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Wilde M, Poulsen RE, Qin W, Arnold J, Favre-Bulle IA, Mattingley JB, Scott EK, Stednitz SJ. EVIDENCE FOR AUDITORY STIMULUS-SPECIFIC ADAPTATION BUT NOT DEVIANCE DETECTION IN LARVAL ZEBRAFISH BRAINS. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.14.597058. [PMID: 38915708 PMCID: PMC11195219 DOI: 10.1101/2024.06.14.597058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Animals receive a constant stream of sensory input, and detecting changes in this sensory landscape is critical to their survival. One signature of change detection in humans is the auditory mismatch negativity (MMN), a neural response to unexpected stimuli that deviate from a predictable sequence. This process requires the auditory system to adapt to specific repeated stimuli while remaining sensitive to novel input (stimulus-specific adaptation). MMN was originally described in humans, and equivalent responses have been found in other mammals and birds, but it is not known to what extent this deviance detection circuitry is evolutionarily conserved. Here we present the first evidence for stimulus-specific adaptation in the brain of a teleost fish, using whole-brain calcium imaging of larval zebrafish at single-neuron resolution with selective plane illumination microscopy. We found frequency-specific responses across the brain with variable response amplitudes for frequencies of the same volume, and created a loudness curve to model this effect. We presented an auditory 'oddball' stimulus in an otherwise predictable train of pure tone stimuli, and did not find a population of neurons with specific responses to deviant tones that were not otherwise explained by stimulus-specific adaptation. Further, we observed no deviance responses to an unexpected omission of a sound in a repetitive sequence of white noise bursts. These findings extend the known scope of auditory adaptation and deviance responses across the evolutionary tree, and lay groundwork for future studies to describe the circuitry underlying auditory adaptation at the level of individual neurons.
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Affiliation(s)
- Maya Wilde
- Queensland Brain Institute, University of Queensland
- Department of Anatomy and Physiology, University of Melbourne
| | - Rebecca E Poulsen
- Department of Linguistics, Faculty of Medicine, Health and Human Sciences, Macquarie University
| | - Wei Qin
- Department of Anatomy and Physiology, University of Melbourne
| | - Joshua Arnold
- Queensland Brain Institute, University of Queensland
| | - Itia A Favre-Bulle
- Queensland Brain Institute, University of Queensland
- School of Mathematics and Physics, University of Queensland
| | - Jason B Mattingley
- Queensland Brain Institute, University of Queensland
- School of Psychology, University of Queensland
| | - Ethan K Scott
- Queensland Brain Institute, University of Queensland
- Department of Anatomy and Physiology, University of Melbourne
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2
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Dibaji H, Kazemi Nasaban Shotorban A, Grattan RM, Lucero S, Schodt DJ, Lidke KA, Petruccelli J, Lidke DS, Liu S, Chakraborty T. Axial de-scanning using remote focusing in the detection arm of light-sheet microscopy. Nat Commun 2024; 15:5019. [PMID: 38866746 PMCID: PMC11169345 DOI: 10.1038/s41467-024-49291-0] [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: 09/20/2023] [Accepted: 05/31/2024] [Indexed: 06/14/2024] Open
Abstract
Rapid, high-resolution volumetric imaging without moving heavy objectives or disturbing delicate samples remains challenging. Pupil-matched remote focusing offers a promising solution for high NA systems, but the fluorescence signal's incoherent and unpolarized nature complicates its application. Thus, remote focusing is mainly used in the illumination arm with polarized laser light to improve optical coupling. Here, we introduce a novel optical design that can de-scan the axial focus movement in the detection arm of a microscope. Our method splits the fluorescence signal into S and P-polarized light, lets them pass through the remote focusing module separately, and combines them with the camera. This allows us to use only one focusing element to perform aberration-free, multi-color, volumetric imaging without (a) compromising the fluorescent signal and (b) needing to perform sample/detection-objective translation. We demonstrate the capabilities of this scheme by acquiring fast dual-color 4D (3D space + time) image stacks with an axial range of 70 μm and camera-limited acquisition speed. Owing to its general nature, we believe this technique will find its application in many other microscopy techniques that currently use an adjustable Z-stage to carry out volumetric imaging, such as confocal, 2-photon, and light sheet variants.
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Affiliation(s)
- Hassan Dibaji
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, NM, USA
| | | | - Rachel M Grattan
- Comprehensive Cancer Center, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
- Department of Pathology, University of New Mexico Health Science Center, Albuquerque, NM, USA
| | - Shayna Lucero
- Comprehensive Cancer Center, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
- Department of Pathology, University of New Mexico Health Science Center, Albuquerque, NM, USA
| | - David J Schodt
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, NM, USA
| | - Keith A Lidke
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, NM, USA
- Comprehensive Cancer Center, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Jonathan Petruccelli
- Department of Physics, University at Albany-State University of NewYork, Albany, NY, USA
| | - Diane S Lidke
- Comprehensive Cancer Center, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
- Department of Pathology, University of New Mexico Health Science Center, Albuquerque, NM, USA
| | - Sheng Liu
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, NM, USA
| | - Tonmoy Chakraborty
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, NM, USA.
- Comprehensive Cancer Center, University of New Mexico Health Sciences Center, Albuquerque, NM, USA.
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3
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Shang CF, Wang YF, Zhao MT, Fan QX, Zhao S, Qian Y, Xu SJ, Mu Y, Hao J, Du JL. Real-time analysis of large-scale neuronal imaging enables closed-loop investigation of neural dynamics. Nat Neurosci 2024; 27:1014-1018. [PMID: 38467902 DOI: 10.1038/s41593-024-01595-6] [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: 08/25/2022] [Accepted: 02/07/2024] [Indexed: 03/13/2024]
Abstract
Large-scale imaging of neuronal activities is crucial for understanding brain functions. However, it is challenging to analyze large-scale imaging data in real time, preventing closed-loop investigation of neural circuitry. Here we develop a real-time analysis system with a field programmable gate array-graphics processing unit design for an up to 500-megabyte-per-second image stream. Adapted to whole-brain imaging of awake larval zebrafish, the system timely extracts activity from up to 100,000 neurons and enables closed-loop perturbations of neural dynamics.
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Affiliation(s)
- Chun-Feng Shang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
- Guangdong-Hongkong-Macau Institute of CNS Regeneration, Ministry of Education CNS Regeneration Collaborative Joint Laboratory, Jinan University, Guangzhou, China
- Shenzhen Institute of Neuroscience, Shenzhen, China
| | - Yu-Fan Wang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Mei-Ting Zhao
- Institute of Automation, Chinese Academy of Sciences, Beijing, China
- Guangdong Institute of Artificial Intelligence and Advanced Computing, Guangzhou, China
| | - Qiu-Xiang Fan
- Institute of Automation, Chinese Academy of Sciences, Beijing, China
- Guangdong Institute of Artificial Intelligence and Advanced Computing, Guangzhou, China
| | - Shan Zhao
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yu Qian
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Sheng-Jin Xu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yu Mu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China.
- University of Chinese Academy of Sciences, Beijing, China.
| | - Jie Hao
- University of Chinese Academy of Sciences, Beijing, China.
- Institute of Automation, Chinese Academy of Sciences, Beijing, China.
- Guangdong Institute of Artificial Intelligence and Advanced Computing, Guangzhou, China.
| | - Jiu-Lin Du
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China.
- University of Chinese Academy of Sciences, Beijing, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
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4
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Dibaji H, Nasaban Shotorban AK, Grattan RM, Lucero S, Schodt DJ, Lidke KA, Petruccelli J, Lidke DS, Liu S, Chakraborty T. Axial de-scanning using remote focusing in the detection arm of light-sheet microscopy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.07.556729. [PMID: 38659774 PMCID: PMC11042218 DOI: 10.1101/2023.09.07.556729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
The ability to image at high speeds is necessary for biological imaging to capture fast-moving or transient events or to efficiently image large samples. However, due to the lack of rigidity of biological specimens, carrying out fast, high-resolution volumetric imaging without moving and agitating the sample has been a challenging problem. Pupil-matched remote focusing has been promising for high NA imaging systems with their low aberrations and wavelength independence, making it suitable for multicolor imaging. However, owing to the incoherent and unpolarized nature of the fluorescence signal, manipulating this emission light through remote focusing is challenging. Therefore, remote focusing has been primarily limited to the illumination arm, using polarized laser light to facilitate coupling in and out of the remote focusing optics. Here, we introduce a novel optical design that can de-scan the axial focus movement in the detection arm of a microscope. Our method splits the fluorescence signal into S and P-polarized light, lets them pass through the remote focusing module separately, and combines them with the camera. This allows us to use only one focusing element to perform aberration-free, multi-color, volumetric imaging without (a) compromising the fluorescent signal and (b) needing to perform sample/detection-objective translation. We demonstrate the capabilities of this scheme by acquiring fast dual-color 4D (3D space + time) image stacks with an axial range of 70 μm and camera-limited acquisition speed. Owing to its general nature, we believe this technique will find its application in many other microscopy techniques that currently use an adjustable Z-stage to carry out volumetric imaging, such as confocal, 2-photon, and light sheet variants.
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5
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Chaoul V, Dib EY, Bedran J, Khoury C, Shmoury O, Harb F, Soueid J. Assessing Drug Administration Techniques in Zebrafish Models of Neurological Disease. Int J Mol Sci 2023; 24:14898. [PMID: 37834345 PMCID: PMC10573323 DOI: 10.3390/ijms241914898] [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: 07/24/2023] [Revised: 08/30/2023] [Accepted: 08/31/2023] [Indexed: 10/15/2023] Open
Abstract
Neurological diseases, including neurodegenerative and neurodevelopmental disorders, affect nearly one in six of the world's population. The burden of the resulting deaths and disability is set to rise during the next few decades as a consequence of an aging population. To address this, zebrafish have become increasingly prominent as a model for studying human neurological diseases and exploring potential therapies. Zebrafish offer numerous benefits, such as genetic homology and brain similarities, complementing traditional mammalian models and serving as a valuable tool for genetic screening and drug discovery. In this comprehensive review, we highlight various drug delivery techniques and systems employed for therapeutic interventions of neurological diseases in zebrafish, and evaluate their suitability. We also discuss the challenges encountered during this process and present potential advancements in innovative techniques.
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Affiliation(s)
- Victoria Chaoul
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut P.O. Box 11-0236, Lebanon; (V.C.); (J.B.); (O.S.)
| | - Emanuel-Youssef Dib
- Department of Biomedical Sciences, Faculty of Medicine and Medical Sciences, University of Balamand, Kalhat P.O. Box 100, Lebanon; (E.-Y.D.); (C.K.)
| | - Joe Bedran
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut P.O. Box 11-0236, Lebanon; (V.C.); (J.B.); (O.S.)
| | - Chakib Khoury
- Department of Biomedical Sciences, Faculty of Medicine and Medical Sciences, University of Balamand, Kalhat P.O. Box 100, Lebanon; (E.-Y.D.); (C.K.)
| | - Omar Shmoury
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut P.O. Box 11-0236, Lebanon; (V.C.); (J.B.); (O.S.)
| | - Frédéric Harb
- Department of Biomedical Sciences, Faculty of Medicine and Medical Sciences, University of Balamand, Kalhat P.O. Box 100, Lebanon; (E.-Y.D.); (C.K.)
| | - Jihane Soueid
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut P.O. Box 11-0236, Lebanon; (V.C.); (J.B.); (O.S.)
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6
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DIBAJI HASSAN, SHOTORBAN ALIKAZEMINASABAN, HABIBI MAHSA, GRATTAN RACHELM, LUCERO SHAYNA, SCHODT DAVIDJ, LIDKE KEITHA, PETRUCCELLI JONATHAN, LIDKE DIANES, LIU SHENG, CHAKRABORTY TONMOY. Axial de-scanning using remote focusing in the detection arm of light-sheet microscopy. RESEARCH SQUARE 2023:rs.3.rs-3338831. [PMID: 37886461 PMCID: PMC10602066 DOI: 10.21203/rs.3.rs-3338831/v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
The ability to image at high speeds is necessary in biological imaging to capture fast-moving or transient events or to efficiently image large samples. However, due to the lack of rigidity of biological specimens, carrying out fast, high-resolution volumetric imaging without moving and agitating the sample has been a challenging problem. Pupil-matched remote focusing has been promising for high NA imaging systems with their low aberrations and wavelength independence, making it suitable for multicolor imaging. However, owing to the incoherent and unpolarized nature of the fluorescence signal, manipulating this emission light through remote focusing is challenging. Therefore, remote focusing has been primarily limited to the illumination arm, using polarized laser light for facilitating coupling in and out of the remote focusing optics. Here we introduce a novel optical design that can de-scan the axial focus movement in the detection arm of a microscope. Our method splits the fluorescence signal into S and P-polarized light and lets them pass through the remote focusing module separately and combines them with the camera. This allows us to use only one focusing element to perform aberration-free, multi-color, volumetric imaging without (a) compromising the fluorescent signal and (b) needing to perform sample/detection-objective translation. We demonstrate the capabilities of this scheme by acquiring fast dual-color 4D (3D space + time) image stacks, with an axial range of 70 μm and camera limited acquisition speed. Owing to its general nature, we believe this technique will find its application to many other microscopy techniques that currently use an adjustable Z-stage to carry out volumetric imaging such as confocal, 2-photon, and light sheet variants.
