prominence, shaping the trajectory of neural circuitry research. Conclusions Our investigation has discerned a paradigmatic reorientation towards neurodynamic processes, anxiety-related mechanisms, and GABAergic neurons within the domain of neural circuit research. This identification intimates a prospective trajectory for the field. In the future, it is imperative for research endeavors to accord priority to the translational application of these discernments, with the aim of materializing tangible clinical solutions.
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Affiliation(s)
- Yuan Liu
- Cancer Research Center Nantong, Affiliated Tumor Hospital of Nantong University, Nantong, China
| | - Wei Lin
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and Institute of Neuroscience, Soochow University, Suzhou, China
- Department of Pediatrics, The First Affiliated Hospital of Fujian Medical University, Fujian, China
| | - Jie Liu
- Department of Orthopedics, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou School of Clinical Medicine, Nanjing Medical University, Taizhou, China
| | - Haixia Zhu
- Cancer Research Center Nantong, Affiliated Tumor Hospital of Nantong University, Nantong, China
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Suryavanshi P, Langton R, Fairhead K, Glykys J. Brief and diverse excitotoxic insults cause an increase in neuronal nuclear membrane permeability in the neonatal brain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.08.22.554167. [PMID: 37662276 PMCID: PMC10473591 DOI: 10.1101/2023.08.22.554167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Neuronal swelling after excitotoxic insults is implicated in neuronal injury and death in the developing brain, yet mitigating brain edema with osmotic and surgical interventions yields poor clinical outcomes. Importantly, neuronal swelling and its downstream consequences during early brain development remain poorly investigated. Using multiphoton Ca2+ imaging in vivo (P12-17) and in acute brain slices (P8-12), we explored Ca2+-dependent downstream effects after neuronal cytotoxic edema. We observed the translocation of cytosolic GCaMP6s into the nucleus of a subpopulation of neurons minutes after various excitotoxic insults. We used automated morphology-detection algorithms for neuronal segmentation and quantified the nuclear translocation of GCaMP6s as the ratio of nuclear and cytosolic intensity (N/C ratio). Elevated neuronal N/C ratios were correlated to higher Ca2+ loads and could occur independently of neuronal swelling. Electron microscopy revealed that the nuclear translocation was associated with increased nuclear pore size. Inhibiting calpains prevented elevated N/C ratios and neuronal swelling. Thus, our results indicate altered nuclear transport in a subpopulation of neurons shortly after injury in the developing brain, which can be used as an early biomarker of acute neuronal injury.
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Affiliation(s)
- P Suryavanshi
- Department of Pediatrics, University of Iowa, Iowa City, IA
- Iowa Neuroscience Institute, University of Iowa, Iowa City, IA
| | - R Langton
- Department of Pediatrics, University of Iowa, Iowa City, IA
- Iowa Neuroscience Institute, University of Iowa, Iowa City, IA
| | - K Fairhead
- Biomedical Sciences, College of Liberal Arts and Sciences, University of Iowa, Iowa City, IA
| | - J Glykys
- Department of Pediatrics, University of Iowa, Iowa City, IA
- Iowa Neuroscience Institute, University of Iowa, Iowa City, IA
- Department of Neurology, University of Iowa, Iowa City, IA
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44
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Paudel S, Yue M, Nalamalapu R, Saha MS. Deciphering the Calcium Code: A Review of Calcium Activity Analysis Methods Employed to Identify Meaningful Activity in Early Neural Development. Biomolecules 2024; 14:138. [PMID: 38275767 PMCID: PMC10813340 DOI: 10.3390/biom14010138] [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: 12/14/2023] [Revised: 01/16/2024] [Accepted: 01/18/2024] [Indexed: 01/27/2024] Open
Abstract
The intracellular and intercellular flux of calcium ions represents an ancient and universal mode of signaling that regulates an extensive array of cellular processes. Evidence for the central role of calcium signaling includes various techniques that allow the visualization of calcium activity in living cells. While extensively investigated in mature cells, calcium activity is equally important in developing cells, particularly the embryonic nervous system where it has been implicated in a wide variety array of determinative events. However, unlike in mature cells, where the calcium dynamics display regular, predictable patterns, calcium activity in developing systems is far more sporadic, irregular, and diverse. This renders the ability to assess calcium activity in a consistent manner extremely challenging, challenges reflected in the diversity of methods employed to analyze calcium activity in neural development. Here we review the wide array of calcium detection and analysis methods used across studies, limiting the extent to which they can be comparatively analyzed. The goal is to provide investigators not only with an overview of calcium activity analysis techniques currently available, but also to offer suggestions for future work and standardization to enable informative comparative evaluations of this fundamental and important process in neural development.
