1
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Baier H, Scott EK. The Visual Systems of Zebrafish. Annu Rev Neurosci 2024; 47:255-276. [PMID: 38663429 DOI: 10.1146/annurev-neuro-111020-104854] [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] [Indexed: 08/09/2024]
Abstract
The zebrafish visual system has become a paradigmatic preparation for behavioral and systems neuroscience. Around 40 types of retinal ganglion cells (RGCs) serve as matched filters for stimulus features, including light, optic flow, prey, and objects on a collision course. RGCs distribute their signals via axon collaterals to 12 retinorecipient areas in forebrain and midbrain. The major visuomotor hub, the optic tectum, harbors nine RGC input layers that combine information on multiple features. The retinotopic map in the tectum is locally adapted to visual scene statistics and visual subfield-specific behavioral demands. Tectal projections to premotor centers are topographically organized according to behavioral commands. The known connectivity in more than 20 processing streams allows us to dissect the cellular basis of elementary perceptual and cognitive functions. Visually evoked responses, such as prey capture or loom avoidance, are controlled by dedicated multistation pathways that-at least in the larva-resemble labeled lines. This architecture serves the neuronal code's purpose of driving adaptive behavior.
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Affiliation(s)
- Herwig Baier
- Department of Genes-Circuits-Behavior, Max Planck Institute for Biological Intelligence, Martinsried, Germany;
| | - Ethan K Scott
- Department of Anatomy and Physiology, School of Biomedical Sciences, The University of Melbourne, Parkville, Victoria, Australia
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2
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Weinreb C, Pearl JE, Lin S, Osman MAM, Zhang L, Annapragada S, Conlin E, Hoffmann R, Makowska S, Gillis WF, Jay M, Ye S, Mathis A, Mathis MW, Pereira T, Linderman SW, Datta SR. Keypoint-MoSeq: parsing behavior by linking point tracking to pose dynamics. Nat Methods 2024; 21:1329-1339. [PMID: 38997595 PMCID: PMC11245396 DOI: 10.1038/s41592-024-02318-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 05/22/2024] [Indexed: 07/14/2024]
Abstract
Keypoint tracking algorithms can flexibly quantify animal movement from videos obtained in a wide variety of settings. However, it remains unclear how to parse continuous keypoint data into discrete actions. This challenge is particularly acute because keypoint data are susceptible to high-frequency jitter that clustering algorithms can mistake for transitions between actions. Here we present keypoint-MoSeq, a machine learning-based platform for identifying behavioral modules ('syllables') from keypoint data without human supervision. Keypoint-MoSeq uses a generative model to distinguish keypoint noise from behavior, enabling it to identify syllables whose boundaries correspond to natural sub-second discontinuities in pose dynamics. Keypoint-MoSeq outperforms commonly used alternative clustering methods at identifying these transitions, at capturing correlations between neural activity and behavior and at classifying either solitary or social behaviors in accordance with human annotations. Keypoint-MoSeq also works in multiple species and generalizes beyond the syllable timescale, identifying fast sniff-aligned movements in mice and a spectrum of oscillatory behaviors in fruit flies. Keypoint-MoSeq, therefore, renders accessible the modular structure of behavior through standard video recordings.
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Affiliation(s)
- Caleb Weinreb
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Jonah E Pearl
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Sherry Lin
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | | | - Libby Zhang
- Department of Electrical Engineering, Stanford University, Stanford, CA, USA
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
| | | | - Eli Conlin
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Red Hoffmann
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Sofia Makowska
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | | | - Maya Jay
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Shaokai Ye
- Brain Mind and Neuro-X Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Alexander Mathis
- Brain Mind and Neuro-X Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Mackenzie W Mathis
- Brain Mind and Neuro-X Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Talmo Pereira
- Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Scott W Linderman
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA.
- Department of Statistics, Stanford University, Stanford, CA, USA.
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3
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Wang R, Wang B, Chen A. Application of machine learning in the study of development, behavior, nerve, and genotoxicity of zebrafish. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 358:124473. [PMID: 38945191 DOI: 10.1016/j.envpol.2024.124473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 05/26/2024] [Accepted: 06/28/2024] [Indexed: 07/02/2024]
Abstract
Machine learning (ML) as a novel model-based approach has been used in studying aquatic toxicology in the environmental field. Zebrafish, as an ideal model organism in aquatic toxicology research, has been widely used to study the toxic effects of various pollutants. However, toxicity testing on organisms may cause significant harm, consume considerable time and resources, and raise ethical concerns. Therefore, ML is used in related research to reduce animal experiments and assist researchers in conducting toxicological research. Although ML techniques have matured in various fields, research on ML-based aquatic toxicology is still in its infancy due to the lack of comprehensive large-scale toxicity databases for environmental pollutants and model organisms. Therefore, to better understand the recent research progress of ML in studying the development, behavior, nerve, and genotoxicity of zebrafish, this review mainly focuses on using ML modeling to assess and predict the toxic effects of zebrafish exposure to different toxic chemicals. Meanwhile, the opportunities and challenges faced by ML in the field of toxicology were analyzed. Finally, suggestions and perspectives were proposed for the toxicity studies of ML on zebrafish in future applications.
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Affiliation(s)
- Rui Wang
- Key Laboratory of Karst Georesources and Environment, Ministry of Education, (Guizhou University), Guiyang, Guizhou, 550025, China
| | - Bing Wang
- Key Laboratory of Karst Georesources and Environment, Ministry of Education, (Guizhou University), Guiyang, Guizhou, 550025, China; College of Resources and Environmental Engineering, Guizhou University, Guiyang, Guizhou, 550025, China.
| | - Anying Chen
- College of Resources and Environmental Engineering, Guizhou University, Guiyang, Guizhou, 550025, China
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4
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Lin S, Gillis WF, Weinreb C, Zeine A, Jones SC, Robinson EM, Markowitz J, Datta SR. Characterizing the structure of mouse behavior using Motion Sequencing. Nat Protoc 2024:10.1038/s41596-024-01015-w. [PMID: 38926589 DOI: 10.1038/s41596-024-01015-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 04/12/2024] [Indexed: 06/28/2024]
Abstract
Spontaneous mouse behavior is composed from repeatedly used modules of movement (e.g., rearing, running or grooming) that are flexibly placed into sequences whose content evolves over time. By identifying behavioral modules and the order in which they are expressed, researchers can gain insight into the effect of drugs, genes, context, sensory stimuli and neural activity on natural behavior. Here we present a protocol for performing Motion Sequencing (MoSeq), an ethologically inspired method that uses three-dimensional machine vision and unsupervised machine learning to decompose spontaneous mouse behavior into a series of elemental modules called 'syllables'. This protocol is based upon a MoSeq pipeline that includes modules for depth video acquisition, data preprocessing and modeling, as well as a standardized set of visualization tools. Users are provided with instructions and code for building a MoSeq imaging rig and acquiring three-dimensional video of spontaneous mouse behavior for submission to the modeling framework; the outputs of this protocol include syllable labels for each frame of the video data as well as summary plots describing how often each syllable was used and how syllables transitioned from one to the other. In addition, we provide instructions for analyzing and visualizing the outputs of keypoint-MoSeq, a recently developed variant of MoSeq that can identify behavioral motifs from keypoints identified from standard (rather than depth) video. This protocol and the accompanying pipeline significantly lower the bar for users without extensive computational ethology experience to adopt this unsupervised, data-driven approach to characterize mouse behavior.
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Affiliation(s)
- Sherry Lin
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | | | - Caleb Weinreb
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Ayman Zeine
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Samuel C Jones
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Emma M Robinson
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Jeffrey Markowitz
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
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5
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Sridhar G, Vergassola M, Marques JC, Orger MB, Costa AC, Wyart C. Uncovering multiscale structure in the variability of larval zebrafish navigation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.16.594521. [PMID: 38798455 PMCID: PMC11118365 DOI: 10.1101/2024.05.16.594521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Animals chain movements into long-lived motor strategies, resulting in variability that ultimately reflects the interplay between internal states and environmental cues. To reveal structure in such variability, we build models that bridges across time scales that enable a quantitative comparison of behavioral phenotypes among individuals. Applied to larval zebrafish exposed to diverse sensory cues, we uncover a hierarchy of long-lived motor strategies, dominated by changes in orientation distinguishing cruising and wandering strategies. Environmental cues induce preferences along these modes at the population level: while fish cruise in the light, they wander in response to aversive (dark) stimuli or in search for prey. Our method enables us to encode the behavioral dynamics of each individual fish in the transitions among coarse-grained motor strategies. By doing so, we uncover a hierarchical structure to the phenotypic variability that corresponds to exploration-exploitation trade-offs. Within a wide range of sensory cues, a major source of variation among fish is driven by prior and immediate exposure to prey that induces exploitation phenotypes. However, a large degree of variability is unexplained by environmental cues, pointing to hidden states that override the sensory context to induce contrasting exploration-exploitation phenotypes. Altogether, our approach extracts the timescales of motor strategies deployed during navigation, exposing undiscovered structure among individuals and pointing to internal states tuned by prior experience.