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Affiliation(s)
- HASSAN DIBAJI
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, New Mexico 87131, USA
| | | | - MAHSA HABIBI
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, New Mexico 87131, USA
| | - RACHEL M GRATTAN
- Comprehensive Cancer Center, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, 87131, USA
- Department of Pathology, University of New Mexico Health Science Center, Albuquerque, NM, USA
| | - SHAYNA LUCERO
- Comprehensive Cancer Center, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, 87131, USA
- Department of Pathology, University of New Mexico Health Science Center, Albuquerque, NM, USA
| | - DAVID J. SCHODT
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, New Mexico 87131, USA
| | - KEITH A. LIDKE
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, New Mexico 87131, USA
- Comprehensive Cancer Center, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, 87131, USA
| | - JONATHAN PETRUCCELLI
- Department of Physics, University at Albany–State University of NewYork,1400 Washington Avenue, Albany, NY 12222, USA
| | - DIANE S. LIDKE
- Comprehensive Cancer Center, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, 87131, USA
- Department of Pathology, University of New Mexico Health Science Center, Albuquerque, NM, USA
| | - SHENG LIU
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, New Mexico 87131, USA
| | - TONMOY CHAKRABORTY
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, New Mexico 87131, USA
- Comprehensive Cancer Center, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, 87131, USA
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7
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Beiza-Canelo N, Moulle H, Pujol T, Panier T, Migault G, Le Goc G, Tapie P, Desprat N, Straka H, Debrégeas G, Bormuth V. Magnetic actuation of otoliths allows behavioral and brain-wide neuronal exploration of vestibulo-motor processing in larval zebrafish. Curr Biol 2023:S0960-9822(23)00621-8. [PMID: 37285844 DOI: 10.1016/j.cub.2023.05.026] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 11/23/2022] [Accepted: 05/11/2023] [Indexed: 06/09/2023]
Abstract
The vestibular system in the inner ear plays a central role in sensorimotor control by informing the brain about the orientation and acceleration of the head. However, most experiments in neurophysiology are performed using head-fixed configurations, depriving animals of vestibular inputs. To overcome this limitation, we decorated the utricular otolith of the vestibular system in larval zebrafish with paramagnetic nanoparticles. This procedure effectively endowed the animal with magneto-sensitive capacities: applied magnetic field gradients induced forces on the otoliths, resulting in robust behavioral responses comparable to those evoked by rotating the animal by up to 25°. We recorded the whole-brain neuronal response to this fictive motion stimulation using light-sheet functional imaging. Experiments performed in unilaterally injected fish revealed the activation of a commissural inhibition between the brain hemispheres. This magnetic-based stimulation technique for larval zebrafish opens new perspectives to functionally dissect the neural circuits underlying vestibular processing and to develop multisensory virtual environments, including vestibular feedback.
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Affiliation(s)
- Natalia Beiza-Canelo
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP), 75005 Paris, France
| | - Hippolyte Moulle
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP), 75005 Paris, France
| | - Thomas Pujol
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP), 75005 Paris, France; IBENS, Département de Biologie, École Normale Supérieure, CNRS, Inserm, PSL Research University, 75005 Paris, France
| | - Thomas Panier
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP), 75005 Paris, France; Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Plateforme d'Imagerie, 75005 Paris, France
| | - Geoffrey Migault
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP), 75005 Paris, France
| | - Guillaume Le Goc
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP), 75005 Paris, France
| | - Pierre Tapie
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP), 75005 Paris, France
| | - Nicolas Desprat
- Laboratoire de Physique de l'École Normale Supérieure, ENS, Université PSL, CNRS, Sorbonne Université, Université Paris Cité, 75005 Paris, France; Université Paris Diderot, 10 Rue Alice Domon et Leonie Duquet, 75013 Paris, France
| | - Hans Straka
- Faculty of Biology, Ludwig-Maximilians-University Munich, Grosshadernerstr. 2, 82152 Planegg, Germany
| | - Georges Debrégeas
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP), 75005 Paris, France
| | - Volker Bormuth
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP), 75005 Paris, France.
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8
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van der Plas TL, Tubiana J, Le Goc G, Migault G, Kunst M, Baier H, Bormuth V, Englitz B, Debrégeas G. Neural assemblies uncovered by generative modeling explain whole-brain activity statistics and reflect structural connectivity. eLife 2023; 12:83139. [PMID: 36648065 PMCID: PMC9940913 DOI: 10.7554/elife.83139] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 01/15/2023] [Indexed: 01/18/2023] Open
Abstract
Patterns of endogenous activity in the brain reflect a stochastic exploration of the neuronal state space that is constrained by the underlying assembly organization of neurons. Yet, it remains to be shown that this interplay between neurons and their assembly dynamics indeed suffices to generate whole-brain data statistics. Here, we recorded the activity from ∼40,000 neurons simultaneously in zebrafish larvae, and show that a data-driven generative model of neuron-assembly interactions can accurately reproduce the mean activity and pairwise correlation statistics of their spontaneous activity. This model, the compositional Restricted Boltzmann Machine (cRBM), unveils ∼200 neural assemblies, which compose neurophysiological circuits and whose various combinations form successive brain states. We then performed in silico perturbation experiments to determine the interregional functional connectivity, which is conserved across individual animals and correlates well with structural connectivity. Our results showcase how cRBMs can capture the coarse-grained organization of the zebrafish brain. Notably, this generative model can readily be deployed to parse neural data obtained by other large-scale recording techniques.
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Affiliation(s)
- Thijs L van der Plas
- Computational Neuroscience Lab, Department of Neurophysiology, Donders Center for Neuroscience, Radboud UniversityNijmegenNetherlands
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP)ParisFrance
- Department of Physiology, Anatomy and Genetics, University of OxfordOxfordUnited Kingdom
| | - Jérôme Tubiana
- Blavatnik School of Computer Science, Tel Aviv UniversityTel AvivIsrael
| | - Guillaume Le Goc
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP)ParisFrance
| | - Geoffrey Migault
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP)ParisFrance
| | - Michael Kunst
- Department Genes – Circuits – Behavior, Max Planck Institute for Biological IntelligenceMartinsriedGermany
- Allen Institute for Brain ScienceSeattleUnited States
| | - Herwig Baier
- Department Genes – Circuits – Behavior, Max Planck Institute for Biological IntelligenceMartinsriedGermany
| | - Volker Bormuth
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP)ParisFrance
| | - Bernhard Englitz
- Computational Neuroscience Lab, Department of Neurophysiology, Donders Center for Neuroscience, Radboud UniversityNijmegenNetherlands
| | - Georges Debrégeas
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP)ParisFrance
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9
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Sy SKH, Chan DCW, Chan RCH, Lyu J, Li Z, Wong KKY, Choi CHJ, Mok VCT, Lai HM, Randlett O, Hu Y, Ko H. An optofluidic platform for interrogating chemosensory behavior and brainwide neural representation in larval zebrafish. Nat Commun 2023; 14:227. [PMID: 36641479 PMCID: PMC9840631 DOI: 10.1038/s41467-023-35836-2] [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: 02/13/2022] [Accepted: 01/03/2023] [Indexed: 01/15/2023] Open
Abstract
Studying chemosensory processing desires precise chemical cue presentation, behavioral response monitoring, and large-scale neuronal activity recording. Here we present Fish-on-Chips, a set of optofluidic tools for highly-controlled chemical delivery while simultaneously imaging behavioral outputs and whole-brain neuronal activities at cellular resolution in larval zebrafish. These include a fluidics-based swimming arena and an integrated microfluidics-light sheet fluorescence microscopy (µfluidics-LSFM) system, both of which utilize laminar fluid flows to achieve spatiotemporally precise chemical cue presentation. To demonstrate the strengths of the platform, we used the navigation arena to reveal binasal input-dependent behavioral strategies that larval zebrafish adopt to evade cadaverine, a death-associated odor. The µfluidics-LSFM system enables sequential presentation of odor stimuli to individual or both nasal cavities separated by only ~100 µm. This allowed us to uncover brainwide neural representations of cadaverine sensing and binasal input summation in the vertebrate model. Fish-on-Chips is readily generalizable and will empower the investigation of neural coding in the chemical senses.
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Affiliation(s)
- Samuel K H Sy
- Division of Neurology, Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Department of Biomedical Engineering, Faculty of Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Department of Electrical and Electronic Engineering, Faculty of Engineering, The University of Hong Kong, Pok Fu Lam, Hong Kong Island, Hong Kong SAR, China
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong SAR, China
| | - Danny C W Chan
- Division of Neurology, Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Department of Anaesthesia and Intensive Care, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Peter Hung Pain Research Institute, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Roy C H Chan
- Division of Neurology, Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Jing Lyu
- Division of Neurology, Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Zhongqi Li
- Division of Neurology, Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Kenneth K Y Wong
- Department of Electrical and Electronic Engineering, Faculty of Engineering, The University of Hong Kong, Pok Fu Lam, Hong Kong Island, Hong Kong SAR, China
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong SAR, China
| | - Chung Hang Jonathan Choi
- Department of Biomedical Engineering, Faculty of Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Peter Hung Pain Research Institute, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Chow Yuk Ho Technology Centre for Innovative Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Vincent C T Mok
- Division of Neurology, Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Margaret K. L. Cheung Research Centre for Management of Parkinsonism, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Gerald Choa Neuroscience Institute, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Hei-Ming Lai
- Division of Neurology, Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Margaret K. L. Cheung Research Centre for Management of Parkinsonism, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Gerald Choa Neuroscience Institute, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Department of Psychiatry, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Owen Randlett
- Institut national de la santé et de la recherche médicale, Université Claude Bernard Lyon 1, Lyon, France
| | - Yu Hu
- Department of Mathematics and Division of Life Science, Faculty of Science, Hong Kong University of Science and Technology, Clear Water Bay, New Territories, Hong Kong SAR, China
| | - Ho Ko
- Division of Neurology, Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.
- Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.
- Peter Hung Pain Research Institute, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.
- Chow Yuk Ho Technology Centre for Innovative Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.
- Margaret K. L. Cheung Research Centre for Management of Parkinsonism, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.
- Gerald Choa Neuroscience Institute, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.
- Department of Psychiatry, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.
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10
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Yang E, Zwart MF, James B, Rubinov M, Wei Z, Narayan S, Vladimirov N, Mensh BD, Fitzgerald JE, Ahrens MB. A brainstem integrator for self-location memory and positional homeostasis in zebrafish. Cell 2022; 185:5011-5027.e20. [PMID: 36563666 DOI: 10.1016/j.cell.2022.11.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 06/28/2022] [Accepted: 11/21/2022] [Indexed: 12/24/2022]
Abstract
To track and control self-location, animals integrate their movements through space. Representations of self-location are observed in the mammalian hippocampal formation, but it is unknown if positional representations exist in more ancient brain regions, how they arise from integrated self-motion, and by what pathways they control locomotion. Here, in a head-fixed, fictive-swimming, virtual-reality preparation, we exposed larval zebrafish to a variety of involuntary displacements. They tracked these displacements and, many seconds later, moved toward their earlier location through corrective swimming ("positional homeostasis"). Whole-brain functional imaging revealed a network in the medulla that stores a memory of location and induces an error signal in the inferior olive to drive future corrective swimming. Optogenetically manipulating medullary integrator cells evoked displacement-memory behavior. Ablating them, or downstream olivary neurons, abolished displacement corrections. These results reveal a multiregional hindbrain circuit in vertebrates that integrates self-motion and stores self-location to control locomotor behavior.
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Affiliation(s)
- En Yang
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA.
| | - Maarten F Zwart
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA; School of Psychology and Neuroscience, Centre for Biophotonics, University of St Andrews, St. Andrews, UK
| | - Ben James
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Mikail Rubinov
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA; Department of Biomedical Engineering, Vanderbilt University, Nashville, TN 37235, USA
| | - Ziqiang Wei
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Sujatha Narayan
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Nikita Vladimirov
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA; URPP Adaptive Brain Circuits in Development and Learning (AdaBD), University of Zurich, Zurich, Switzerland
| | - Brett D Mensh
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - James E Fitzgerald
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Misha B Ahrens
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA.
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11
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Etchegaray E, Baas D, Naville M, Haftek-Terreau Z, Volff JN. The neurodevelopmental gene MSANTD2 belongs to a gene family formed by recurrent molecular domestication of Harbinger transposons at the base of vertebrates. Mol Biol Evol 2022; 39:msac173. [PMID: 35980103 PMCID: PMC9392472 DOI: 10.1093/molbev/msac173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 07/06/2022] [Accepted: 08/02/2022] [Indexed: 11/18/2022] Open
Abstract
The formation of new genes is a major source of organism evolutionary innovation. Beyond their mutational effects, transposable elements can be co-opted by host genomes to form different types of sequences including novel genes, through a mechanism named molecular domestication.We report the formation of four genes through molecular domestication of Harbinger transposons, three in a common ancestor of jawed vertebrates about 500 million years ago and one in sarcopterygians approx. 430 million years ago. Additionally, one processed pseudogene arose approx. 60 million years ago in simians. In zebrafish, Harbinger-derived genes are expressed during early development but also in adult tissues, and predominantly co-expressed in male brain. In human, expression was detected in multiple organs, with major expression in the brain particularly during fetal development. We used CRISPR/Cas9 with direct gene knock-out in the F0 generation and the morpholino antisense oligonucleotide knock-down technique to study in zebrafish the function of one of these genes called MSANTD2, which has been suggested to be associated to neuro-developmental diseases such as autism spectrum disorders and schizophrenia in human. MSANTD2 inactivation led to developmental delays including tail and nervous system malformation at one day post fertilization. Affected embryos showed dead cell accumulation, major anatomical defects characterized by impaired brain ventricle formation and alterations in expression of some characteristic genes involved in vertebrate nervous system development. Hence, the characterization of MSANTD2 and other Harbinger-derived genes might contribute to a better understanding of the genetic innovations having driven the early evolution of the vertebrate nervous system.