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Affiliation(s)
- Sudip Paudel
- Wyss Institute, Harvard University, Boston, MA 02215, USA; (S.P.); (M.Y.)
| | - Michelle Yue
- Wyss Institute, Harvard University, Boston, MA 02215, USA; (S.P.); (M.Y.)
| | - Rithvik Nalamalapu
- School of Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA;
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45
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Jose A, Cheung PY, Laouby Z, Vanholsbeeck F, Cheyne JE. Low-cost reversible tandem lens mesoscope for brain imaging in rodents. NEUROPHOTONICS 2024; 11:014306. [PMID: 38464865 PMCID: PMC10924044 DOI: 10.1117/1.nph.11.1.014306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 02/07/2024] [Accepted: 02/09/2024] [Indexed: 03/12/2024]
Abstract
Significance The development of imaging systems that are cost-efficient and modular is essential for modern neuroscience research. Aim In the current study, we designed, developed, and characterized a low-cost reversible tandem lens mesoscope for brain imaging in rodents. Approach Using readily available components, we assembled a robust imaging system that is highly efficient and cost-effective. We developed a mesoscope that offers high-resolution structural and functional imaging with cost-effective lenses and CMOS camera. Results The reversible tandem lens configuration of the mesoscope offers two fields of view (FOVs), which can be achieved by swapping the objective and imaging lenses. The large FOV configuration of 12.6 × 10.5 mm provides a spatial resolution up to 4.92 μ m , and the small FOV configuration of 6 × 5 mm provides a resolution of up to 2.46 μ m . We demonstrate the efficiency of our system for imaging neuronal calcium activity in both rat and mouse brains in vivo. Conclusions The careful selection of the mesoscope components ensured its compactness, portability, and versatility, meaning that different types of samples and sample holders can be easily accommodated, enabling a range of different experiments both in vivo and in vitro. The custom-built reversible FOV mesoscope is cost-effective and was developed for under US$10,000 with excellent performance.
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Affiliation(s)
- Ashly Jose
- University of Auckland, Department of Physics, Auckland, New Zealand
- Dodd-Walls Centre for Photonic and Quantum Technologies (DWC), Dunedin, New Zealand
| | - Pang Ying Cheung
- Dodd-Walls Centre for Photonic and Quantum Technologies (DWC), Dunedin, New Zealand
- University of Auckland, Department of Physiology, Auckland, New Zealand
| | - Zahra Laouby
- Dodd-Walls Centre for Photonic and Quantum Technologies (DWC), Dunedin, New Zealand
- University of Auckland, Department of Physiology, Auckland, New Zealand
| | - Frédérique Vanholsbeeck
- University of Auckland, Department of Physics, Auckland, New Zealand
- Dodd-Walls Centre for Photonic and Quantum Technologies (DWC), Dunedin, New Zealand
| | - Juliette E. Cheyne
- Dodd-Walls Centre for Photonic and Quantum Technologies (DWC), Dunedin, New Zealand
- University of Auckland, Department of Physiology, Auckland, New Zealand
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46
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Zhou ZC, Gordon-Fennell A, Piantadosi SC, Ji N, Smith SL, Bruchas MR, Stuber GD. Deep-brain optical recording of neural dynamics during behavior. Neuron 2023; 111:3716-3738. [PMID: 37804833 PMCID: PMC10843303 DOI: 10.1016/j.neuron.2023.09.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 08/24/2023] [Accepted: 09/06/2023] [Indexed: 10/09/2023]
Abstract
In vivo fluorescence recording techniques have produced landmark discoveries in neuroscience, providing insight into how single cell and circuit-level computations mediate sensory processing and generate complex behaviors. While much attention has been given to recording from cortical brain regions, deep-brain fluorescence recording is more complex because it requires additional measures to gain optical access to harder to reach brain nuclei. Here we discuss detailed considerations and tradeoffs regarding deep-brain fluorescence recording techniques and provide a comprehensive guide for all major steps involved, from project planning to data analysis. The goal is to impart guidance for new and experienced investigators seeking to use in vivo deep fluorescence optical recordings in awake, behaving rodent models.