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6
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Lee HB, Shams S, Dang Thi VH, Boyum GE, Modhurima R, Hall EM, Green IK, Cervantes EM, Miguez FE, Clark KJ. Key HPI axis receptors facilitate light adaptive behavior in larval zebrafish. Sci Rep 2024; 14:7759. [PMID: 38565594 PMCID: PMC10987622 DOI: 10.1038/s41598-024-57707-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 03/21/2024] [Indexed: 04/04/2024] Open
Abstract
The vertebrate stress response (SR) is mediated by the hypothalamic-pituitary-adrenal (HPA) axis and contributes to generating context appropriate physiological and behavioral changes. Although the HPA axis plays vital roles both in stressful and basal conditions, research has focused on the response under stress. To understand broader roles of the HPA axis in a changing environment, we characterized an adaptive behavior of larval zebrafish during ambient illumination changes. Genetic abrogation of glucocorticoid receptor (nr3c1) decreased basal locomotor activity in light and darkness. Some key HPI axis receptors (mc2r [ACTH receptor], nr3c1), but not nr3c2 (mineralocorticoid receptor), were required to adapt to light more efficiently but became dispensable when longer illumination was provided. Such light adaptation was more efficient in dimmer light. Our findings show that the HPI axis contributes to the SR, facilitating the phasic response and maintaining an adapted basal state, and that certain adaptations occur without HPI axis activity.
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Affiliation(s)
- Han B Lee
- Department of Neurology, Mayo Clinic, Rochester, MN, USA
| | - Soaleha Shams
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Viet Ha Dang Thi
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Grace E Boyum
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Rodsy Modhurima
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Emma M Hall
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Izzabella K Green
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | | | | | - Karl J Clark
- Department of Neurology, Mayo Clinic, Rochester, MN, USA.
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA.
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA.
- Neuroscience, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, MN, USA.
- Department of Animal Science, Texas A&M University, College Station, TX, USA.
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7
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Braun D, Rosenberg AM, Rabaniam E, Haruvi R, Malamud D, Barbara R, Aiznkot T, Levavi-Sivan B, Kawashima T. High-resolution tracking of unconfined zebrafish behavior reveals stimulatory and anxiolytic effects of psilocybin. Mol Psychiatry 2024; 29:1046-1062. [PMID: 38233467 PMCID: PMC11176078 DOI: 10.1038/s41380-023-02391-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 12/12/2023] [Accepted: 12/19/2023] [Indexed: 01/19/2024]
Abstract
Serotonergic psychedelics are emerging therapeutics for psychiatric disorders, yet their underlying mechanisms of action in the brain remain largely elusive. Here, we developed a wide-field behavioral tracking system for larval zebrafish and investigated the effects of psilocybin, a psychedelic serotonin receptor agonist. Machine learning analyses of precise body kinematics identified latent behavioral states reflecting spontaneous exploration, visually-driven rapid swimming, and irregular swim patterns following stress exposure. Using this method, we found that acute psilocybin treatment has two behavioral effects: [i] facilitation of spontaneous exploration ("stimulatory") and [ii] prevention of irregular swim patterns following stress exposure ("anxiolytic"). These effects differed from the effect of acute SSRI treatment and were rather similar to the effect of ketamine treatment. Neural activity imaging in the dorsal raphe nucleus suggested that psilocybin inhibits serotonergic neurons by activating local GABAergic neurons, consistent with psychedelic-induced suppression of serotonergic neurons in mammals. These findings pave the way for using larval zebrafish to elucidate neural mechanisms underlying the behavioral effects of serotonergic psychedelics.
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Affiliation(s)
- Dotan Braun
- Department of Brain Sciences, Weizmann Institute of Science, 234 Herzl Street, Rehovot, Israel
- The Jerusalem Mental Health Center, Jerusalem, Israel
| | - Ayelet M Rosenberg
- Department of Brain Sciences, Weizmann Institute of Science, 234 Herzl Street, Rehovot, Israel
| | - Elad Rabaniam
- Department of Brain Sciences, Weizmann Institute of Science, 234 Herzl Street, Rehovot, Israel
| | - Ravid Haruvi
- Department of Brain Sciences, Weizmann Institute of Science, 234 Herzl Street, Rehovot, Israel
| | - Dorel Malamud
- Department of Brain Sciences, Weizmann Institute of Science, 234 Herzl Street, Rehovot, Israel
| | - Rani Barbara
- Department of Brain Sciences, Weizmann Institute of Science, 234 Herzl Street, Rehovot, Israel
| | - Tomer Aiznkot
- Department of Animal Sciences, The Robert H. Smith Faculty of Agriculture, Food, and Environment, Hebrew University of Jerusalem, 229 Herzl Street, Rehovot, Israel
| | - Berta Levavi-Sivan
- Department of Animal Sciences, The Robert H. Smith Faculty of Agriculture, Food, and Environment, Hebrew University of Jerusalem, 229 Herzl Street, Rehovot, Israel
| | - Takashi Kawashima
- Department of Brain Sciences, Weizmann Institute of Science, 234 Herzl Street, Rehovot, Israel.
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8
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Laeverenz-Schlogelhofer H, Wan KY. Bioelectric control of locomotor gaits in the walking ciliate Euplotes. Curr Biol 2024; 34:697-709.e6. [PMID: 38237598 DOI: 10.1016/j.cub.2023.12.051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 11/20/2023] [Accepted: 12/18/2023] [Indexed: 02/29/2024]
Abstract
Diverse animal species exhibit highly stereotyped behavioral actions and locomotor sequences as they explore their natural environments. In many such cases, the neural basis of behavior is well established, where dedicated neural circuitry contributes to the initiation and regulation of certain response sequences. At the microscopic scale, single-celled eukaryotes (protists) also exhibit remarkably complex behaviors and yet are completely devoid of nervous systems. Here, to address the question of how single cells control behavior, we study locomotor patterning in the exemplary hypotrich ciliate Euplotes, a highly polarized cell, which actuates a large number of leg-like appendages called cirri (each a bundle of ∼25-50 cilia) to swim in fluids or walk on surfaces. As it navigates its surroundings, a walking Euplotes cell is routinely observed to perform side-stepping reactions, one of the most sophisticated maneuvers ever observed in a single-celled organism. These are spontaneous and stereotyped reorientation events involving a transient and fast backward motion followed by a turn. Combining high-speed imaging with simultaneous time-resolved electrophysiological recordings, we show that this complex coordinated motion sequence is tightly regulated by rapid membrane depolarization events, which orchestrate the activity of different cirri on the cell. Using machine learning and computer vision methods, we map detailed measurements of cirri dynamics to the cell's membrane bioelectrical activity, revealing a differential response in the front and back cirri. We integrate these measurements with a minimal model to understand how Euplotes-a unicellular organism-manipulates its membrane potential to achieve real-time control over its motor apparatus.
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Affiliation(s)
| | - Kirsty Y Wan
- Living Systems Institute, University of Exeter, Stocker Road, Exeter EX4 4QD, UK.