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Affiliation(s)
- Ema Etchegaray
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, UCBL1, CNRS UMR 5242, Lyon, France
| | - Dominique Baas
- Unité MeLiS, UCBL-CNRS UMR 5284, INSERM U1314, Lyon, France
| | - Magali Naville
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, UCBL1, CNRS UMR 5242, Lyon, France
| | - Zofia Haftek-Terreau
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, UCBL1, CNRS UMR 5242, Lyon, France
| | - Jean Nicolas Volff
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, UCBL1, CNRS UMR 5242, Lyon, France
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12
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Wlodkowic D, Bownik A, Leitner C, Stengel D, Braunbeck T. Beyond the behavioural phenotype: Uncovering mechanistic foundations in aquatic eco-neurotoxicology. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 829:154584. [PMID: 35306067 DOI: 10.1016/j.scitotenv.2022.154584] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 03/09/2022] [Accepted: 03/11/2022] [Indexed: 06/14/2023]
Abstract
During the last decade, there has been an increase in awareness of how anthropogenic pollution can alter behavioural traits of diverse aquatic organisms. Apart from understanding profound ecological implications, alterations in neuro-behavioural indices have emerged as sensitive and physiologically integrative endpoints in chemical risk assessment. Accordingly, behavioural ecotoxicology and broader eco-neurotoxicology are becoming increasingly popular fields of research that span a plethora of fundamental laboratory experimentations as well as applied field-based studies. Despite mounting interest in aquatic behavioural ecotoxicology studies, there is, however, a considerable paucity in deciphering the mechanistic foundations underlying behavioural alterations upon exposure to pollutants. The behavioural phenotype is indeed the highest-level integrative neurobiological phenomenon, but at its core lie myriads of intertwined biochemical, cellular, and physiological processes. Therefore, the mechanisms that underlie changes in behavioural phenotypes can stem among others from dysregulation of neurotransmitter pathways, electrical signalling, and cell death of discrete cell populations in the central and peripheral nervous systems. They can, however, also be a result of toxicity to sensory organs and even metabolic dysfunctions. In this critical review, we outline why behavioural phenotyping should be the starting point that leads to actual discovery of fundamental mechanisms underlying actions of neurotoxic and neuromodulating contaminants. We highlight potential applications of the currently existing and emerging neurobiology and neurophysiology analytical strategies that should be embraced and more broadly adopted in behavioural ecotoxicology. Such strategies can provide new mechanistic discoveries instead of only observing the end sum phenotypic effects.
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Affiliation(s)
- Donald Wlodkowic
- The Neurotox Laboratory, School of Science, RMIT University, Melbourne, Australia.
| | - Adam Bownik
- Department of Hydrobiology and Protection of Ecosystems, Faculty of Environmental Biology, University of Life Sciences, Lublin, Poland
| | - Carola Leitner
- Aquatic Ecology and Toxicology, Centre for Organismal Studies, University of Heidelberg, Im Neuenheimer Feld 504, D-69120 Heidelberg, Germany
| | - Daniel Stengel
- Aquatic Ecology and Toxicology, Centre for Organismal Studies, University of Heidelberg, Im Neuenheimer Feld 504, D-69120 Heidelberg, Germany
| | - Thomas Braunbeck
- Aquatic Ecology and Toxicology, Centre for Organismal Studies, University of Heidelberg, Im Neuenheimer Feld 504, D-69120 Heidelberg, Germany
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13
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Barbara R, Nagathihalli Kantharaju M, Haruvi R, Harrington K, Kawashima T. PyZebrascope: An Open-Source Platform for Brain-Wide Neural Activity Imaging in Zebrafish. Front Cell Dev Biol 2022; 10:875044. [PMID: 35663407 PMCID: PMC9161555 DOI: 10.3389/fcell.2022.875044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 04/18/2022] [Indexed: 11/13/2022] Open
Abstract
Understanding how neurons interact across the brain to control animal behaviors is one of the central goals in neuroscience. Recent developments in fluorescent microscopy and genetically-encoded calcium indicators led to the establishment of whole-brain imaging methods in zebrafish, which record neural activity across a brain-wide volume with single-cell resolution. Pioneering studies of whole-brain imaging used custom light-sheet microscopes, and their operation relied on commercially developed and maintained software not available globally. Hence it has been challenging to disseminate and develop the technology in the research community. Here, we present PyZebrascope, an open-source Python platform designed for neural activity imaging in zebrafish using light-sheet microscopy. PyZebrascope has intuitive user interfaces and supports essential features for whole-brain imaging, such as two orthogonal excitation beams and eye damage prevention. Its camera module can handle image data throughput of up to 800 MB/s from camera acquisition to file writing while maintaining stable CPU and memory usage. Its modular architecture allows the inclusion of advanced algorithms for microscope control and image processing. As a proof of concept, we implemented a novel automatic algorithm for maximizing the image resolution in the brain by precisely aligning the excitation beams to the image focal plane. PyZebrascope enables whole-brain neural activity imaging in fish behaving in a virtual reality environment. Thus, PyZebrascope will help disseminate and develop light-sheet microscopy techniques in the neuroscience community and advance our understanding of whole-brain neural dynamics during animal behaviors.
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Affiliation(s)
- Rani Barbara
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Madhu Nagathihalli Kantharaju
- Max-Delbrück-Centrum for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Humboldt University of Berlin, Berlin, Germany
| | - Ravid Haruvi
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Kyle Harrington
- Max-Delbrück-Centrum for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Oak Ridge National Laboratory, Oak Ridge, TN, United States
- *Correspondence: Kyle Harrington, ; Takashi Kawashima,
| | - Takashi Kawashima
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel
- *Correspondence: Kyle Harrington, ; Takashi Kawashima,
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14
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Sovrano VA, Vicidomini S, Potrich D, Miletto Petrazzini ME, Baratti G, Rosa-Salva O. Visual discrimination and amodal completion in zebrafish. PLoS One 2022; 17:e0264127. [PMID: 35235595 PMCID: PMC8890640 DOI: 10.1371/journal.pone.0264127] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 02/03/2022] [Indexed: 01/16/2023] Open
Abstract
While zebrafish represent an important model for the study of the visual system, visual perception in this species is still less investigated than in other teleost fish. In this work, we validated for zebrafish two versions of a visual discrimination learning task, which is based on the motivation to reach food and companions. Using this task, we investigated zebrafish ability to discriminate between two different shape pairs (i.e., disk vs. cross and full vs. amputated disk). Once zebrafish were successfully trained to discriminate a full from an amputated disk, we also tested their ability to visually complete partially occluded objects (amodal completion). After training, animals were presented with two amputated disks. In these test stimuli, another shape was either exactly juxtaposed or only placed close to the missing sectors of the disk. Only the former stimulus should elicit amodal completion. In human observers, this stimulus causes the impression that the other shape is occluding the missing sector of the disk, which is thus perceived as a complete, although partially hidden, disk. In line with our predictions, fish reinforced on the full disk chose the stimulus eliciting amodal completion, while fish reinforced on the amputated disk chose the other stimulus. This represents the first demonstration of amodal completion perception in zebrafish. Moreover, our results also indicated that a specific shape pair (disk vs. cross) might be particularly difficult to discriminate for this species, confirming previous reports obtained with different procedures.
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Affiliation(s)
- Valeria Anna Sovrano
- Center for Mind/Brain Sciences, University of Trento, Rovereto, Italy
- Department of Psychology and Cognitive Science, University of Trento, Rovereto, Italy
- * E-mail: (VAS); (ORS)
| | | | - Davide Potrich
- Center for Mind/Brain Sciences, University of Trento, Rovereto, Italy
| | | | - Greta Baratti
- Center for Mind/Brain Sciences, University of Trento, Rovereto, Italy
| | - Orsola Rosa-Salva
- Center for Mind/Brain Sciences, University of Trento, Rovereto, Italy
- * E-mail: (VAS); (ORS)
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15
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de Vito G, Turrini L, Müllenbroich C, Ricci P, Sancataldo G, Mazzamuto G, Tiso N, Sacconi L, Fanelli D, Silvestri L, Vanzi F, Pavone FS. Fast whole-brain imaging of seizures in zebrafish larvae by two-photon light-sheet microscopy. BIOMEDICAL OPTICS EXPRESS 2022; 13:1516-1536. [PMID: 35414999 PMCID: PMC8973167 DOI: 10.1364/boe.434146] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 11/22/2021] [Accepted: 11/22/2021] [Indexed: 05/27/2023]
Abstract
Light-sheet fluorescence microscopy (LSFM) enables real-time whole-brain functional imaging in zebrafish larvae. Conventional one-photon LSFM can however induce undesirable visual stimulation due to the use of visible excitation light. The use of two-photon (2P) excitation, employing near-infrared invisible light, provides unbiased investigation of neuronal circuit dynamics. However, due to the low efficiency of the 2P absorption process, the imaging speed of this technique is typically limited by the signal-to-noise-ratio. Here, we describe a 2P LSFM setup designed for non-invasive imaging that enables quintuplicating state-of-the-art volumetric acquisition rate of the larval zebrafish brain (5 Hz) while keeping low the laser intensity on the specimen. We applied our system to the study of pharmacologically-induced acute seizures, characterizing the spatial-temporal dynamics of pathological activity and describing for the first time the appearance of caudo-rostral ictal waves (CRIWs).
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Affiliation(s)
- Giuseppe de Vito
- University of Florence, Department of Neuroscience, Psychology, Drug Research and Child Health, Viale Pieraccini 6, Florence, Italy, 50139, Italy
- European Laboratory for Non-Linear Spectroscopy, Via Nello Carrara 1, Sesto Fiorentino 50019, Italy
- Co-first authors with equal contribution
| | - Lapo Turrini
- European Laboratory for Non-Linear Spectroscopy, Via Nello Carrara 1, Sesto Fiorentino 50019, Italy
- University of Florence, Department of Physics and Astronomy, Via Sansone 1, Sesto Fiorentino 50019, Italy
- Co-first authors with equal contribution
| | - Caroline Müllenbroich
- European Laboratory for Non-Linear Spectroscopy, Via Nello Carrara 1, Sesto Fiorentino 50019, Italy
- School of Physics and Astronomy, Kelvin Building, University of Glasgow, G12 8QQ, Glasgow, UK
- National Institute of Optics, National Research Council, Via Nello Carrara 1, Sesto Fiorentino 50019, Italy
| | - Pietro Ricci
- European Laboratory for Non-Linear Spectroscopy, Via Nello Carrara 1, Sesto Fiorentino 50019, Italy
| | - Giuseppe Sancataldo
- European Laboratory for Non-Linear Spectroscopy, Via Nello Carrara 1, Sesto Fiorentino 50019, Italy
- University of Florence, Department of Physics and Astronomy, Via Sansone 1, Sesto Fiorentino 50019, Italy
| | - Giacomo Mazzamuto
- European Laboratory for Non-Linear Spectroscopy, Via Nello Carrara 1, Sesto Fiorentino 50019, Italy
- National Institute of Optics, National Research Council, Via Nello Carrara 1, Sesto Fiorentino 50019, Italy
| | - Natascia Tiso
- University of Padova, Department of Biology, Via U. Bassi 58/B, Padova 35131, Italy
| | - Leonardo Sacconi
- European Laboratory for Non-Linear Spectroscopy, Via Nello Carrara 1, Sesto Fiorentino 50019, Italy
- National Institute of Optics, National Research Council, Via Nello Carrara 1, Sesto Fiorentino 50019, Italy
| | - Duccio Fanelli
- University of Florence, Department of Physics and Astronomy, Via Sansone 1, Sesto Fiorentino 50019, Italy
| | - Ludovico Silvestri
- European Laboratory for Non-Linear Spectroscopy, Via Nello Carrara 1, Sesto Fiorentino 50019, Italy
- University of Florence, Department of Physics and Astronomy, Via Sansone 1, Sesto Fiorentino 50019, Italy
- National Institute of Optics, National Research Council, Via Nello Carrara 1, Sesto Fiorentino 50019, Italy
| | - Francesco Vanzi
- European Laboratory for Non-Linear Spectroscopy, Via Nello Carrara 1, Sesto Fiorentino 50019, Italy
- University of Florence, Department of Biology, Via Madonna del Piano 6, Sesto Fiorentino 50019, Italy
| | - Francesco Saverio Pavone
- European Laboratory for Non-Linear Spectroscopy, Via Nello Carrara 1, Sesto Fiorentino 50019, Italy
- University of Florence, Department of Physics and Astronomy, Via Sansone 1, Sesto Fiorentino 50019, Italy
- National Institute of Optics, National Research Council, Via Nello Carrara 1, Sesto Fiorentino 50019, Italy
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16
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Crouzier L, Richard EM, Sourbron J, Lagae L, Maurice T, Delprat B. Use of Zebrafish Models to Boost Research in Rare Genetic Diseases. Int J Mol Sci 2021; 22:13356. [PMID: 34948153 PMCID: PMC8706563 DOI: 10.3390/ijms222413356] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 12/09/2021] [Accepted: 12/10/2021] [Indexed: 02/06/2023] Open
Abstract
Rare genetic diseases are a group of pathologies with often unmet clinical needs. Even if rare by a single genetic disease (from 1/2000 to 1/more than 1,000,000), the total number of patients concerned account for approximatively 400 million peoples worldwide. Finding treatments remains challenging due to the complexity of these diseases, the small number of patients and the challenge in conducting clinical trials. Therefore, innovative preclinical research strategies are required. The zebrafish has emerged as a powerful animal model for investigating rare diseases. Zebrafish combines conserved vertebrate characteristics with high rate of breeding, limited housing requirements and low costs. More than 84% of human genes responsible for diseases present an orthologue, suggesting that the majority of genetic diseases could be modelized in zebrafish. In this review, we emphasize the unique advantages of zebrafish models over other in vivo models, particularly underlining the high throughput phenotypic capacity for therapeutic screening. We briefly introduce how the generation of zebrafish transgenic lines by gene-modulating technologies can be used to model rare genetic diseases. Then, we describe how zebrafish could be phenotyped using state-of-the-art technologies. Two prototypic examples of rare diseases illustrate how zebrafish models could play a critical role in deciphering the underlying mechanisms of rare genetic diseases and their use to identify innovative therapeutic solutions.