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Affiliation(s)
- Zhe Charles Zhou
- Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, WA 98195, USA; Center for Neurobiology of Addiction, Pain, and Emotion, University of Washington, Seattle, WA 98195, USA
| | - Adam Gordon-Fennell
- Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, WA 98195, USA; Center for Neurobiology of Addiction, Pain, and Emotion, University of Washington, Seattle, WA 98195, USA
| | - Sean C Piantadosi
- Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, WA 98195, USA; Center for Neurobiology of Addiction, Pain, and Emotion, University of Washington, Seattle, WA 98195, USA
| | - Na Ji
- Department of Physics, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Spencer LaVere Smith
- Department of Electrical and Computer Engineering, University of California Santa Barbara, Santa Barbara, CA 93106, USA
| | - Michael R Bruchas
- Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, WA 98195, USA; Center for Neurobiology of Addiction, Pain, and Emotion, University of Washington, Seattle, WA 98195, USA; Department of Pharmacology, University of Washington, Seattle, WA 98195, USA; Department of Bioengineering, University of Washington, Seattle, WA 98195, USA.
| | - Garret D Stuber
- Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, WA 98195, USA; Center for Neurobiology of Addiction, Pain, and Emotion, University of Washington, Seattle, WA 98195, USA; Department of Pharmacology, University of Washington, Seattle, WA 98195, USA.
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47
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Ghosh S, Dahiya M, Kumar A, Bheri M, Pandey GK. Calcium imaging: a technique to monitor calcium dynamics in biological systems. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2023; 29:1777-1811. [PMID: 38222278 PMCID: PMC10784449 DOI: 10.1007/s12298-023-01405-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 12/07/2023] [Accepted: 12/11/2023] [Indexed: 01/16/2024]
Abstract
Calcium ion (Ca2+) is a multifaceted signaling molecule that acts as an important second messenger. During the course of evolution, plants and animals have developed Ca2+ signaling in order to respond against diverse stimuli, to regulate a large number of physiological and developmental pathways. Our understanding of Ca2+ signaling and its components in physiological phenomena ranging from lower to higher organisms, and from single cell to multiple tissues has grown exponentially. The generation of Ca2+ transients or signatures for various stress factor is a well-known mechanism adopted in plant and animal systems. However, the decoding of such remarkable signatures is an uphill task and is always an interesting goal for the scientific community. In the past few decades, studies on the concentration and dynamics of intracellular Ca2+ are significantly increasing and have become a trend in modern biology. The advancement in approaches from Ca2+ binding dyes to in vivo Ca2+ imaging through the use of Ca2+ biosensors to achieve spatio-temporal resolution in micro and milliseconds range, provide us phenomenal opportunities to study live cell Ca2+ imaging or dynamics. Here, we describe the usage, improvement and advancement of Ca2+ based dyes, genetically encoded probes and sensors to achieve extraordinary Ca2+ imaging in plants and animals. Graphical abstract
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Affiliation(s)
- Soma Ghosh
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, Dhaula Kuan, New Delhi, 110021 India
| | - Monika Dahiya
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, Dhaula Kuan, New Delhi, 110021 India
| | - Amit Kumar
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, Dhaula Kuan, New Delhi, 110021 India
| | - Malathi Bheri
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, Dhaula Kuan, New Delhi, 110021 India
| | - Girdhar K. Pandey
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, Dhaula Kuan, New Delhi, 110021 India
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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: 1.0] [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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Bonney SK, Nielson CD, Sosa MJ, Shih AY. Capillary regression leads to sustained local hypoperfusion by inducing constriction of upstream transitional vessels. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.28.564529. [PMID: 37961686 PMCID: PMC10635020 DOI: 10.1101/2023.10.28.564529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