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9
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Palieri V, Paoli E, Wu YK, Haesemeyer M, Grunwald Kadow IC, Portugues R. The preoptic area and dorsal habenula jointly support homeostatic navigation in larval zebrafish. Curr Biol 2024; 34:489-504.e7. [PMID: 38211586 PMCID: PMC10849091 DOI: 10.1016/j.cub.2023.12.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 11/22/2023] [Accepted: 12/11/2023] [Indexed: 01/13/2024]
Abstract
Animals must maintain physiological processes within an optimal temperature range despite changes in their environment. Through behavioral assays, whole-brain functional imaging, and neural ablations, we show that larval zebrafish, an ectothermic vertebrate, achieves thermoregulation through homeostatic navigation-non-directional and directional movements toward the temperature closest to its physiological setpoint. A brain-wide circuit encompassing several brain regions enables this behavior. We identified the preoptic area of the hypothalamus (PoA) as a key brain structure in triggering non-directional reorientation when thermal conditions are worsening. This result shows an evolutionary conserved role of the PoA as principal thermoregulator of the brain also in ectotherms. We further show that the habenula (Hb)-interpeduncular nucleus (IPN) circuit retains a short-term memory of the sensory history to support the generation of coherent directed movements even in the absence of continuous sensory cues. We finally provide evidence that this circuit may not be exclusive for temperature but may convey a more abstract representation of relative valence of physiologically meaningful stimuli regardless of their specific identity to enable homeostatic navigation.
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Affiliation(s)
- Virginia Palieri
- Institute of Neuroscience, Technical University of Munich, Biedersteiner Strasse 29, 80802 Munich, Germany; School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Emanuele Paoli
- Institute of Neuroscience, Technical University of Munich, Biedersteiner Strasse 29, 80802 Munich, Germany
| | - You Kure Wu
- Institute of Neuroscience, Technical University of Munich, Biedersteiner Strasse 29, 80802 Munich, Germany
| | - Martin Haesemeyer
- Department of Neuroscience, The Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Ilona C Grunwald Kadow
- School of Life Sciences, Technical University of Munich, Freising, Germany; Institute of Physiology II, University of Bonn, Medical Faculty (UKB), Nussallee 11, 53115 Bonn, Germany.
| | - Ruben Portugues
- Institute of Neuroscience, Technical University of Munich, Biedersteiner Strasse 29, 80802 Munich, Germany; Munich Cluster of Systems Neurology (SyNergy), Feodor-Lynen-Str. 17, 81377 Munich, Germany.
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10
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Davis SN, Zhu Y, Schoppik D. Multisensory strategies for postural compensation after lateral line loss. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.23.576760. [PMID: 38328242 PMCID: PMC10849565 DOI: 10.1101/2024.01.23.576760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
To control elevation underwater, aquatic vertebrates integrate multisensory information (e.g., vestibular, visual, proprioceptive) to guide posture and swim kinematics. Here we characterized how larval zebrafish changed posture and locomotive strategies after imposed instability (decreased buoyancy) in the presence and absence of visual cues. We discovered that larvae sank more after acute loss of lateral line (flow-sensing) hair cells. In response, larvae engaged different compensatory strategies, depending on whether they were in the light or dark. In the dark, larvae swam more frequently, engaging their trunk to steer their nose up and climb more effectively. However, in the light, larvae climbed more often, engaging both pectoral fins and trunk to elevate. We conclude that larvae sense instability and use vestibular and visual information as available to control posture and trajectory. Our work is a step towards understanding the multisensory neural computations responsible for control strategies that allow orientation and navigation in depth.
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Affiliation(s)
- Samantha N. Davis
- Depts. of Otolaryngology, Neuroscience & Physiology, and the Neuroscience Institute, NYU Grossman School of Medicine
| | - Yunlu Zhu
- Depts. of Otolaryngology, Neuroscience & Physiology, and the Neuroscience Institute, NYU Grossman School of Medicine
| | - David Schoppik
- Depts. of Otolaryngology, Neuroscience & Physiology, and the Neuroscience Institute, NYU Grossman School of Medicine
- Lead Contact
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11
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Chai Y, Qi K, Wu Y, Li D, Tan G, Guo Y, Chu J, Mu Y, Shen C, Wen Q. All-optical interrogation of brain-wide activity in freely swimming larval zebrafish. iScience 2024; 27:108385. [PMID: 38205255 PMCID: PMC10776927 DOI: 10.1016/j.isci.2023.108385] [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: 06/12/2023] [Revised: 09/22/2023] [Accepted: 10/30/2023] [Indexed: 01/12/2024] Open
Abstract
We introduce an all-optical technique that enables volumetric imaging of brain-wide calcium activity and targeted optogenetic stimulation of specific brain regions in unrestrained larval zebrafish. The system consists of three main components: a 3D tracking module, a dual-color fluorescence imaging module, and a real-time activity manipulation module. Our approach uses a sensitive genetically encoded calcium indicator in combination with a long Stokes shift red fluorescence protein as a reference channel, allowing the extraction of Ca2+ activity from signals contaminated by motion artifacts. The method also incorporates rapid 3D image reconstruction and registration, facilitating real-time selective optogenetic stimulation of different regions of the brain. By demonstrating that selective light activation of the midbrain regions in larval zebrafish could reliably trigger biased turning behavior and changes of brain-wide neural activity, we present a valuable tool for investigating the causal relationship between distributed neural circuit dynamics and naturalistic behavior.
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Affiliation(s)
- Yuming Chai
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Hefei National Research Center for Physical Sciences at the Microscale, Center for Integrative Imaging, University of Science and Technology of China, Hefei, China
| | - Kexin Qi
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Hefei National Research Center for Physical Sciences at the Microscale, Center for Integrative Imaging, University of Science and Technology of China, Hefei, China
| | - Yubin Wu
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Hefei National Research Center for Physical Sciences at the Microscale, Center for Integrative Imaging, University of Science and Technology of China, Hefei, China
| | - Daguang Li
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Hefei National Research Center for Physical Sciences at the Microscale, Center for Integrative Imaging, University of Science and Technology of China, Hefei, China
| | - Guodong Tan
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Hefei National Research Center for Physical Sciences at the Microscale, Center for Integrative Imaging, University of Science and Technology of China, Hefei, China
| | - Yuqi Guo
- Guangdong Provincial Key Laboratory of Biomedical Optical Imaging Technology and Center for Biomedical Optics and Molecular Imaging, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Jun Chu
- Guangdong Provincial Key Laboratory of Biomedical Optical Imaging Technology and Center for Biomedical Optics and Molecular Imaging, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 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
| | - Chen Shen
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Hefei National Research Center for Physical Sciences at the Microscale, Center for Integrative Imaging, University of Science and Technology of China, Hefei, China
| | - Quan Wen
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Hefei National Research Center for Physical Sciences at the Microscale, Center for Integrative Imaging, University of Science and Technology of China, Hefei, China
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12
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Kanwal JS, Sanghera B, Dabbi R, Glasgow E. Pose analysis in free-swimming adult zebrafish, Danio rerio : "fishy" origins of movement design. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.31.573780. [PMID: 38260397 PMCID: PMC10802288 DOI: 10.1101/2023.12.31.573780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Movement requires maneuvers that generate thrust to either make turns or move the body forward in physical space. The computational space for perpetually controlling the relative position of every point on the body surface can be vast. We hypothesize the evolution of efficient design for movement that minimizes active (neural) control by leveraging the passive (reactive) forces between the body and the surrounding medium at play. To test our hypothesis, we investigate the presence of stereotypical postures during free-swimming in adult zebrafish, Danio rerio . We perform markerless tracking using DeepLabCut, a deep learning pose estimation toolkit, to track geometric relationships between body parts. To identify putative clusters of postural configurations obtained from twelve freely behaving zebrafish, we use unsupervised multivariate time-series analysis (B-SOiD machine learning software). When applied to single individuals, this method reveals a best-fit for 36 to 50 clusters in contrast 86 clusters for data pooled from all 12 animals. The centroids of each cluster obtained over 14,000 sequential frames recorded for a single fish represent an apriori classification into relatively stable "target body postures" and inter-pose "transitional postures" that lead to and away from a target pose. We use multidimensional scaling of mean parameter values for each cluster to map cluster-centroids within two dimensions of postural space. From a post-priori visual analysis, we condense neighboring postural variants into 15 superclusters or core body configurations. We develop a nomenclature specifying the anteroposterior level/s (upper, mid and lower) and degree of bending. Our results suggest that constraining bends to mainly three levels in adult zebrafish preempts the neck, fore- and hindlimb design for maneuverability in land vertebrates.