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Affiliation(s)
- Lucie Crouzier
- MMDN, University of Montpellier, EPHE, INSERM, 34095 Montpellier, France; (L.C.); (E.M.R.); (T.M.)
| | - Elodie M. Richard
- MMDN, University of Montpellier, EPHE, INSERM, 34095 Montpellier, France; (L.C.); (E.M.R.); (T.M.)
| | - Jo Sourbron
- Department of Development and Regeneration, Section Pediatric Neurology, University Hospital KU Leuven, 3000 Leuven, Belgium; (J.S.); (L.L.)
| | - Lieven Lagae
- Department of Development and Regeneration, Section Pediatric Neurology, University Hospital KU Leuven, 3000 Leuven, Belgium; (J.S.); (L.L.)
| | - Tangui Maurice
- MMDN, University of Montpellier, EPHE, INSERM, 34095 Montpellier, France; (L.C.); (E.M.R.); (T.M.)
| | - Benjamin Delprat
- MMDN, University of Montpellier, EPHE, INSERM, 34095 Montpellier, France; (L.C.); (E.M.R.); (T.M.)
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17
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Gagliano G, Nelson T, Saliba N, Vargas-Hernández S, Gustavsson AK. Light Sheet Illumination for 3D Single-Molecule Super-Resolution Imaging of Neuronal Synapses. Front Synaptic Neurosci 2021; 13:761530. [PMID: 34899261 PMCID: PMC8651567 DOI: 10.3389/fnsyn.2021.761530] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 10/27/2021] [Indexed: 01/02/2023] Open
Abstract
The function of the neuronal synapse depends on the dynamics and interactions of individual molecules at the nanoscale. With the development of single-molecule super-resolution microscopy over the last decades, researchers now have a powerful and versatile imaging tool for mapping the molecular mechanisms behind the biological function. However, imaging of thicker samples, such as mammalian cells and tissue, in all three dimensions is still challenging due to increased fluorescence background and imaging volumes. The combination of single-molecule imaging with light sheet illumination is an emerging approach that allows for imaging of biological samples with reduced fluorescence background, photobleaching, and photodamage. In this review, we first present a brief overview of light sheet illumination and previous super-resolution techniques used for imaging of neurons and synapses. We then provide an in-depth technical review of the fundamental concepts and the current state of the art in the fields of three-dimensional single-molecule tracking and super-resolution imaging with light sheet illumination. We review how light sheet illumination can improve single-molecule tracking and super-resolution imaging in individual neurons and synapses, and we discuss emerging perspectives and new innovations that have the potential to enable and improve single-molecule imaging in brain tissue.
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Affiliation(s)
- Gabriella Gagliano
- Department of Chemistry, Rice University, Houston, TX, United States
- Applied Physics Program, Rice University, Houston, TX, United States
- Smalley-Curl Institute, Rice University, Houston, TX, United States
| | - Tyler Nelson
- Department of Chemistry, Rice University, Houston, TX, United States
- Applied Physics Program, Rice University, Houston, TX, United States
- Smalley-Curl Institute, Rice University, Houston, TX, United States
| | - Nahima Saliba
- Department of Chemistry, Rice University, Houston, TX, United States
| | - Sofía Vargas-Hernández
- Department of Chemistry, Rice University, Houston, TX, United States
- Systems, Synthetic, and Physical Biology Program, Rice University, Houston, TX, United States
- Institute of Biosciences & Bioengineering, Rice University, Houston, TX, United States
| | - Anna-Karin Gustavsson
- Department of Chemistry, Rice University, Houston, TX, United States
- Smalley-Curl Institute, Rice University, Houston, TX, United States
- Institute of Biosciences & Bioengineering, Rice University, Houston, TX, United States
- Department of Biosciences, Rice University, Houston, TX, United States
- Laboratory for Nanophotonics, Rice University, Houston, TX, United States
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18
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Zaupa M, Naini SMA, Younes MA, Bullier E, Duboué ER, Le Corronc H, Soula H, Wolf S, Candelier R, Legendre P, Halpern ME, Mangin JM, Hong E. Trans-inhibition of axon terminals underlies competition in the habenulo-interpeduncular pathway. Curr Biol 2021; 31:4762-4772.e5. [PMID: 34529937 DOI: 10.1016/j.cub.2021.08.051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 07/12/2021] [Accepted: 08/18/2021] [Indexed: 11/19/2022]
Abstract
Survival of animals is dependent on the correct selection of an appropriate behavioral response to competing external stimuli. Theoretical models have been proposed and underlying mechanisms are emerging to explain how one circuit is selected among competing neural circuits. The evolutionarily conserved forebrain to midbrain habenulo-interpeduncular nucleus (Hb-IPN) pathway consists of cholinergic and non-cholinergic neurons, which mediate different aversive behaviors. Simultaneous calcium imaging of neuronal cell bodies and of the population dynamics of their axon terminals reveals that signals in the cell bodies are not reflective of terminal activity. We find that axon terminals of cholinergic and non-cholinergic habenular neurons exhibit stereotypic patterns of spontaneous activity that are negatively correlated and localize to discrete subregions of the target IPN. Patch-clamp recordings show that calcium bursts in cholinergic terminals at the ventral IPN trigger excitatory currents in IPN neurons, which precede inhibition of non-cholinergic terminals at the adjacent dorsal IPN. Inhibition is mediated through presynaptic GABAB receptors activated in non-cholinergic habenular neurons upon GABA release from the target IPN. Together, the results reveal a hardwired mode of competition at the terminals of two excitatory neuronal populations, providing a physiological framework to explore the relationship between different aversive responses.
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Affiliation(s)
- Margherita Zaupa
- INSERM, CNRS, Neurosciences Paris Seine - Institut de Biologie Paris Seine (NPS - IBPS), Sorbonne Université, 75005 Paris, France
| | - Seyedeh Maryam Alavi Naini
- INSERM, CNRS, Neurosciences Paris Seine - Institut de Biologie Paris Seine (NPS - IBPS), Sorbonne Université, 75005 Paris, France
| | - Maroun Abi Younes
- INSERM, CNRS, Neurosciences Paris Seine - Institut de Biologie Paris Seine (NPS - IBPS), Sorbonne Université, 75005 Paris, France
| | - Erika Bullier
- INSERM, CNRS, Neurosciences Paris Seine - Institut de Biologie Paris Seine (NPS - IBPS), Sorbonne Université, 75005 Paris, France
| | - Erik R Duboué
- Jupiter Life Science Initiative, Wilkes Honors College and Charles E. Schmidt College of Science, Florida Atlantic University, Jupiter, FL 33458, USA
| | - Hervé Le Corronc
- INSERM, CNRS, Neurosciences Paris Seine - Institut de Biologie Paris Seine (NPS - IBPS), Sorbonne Université, 75005 Paris, France
| | - Hédi Soula
- INSERM, Sorbonne Université, Nutriomics, La Pitié Salpétrière, 75013 Paris, France
| | - Sebastien Wolf
- Laboratoire Jean Perrin, CNRS, Sorbonne Université, 75005 Paris, France
| | - Raphaël Candelier
- Laboratoire Jean Perrin, CNRS, Sorbonne Université, 75005 Paris, France
| | - Pascal Legendre
- INSERM, CNRS, Neurosciences Paris Seine - Institut de Biologie Paris Seine (NPS - IBPS), Sorbonne Université, 75005 Paris, France
| | - Marnie E Halpern
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Jean-Marie Mangin
- INSERM, CNRS, Neurosciences Paris Seine - Institut de Biologie Paris Seine (NPS - IBPS), Sorbonne Université, 75005 Paris, France
| | - Elim Hong
- INSERM, CNRS, Neurosciences Paris Seine - Institut de Biologie Paris Seine (NPS - IBPS), Sorbonne Université, 75005 Paris, France.
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19
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Cho ES, Han S, Lee KH, Kim CH, Yoon YG. 3DM: deep decomposition and deconvolution microscopy for rapid neural activity imaging. OPTICS EXPRESS 2021; 29:32700-32711. [PMID: 34615335 DOI: 10.1364/oe.439619] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 09/14/2021] [Indexed: 05/18/2023]
Abstract
We report the development of deep decomposition and deconvolution microscopy (3DM), a computational microscopy method for the volumetric imaging of neural activity. 3DM overcomes the major challenge of deconvolution microscopy, the ill-posed inverse problem. We take advantage of the temporal sparsity of neural activity to reformulate and solve the inverse problem using two neural networks which perform sparse decomposition and deconvolution. We demonstrate the capability of 3DM via in vivo imaging of the neural activity of a whole larval zebrafish brain with a field of view of 1040 µm × 400 µm × 235 µm and with estimated lateral and axial resolutions of 1.7 µm and 5.4 µm, respectively, at imaging rates of up to 4.2 volumes per second.
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20
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Goc GL, Lafaye J, Karpenko S, Bormuth V, Candelier R, Debrégeas G. Thermal modulation of Zebrafish exploratory statistics reveals constraints on individual behavioral variability. BMC Biol 2021; 19:208. [PMID: 34548084 PMCID: PMC8456632 DOI: 10.1186/s12915-021-01126-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 08/18/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Variability is a hallmark of animal behavior. It contributes to survival by endowing individuals and populations with the capacity to adapt to ever-changing environmental conditions. Intra-individual variability is thought to reflect both endogenous and exogenous modulations of the neural dynamics of the central nervous system. However, how variability is internally regulated and modulated by external cues remains elusive. Here, we address this question by analyzing the statistics of spontaneous exploration of freely swimming zebrafish larvae and by probing how these locomotor patterns are impacted when changing the water temperatures within an ethologically relevant range. RESULTS We show that, for this simple animal model, five short-term kinematic parameters - interbout interval, turn amplitude, travelled distance, turn probability, and orientational flipping rate - together control the long-term exploratory dynamics. We establish that the bath temperature consistently impacts the means of these parameters, but leave their pairwise covariance unchanged. These results indicate that the temperature merely controls the sampling statistics within a well-defined kinematic space delineated by this robust statistical structure. At a given temperature, individual animals explore the behavioral space over a timescale of tens of minutes, suggestive of a slow internal state modulation that could be externally biased through the bath temperature. By combining these various observations into a minimal stochastic model of navigation, we show that this thermal modulation of locomotor kinematics results in a thermophobic behavior, complementing direct gradient-sensing mechanisms. CONCLUSIONS This study establishes the existence of a well-defined locomotor space accessible to zebrafish larvae during spontaneous exploration, and quantifies self-generated modulation of locomotor patterns. Intra-individual variability reflects a slow diffusive-like probing of this space by the animal. The bath temperature in turn restricts the sampling statistics to sub-regions, endowing the animal with basic thermophobicity. This study suggests that in zebrafish, as well as in other ectothermic animals, ambient temperature could be used to efficiently manipulate internal states in a simple and ethological way.
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Affiliation(s)
- Guillaume Le Goc
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP), Paris, France
| | - Julie Lafaye
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP), Paris, France
| | - Sophia Karpenko
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP), Paris, France.,Université Paris Sciences et Lettres, Paris, France.,Present address : Department of Collective Behavior, Max Planck Institute of Animal Behavior, Konstanz, Germany
| | - Volker Bormuth
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP), Paris, France
| | - Raphaël Candelier
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP), Paris, France
| | - Georges Debrégeas
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP), Paris, France.
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21
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Choe CP, Choi SY, Kee Y, Kim MJ, Kim SH, Lee Y, Park HC, Ro H. Transgenic fluorescent zebrafish lines that have revolutionized biomedical research. Lab Anim Res 2021; 37:26. [PMID: 34496973 PMCID: PMC8424172 DOI: 10.1186/s42826-021-00103-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 08/26/2021] [Indexed: 12/22/2022] Open
Abstract
Since its debut in the biomedical research fields in 1981, zebrafish have been used as a vertebrate model organism in more than 40,000 biomedical research studies. Especially useful are zebrafish lines expressing fluorescent proteins in a molecule, intracellular organelle, cell or tissue specific manner because they allow the visualization and tracking of molecules, intracellular organelles, cells or tissues of interest in real time and in vivo. In this review, we summarize representative transgenic fluorescent zebrafish lines that have revolutionized biomedical research on signal transduction, the craniofacial skeletal system, the hematopoietic system, the nervous system, the urogenital system, the digestive system and intracellular organelles.
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Affiliation(s)
- Chong Pyo Choe
- Division of Life Science, Gyeongsang National University, Jinju, 52828, Republic of Korea.,Division of Applied Life Science, Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Seok-Yong Choi
- Department of Biomedical Sciences, Chonnam National University Medical School, Hwasun, 58128, Republic of Korea
| | - Yun Kee
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon, 24341, Republic of Korea.
| | - Min Jung Kim
- Department of Biological Sciences, Sookmyung Women's University, Seoul, 04310, Republic of Korea
| | - Seok-Hyung Kim
- Department of Marine Life Sciences and Fish Vaccine Research Center, Jeju National University, Jeju, 63243, Republic of Korea
| | - Yoonsung Lee
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan, 44919, Republic of Korea
| | - Hae-Chul Park
- Department of Biomedical Sciences, College of Medicine, Korea University, Ansan, 15355, Republic of Korea
| | - Hyunju Ro
- Department of Biological Sciences, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, 34134, Republic of Korea
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22
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Redolfi N, García-Casas P, Fornetto C, Sonda S, Pizzo P, Pendin D. Lighting Up Ca 2+ Dynamics in Animal Models. Cells 2021; 10:2133. [PMID: 34440902 PMCID: PMC8392631 DOI: 10.3390/cells10082133] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/08/2021] [Accepted: 08/16/2021] [Indexed: 12/11/2022] Open
Abstract
Calcium (Ca2+) signaling coordinates are crucial processes in brain physiology. Particularly, fundamental aspects of neuronal function such as synaptic transmission and neuronal plasticity are regulated by Ca2+, and neuronal survival itself relies on Ca2+-dependent cascades. Indeed, impaired Ca2+ homeostasis has been reported in aging as well as in the onset and progression of neurodegeneration. Understanding the physiology of brain function and the key processes leading to its derangement is a core challenge for neuroscience. In this context, Ca2+ imaging represents a powerful tool, effectively fostered by the continuous amelioration of Ca2+ sensors in parallel with the improvement of imaging instrumentation. In this review, we explore the potentiality of the most used animal models employed for Ca2+ imaging, highlighting their application in brain research to explore the pathogenesis of neurodegenerative diseases.