In the brain, a microvascular sensory web coordinates oxygen delivery to regions of neuronal activity. This involves a dense network of capillaries that send conductive signals upstream to feeding arterioles to promote vasodilation and blood flow. Although this process is critical to the metabolic supply of healthy brain tissue, it may also be a point of vulnerability in disease. Deterioration of capillary networks is a hallmark of many neurological disorders and how this web is engaged during vascular damage remains unknown. We performed in vivo two-photon microscopy on young adult mural cell reporter mice and induced focal capillary injuries using precise two-photon laser irradiation of single capillaries. We found that ∼63% of the injuries resulted in regression of the capillary segment 7-14 days following injury, and the remaining repaired to re-establish blood flow within 7 days. Injuries that resulted in capillary regression induced sustained vasoconstriction in the upstream arteriole-capillary transition (ACT) zone at least 21 days post-injury in both awake and anesthetized mice. This abnormal vasoconstriction involved attenuation of vasomotor dynamics and uncoupling from mural cell calcium signaling following capillary regression. Consequently, blood flow was reduced in the ACT zone and in secondary, uninjured downstream capillaries. These findings demonstrate how capillary injury and regression, as often seen in age-related neurological disease, can impair the microvascular sensory web and contribute to cerebral hypoperfusion. SIGNIFICANCE Deterioration of the capillary network is a characteristic of many neurological diseases and can exacerbate neuronal dysfunction and degeneration due to poor blood perfusion. Here we show that focal capillary injuries can induce vessel regression and elicit sustained vasoconstriction in upstream transitional vessels that branch from cortical penetrating arterioles. This reduces blood flow to broader, uninjured regions of the same microvascular network. These findings suggest that widespread and cumulative damage to brain capillaries in neurological disease may broadly affect blood supply and contribute to hypoperfusion through their remote actions.
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50
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Nakasone K, Zavik C, Liu E, Ahmed B, Griffith D, Maisenbacher L, Singh A, Zhou Y, Cui B, Müller H. Compact Electrochromic Optical Recording of Bioelectric Potentials. ARXIV 2023:arXiv:2311.15506v1. [PMID: 38076511 PMCID: PMC10705589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Electrochromic optical recording (ECORE) is a label-free method that utilizes electrochromism to optically detect electrical signals in biological cells with a high signal-to-noise ratio and is suitable for long-term recording. However, ECORE usually requires a large and intricate optical setup, making it relatively difficult to transport and to study specimens on a large scale. Here, we present a Compact ECORE (CECORE) apparatus that drastically reduces the spatial footprint and complexity of the ECORE setup whilst maintaining high sensitivity. An autobalancing differential photodetector automates common-mode noise rejection, removing the need for manually adjustable optics, and a compact laser module conserves space compared to a typical laser mount. The result is a simple, easy-to-use, and relatively low cost system that achieves a sensitivity of 16.7 μV (within a factor of 5 of the shot noise limit), and reliably detects action potentials from Human-induced pluripotent stem cell (HiPSC) derived cardiomyocytes. This setup can be further improved to within 1.5 dB of the shot noise limit by filtering out power-line interference.
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Affiliation(s)
- Kenneth Nakasone
- Department of Physics, 366 Physics South, University of California, Berkeley, CA 94720
| | - Chris Zavik
- Department of Physics, 366 Physics South, University of California, Berkeley, CA 94720
| | - Erica Liu
- Department of Chemistry, 290 Jane Stanford Way, Stanford University, Stanford, CA 94305
- Wu Tsai Neurosciences Institute, 290 Jane Stanford Way, Stanford University, Stanford, CA 94305
| | - Burhan Ahmed
- Department of Physics, 366 Physics South, University of California, Berkeley, CA 94720
| | - Dana Griffith
- Department of Physics, 366 Physics South, University of California, Berkeley, CA 94720
| | - Lothar Maisenbacher
- Department of Physics, 366 Physics South, University of California, Berkeley, CA 94720
| | - Ashwin Singh
- Department of Physics, 366 Physics South, University of California, Berkeley, CA 94720
| | - Yuecheng Zhou
- Department of Chemistry, 290 Jane Stanford Way, Stanford University, Stanford, CA 94305
- Wu Tsai Neurosciences Institute, 290 Jane Stanford Way, Stanford University, Stanford, CA 94305
| | - Bianxiao Cui
- Department of Chemistry, 290 Jane Stanford Way, Stanford University, Stanford, CA 94305
- Wu Tsai Neurosciences Institute, 290 Jane Stanford Way, Stanford University, Stanford, CA 94305
| | - Holger Müller
- Department of Physics, 366 Physics South, University of California, Berkeley, CA 94720
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