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13
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Weinreb C, Pearl J, Lin S, Osman MAM, Zhang L, Annapragada S, Conlin E, Hoffman R, Makowska S, Gillis WF, Jay M, Ye S, Mathis A, Mathis MW, Pereira T, Linderman SW, Datta SR. Keypoint-MoSeq: parsing behavior by linking point tracking to pose dynamics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.16.532307. [PMID: 36993589 PMCID: PMC10055085 DOI: 10.1101/2023.03.16.532307] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Keypoint tracking algorithms have revolutionized the analysis of animal behavior, enabling investigators to flexibly quantify behavioral dynamics from conventional video recordings obtained in a wide variety of settings. However, it remains unclear how to parse continuous keypoint data into the modules out of which behavior is organized. This challenge is particularly acute because keypoint data is susceptible to high frequency jitter that clustering algorithms can mistake for transitions between behavioral modules. Here we present keypoint-MoSeq, a machine learning-based platform for identifying behavioral modules ("syllables") from keypoint data without human supervision. Keypoint-MoSeq uses a generative model to distinguish keypoint noise from behavior, enabling it to effectively identify syllables whose boundaries correspond to natural sub-second discontinuities inherent to mouse behavior. Keypoint-MoSeq outperforms commonly used alternative clustering methods at identifying these transitions, at capturing correlations between neural activity and behavior, and at classifying either solitary or social behaviors in accordance with human annotations. Keypoint-MoSeq therefore renders behavioral syllables and grammar accessible to the many researchers who use standard video to capture animal behavior.
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Affiliation(s)
- Caleb Weinreb
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Jonah Pearl
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Sherry Lin
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | | | - Libby Zhang
- Department of Electrical Engineering, Stanford University, Stanford, CA, USA
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
| | | | - Eli Conlin
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Red Hoffman
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Sofia Makowska
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | | | - Maya Jay
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Shaokai Ye
- Brain Mind and Neuro-X Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Alexander Mathis
- Brain Mind and Neuro-X Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Mackenzie Weygandt Mathis
- Brain Mind and Neuro-X Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Talmo Pereira
- Salk Institute for Biological Studies, La Jolla, USA
| | - Scott W. Linderman
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
- Department of Statistics, Stanford University, Stanford, CA, USA
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14
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Myrov VO, Polovian AI, Kolchanova S, Galumov GK, Schiöth HB, Bozhko DV. Artificial Neural Network (ANN)-Based Pattern Recognition Approach Illustrates a Biphasic Behavioral Effect of Ethanol in Zebrafish: A High-Throughput Method for Animal Locomotor Analysis. Biomedicines 2023; 11:3215. [PMID: 38137436 PMCID: PMC10740670 DOI: 10.3390/biomedicines11123215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 10/28/2023] [Accepted: 10/30/2023] [Indexed: 12/24/2023] Open
Abstract
Variations in stress responses between individuals are linked to factors ranging from stress coping styles to the sensitivity of neurotransmitter systems. Many anxiolytic compounds can increase stressor engagement through the modulation of neurotransmitter systems and are used to investigate stress response mechanisms. The effect of such modulation may vary in time depending on concentration or environment, but those effects are hard to dissect because of the slow transition. We investigated the temporal effect of ethanol and found that ethanol-treated individual zebrafish larvae showed altered behavior that is different between drug concentrations and decreases with time. We used an artificial neural network approach with a time-dependent method for analyzing long (90 min) experiments on zebrafish larvae and found that individuals from the 0.5% group begin to show locomotor activity corresponding to the control group starting from the 60th minute. The locomotor activity of individuals from the 2% group after the 80th minute is classified as the activity of individuals from the 1.5% group. Our method shows three clusters of different concentrations in comparison with two clusters, which were obtained with the usage of a statistical approach for analyzing just the speed of fish movements. In addition, we show that such changes are not explained by basic behavior statistics such as speed and are caused by shifts in locomotion patterns.
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Affiliation(s)
| | - Aleksandr I. Polovian
- ZebraML, Inc., Houston, TX 77043, USA
- Department of Surgical Sciences, Division of Functional Pharmacology and Neuroscience, Uppsala University, 751 24 Uppsala, Sweden;
| | | | | | - Helgi B. Schiöth
- Department of Surgical Sciences, Division of Functional Pharmacology and Neuroscience, Uppsala University, 751 24 Uppsala, Sweden;
| | - Dmitrii V. Bozhko
- ZebraML, Inc., Houston, TX 77043, USA
- Department of Surgical Sciences, Division of Functional Pharmacology and Neuroscience, Uppsala University, 751 24 Uppsala, Sweden;
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15
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Ahn JC, Coyle SM. Comparative profiling of cellular gait on adhesive micropatterns defines statistical patterns of activity that underlie native and cancerous cell dynamics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.27.564389. [PMID: 37961146 PMCID: PMC10634873 DOI: 10.1101/2023.10.27.564389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Cell dynamics are powered by patterns of activity, but it is not straightforward to quantify these patterns or compare them across different environmental conditions or cell-types. Here we digitize the long-term shape fluctuations of metazoan cells grown on micropatterned fibronectin islands to define and extract statistical features of cell dynamics without the need for genetic modification or fluorescence imaging. These shape fluctuations generate single-cell morphological signals that can be decomposed into two major components: a continuous, slow-timescale meandering of morphology about an average steady-state shape; and short-lived "events" of rapid morphology change that sporadically occur throughout the timecourse. By developing statistical metrics for each of these components, we used thousands of hours of single-cell data to quantitatively define how each axis of cell dynamics was impacted by environmental conditions or cell-type. We found the size and spatial complexity of the micropattern island modulated the statistics of morphological events-lifetime, frequency, and orientation-but not its baseline shape fluctuations. Extending this approach to profile a panel of triple negative breast cancer cell-lines, we found that different cell-types could be distinguished from one another along specific and unique statistical axes of their behavior. Our results suggest that micropatterned substrates provide a generalizable method to build statistical profiles of cell dynamics to classify and compare emergent cell behaviors.
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Affiliation(s)
- John C. Ahn
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- Integrated Program in Biochemistry Graduate Program, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Scott M. Coyle
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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16
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Ravan A, Feng R, Gruebele M, Chemla YR. Rapid automated 3-D pose estimation of larval zebrafish using a physical model-trained neural network. PLoS Comput Biol 2023; 19:e1011566. [PMID: 37871114 PMCID: PMC10621986 DOI: 10.1371/journal.pcbi.1011566] [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: 01/09/2023] [Revised: 11/02/2023] [Accepted: 10/02/2023] [Indexed: 10/25/2023] Open
Abstract
Quantitative ethology requires an accurate estimation of an organism's postural dynamics in three dimensions plus time. Technological progress over the last decade has made animal pose estimation in challenging scenarios possible with unprecedented detail. Here, we present (i) a fast automated method to record and track the pose of individual larval zebrafish in a 3-D environment, applicable when accurate human labeling is not possible; (ii) a rich annotated dataset of 3-D larval poses for ethologists and the general zebrafish and machine learning community; and (iii) a technique to generate realistic, annotated larval images in different behavioral contexts. Using a three-camera system calibrated with refraction correction, we record diverse larval swims under free swimming conditions and in response to acoustic and optical stimuli. We then employ a convolutional neural network to estimate 3-D larval poses from video images. The network is trained against a set of synthetic larval images rendered using a 3-D physical model of larvae. This 3-D model samples from a distribution of realistic larval poses that we estimate a priori using a template-based pose estimation of a small number of swim bouts. Our network model, trained without any human annotation, performs larval pose estimation three orders of magnitude faster and with accuracy comparable to the template-based approach, capturing detailed kinematics of 3-D larval swims. It also applies accurately to other datasets collected under different imaging conditions and containing behavioral contexts not included in our training.