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Affiliation(s)
- Nelly Redolfi
- Department of Biomedical Sciences, University of Padua, 35131 Padua, Italy; (N.R.); (P.G.-C.); (C.F.); (S.S.); (P.P.)
| | - Paloma García-Casas
- Department of Biomedical Sciences, University of Padua, 35131 Padua, Italy; (N.R.); (P.G.-C.); (C.F.); (S.S.); (P.P.)
| | - Chiara Fornetto
- Department of Biomedical Sciences, University of Padua, 35131 Padua, Italy; (N.R.); (P.G.-C.); (C.F.); (S.S.); (P.P.)
| | - Sonia Sonda
- Department of Biomedical Sciences, University of Padua, 35131 Padua, Italy; (N.R.); (P.G.-C.); (C.F.); (S.S.); (P.P.)
| | - Paola Pizzo
- Department of Biomedical Sciences, University of Padua, 35131 Padua, Italy; (N.R.); (P.G.-C.); (C.F.); (S.S.); (P.P.)
- Neuroscience Institute, National Research Council (CNR), 35131 Padua, Italy
| | - Diana Pendin
- Department of Biomedical Sciences, University of Padua, 35131 Padua, Italy; (N.R.); (P.G.-C.); (C.F.); (S.S.); (P.P.)
- Neuroscience Institute, National Research Council (CNR), 35131 Padua, Italy
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23
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Poulsen RE, Scholz LA, Constantin L, Favre-Bulle I, Vanwalleghem GC, Scott EK. Broad frequency sensitivity and complex neural coding in the larval zebrafish auditory system. Curr Biol 2021; 31:1977-1987.e4. [PMID: 33657408 PMCID: PMC8443405 DOI: 10.1016/j.cub.2021.01.103] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 12/16/2020] [Accepted: 01/28/2021] [Indexed: 02/02/2023]
Abstract
Most animals have complex auditory systems that identify salient features of the acoustic landscape to direct appropriate responses. In fish, these features include the volume, frequency, complexity, and temporal structure of acoustic stimuli transmitted through water. Larval fish have simple brains compared to adults but swim freely and depend on sophisticated sensory processing for survival.1-5 Zebrafish larvae, an important model for studying brain-wide neural networks, have thus far been found to possess a rudimentary auditory system, sensitive to a narrow range of frequencies and without evident sensitivity to acoustic features that are salient and ethologically important to adult fish.6,7 Here, we have combined a novel method for delivering water-borne sounds, a diverse assembly of acoustic stimuli, and whole-brain calcium imaging to describe the responses of individual auditory-responsive neurons across the brains of zebrafish larvae. Our results reveal responses to frequencies ranging from 100 Hz to 4 kHz, with evidence of frequency discrimination from 100 Hz to 2.5 kHz. Frequency-selective neurons are located in numerous regions of the brain, and neurons responsive to the same frequency are spatially grouped in some regions. Using functional clustering, we identified categories of neurons that are selective for a single pure-tone frequency, white noise, the sharp onset of acoustic stimuli, and stimuli involving a gradual crescendo. These results suggest a more nuanced auditory system than has previously been described in larval fish and provide insights into how a young animal's auditory system can both function acutely and serve as the scaffold for a more complex adult system.
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Affiliation(s)
- Rebecca E Poulsen
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Leandro A Scholz
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Lena Constantin
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Itia Favre-Bulle
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia; School of Mathematics and Physics, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Gilles C Vanwalleghem
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia.
| | - Ethan K Scott
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia.
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24
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Daria VR, Castañares ML, Bachor HA. Spatio-temporal parameters for optical probing of neuronal activity. Biophys Rev 2021; 13:13-33. [PMID: 33747244 PMCID: PMC7930150 DOI: 10.1007/s12551-021-00780-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 01/01/2021] [Indexed: 12/28/2022] Open
Abstract
The challenge to understand the complex neuronal circuit functions in the mammalian brain has brought about a revolution in light-based neurotechnologies and optogenetic tools. However, while recent seminal works have shown excellent insights on the processing of basic functions such as sensory perception, memory, and navigation, understanding more complex brain functions is still unattainable with current technologies. We are just scratching the surface, both literally and figuratively. Yet, the path towards fully understanding the brain is not totally uncertain. Recent rapid technological advancements have allowed us to analyze the processing of signals within dendritic arborizations of single neurons and within neuronal circuits. Understanding the circuit dynamics in the brain requires a good appreciation of the spatial and temporal properties of neuronal activity. Here, we assess the spatio-temporal parameters of neuronal responses and match them with suitable light-based neurotechnologies as well as photochemical and optogenetic tools. We focus on the spatial range that includes dendrites and certain brain regions (e.g., cortex and hippocampus) that constitute neuronal circuits. We also review some temporal characteristics of some proteins and ion channels responsible for certain neuronal functions. With the aid of the photochemical and optogenetic markers, we can use light to visualize the circuit dynamics of a functioning brain. The challenge to understand how the brain works continue to excite scientists as research questions begin to link macroscopic and microscopic units of brain circuits.
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Affiliation(s)
- Vincent R. Daria
- Research School of Physics, The Australian National University, Canberra, Australia
- John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | | | - Hans-A. Bachor
- Research School of Physics, The Australian National University, Canberra, Australia
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25
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Larval Zebrafish Use Olfactory Detection of Sodium and Chloride to Avoid Salt Water. Curr Biol 2020; 31:782-793.e3. [PMID: 33338431 DOI: 10.1016/j.cub.2020.11.051] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 11/17/2020] [Accepted: 11/18/2020] [Indexed: 12/19/2022]
Abstract
Salinity levels constrain the habitable environment of all aquatic organisms. Zebrafish are freshwater fish that cannot tolerate high-salt environments and would therefore benefit from neural mechanisms that enable the navigation of salt gradients to avoid high salinity. Yet zebrafish lack epithelial sodium channels, the primary conduit land animals use to taste sodium. This suggests fish may possess novel, undescribed mechanisms for salt detection. In the present study, we show that zebrafish indeed respond to small temporal increases in salt by reorienting more frequently. Further, we use calcium imaging techniques to identify the olfactory system as the primary sense used for salt detection, and we find that a specific subset of olfactory receptor neurons encodes absolute salinity concentrations by detecting monovalent anions and cations. In summary, our study establishes that zebrafish larvae have the ability to navigate and thus detect salinity gradients and that this is achieved through previously undescribed sensory mechanisms for salt detection.
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26
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Kang B, Druckmann S. Approaches to inferring multi-regional interactions from simultaneous population recordings: Inferring multi-regional interactions from simultaneous population recordings. Curr Opin Neurobiol 2020; 65:108-119. [PMID: 33227602 PMCID: PMC7853322 DOI: 10.1016/j.conb.2020.10.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 09/28/2020] [Accepted: 10/03/2020] [Indexed: 12/20/2022]
Abstract
Most past studies of neural representations and dynamics have focused on recordings from single brain areas. However, growing evidence of brain-wide, parallel representations of cognitive variables suggests that analyzing neural representations and dynamics in individual brain areas can benefit from understanding the context of multi-regional interactions that support them. Moreover, perturbation experiments revealed that the manner in which these parallel representations interact with each other can differ dramatically across different pairs of brain areas. Recent advances in recording technology offer a potentially powerful substrate to study how multi-regional interactions coordinate neural representations in individual brain areas and dictate behavior on a single-trial basis through simultaneous recordings of multiple brain areas. We review pragmatic approaches to studying multi-regional interactions and illustrate them in the concrete context of a rodent delayed response task paradigm.
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Affiliation(s)
- Byungwoo Kang
- Dept. of Neurobiology, Stanford University, Stanford, CA, United States; Physics Department, Stanford University, Stanford, CA, United States
| | - Shaul Druckmann
- Dept. of Neurobiology, Stanford University, Stanford, CA, United States.
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27
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Mu Y, Narayan S, Mensh BD, Ahrens MB. Brain-wide, scale-wide physiology underlying behavioral flexibility in zebrafish. Curr Opin Neurobiol 2020; 64:151-160. [PMID: 33091825 DOI: 10.1016/j.conb.2020.08.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 08/25/2020] [Accepted: 08/31/2020] [Indexed: 01/04/2023]
Abstract
The brain is tasked with choosing actions that maximize an animal's chances of survival and reproduction. These choices must be flexible and informed by the current state of the environment, the needs of the body, and the outcomes of past actions. This information is physiologically encoded and processed across different brain regions on a wide range of spatial scales, from molecules in single synapses to networks of brain areas. Uncovering these spatially distributed neural interactions underlying behavior requires investigations that span a similar range of spatial scales. Larval zebrafish, given their small size, transparency, and ease of genetic access, are a good model organism for such investigations, allowing the use of modern microscopy, molecular biology, and computational techniques. These approaches are yielding new insights into the mechanistic basis of behavioral states, which we review here and compare to related studies in mammalian species.
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Affiliation(s)
- Yu Mu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA; Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, and Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, China.
| | - Sujatha Narayan
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Brett D Mensh
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Misha B Ahrens
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.
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28
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Knockout of stim2a Increases Calcium Oscillations in Neurons and Induces Hyperactive-Like Phenotype in Zebrafish Larvae. Int J Mol Sci 2020; 21:ijms21176198. [PMID: 32867296 PMCID: PMC7503814 DOI: 10.3390/ijms21176198] [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: 06/03/2020] [Revised: 08/20/2020] [Accepted: 08/24/2020] [Indexed: 11/17/2022] Open
Abstract
Stromal interaction molecule (STIM) proteins play a crucial role in store-operated calcium entry (SOCE) as endoplasmic reticulum Ca2+ sensors. In neurons, STIM2 was shown to have distinct functions from STIM1. However, its role in brain activity and behavior was not fully elucidated. The present study analyzed behavior in zebrafish (Danio rerio) that lacked stim2a. The mutant animals had no morphological abnormalities and were fertile. RNA-sequencing revealed alterations of the expression of transcription factor genes and several members of the calcium toolkit. Neuronal Ca2+ activity was measured in vivo in neurons that expressed the GCaMP5G sensor. Optic tectum neurons in stim2a-/- fish had more frequent Ca2+ signal oscillations compared with neurons in wildtype (WT) fish. We detected an increase in activity during the visual-motor response test, an increase in thigmotaxis in the open field test, and the disruption of phototaxis in the dark/light preference test in stim2a-/- mutants compared with WT. Both groups of animals reacted to glutamate and pentylenetetrazol with an increase in activity during the visual-motor response test, with no major differences between groups. Altogether, our results suggest that the hyperactive-like phenotype of stim2a-/- mutant zebrafish is caused by the dysregulation of Ca2+ homeostasis and signaling.
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29
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Gatto E, Lucon-Xiccato T, Bisazza A, Manabe K, Dadda M. The devil is in the detail: Zebrafish learn to discriminate visual stimuli only if salient. Behav Processes 2020; 179:104215. [PMID: 32763462 DOI: 10.1016/j.beproc.2020.104215] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 07/30/2020] [Accepted: 07/31/2020] [Indexed: 10/23/2022]
Abstract
Due to their unique characteristics, the zebrafish plays a key role in the comprehension of neurobiology of cognition and its pathologies, such as neurodegenerative diseases. More and more molecular tools for this aim are being developed, but our knowledge about the cognitive abilities of zebrafish remains extremely scarce compared to other teleost fish. We aimed to investigate the complex cognitive abilities of zebrafish using a tracking-based automated conditioning chamber that allowed precise experimental control, avoided potential cueing provided by the observer (Clever Hans phenomenon), and was shown to considerably improve learning in other teleosts. A computer presented two visual stimuli in two sectors of the chamber, and zebrafish had to enter the correct sector to obtain a food reward. Zebrafish quickly learned to use the conditioning device and easily performed up to 80 trials per day. In Experiment 1, zebrafish efficiently discriminated between two differently coloured sides, reaching a 75 % accuracy in only 10 training sessions. Surprisingly, zebrafish failed to choose the correct chamber when the stimuli were two shapes, a small circle and a small triangle, even when, in Experiment 2, training on shape discrimination was prolonged for up to 30 sessions. In Experiment 3, we tested the hypothesis that simultaneously learning to use the conditioning chamber and learning discrimination imposes a too-high cognitive load. However, zebrafish that first successfully learned how the conditioning chamber functioned (in the colour discrimination) subsequently failed in the shape discrimination. Conversely, zebrafish that firstly failed the shape discrimination subsequently learned colour discrimination. In Experiment 4, zebrafish showed some evidence of learning when the stimuli were two large shapes, suggesting that zebrafish did not discriminate between the shapes of the previous experiments because they were not salient enough. Altogether, results suggest constraints in the discrimination learning abilities of zebrafish, which should be taken into account when developing cognitive tasks for this species.