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Affiliation(s)
- Aniket Ravan
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Ruopei Feng
- Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Martin Gruebele
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Yann R. Chemla
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
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17
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Kozol RA, Dallman JE. Drugs prescribed for Phelan-McDermid syndrome differentially impact sensory behaviors in shank3 zebrafish models. F1000Res 2023; 12:84. [PMID: 37868296 PMCID: PMC10589628 DOI: 10.12688/f1000research.127830.2] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/07/2023] [Indexed: 10/24/2023] Open
Abstract
Background: Altered sensory processing is a pervasive symptom in individuals with Autism Spectrum Disorders (ASD); people with Phelan McDermid syndrome (PMS), in particular, show reduced responses to sensory stimuli. PMS is caused by deletions of the terminal end of chromosome 22 or point mutations in Shank3. People with PMS can present with an array of symptoms including ASD, epilepsy, gastrointestinal distress, and reduced responses to sensory stimuli. People with PMS are often medicated to manage behaviors like aggression and/or self-harm and/or epilepsy, and it remains unclear how these medications might impact perception/sensory processing. Here we test this using zebrafish mutant shank3ab PMS models that likewise show reduced sensory responses in a visual motor response (VMR) assay, in which increased locomotion is triggered by light to dark transitions. Methods: We screened three medications, risperidone, lithium chloride (LiCl), and carbamazepine (CBZ), prescribed to people with PMS and one drug, 2-methyl-6-(phenylethynyl) pyridine (MPEP) tested in rodent models of PMS, for their effects on a sensory-induced behavior in two zebrafish PMS models with frameshift mutations in either the N- or C- termini. To test how pharmacological treatments affect the VMR, we exposed larvae to selected drugs for 24 hours and then quantified their locomotion during four ten-minute cycles of lights on-to-off stimuli. Results: We found that risperidone normalized the VMR in shank3 models. LiCl and CBZ had no effect on the VMR in any of the three genotypes. MPEP reduced the VMR in wildtype (WT) to levels seen in shank3 models but caused no changes in either shank3 model. Finally, shank3 mutants showed resistance to the seizure-inducing drug pentylenetetrazol (PTZ), at a dosage that results in hyperactive swimming in WT zebrafish. Conclusions: Our work shows that the effects of drugs on sensory processing are varied in ways that can be highly genotype- and drug-dependent.
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Affiliation(s)
- Robert A. Kozol
- Charles E. Schmidt College of Science, Florida Atlantic University, Jupiter, Fl., USA
| | - Julia E. Dallman
- Department of Biology, University of Miami, Coral Gables, FL, 33146, USA
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18
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Lee H, Shams S, Dang Thi VH, Boyum G, Modhurima R, Hall E, Green I, Cervantes E, Miguez F, Clark K. The canonical HPA axis facilitates and maintains light adaptive behavior. RESEARCH SQUARE 2023:rs.3.rs-3240080. [PMID: 37720015 PMCID: PMC10503838 DOI: 10.21203/rs.3.rs-3240080/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/19/2023]
Abstract
The vertebrate stress response (SR) is mediated by the hypothalamic-pituitary-adrenal (HPA) axis and contributes to generating context appropriate physiological and behavioral changes. Although the HPA axis plays vital roles both in stressful and basal conditions, research has focused on the response under stress. To understand broader roles of the HPA axis in a changing environment, we characterized an adaptive behavior of larval zebrafish during ambient illumination changes. The glucocorticoid receptor (nr3c1) was necessary to maintain basal locomotor activity in light and darkness. The HPA axis was required to adapt to light more efficiently but became dispensable when longer illumination was provided. Light adaptation was more efficient in dimmer light and did not require the mineralocorticoid receptor (nr3c2). Our findings show that the HPA axis contributes to the SR at various stages, facilitating the phasic response and maintaining an adapted basal state, and that certain adaptations occur without HPA axis activity.
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19
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Khan B, Jaesiri OM, Lazarte IP, Li Y, Tian G, Zhao P, Zhao Y, Ho VD, Semmelhack JL. Zebrafish larvae use stimulus intensity and contrast to estimate distance to prey. Curr Biol 2023; 33:3179-3191.e4. [PMID: 37437573 DOI: 10.1016/j.cub.2023.06.046] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 05/15/2023] [Accepted: 06/16/2023] [Indexed: 07/14/2023]
Abstract
The ability to determine the distance to objects is an important feature of most visual systems, but little is known about the neuronal mechanisms for distance estimation. Larval zebrafish execute different visual behaviors depending on distance; at medium distances, they converge their eyes and approach, but when the prey is close enough, they execute a strike and suck the prey into their mouths. To study distance estimation, we developed a head-fixed strike assay. We found that we could evoke strike behavior in head-fixed larvae and quantify head movements to classify the behavior as a strike. Strikes were dependent on distance to prey, allowing us to use them to study distance estimation. Light intensity is rapidly attenuated as it travels through water, so we hypothesized that larvae could use intensity as a distance cue. We found that increasing stimulus intensity could cause larvae to strike at prey that would normally be out of range, and decreasing the intensity could lower the strike rate even for very proximal stimuli. In addition, stimulus contrast is a key parameter, and this could allow larvae to estimate distance over the range of natural illumination. Finally, we presented prey in the binocular vs. monocular visual field and found that monocular prey did evoke strikes, although the binocular input produced more. These results suggest that strike behavior is optimally evoked by bright UV dots in the binocular zone with minimal UV background light and provide a foundation to study the neuronal mechanisms of distance estimation.
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Affiliation(s)
- Biswadeep Khan
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - On-Mongkol Jaesiri
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Ivan P Lazarte
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China; Department of Physiology, Anatomy and Genetics, University of Oxford, Sherrington Building, Parks Road, Oxford OX1 3PT, UK
| | - Yang Li
- Department of Biology, Stanford University, Gilbert Building, 371 Jane Stanford Way, Stanford, CA 94305, USA
| | - Guangnan Tian
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Peixiong Zhao
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Yicheng Zhao
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Viet Duc Ho
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Julie L Semmelhack
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China; Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China.
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20
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Cao S, Wu Y, Gao Z, Tang J, Xiong L, Hu J, Li C. Automated phenotyping of postoperative delirium-like behaviour in mice reveals the therapeutic efficacy of dexmedetomidine. Commun Biol 2023; 6:807. [PMID: 37532767 PMCID: PMC10397202 DOI: 10.1038/s42003-023-05149-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 07/17/2023] [Indexed: 08/04/2023] Open
Abstract
Postoperative delirium (POD) is a complicated and harmful clinical syndrome. Traditional behaviour analysis mostly focuses on static parameters. However, animal behaviour is a bottom-up and hierarchical organizational structure composed of time-varying posture dynamics. Spontaneous and task-driven behaviours are used to conduct comprehensive profiling of behavioural data of various aspects of model animals. A machine-learning based method is used to assess the effect of dexmedetomidine. Fourteen statistically different spontaneous behaviours are used to distinguish the non-POD group from the POD group. In the task-driven behaviour, the non-POD group has greater deep versus shallow investigation preference, with no significant preference in the POD group. Hyperactive and hypoactive subtypes can be distinguished through pose evaluation. Dexmedetomidine at a dose of 25 μg kg-1 reduces the severity and incidence of POD. Here we propose a multi-scaled clustering analysis framework that includes pose, behaviour and action sequence evaluation. This may represent the hierarchical dynamics of delirium-like behaviours.
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Affiliation(s)
- Silu Cao
- Department of Anesthesiology and Perioperative Medicine, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai, 200434, China
- Translational Research Institute of Brain and Brain-like Intelligence, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai, 200434, China
- Clinical Research Center for Anesthesiology and Perioperative Medicine, Tongji University, Shanghai, 200434, China
- Shanghai Key Laboratory of Anesthesiology and Brain Functional Modulation, Shanghai, 200434, China
| | - Yiling Wu
- School of Life Sciences and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Zilong Gao
- School of Life Sciences and Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, Westlake University, Hangzhou, 310024, China
- Chinese Institute for Brain Research, Beijing, 102206, China
| | - Jinxuan Tang
- Department of Anesthesiology and Perioperative Medicine, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai, 200434, China
- Translational Research Institute of Brain and Brain-like Intelligence, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai, 200434, China
- Clinical Research Center for Anesthesiology and Perioperative Medicine, Tongji University, Shanghai, 200434, China
- Shanghai Key Laboratory of Anesthesiology and Brain Functional Modulation, Shanghai, 200434, China
| | - Lize Xiong
- Department of Anesthesiology and Perioperative Medicine, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai, 200434, China
- Translational Research Institute of Brain and Brain-like Intelligence, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai, 200434, China
- Clinical Research Center for Anesthesiology and Perioperative Medicine, Tongji University, Shanghai, 200434, China
- Shanghai Key Laboratory of Anesthesiology and Brain Functional Modulation, Shanghai, 200434, China
| | - Ji Hu
- School of Life Sciences and Technology, ShanghaiTech University, Shanghai, 201210, China.
| | - Cheng Li
- Department of Anesthesiology and Perioperative Medicine, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai, 200434, China.
- Translational Research Institute of Brain and Brain-like Intelligence, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai, 200434, China.
- Clinical Research Center for Anesthesiology and Perioperative Medicine, Tongji University, Shanghai, 200434, China.