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Affiliation(s)
- Elia Gatto
- Department of General Psychology, University of Padova, Padova, Italy.
| | - Tyrone Lucon-Xiccato
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Angelo Bisazza
- Department of General Psychology, University of Padova, Padova, Italy; Padova Neuroscience Center, University of Padova, Padova, Italy
| | - Kazuchika Manabe
- Graduate School of Social and Cultural Studies, Nihon University, Saitama, Japan; College of Bioresource Sciences, Nihon University, Fujisawa, Japan
| | - Marco Dadda
- Department of General Psychology, University of Padova, Padova, Italy
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30
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Tubiana J, Wolf S, Panier T, Debregeas G. Blind deconvolution for spike inference from fluorescence recordings. J Neurosci Methods 2020; 342:108763. [PMID: 32479972 DOI: 10.1016/j.jneumeth.2020.108763] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 05/05/2020] [Accepted: 05/06/2020] [Indexed: 10/24/2022]
Abstract
The parallel developments of genetically-encoded calcium indicators and fast fluorescence imaging techniques allows one to simultaneously record neural activity of extended neuronal populations in vivo. To fully harness the potential of functional imaging, one needs to infer the sequence of action potentials from fluorescence traces. Here we build on recently proposed computational approaches to develop a blind sparse deconvolution (BSD) algorithm based on a generative model for inferring spike trains from fluorescence traces. BSD features, (1) automatic (fully unsupervised) estimation of the hyperparameters, such as spike amplitude, noise level and rise and decay time constants, (2) a novel analytical estimate of the sparsity prior, which yields enhanced robustness and computational speed with respect to existing methods, (3) automatic thresholding for binarizing spikes that maximizes the precision-recall performance, (4) super-resolution capabilities increasing the temporal resolution beyond the fluorescence signal acquisition rate. BSD also uniquely provides theoretically-grounded estimates of the expected performance of the spike reconstruction in terms of precision-recall and temporal accuracy for each recording. The performance of the algorithm is established using synthetic data and through the SpikeFinder challenge, a community-based initiative for spike-rate inference benchmarking based on a collection of joint electrophysiological and fluorescence recordings. Our method outperforms classical sparse deconvolution algorithms in terms of robustness, speed and/or accuracy and performs competitively in the SpikeFinder challenge. This algorithm is modular, easy-to-use and made freely available. Its novel features can thus be incorporated in a straightforward way into existing calcium imaging packages.
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Affiliation(s)
- Jérôme Tubiana
- Blavatnik School of Computer Science, Tel Aviv University, Israel
| | - Sébastien Wolf
- Laboratoire de Physique de l'Ecole Normale Supérieure, CNRS UMR 8023 & PSL Research, France; Institut de Biologie de l'Ecole Normale Supérieure, CNRS, INSERM, UMR 8197 & PSL Research, France
| | - Thomas Panier
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP), France
| | - Georges Debregeas
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP), France.
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31
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Ricci P, Sancataldo G, Gavryusev V, Franceschini A, Müllenbroich MC, Silvestri L, Pavone FS. Fast multi-directional DSLM for confocal detection without striping artifacts. BIOMEDICAL OPTICS EXPRESS 2020; 11:3111-3124. [PMID: 32637245 PMCID: PMC7316030 DOI: 10.1364/boe.390916] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 04/19/2020] [Accepted: 04/28/2020] [Indexed: 05/02/2023]
Abstract
In recent years light-sheet fluorescence microscopy (LSFM) has become a cornerstone technology for neuroscience, improving the quality and capabilities of 3D imaging. By selectively illuminating a single plane, it provides intrinsic optical sectioning and fast image recording, while minimizing out of focus fluorescence background, sample photo-damage and photo-bleaching. However, images acquired with LSFM are often affected by light absorption or scattering effects, leading to un-even illumination and striping artifacts. In this work we present an optical solution to this problem, via fast multi-directional illumination of the sample, based on an acousto-optical deflector (AOD). We demonstrate that this pivoting system is compatible with confocal detection in digital scanned laser light-sheet fluorescence microscopy (DSLM) by using a pivoted elliptical-Gaussian beam. We tested its performance by acquiring signals emitted by specific fluorophores in several mouse brain areas, comparing the pivoting beam illumination and a traditional static one, measuring the point spread function response and quantifying the striping reduction. We observed real-time shadow suppression, while preserving the advantages of confocal detection for image contrast.
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Affiliation(s)
- Pietro Ricci
- European Laboratory for Non-Linear Spectroscopy, Sesto Fiorentino, 50019, Italy
- University of Florence, Department of Physics and Astronomy, Sesto Fiorentino, 50019, Italy
| | - Giuseppe Sancataldo
- European Laboratory for Non-Linear Spectroscopy, Sesto Fiorentino, 50019, Italy
- University of Palermo, Department of Physics and Chemistry, Palermo, 90128, Italy
| | - Vladislav Gavryusev
- European Laboratory for Non-Linear Spectroscopy, Sesto Fiorentino, 50019, Italy
- University of Florence, Department of Physics and Astronomy, Sesto Fiorentino, 50019, Italy
| | - Alessandra Franceschini
- European Laboratory for Non-Linear Spectroscopy, Sesto Fiorentino, 50019, Italy
- National Institute of Optics, Sesto Fiorentino, 50019, Italy
| | | | - Ludovico Silvestri
- European Laboratory for Non-Linear Spectroscopy, Sesto Fiorentino, 50019, Italy
- University of Florence, Department of Physics and Astronomy, Sesto Fiorentino, 50019, Italy
- National Institute of Optics, Sesto Fiorentino, 50019, Italy
| | - Francesco Saverio Pavone
- European Laboratory for Non-Linear Spectroscopy, Sesto Fiorentino, 50019, Italy
- University of Florence, Department of Physics and Astronomy, Sesto Fiorentino, 50019, Italy
- National Institute of Optics, Sesto Fiorentino, 50019, Italy
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Wasilewska I, Gupta RK, Wojtaś B, Palchevska O, Kuźnicki J. stim2b Knockout Induces Hyperactivity and Susceptibility to Seizures in Zebrafish Larvae. Cells 2020; 9:cells9051285. [PMID: 32455839 PMCID: PMC7291033 DOI: 10.3390/cells9051285] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 05/19/2020] [Accepted: 05/20/2020] [Indexed: 12/13/2022] Open
Abstract
In neurons, stromal interaction molecule (STIM) proteins regulate store-operated Ca2+ entry (SOCE) and are involved in calcium signaling pathways. However, STIM activity in neurological diseases is unclear and should be clarified by studies that are performed in vivo rather than in cultured cells in vitro. The present study investigated the role of neuronal Stim2b protein in zebrafish. We generated stim2b knockout zebrafish, which were fertile and had a regular lifespan. Using various behavioral tests, we found that stim2b−/− zebrafish larvae were hyperactive compared with wild-type fish. The mutants exhibited increases in mobility and thigmotaxis and disruptions of phototaxis. They were also more sensitive to pentylenetetrazol and glutamate treatments. Using lightsheet microscopy, a higher average oscillation frequency and higher average amplitude of neuronal Ca2+ oscillations were observed in stim2b−/− larvae. RNA sequencing detected upregulation of the annexin 3a and gpr39 genes and downregulation of the rrm2, neuroguidin, and homer2 genes. The latter gene encodes a protein that is involved in several processes that are involved in Ca2+ homeostasis in neurons, including metabotropic glutamate receptors. We propose that Stim2b deficiency in neurons dysregulates SOCE and triggers changes in gene expression, thereby causing abnormal behavior, such as hyperactivity and susceptibility to seizures.
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Affiliation(s)
- Iga Wasilewska
- International Institute of Molecular and Cell Biology, 4 Ks. Trojdena Street, 02-109 Warsaw, Poland; (I.W.); (R.K.G.); (O.P.)
| | - Rishikesh Kumar Gupta
- International Institute of Molecular and Cell Biology, 4 Ks. Trojdena Street, 02-109 Warsaw, Poland; (I.W.); (R.K.G.); (O.P.)
| | - Bartosz Wojtaś
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur Street, 02-093 Warsaw, Poland;
| | - Oksana Palchevska
- International Institute of Molecular and Cell Biology, 4 Ks. Trojdena Street, 02-109 Warsaw, Poland; (I.W.); (R.K.G.); (O.P.)
| | - Jacek Kuźnicki
- International Institute of Molecular and Cell Biology, 4 Ks. Trojdena Street, 02-109 Warsaw, Poland; (I.W.); (R.K.G.); (O.P.)
- Correspondence:
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Ueda HR, Dodt HU, Osten P, Economo MN, Chandrashekar J, Keller PJ. Whole-Brain Profiling of Cells and Circuits in Mammals by Tissue Clearing and Light-Sheet Microscopy. Neuron 2020; 106:369-387. [PMID: 32380050 PMCID: PMC7213014 DOI: 10.1016/j.neuron.2020.03.004] [Citation(s) in RCA: 124] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 01/11/2020] [Accepted: 03/04/2020] [Indexed: 01/12/2023]
Abstract
Tissue clearing and light-sheet microscopy have a 100-year-plus history, yet these fields have been combined only recently to facilitate novel experiments and measurements in neuroscience. Since tissue-clearing methods were first combined with modernized light-sheet microscopy a decade ago, the performance of both technologies has rapidly improved, broadening their applications. Here, we review the state of the art of tissue-clearing methods and light-sheet microscopy and discuss applications of these techniques in profiling cells and circuits in mice. We examine outstanding challenges and future opportunities for expanding these techniques to achieve brain-wide profiling of cells and circuits in primates and humans. Such integration will help provide a systems-level understanding of the physiology and pathology of our central nervous system.
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Affiliation(s)
- Hiroki R Ueda
- Department of Systems Pharmacology, The University of Tokyo, Tokyo 113-0033, Japan; Laboratory for Synthetic Biology, RIKEN BDR, Suita, Osaka 565-0871, Japan.
| | - Hans-Ulrich Dodt
- Department of Bioelectronics, FKE, Vienna University of Technology-TU Wien, Vienna, Austria; Section of Bioelectronics, Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Pavel Osten
- Cold Spring Harbor Laboratories, Cold Spring Harbor, NY 11724, USA
| | - Michael N Economo
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | | | - Philipp J Keller
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
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Kaplan HS, Zimmer M. Brain-wide representations of ongoing behavior: a universal principle? Curr Opin Neurobiol 2020; 64:60-69. [PMID: 32203874 DOI: 10.1016/j.conb.2020.02.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 02/16/2020] [Accepted: 02/17/2020] [Indexed: 12/13/2022]
Abstract
Recent neuronal activity recordings of unprecedented breadth and depth in worms, flies, and mice have uncovered a surprising common feature: brain-wide behavior-related signals. These signals pervade, and even dominate, neuronal populations thought to function primarily in sensory processing. Such convergent findings across organisms suggest that brain-wide representations of behavior might be a universal neuroscientific principle. What purpose(s) do these representations serve? Here we review these findings along with suggested functions, including sensory prediction, context-dependent sensory processing, and, perhaps most speculatively, distributed motor command generation. It appears that a large proportion of the brain's energy and coding capacity is used to represent ongoing behavior; understanding the function of these representations should therefore be a major goal in neuroscience research.
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Affiliation(s)
- Harris S Kaplan
- Department of Neuroscience and Developmental Biology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria; Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria.
| | - Manuel Zimmer
- Department of Neuroscience and Developmental Biology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria; Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
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A virtual reality system to analyze neural activity and behavior in adult zebrafish. Nat Methods 2020; 17:343-351. [PMID: 32123394 PMCID: PMC7100911 DOI: 10.1038/s41592-020-0759-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 01/22/2020] [Indexed: 11/09/2022]
Abstract
Virtual realities are powerful tools to analyze and manipulate interactions between animals and their environment and to enable measurements of neuronal activity during behavior. In many species, however, optical access to the brain and/or the behavioral repertoire are limited. We developed a high-resolution virtual reality for head-restrained adult zebrafish, which exhibit cognitive behaviors not shown by larvae. We noninvasively measured activity throughout the dorsal telencephalon by multiphoton calcium imaging. Fish in the virtual reality showed regular swimming patterns and were attracted to animations of conspecifics. Manipulations of visuo-motor feedback revealed neurons that responded selectively to the mismatch between the expected and the actual visual consequences of motor output. Such error signals were prominent in multiple telencephalic areas, consistent with models of predictive processing. A virtual reality system for adult zebrafish therefore provides opportunities to analyze neuronal processing mechanisms underlying higher brain functions including decision making, associative learning, and social interactions.
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Betzel RF. Organizing principles of whole-brain functional connectivity in zebrafish larvae. Netw Neurosci 2020; 4:234-256. [PMID: 32166210 PMCID: PMC7055648 DOI: 10.1162/netn_a_00121] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Accepted: 12/04/2019] [Indexed: 12/13/2022] Open
Abstract
Network science has begun to reveal the fundamental principles by which large-scale brain networks are organized, including geometric constraints, a balance between segregative and integrative features, and functionally flexible brain areas. However, it remains unknown whether whole-brain networks imaged at the cellular level are organized according to similar principles. Here, we analyze whole-brain functional networks reconstructed from calcium imaging data recorded in larval zebrafish. Our analyses reveal that functional connections are distance-dependent and that networks exhibit hierarchical modular structure and hubs that span module boundaries. We go on to show that spontaneous network structure places constraints on stimulus-evoked reconfigurations of connections and that networks are highly consistent across individuals. Our analyses reveal basic organizing principles of whole-brain functional brain networks at the mesoscale. Our overarching methodological framework provides a blueprint for studying correlated activity at the cellular level using a low-dimensional network representation. Our work forms a conceptual bridge between macro- and mesoscale network neuroscience and opens myriad paths for future studies to investigate network structure of nervous systems at the cellular level.