- Shanghai Key Laboratory of Anesthesiology and Brain Functional Modulation, Shanghai, 200434, China.
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21
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Berry JA, Marjaninejad A, Valero-Cuevas FJ. Edge Computing in Nature: Minimal pre-processing of multi-muscle ensembles of spindle signals improves discriminability of limb movements. Front Physiol 2023; 14:1183492. [PMID: 37457034 PMCID: PMC10345157 DOI: 10.3389/fphys.2023.1183492] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 06/12/2023] [Indexed: 07/18/2023] Open
Abstract
Multiple proprioceptive signals, like those from muscle spindles, are thought to enable robust estimates of body configuration. Yet, it remains unknown whether spindle signals suffice to discriminate limb movements. Here, a simulated 4-musculotendon, 2-joint planar limb model produced repeated cycles of five end-point trajectories in forward and reverse directions, which generated spindle Ia and II afferent signals (proprioceptors for velocity and length, respectively) from each musculotendon. We find that cross-correlation of the 8D time series of raw firing rates (four Ia, four II) cannot discriminate among most movement pairs (∼ 29% accuracy). However, projecting these signals onto their 1st and 2nd principal components greatly improves discriminability of movement pairs (82% accuracy). We conclude that high-dimensional ensembles of muscle proprioceptors can discriminate among limb movements-but only after dimensionality reduction. This may explain the pre-processing of some afferent signals before arriving at the somatosensory cortex, such as processing of cutaneous signals at the cat's cuneate nucleus.
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Affiliation(s)
- Jasmine A. Berry
- Brain-Body Dynamics Lab, Department of Computer Science, University of Southern California, Los Angeles, CA, United States
| | - Ali Marjaninejad
- Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, United States
| | - Francisco J. Valero-Cuevas
- Brain-Body Dynamics Lab, Department of Computer Science, University of Southern California, Los Angeles, CA, United States
- Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, United States
- Division of Biokinesiology and Physical Therapy, University of Southern California, Los Angeles, CA, United States
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22
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Zhu Y, Auer F, Gelnaw H, Davis SN, Hamling KR, May CE, Ahamed H, Ringstad N, Nagel KI, Schoppik D. SAMPL is a high-throughput solution to study unconstrained vertical behavior in small animals. Cell Rep 2023; 42:112573. [PMID: 37267107 PMCID: PMC10592459 DOI: 10.1016/j.celrep.2023.112573] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 03/27/2023] [Accepted: 05/11/2023] [Indexed: 06/04/2023] Open
Abstract
Balance and movement are impaired in many neurological disorders. Recent advances in behavioral monitoring provide unprecedented access to posture and locomotor kinematics but without the throughput and scalability necessary to screen candidate genes/potential therapeutics. Here, we present a scalable apparatus to measure posture and locomotion (SAMPL). SAMPL includes extensible hardware and open-source software with real-time processing and can acquire data from D. melanogaster, C. elegans, and D. rerio as they move vertically. Using SAMPL, we define how zebrafish balance as they navigate vertically and discover small but systematic variations among kinematic parameters between genetic backgrounds. We demonstrate SAMPL's ability to resolve differences in posture and navigation as a function of effect size and data gathered, providing key data for screens. SAMPL is therefore both a tool to model balance and locomotor disorders and an exemplar of how to scale apparatus to support screens.
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Affiliation(s)
- Yunlu Zhu
- Department of Otolaryngology, New York University Grossman School of Medicine, New York, NY 10016, USA; The Neuroscience Institute, New York University Grossman School of Medicine, New York, NY 10016, USA; Department of Neuroscience & Physiology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Franziska Auer
- Department of Otolaryngology, New York University Grossman School of Medicine, New York, NY 10016, USA; The Neuroscience Institute, New York University Grossman School of Medicine, New York, NY 10016, USA; Department of Neuroscience & Physiology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Hannah Gelnaw
- Department of Otolaryngology, New York University Grossman School of Medicine, New York, NY 10016, USA; The Neuroscience Institute, New York University Grossman School of Medicine, New York, NY 10016, USA; Department of Neuroscience & Physiology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Samantha N Davis
- Department of Otolaryngology, New York University Grossman School of Medicine, New York, NY 10016, USA; The Neuroscience Institute, New York University Grossman School of Medicine, New York, NY 10016, USA; Department of Neuroscience & Physiology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Kyla R Hamling
- Department of Otolaryngology, New York University Grossman School of Medicine, New York, NY 10016, USA; The Neuroscience Institute, New York University Grossman School of Medicine, New York, NY 10016, USA; Department of Neuroscience & Physiology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Christina E May
- The Neuroscience Institute, New York University Grossman School of Medicine, New York, NY 10016, USA; Department of Neuroscience & Physiology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Hassan Ahamed
- Department of Cell Biology, Skirball Institute of Biomolecular Medicine, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Niels Ringstad
- Department of Cell Biology, Skirball Institute of Biomolecular Medicine, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Katherine I Nagel
- The Neuroscience Institute, New York University Grossman School of Medicine, New York, NY 10016, USA; Department of Neuroscience & Physiology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - David Schoppik
- Department of Otolaryngology, New York University Grossman School of Medicine, New York, NY 10016, USA; The Neuroscience Institute, New York University Grossman School of Medicine, New York, NY 10016, USA; Department of Neuroscience & Physiology, New York University Grossman School of Medicine, New York, NY 10016, USA.
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23
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Widrick JJ, Lambert MR, Kunkel LM, Beggs AH. Optimizing assays of zebrafish larvae swimming performance for drug discovery. Expert Opin Drug Discov 2023; 18:629-641. [PMID: 37183669 PMCID: PMC10485652 DOI: 10.1080/17460441.2023.2211802] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 05/04/2023] [Indexed: 05/16/2023]
Abstract
INTRODUCTION Zebrafish larvae are one of the few vertebrates amenable to large-scale drug discovery screens. Larval swimming behavior is often used as an outcome variable and many fields of study have developed assays for evaluating swimming performance. An unintended consequence of this wide interest is that details related to assay methodology and interpretation become scattered across the literature. The aim of this review is to consolidate this information, particularly as it relates to high-throughput approaches. AREAS COVERED The authors describe larval swimming behaviors as this forms the basis for understanding their experimentally evoked swimming or spontaneous activity. Next, they detail how swimming activity can serve as an outcome variable, particularly in the multi-well formats used in large-scale screening studies. They also highlight biological and technical factors that can impact the sensitivity and variability of these measurements. EXPERT OPINION Careful attention to animal husbandry, experimental design, data acquisition, and interpretation of results can improve screen outcomes by maximizing swimming activity while minimizing intra- and inter-larval variability. The development of more sensitive, quantitative methods of assessing swimming performance that can be incorporated into high-throughput workflows will be important in order to take full advantage of the zebrafish model.
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Affiliation(s)
- Jeffrey J. Widrick
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA 02115, USA; The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Matthias R. Lambert
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA 02115, USA; The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Louis M. Kunkel
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA 02115, USA; The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
- The Stem Cell Program, Boston Children’s Hospital, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Alan H. Beggs
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA 02115, USA; The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
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24
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Hasani H, Sun J, Zhu SI, Rong Q, Willomitzer F, Amor R, McConnell G, Cossairt O, Goodhill GJ. Whole-brain imaging of freely-moving zebrafish. Front Neurosci 2023; 17:1127574. [PMID: 37139528 PMCID: PMC10150962 DOI: 10.3389/fnins.2023.1127574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 03/28/2023] [Indexed: 05/05/2023] Open
Abstract
One of the holy grails of neuroscience is to record the activity of every neuron in the brain while an animal moves freely and performs complex behavioral tasks. While important steps forward have been taken recently in large-scale neural recording in rodent models, single neuron resolution across the entire mammalian brain remains elusive. In contrast the larval zebrafish offers great promise in this regard. Zebrafish are a vertebrate model with substantial homology to the mammalian brain, but their transparency allows whole-brain recordings of genetically-encoded fluorescent indicators at single-neuron resolution using optical microscopy techniques. Furthermore zebrafish begin to show a complex repertoire of natural behavior from an early age, including hunting small, fast-moving prey using visual cues. Until recently work to address the neural bases of these behaviors mostly relied on assays where the fish was immobilized under the microscope objective, and stimuli such as prey were presented virtually. However significant progress has recently been made in developing brain imaging techniques for zebrafish which are not immobilized. Here we discuss recent advances, focusing particularly on techniques based on light-field microscopy. We also draw attention to several important outstanding issues which remain to be addressed to increase the ecological validity of the results obtained.