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Affiliation(s)
- Richard F. Betzel
- Department of Psychological and Brain Sciences, Indiana University, Bloomington, IN, USA
- Cognitive Science Program, Indiana University, Bloomington, IN, USA
- Program in Neuroscience, Indiana University, Bloomington, IN, USA
- IU Network Science Institute, Indiana University, Bloomington, IN, USA
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37
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Karpenko S, Wolf S, Lafaye J, Le Goc G, Panier T, Bormuth V, Candelier R, Debrégeas G. From behavior to circuit modeling of light-seeking navigation in zebrafish larvae. eLife 2020; 9:52882. [PMID: 31895038 PMCID: PMC6989119 DOI: 10.7554/elife.52882] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Accepted: 01/02/2020] [Indexed: 01/18/2023] Open
Abstract
Bridging brain-scale circuit dynamics and organism-scale behavior is a central challenge in neuroscience. It requires the concurrent development of minimal behavioral and neural circuit models that can quantitatively capture basic sensorimotor operations. Here, we focus on light-seeking navigation in zebrafish larvae. Using a virtual reality assay, we first characterize how motor and visual stimulation sequences govern the selection of discrete swim-bout events that subserve the fish navigation in the presence of a distant light source. These mechanisms are combined into a comprehensive Markov-chain model of navigation that quantitatively predicts the stationary distribution of the fish’s body orientation under any given illumination profile. We then map this behavioral description onto a neuronal model of the ARTR, a small neural circuit involved in the orientation-selection of swim bouts. We demonstrate that this visually-biased decision-making circuit can capture the statistics of both spontaneous and contrast-driven navigation. All animals with the ability to move use sensory signals to help them navigate towards areas that seem better than their current location. Such areas might contain desirable things like food and mates, or they might allow an animal to escape from threats such as predators. But how the brain gives rise to this navigation behavior is unclear. Karpenko et al. have now obtained insights into the underlying mechanism by studying a behavior in zebrafish larvae called phototaxis. Phototaxis is the tendency to move in response to light. The advantage of using zebrafish larvae to study this behavior is that their brains are small and semi-transparent. This makes it possible to record the activity of almost every neuron. As a result, an individual’s brain activity can be mapped on to their behavior more precisely than in most other species. To probe how visual cues influence fish behavior, Karpenko et al. exposed individual fish to a carefully controlled virtual light source and then tracked their movements with a camera. The fish used two strategies to move towards the light. They selected their next movement based partly on the difference in the amount of light reaching each of their eyes, and partly on the change in overall brightness with each swim movement. Karpenko et al. used this information to build a numerical model of fish phototaxis, and to show how a simple brain circuit could generate this behavior. Species whose brains differ in size and structure may nevertheless develop similar strategies to perform similar tasks. By quantifying a generic behavior in a simple animal model, this study could provide insights into comparable behaviors in other species. In addition, the study suggests a simple mechanism for how animals select actions on the basis of sensory signals, which may also be relevant to other species and other tasks.
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Affiliation(s)
- Sophia Karpenko
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP), Paris, France.,Université Paris Sciences et Lettres, Paris, France
| | - Sebastien Wolf
- Laboratoire de Physique de l'Ecole Normale Supérieure, CNRS UMR 8023 & PSL Research, Paris, France.,Institut de Biologie de l'Ecole Normale Supérieure, CNRS, INSERM, UMR 8197 & PSL Research, Paris, France
| | - Julie Lafaye
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP), Paris, France
| | - Guillaume Le Goc
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP), Paris, France
| | - Thomas Panier
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP), Paris, France
| | - Volker Bormuth
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP), Paris, France
| | - Raphaël Candelier
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP), Paris, France
| | - Georges Debrégeas
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP), Paris, France
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Soman SK, Bazała M, Keatinge M, Bandmann O, Kuznicki J. Restriction of mitochondrial calcium overload by mcu inactivation renders a neuroprotective effect in zebrafish models of Parkinson's disease. Biol Open 2019; 8:bio044347. [PMID: 31548178 PMCID: PMC6826286 DOI: 10.1242/bio.044347] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 09/13/2019] [Indexed: 12/21/2022] Open
Abstract
The loss of dopaminergic neurons (DA) is a pathological hallmark of sporadic and familial forms of Parkinson's disease (PD). We have previously shown that inhibiting mitochondrial calcium uniporter (mcu) using morpholinos can rescue DA neurons in the PTEN-induced putative kinase 1 (pink1)-/- zebrafish model of PD. In this article, we show results from our studies in mcu knockout zebrafish, which was generated using the CRISPR/Cas9 system. Functional assays confirmed impaired mitochondrial calcium influx in mcu -/- zebrafish. We also used in vivo calcium imaging and fluorescent assays in purified mitochondria to investigate mitochondrial calcium dynamics in a pink1 -/- zebrafish model of PD. Mitochondrial morphology was evaluated in DA neurons and muscle fibers using immunolabeling and transgenic lines, respectively. We observed diminished mitochondrial area in DA neurons of pink1 -/- zebrafish, while deletion of mcu restored mitochondrial area. In contrast, the mitochondrial volume in muscle fibers was not restored after inactivation of mcu in pink1 -/- zebrafish. Mitochondrial calcium overload coupled with depolarization of mitochondrial membrane potential leads to mitochondrial dysfunction in the pink1 -/- zebrafish model of PD. We used in situ hybridization and immunohistochemical labeling of DA neurons to evaluate the effect of mcu deletion on DA neuronal clusters in the ventral telencephalon of zebrafish brain. We show that DA neurons are rescued after deletion of mcu in pink1 -/- and the 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) zebrafish model of PD. Thus, inactivation of mcu is protective in both genetic and chemical models of PD. Our data reveal that regulating mcu function could be an effective therapeutic target in PD pathology.
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Affiliation(s)
- Smijin K Soman
- Laboratory of Neurodegeneration, International Institute of Molecular and Cell Biology, Księcia Trojdena 4, 02-109, Warsaw, Poland
| | - Michal Bazała
- Laboratory of Neurodegeneration, International Institute of Molecular and Cell Biology, Księcia Trojdena 4, 02-109, Warsaw, Poland
| | - Marcus Keatinge
- Medical Research Council Centre for Developmental and Biomedical Genetics, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, 385a Glossop Road, Sheffield, S10 2HQ, UK
| | - Oliver Bandmann
- Medical Research Council Centre for Developmental and Biomedical Genetics, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, 385a Glossop Road, Sheffield, S10 2HQ, UK
| | - Jacek Kuznicki
- Laboratory of Neurodegeneration, International Institute of Molecular and Cell Biology, Księcia Trojdena 4, 02-109, Warsaw, Poland
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Mu Y, Bennett DV, Rubinov M, Narayan S, Yang CT, Tanimoto M, Mensh BD, Looger LL, Ahrens MB. Glia Accumulate Evidence that Actions Are Futile and Suppress Unsuccessful Behavior. Cell 2019; 178:27-43.e19. [PMID: 31230713 DOI: 10.1016/j.cell.2019.05.050] [Citation(s) in RCA: 152] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 01/31/2019] [Accepted: 05/23/2019] [Indexed: 11/29/2022]
Abstract
When a behavior repeatedly fails to achieve its goal, animals often give up and become passive, which can be strategic for preserving energy or regrouping between attempts. It is unknown how the brain identifies behavioral failures and mediates this behavioral-state switch. In larval zebrafish swimming in virtual reality, visual feedback can be withheld so that swim attempts fail to trigger expected visual flow. After tens of seconds of such motor futility, animals became passive for similar durations. Whole-brain calcium imaging revealed noradrenergic neurons that responded specifically to failed swim attempts and radial astrocytes whose calcium levels accumulated with increasing numbers of failed attempts. Using cell ablation and optogenetic or chemogenetic activation, we found that noradrenergic neurons progressively activated brainstem radial astrocytes, which then suppressed swimming. Thus, radial astrocytes perform a computation critical for behavior: they accumulate evidence that current actions are ineffective and consequently drive changes in behavioral states. VIDEO ABSTRACT.
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Affiliation(s)
- Yu Mu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.
| | - Davis V Bennett
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA; Department of Organismal Biology and Anatomy, University of Chicago, Chicago, IL, USA
| | - Mikail Rubinov
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA; Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Sujatha Narayan
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Chao-Tsung Yang
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Masashi Tanimoto
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Brett D Mensh
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Loren L Looger
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Misha B Ahrens
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.
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Engineering brain activity patterns by neuromodulator polytherapy for treatment of disorders. Nat Commun 2019; 10:2620. [PMID: 31197165 PMCID: PMC6565674 DOI: 10.1038/s41467-019-10541-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 05/15/2019] [Indexed: 11/08/2022] Open
Abstract
Conventional drug screens and treatments often ignore the underlying complexity of brain network dysfunctions, resulting in suboptimal outcomes. Here we ask whether we can correct abnormal functional connectivity of the entire brain by identifying and combining multiple neuromodulators that perturb connectivity in complementary ways. Our approach avoids the combinatorial complexity of screening all drug combinations. We develop a high-speed platform capable of imaging more than 15000 neurons in 50ms to map the entire brain functional connectivity in large numbers of vertebrates under many conditions. Screening a panel of drugs in a zebrafish model of human Dravet syndrome, we show that even drugs with related mechanisms of action can modulate functional connectivity in significantly different ways. By clustering connectivity fingerprints, we algorithmically select small subsets of complementary drugs and rapidly identify combinations that are significantly more effective at correcting abnormal networks and reducing spontaneous seizures than monotherapies, while minimizing behavioral side effects. Even at low concentrations, our polytherapy performs superior to individual drugs even at highest tolerated concentrations. Brain disorders are associated with network dysfunctions that are not addressed by conventional drug screens. Here, the authors use high-throughput functional imaging of brain activity in zebrafish larvae to study the effects of individual drugs on network connectivity and demonstrate an algorithm that predicts the most effective drug combinations to normalize both the activity patterns and the animal behavior.
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41
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Corsetti S, Gunn-Moore F, Dholakia K. Light sheet fluorescence microscopy for neuroscience. J Neurosci Methods 2019; 319:16-27. [DOI: 10.1016/j.jneumeth.2018.07.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 06/03/2018] [Accepted: 07/16/2018] [Indexed: 12/29/2022]
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42
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DiLoreto EM, Chute CD, Bryce S, Srinivasan J. Novel Technological Advances in Functional Connectomics in C. elegans. J Dev Biol 2019; 7:E8. [PMID: 31018525 PMCID: PMC6630759 DOI: 10.3390/jdb7020008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 02/08/2019] [Accepted: 02/13/2019] [Indexed: 12/11/2022] Open
Abstract
The complete structure and connectivity of the Caenorhabditis elegans nervous system ("mind of a worm") was first published in 1986, representing a critical milestone in the field of connectomics. The reconstruction of the nervous system (connectome) at the level of synapses provided a unique perspective of understanding how behavior can be coded within the nervous system. The following decades have seen the development of technologies that help understand how neural activity patterns are connected to behavior and modulated by sensory input. Investigations on the developmental origins of the connectome highlight the importance of role of neuronal cell lineages in the final connectivity matrix of the nervous system. Computational modeling of neuronal dynamics not only helps reconstruct the biophysical properties of individual neurons but also allows for subsequent reconstruction of whole-organism neuronal network models. Hence, combining experimental datasets with theoretical modeling of neurons generates a better understanding of organismal behavior. This review discusses some recent technological advances used to analyze and perturb whole-organism neuronal function along with developments in computational modeling, which allows for interrogation of both local and global neural circuits, leading to different behaviors. Combining these approaches will shed light into how neural networks process sensory information to generate the appropriate behavioral output, providing a complete understanding of the worm nervous system.
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Affiliation(s)
- Elizabeth M DiLoreto
- Biology and Biotechnology Department, Worcester Polytechnic Institute, Worcester, MA 01605, USA.
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Abstract
We describe the implementation and use of an adaptive imaging framework for optimizing spatial resolution and signal strength in a light-sheet microscope. The framework, termed AutoPilot, comprises hardware and software modules for automatically measuring and compensating for mismatches between light-sheet and detection focal planes in living specimens. Our protocol enables researchers to introduce adaptive imaging capabilities in an existing light-sheet microscope or use our SiMView microscope blueprint to set up a new adaptive multiview light-sheet microscope. The protocol describes (i) the mechano-optical implementation of the adaptive imaging hardware, including technical drawings for all custom microscope components; (ii) the algorithms and software library for automated adaptive imaging, including the pseudocode and annotated source code for all software modules; and (iii) the execution of adaptive imaging experiments, as well as the configuration and practical use of the AutoPilot framework. Setup of the adaptive imaging hardware and software takes 1-2 weeks each. Previous experience with light-sheet microscopy and some familiarity with software engineering and building of optical instruments are recommended. Successful implementation of the protocol recovers near diffraction-limited performance in many parts of typical multicellular organisms studied with light-sheet microscopy, such as fruit fly and zebrafish embryos, for which resolution and signal strength are improved two- to fivefold.
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44
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Basnet RM, Zizioli D, Taweedet S, Finazzi D, Memo M. Zebrafish Larvae as a Behavioral Model in Neuropharmacology. Biomedicines 2019; 7:biomedicines7010023. [PMID: 30917585 PMCID: PMC6465999 DOI: 10.3390/biomedicines7010023] [Citation(s) in RCA: 189] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 03/22/2019] [Accepted: 03/22/2019] [Indexed: 12/21/2022] Open
Abstract
Zebrafish larvae show a clear and distinct pattern of swimming in response to light and dark conditions, following the development of a swim bladder at 4 days post fertilization. This swimming behavior is increasingly employed in the screening of neuroactive drugs. The recent emergence of high-throughput techniques for the automatic tracking of zebrafish larvae has further allowed an objective and efficient way of finding subtle behavioral changes that could go unnoticed during manual observations. This review highlights the use of zebrafish larvae as a high-throughput behavioral model for the screening of neuroactive compounds. We describe, in brief, the behavior repertoire of zebrafish larvae. Then, we focus on the utilization of light-dark locomotion test in identifying and screening of neuroactive compounds.
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Affiliation(s)
- Ram Manohar Basnet
- Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy.
| | - Daniela Zizioli
- Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy.
| | - Somrat Taweedet
- Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy.
| | - Dario Finazzi
- Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy.
- Clinical Chemistry Laboratory, ASST-Spedali Civili di Brescia, 25123 Brescia, Italy.
| | - Maurizio Memo
- Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy.
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Bercier V, Rosello M, Del Bene F, Revenu C. Zebrafish as a Model for the Study of Live in vivo Processive Transport in Neurons. Front Cell Dev Biol 2019; 7:17. [PMID: 30838208 PMCID: PMC6389722 DOI: 10.3389/fcell.2019.00017] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 02/01/2019] [Indexed: 12/13/2022] Open
Abstract
Motor proteins are responsible for transport of vesicles and organelles within the cell cytoplasm. They interact with the actin cytoskeleton and with microtubules to ensure communication and supply throughout the cell. Much work has been done in vitro and in silico to unravel the key players, including the dynein motor complex, the kinesin and myosin superfamilies, and their interacting regulatory complexes, but there is a clear need for in vivo data as recent evidence suggests previous models might not recapitulate physiological conditions. The zebrafish embryo provides an excellent system to study these processes in intact animals due to the ease of genetic manipulation and the optical transparency allowing live imaging. We present here the advantages of the zebrafish embryo as a system to study live in vivo processive transport in neurons and provide technical recommendations for successful analysis.
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Affiliation(s)
- Valérie Bercier
- Institut Curie, PSL Research University, Inserm U934, CNRS UMR3215, Paris, France.,Laboratory of Neurobiology, Center for Brain and Disease Research, Research Group Experimental Neurology, Department of Neurosciences, VIB-KU Leuven, Leuven, Belgium
| | - Marion Rosello
- Institut Curie, PSL Research University, Inserm U934, CNRS UMR3215, Paris, France
| | - Filippo Del Bene
- Institut Curie, PSL Research University, Inserm U934, CNRS UMR3215, Paris, France
| | - Céline Revenu
- Institut Curie, PSL Research University, Inserm U934, CNRS UMR3215, Paris, France
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46
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Sancataldo G, Gavryusev V, de Vito G, Turrini L, Locatelli M, Fornetto C, Tiso N, Vanzi F, Silvestri L, Pavone FS. Flexible Multi-Beam Light-Sheet Fluorescence Microscope for Live Imaging Without Striping Artifacts. Front Neuroanat 2019; 13:7. [PMID: 30800060 PMCID: PMC6376877 DOI: 10.3389/fnana.2019.00007] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 01/21/2019] [Indexed: 11/24/2022] Open
Abstract
The development of light-sheet fluorescence microscopy (LSFM) has greatly expanded the experimental capabilities in many biological and biomedical research fields, enabling for example live studies of murine and zebrafish neural activity or of cell growth and division. The key feature of the method is the selective illumination of a sample single plane, providing an intrinsic optical sectioning and allowing direct 2D image recording. On the other hand, this excitation scheme is more affected by absorption or scattering artifacts in comparison to point scanning methods, leading to un-even illumination. We present here an easily implementable method, based on acousto-optical deflectors (AOD), to overcome this obstacle. We report the advantages provided by flexible and fast AODs in generating simultaneous angled multiple beams from a single laser beam and in fast light sheet pivoting and we demonstrate the suppression of illumination artifacts.
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Affiliation(s)
- Giuseppe Sancataldo
- Department of Physics and Astronomy, University of Florence, Sesto Fiorentino, Italy.,European Laboratory for Non-Linear Spectroscopy, University of Florence, Sesto Fiorentino, Italy
| | - Vladislav Gavryusev
- Department of Physics and Astronomy, University of Florence, Sesto Fiorentino, Italy.,European Laboratory for Non-Linear Spectroscopy, University of Florence, Sesto Fiorentino, Italy
| | - Giuseppe de Vito
- European Laboratory for Non-Linear Spectroscopy, University of Florence, Sesto Fiorentino, Italy.,National Institute of Optics, National Research Council, Sesto Fiorentino, Italy
| | - Lapo Turrini
- Department of Physics and Astronomy, University of Florence, Sesto Fiorentino, Italy.,European Laboratory for Non-Linear Spectroscopy, University of Florence, Sesto Fiorentino, Italy
| | - Massimiliano Locatelli
- Department of Physics and Astronomy, University of Florence, Sesto Fiorentino, Italy.,European Laboratory for Non-Linear Spectroscopy, University of Florence, Sesto Fiorentino, Italy
| | - Chiara Fornetto
- Department of Physics and Astronomy, University of Florence, Sesto Fiorentino, Italy.,European Laboratory for Non-Linear Spectroscopy, University of Florence, Sesto Fiorentino, Italy
| | - Natascia Tiso
- Department of Biology, University of Padova, Padua, Italy
| | - Francesco Vanzi
- European Laboratory for Non-Linear Spectroscopy, University of Florence, Sesto Fiorentino, Italy.,Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | - Ludovico Silvestri
- European Laboratory for Non-Linear Spectroscopy, University of Florence, Sesto Fiorentino, Italy.,National Institute of Optics, National Research Council, Sesto Fiorentino, Italy
| | - Francesco Saverio Pavone
- Department of Physics and Astronomy, University of Florence, Sesto Fiorentino, Italy.,European Laboratory for Non-Linear Spectroscopy, University of Florence, Sesto Fiorentino, Italy
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47
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Liu Y, Dale S, Ball R, VanLeuven AJ, Sornborger A, Lauderdale JD, Kner P. Imaging neural events in zebrafish larvae with linear structured illumination light sheet fluorescence microscopy. NEUROPHOTONICS 2019; 6:015009. [PMID: 30854407 PMCID: PMC6400141 DOI: 10.1117/1.nph.6.1.015009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 02/13/2019] [Indexed: 05/02/2023]
Abstract
Light sheet fluorescence microscopy (LSFM) is a powerful tool for investigating model organisms including zebrafish. However, due to scattering and refractive index variations within the sample, the resulting image often suffers from low contrast. Structured illumination (SI) has been combined with scanned LSFM to remove out-of-focus and scattered light using square-law detection. Here, we demonstrate that the combination of LSFM with linear reconstruction SI can further increase resolution and contrast in the vertical and axial directions compared to the widely adopted root-mean square reconstruction method while using the same input images. We apply this approach to imaging neural activity in 7-day postfertilization zebrafish larvae. We imaged two-dimensional sections of the zebrafish central nervous system in two colors at an effective frame rate of 7 frames per second.
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Affiliation(s)
- Yang Liu
- University of Georgia, College of Engineering, Athens, Georgia, United States
| | - Savannah Dale
- Clemson University, Department of Bioengineering, Clemson, South Carolina, United States
| | - Rebecca Ball
- University of Georgia, Department of Cellular Biology, Athens, Georgia, United States
| | - Ariel J. VanLeuven
- University of Georgia, Department of Cellular Biology, Athens, Georgia, United States
| | - Andrew Sornborger
- Los Alamos National Laboratory, Information Sciences, CCS-3, Los Alamos, New Mexico, United States
| | - James D. Lauderdale
- University of Georgia, Department of Cellular Biology, Athens, Georgia, United States
- University of Georgia, Neuroscience Division of the Biomedical Health Sciences Institute, Athens, Georgia, United States
| | - Peter Kner
- University of Georgia, College of Engineering, Athens, Georgia, United States
- Address all correspondence to Peter Kner, E-mail:
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48
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Licea-Rodriguez J, Figueroa-Melendez A, Falaggis K, Plata-Sanchez M, Riquelme M, Rocha-Mendoza I. Multicolor fluorescence microscopy using static light sheets and a single-channel detection. JOURNAL OF BIOMEDICAL OPTICS 2019; 24:1-8. [PMID: 30612379 PMCID: PMC6985699 DOI: 10.1117/1.jbo.24.1.016501] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 12/06/2018] [Indexed: 05/25/2023]
Abstract
We present a multicolor fluorescence microscope system, under a selective plane illumination microscopy (SPIM) configuration, using three continuous wave-lasers and a single-channel-detection camera. The laser intensities are modulated with three time-delayed pulse trains that operate synchronously at one third of the camera frame rate, allowing a sequential excitation and an image acquisition of up to three different biomarkers. The feasibility of this imaging acquisition mode is demonstrated by acquiring single-plane multicolor images of living hyphae of Neurospora crassa. This allows visualizing simultaneously the localization and dynamics of different cellular components involved in apical growth in living hyphae. The configuration presented represents a noncommercial, cost-effective alternative microscopy system for the rapid and simultaneous acquisition of multifluorescent images and can be potentially useful for three-dimensional imaging of large biological samples.
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Affiliation(s)
- Jacob Licea-Rodriguez
- Centro de Investigación Científica y de Educación Superior de Ensenada, Department of Optics, Ensenada, Baja California, Mexico
- Cátedras Conacyt, Centro de Investigación Científica y de Educación Superior de Ensenada, Ensenada, Baja California, Mexico
| | - Alfredo Figueroa-Melendez
- Centro de Investigación Científica y de Educación Superior de Ensenada, Department of Microbiology, Ensenada, Baja California, Mexico
| | - Konstantinos Falaggis
- Cátedras Conacyt, Centro de Investigación Científica y de Educación Superior de Ensenada, Ensenada, Baja California, Mexico
- University of North Carolina, Department of Mechanical Engineering and Engineering Science, Charlotte, North Carolina, United States
| | - Marcos Plata-Sanchez
- Centro de Investigación Científica y de Educación Superior de Ensenada, Department of Optics, Ensenada, Baja California, Mexico
| | - Meritxell Riquelme
- Centro de Investigación Científica y de Educación Superior de Ensenada, Department of Microbiology, Ensenada, Baja California, Mexico
| | - Israel Rocha-Mendoza
- Centro de Investigación Científica y de Educación Superior de Ensenada, Department of Optics, Ensenada, Baja California, Mexico
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49
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Ponce-Alvarez A, Jouary A, Privat M, Deco G, Sumbre G. Whole-Brain Neuronal Activity Displays Crackling Noise Dynamics. Neuron 2018; 100:1446-1459.e6. [PMID: 30449656 PMCID: PMC6307982 DOI: 10.1016/j.neuron.2018.10.045] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 07/05/2018] [Accepted: 10/24/2018] [Indexed: 12/24/2022]
Abstract
Previous studies suggest that the brain operates at a critical point in which phases of order and disorder coexist, producing emergent patterned dynamics at all scales and optimizing several brain functions. Here, we combined light-sheet microscopy with GCaMP zebrafish larvae to study whole-brain dynamics in vivo at near single-cell resolution. We show that spontaneous activity propagates in the brain's three-dimensional space, generating scale-invariant neuronal avalanches with time courses and recurrence times that exhibit statistical self-similarity at different magnitude, temporal, and frequency scales. This suggests that the nervous system operates close to a non-equilibrium phase transition, where a large repertoire of spatial, temporal, and interactive modes can be supported. Finally, we show that gap junctions contribute to the maintenance of criticality and that, during interactions with the environment (sensory inputs and self-generated behaviors), the system is transiently displaced to a more ordered regime, conceivably to limit the potential sensory representations and motor outcomes.
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Affiliation(s)
- Adrián Ponce-Alvarez
- Center for Brain and Cognition, Computational Neuroscience Group, Department of Information and Communication Technologies, Universitat Pompeu Fabra, Barcelona 08005, Spain.
| | - Adrien Jouary
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Université Paris, Paris 75005, France; Champalimaud Research, Champalimaud Centre for the Unknown, Lisbon 1400-038, Portugal
| | - Martin Privat
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Université Paris, Paris 75005, France
| | - Gustavo Deco
- Center for Brain and Cognition, Computational Neuroscience Group, Department of Information and Communication Technologies, Universitat Pompeu Fabra, Barcelona 08005, Spain; Institució Catalana de la Recerca i Estudis Avançats (ICREA), Barcelona 08010, Spain; Department of Neuropsychology, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig 04103, Germany; School of Psychological Sciences, Monash University, Melbourne, Clayton VIC 3800, Australia
| | - Germán Sumbre
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Université Paris, Paris 75005, France.
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50
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Taylor MA, Vanwalleghem GC, Favre-Bulle IA, Scott EK. Diffuse light-sheet microscopy for stripe-free calcium imaging of neural populations. JOURNAL OF BIOPHOTONICS 2018; 11:e201800088. [PMID: 29920963 DOI: 10.1002/jbio.201800088] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 06/14/2018] [Indexed: 05/06/2023]
Abstract
Light-sheet microscopy is used extensively in developmental biology and neuroscience. One limitation of this approach is that absorption and scattering produces shadows in the illuminating light sheet, resulting in stripe artifacts. Here, we introduce diffuse light-sheet microscopes that use a line diffuser to randomize the light propagation within the image plane, allowing the light sheets to reform after obstacles. We incorporate diffuse light sheets in two existing configurations: selective plane illumination microscopy in which the sample is illuminated with a static sheet of light, and digitally scanned light sheet (DSLS) in which a thin Gaussian beam is scanned across the image plane during each acquisition. We compare diffuse light-sheet microscopes to their conventional counterparts for calcium imaging of neural activity in larval zebrafish. We show that stripe artifacts can cast deep shadows that conceal some neurons, and that the stripes can flicker, producing spurious signals that could be interpreted as biological activity. Diffuse light-sheets mitigate these problems, illuminating the blind spots produced by stripes and removing artifacts produced by the stripes' movements. The upgrade to diffuse light sheets is simple and inexpensive, especially in the case of DSLS, where it requires the addition of one optical element.
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Affiliation(s)
- Michael A Taylor
- School of Biomedical Sciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Gilles C Vanwalleghem
- School of Biomedical Sciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Itia A Favre-Bulle
- School of Biomedical Sciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Ethan K Scott
- School of Biomedical Sciences, The University of Queensland, St. Lucia, QLD, Australia
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