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Affiliation(s)
- Hamid Hasani
- Department of Electrical and Computer Engineering, Northwestern University, Evanston, IL, United States
| | - Jipeng Sun
- Department of Computer Science, Northwestern University, Evanston, IL, United States
| | - Shuyu I. Zhu
- Departments of Developmental Biology and Neuroscience, Washington University in St. Louis, St. Louis, MO, United States
| | - Qiangzhou Rong
- Departments of Developmental Biology and Neuroscience, Washington University in St. Louis, St. Louis, MO, United States
| | - Florian Willomitzer
- Wyant College of Optical Sciences, University of Arizona, Tucson, AZ, United States
| | - Rumelo Amor
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Gail McConnell
- Centre for Biophotonics, Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Oliver Cossairt
- Department of Computer Science, Northwestern University, Evanston, IL, United States
| | - Geoffrey J. Goodhill
- Departments of Developmental Biology and Neuroscience, Washington University in St. Louis, St. Louis, MO, United States
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Zhu Y, Auer F, Gelnaw H, Davis SN, Hamling KR, May CE, Ahamed H, Ringstad N, Nagel KI, Schoppik D. Scalable Apparatus to Measure Posture and Locomotion (SAMPL): a high-throughput solution to study unconstrained vertical behavior in small animals. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.07.523102. [PMID: 36712122 PMCID: PMC9881893 DOI: 10.1101/2023.01.07.523102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Balance and movement are impaired in a wide variety of neurological disorders. Recent advances in behavioral monitoring provide unprecedented access to posture and locomotor kinematics, but without the throughput and scalability necessary to screen candidate genes / potential therapeutics. We present a powerful solution: a Scalable Apparatus to Measure Posture and Locomotion (SAMPL). SAMPL includes extensible imaging hardware and low-cost open-source acquisition software with real-time processing. We first demonstrate that SAMPL's hardware and acquisition software can acquire data from from D. melanogaster, C. elegans, and D. rerio as they move vertically. Next, we leverage SAMPL's throughput to rapidly (two weeks) gather a new zebrafish dataset. We use SAMPL's analysis and visualization tools to replicate and extend our current understanding of how zebrafish balance as they navigate through a vertical environment. Next, we discover (1) that key kinematic parameters vary systematically with genetic background, and (2) that such background variation is small relative to the changes that accompany early development. Finally, we simulate SAMPL's ability to resolve differences in posture or vertical navigation as a function of affect size and data gathered -- key data for screens. Taken together, our apparatus, data, and analysis provide a powerful solution for labs using small animals to investigate balance and locomotor disorders at scale. More broadly, SAMPL is both an adaptable resource for labs looking process videographic measures of behavior in real-time, and an exemplar of how to scale hardware to enable the throughput necessary for screening.
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Affiliation(s)
- Yunlu Zhu
- Department. of Otolaryngology, New York University Grossman School of Medicine
- The Neuroscience Institute, New York University Grossman School of Medicine
- Department of Neuroscience & Physiology, New York University Grossman School of Medicine
| | - Franziska Auer
- Department. of Otolaryngology, New York University Grossman School of Medicine
- The Neuroscience Institute, New York University Grossman School of Medicine
- Department of Neuroscience & Physiology, New York University Grossman School of Medicine
| | - Hannah Gelnaw
- Department. of Otolaryngology, New York University Grossman School of Medicine
- The Neuroscience Institute, New York University Grossman School of Medicine
- Department of Neuroscience & Physiology, New York University Grossman School of Medicine
| | - Samantha N. Davis
- Department. of Otolaryngology, New York University Grossman School of Medicine
- The Neuroscience Institute, New York University Grossman School of Medicine
- Department of Neuroscience & Physiology, New York University Grossman School of Medicine
| | - Kyla R. Hamling
- Department. of Otolaryngology, New York University Grossman School of Medicine
- The Neuroscience Institute, New York University Grossman School of Medicine
- Department of Neuroscience & Physiology, New York University Grossman School of Medicine
| | - Christina E. May
- The Neuroscience Institute, New York University Grossman School of Medicine
- Department of Neuroscience & Physiology, New York University Grossman School of Medicine
| | - Hassan Ahamed
- Department of Cell Biology, Skirball Institute of Biomolecular Medicine, New York University Grossman School of Medicine
| | - Niels Ringstad
- Department of Cell Biology, Skirball Institute of Biomolecular Medicine, New York University Grossman School of Medicine
| | - Katherine I. Nagel
- The Neuroscience Institute, New York University Grossman School of Medicine
- Department of Neuroscience & Physiology, New York University Grossman School of Medicine
| | - David Schoppik
- Department. of Otolaryngology, New York University Grossman School of Medicine
- The Neuroscience Institute, New York University Grossman School of Medicine
- Department of Neuroscience & Physiology, New York University Grossman School of Medicine
- Lead Contact
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26
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Reemst K, Shahin H, Shahar OD. Learning and memory formation in zebrafish: Protein dynamics and molecular tools. Front Cell Dev Biol 2023; 11:1120984. [PMID: 36968211 PMCID: PMC10034119 DOI: 10.3389/fcell.2023.1120984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 02/20/2023] [Indexed: 03/12/2023] Open
Abstract
Research on learning and memory formation at the level of neural networks, as well as at the molecular level, is challenging due to the immense complexity of the brain. The zebrafish as a genetically tractable model organism can overcome many of the current challenges of studying molecular mechanisms of learning and memory formation. Zebrafish have a translucent, smaller and more accessible brain than that of mammals, allowing imaging of the entire brain during behavioral manipulations. Recent years have seen an extensive increase in published brain research describing the use of zebrafish for the study of learning and memory. Nevertheless, due to the complexity of the brain comprising many neural cell types that are difficult to isolate, it has been difficult to elucidate neural networks and molecular mechanisms involved in memory formation in an unbiased manner, even in zebrafish larvae. Therefore, data regarding the identity, location, and intensity of nascent proteins during memory formation is still sparse and our understanding of the molecular networks remains limited, indicating a need for new techniques. Here, we review recent progress in establishing learning paradigms for zebrafish and the development of methods to elucidate neural and molecular networks of learning. We describe various types of learning and highlight directions for future studies, focusing on molecular mechanisms of long-term memory formation and promising state-of-the-art techniques such as cell-type-specific metabolic labeling.
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Affiliation(s)
- Kitty Reemst
- Migal—Galilee Research Institute, Kiryat Shmona, Israel
- Department of Biotechnology, Tel-Hai College, Kiryat Shmona, Israel
| | - Heba Shahin
- Migal—Galilee Research Institute, Kiryat Shmona, Israel
- Department of Biotechnology, Tel-Hai College, Kiryat Shmona, Israel
| | - Or David Shahar
- Migal—Galilee Research Institute, Kiryat Shmona, Israel
- Department of Biotechnology, Tel-Hai College, Kiryat Shmona, Israel
- *Correspondence: Or David Shahar,
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27
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Xu H, Tang X, Chen J, Shi Y, Liu J, Han C, Zhu X, Zhang T, Zhou J, Miao W. Development and optimization of an effective method for evaluating habituation learning behavior in larval zebrafish. J Neurosci Methods 2023; 386:109793. [PMID: 36640926 DOI: 10.1016/j.jneumeth.2023.109793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 01/09/2023] [Accepted: 01/09/2023] [Indexed: 01/13/2023]
Abstract
BACKGROUND Habituation learning is a simple and conserved behavior in all organisms which could be induced by repeated stimuli. However, no standard and universal methods for training and evaluating the habituation learning behavior in larval zebrafish were available. NEW METHOD This study aims to establish effective training and detection protocols for habituation learning behavior in larval zebrafish by using the ViewPoint system. For this purpose, the detection threshold of velocity-a parameter for distinguishing the escape reaction and the spontaneous motion, the detection sensitivity-a parameter for determining the size of the identified object, the number of stimuli, and the age of larvae were optimized to obtain the best performance. RESULTS In this study, the optimized parameters were as follows: the detection threshold of velocity at 13, the luminous intensity at 8 %, the detection sensitivity at 32, the number of stimuli at 150, and the age of larvae at 6 dpf. Furthermore, we validated the utility of the established protocol by showing a consistent memory impairment induced by cycloheximide (CHX). COMPARISON WITH EXISTING METHOD A similar method was reported previously. However, the equipment used in those assays, including the hardware and software, were neither standard nor universal, which might impede the extensive application of the habituation learning assays. Here, we developed an alternative method for studying the habituation learning behavior in larval zebrafish using the ViewPoint system. CONCLUSIONS Our study provided an alternative method for studying the habituation learning behavior in larval zebrafish.
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Affiliation(s)
- Huifang Xu
- Otolaryngology Department, Zhejiang Provincial Hospital of Traditional Chinese Medical, Hangzhou, China
| | - Xuxia Tang
- Otolaryngology Department, Zhejiang Provincial Hospital of Traditional Chinese Medical, Hangzhou, China
| | - Jingjing Chen
- Otolaryngology Department, Zhejiang Provincial Hospital of Traditional Chinese Medical, Hangzhou, China
| | - Ya Shi
- Otolaryngology Department, Zhejiang Provincial Hospital of Traditional Chinese Medical, Hangzhou, China
| | - Jun Liu
- Otolaryngology Department, Zhejiang Provincial Hospital of Traditional Chinese Medical, Hangzhou, China
| | - Cheng Han
- Hunter Biotechnology, Hangzhou, China
| | | | - Tao Zhang
- Hunter Biotechnology, Hangzhou, China
| | - Jinghe Zhou
- Department of Plastic Surgery, Affiliated Hangzhou First People's Hospital Zhejiang University School of Medicine, Hangzhou, China.
| | - Wenyu Miao
- School of Public Health, Zhejiang University School of Medicine, Hangzhou, China; Hunter Biotechnology, Hangzhou, China.
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28
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Ehlman SM, Scherer U, Bierbach D, Francisco FA, Laskowski KL, Krause J, Wolf M. Leveraging big data to uncover the eco-evolutionary factors shaping behavioural development. Proc Biol Sci 2023; 290:20222115. [PMID: 36722081 PMCID: PMC9890127 DOI: 10.1098/rspb.2022.2115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Mapping the eco-evolutionary factors shaping the development of animals' behavioural phenotypes remains a great challenge. Recent advances in 'big behavioural data' research-the high-resolution tracking of individuals and the harnessing of that data with powerful analytical tools-have vastly improved our ability to measure and model developing behavioural phenotypes. Applied to the study of behavioural ontogeny, the unfolding of whole behavioural repertoires can be mapped in unprecedented detail with relative ease. This overcomes long-standing experimental bottlenecks and heralds a surge of studies that more finely define and explore behavioural-experiential trajectories across development. In this review, we first provide a brief guide to state-of-the-art approaches that allow the collection and analysis of high-resolution behavioural data across development. We then outline how such approaches can be used to address key issues regarding the ecological and evolutionary factors shaping behavioural development: developmental feedbacks between behaviour and underlying states, early life effects and behavioural transitions, and information integration across development.
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Affiliation(s)
- Sean M. Ehlman
- SCIoI Excellence Cluster, 10587 Berlin, Germany,Faculty of Life Sciences, Humboldt University, 10117 Berlin, Germany,Department of Fish Biology, Fisheries, and Aquaculture, Leibniz Institute of Freshwater Ecology and Inland Fisheries, 12587 Berlin, Germany
| | - Ulrike Scherer
- SCIoI Excellence Cluster, 10587 Berlin, Germany,Faculty of Life Sciences, Humboldt University, 10117 Berlin, Germany,Department of Fish Biology, Fisheries, and Aquaculture, Leibniz Institute of Freshwater Ecology and Inland Fisheries, 12587 Berlin, Germany
| | - David Bierbach
- SCIoI Excellence Cluster, 10587 Berlin, Germany,Faculty of Life Sciences, Humboldt University, 10117 Berlin, Germany,Department of Fish Biology, Fisheries, and Aquaculture, Leibniz Institute of Freshwater Ecology and Inland Fisheries, 12587 Berlin, Germany
| | - Fritz A. Francisco
- SCIoI Excellence Cluster, 10587 Berlin, Germany,Faculty of Life Sciences, Humboldt University, 10117 Berlin, Germany
| | - Kate L. Laskowski
- Department of Evolution and Ecology, University of California – Davis, Davis, CA 95616, USA
| | - Jens Krause
- SCIoI Excellence Cluster, 10587 Berlin, Germany,Faculty of Life Sciences, Humboldt University, 10117 Berlin, Germany,Department of Fish Biology, Fisheries, and Aquaculture, Leibniz Institute of Freshwater Ecology and Inland Fisheries, 12587 Berlin, Germany
| | - Max Wolf
- SCIoI Excellence Cluster, 10587 Berlin, Germany,Department of Fish Biology, Fisheries, and Aquaculture, Leibniz Institute of Freshwater Ecology and Inland Fisheries, 12587 Berlin, Germany
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29
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Zhu SI, Goodhill GJ. From perception to behavior: The neural circuits underlying prey hunting in larval zebrafish. Front Neural Circuits 2023; 17:1087993. [PMID: 36817645 PMCID: PMC9928868 DOI: 10.3389/fncir.2023.1087993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 01/10/2023] [Indexed: 02/04/2023] Open
Abstract
A key challenge for neural systems is to extract relevant information from the environment and make appropriate behavioral responses. The larval zebrafish offers an exciting opportunity for studying these sensing processes and sensory-motor transformations. Prey hunting is an instinctual behavior of zebrafish that requires the brain to extract and combine different attributes of the sensory input and form appropriate motor outputs. Due to its small size and transparency the larval zebrafish brain allows optical recording of whole-brain activity to reveal the neural mechanisms involved in prey hunting and capture. In this review we discuss how the larval zebrafish brain processes visual information to identify and locate prey, the neural circuits governing the generation of motor commands in response to prey, how hunting behavior can be modulated by internal states and experience, and some outstanding questions for the field.
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Affiliation(s)
- Shuyu I. Zhu
- Departments of Developmental Biology and Neuroscience, Washington University in St. Louis, St. Louis, MO, United States
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30
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Geng Y, Yates C, Peterson RT. Social behavioral profiling by unsupervised deep learning reveals a stimulative effect of dopamine D3 agonists on zebrafish sociality. CELL REPORTS METHODS 2023; 3:100381. [PMID: 36814839 PMCID: PMC9939379 DOI: 10.1016/j.crmeth.2022.100381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 11/15/2022] [Accepted: 12/12/2022] [Indexed: 01/07/2023]
Abstract
It has been a major challenge to systematically evaluate and compare how pharmacological perturbations influence social behavioral outcomes. Although some pharmacological agents are known to alter social behavior, precise description and quantification of such effects have proven difficult. We developed a scalable social behavioral assay for zebrafish named ZeChat based on unsupervised deep learning to characterize sociality at high resolution. High-dimensional and dynamic social behavioral phenotypes are automatically classified using this method. By screening a neuroactive compound library, we found that different classes of chemicals evoke distinct patterns of social behavioral fingerprints. By examining these patterns, we discovered that dopamine D3 agonists possess a social stimulative effect on zebrafish. The D3 agonists pramipexole, piribedil, and 7-hydroxy-DPAT-HBr rescued social deficits in a valproic-acid-induced zebrafish autism model. The ZeChat platform provides a promising approach for dissecting the pharmacology of social behavior and discovering novel social-modulatory compounds.
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Affiliation(s)
- Yijie Geng
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Utah, Salt Lake City, UT 84112, USA
| | - Christopher Yates
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Utah, Salt Lake City, UT 84112, USA
| | - Randall T. Peterson
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Utah, Salt Lake City, UT 84112, USA
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31
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Burgess HA, Burton EA. A Critical Review of Zebrafish Neurological Disease Models-1. The Premise: Neuroanatomical, Cellular and Genetic Homology and Experimental Tractability. OXFORD OPEN NEUROSCIENCE 2023; 2:kvac018. [PMID: 37649777 PMCID: PMC10464506 DOI: 10.1093/oons/kvac018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 11/13/2022] [Indexed: 09/01/2023]
Abstract
The last decade has seen a dramatic rise in the number of genes linked to neurological disorders, necessitating new models to explore underlying mechanisms and to test potential therapies. Over a similar period, many laboratories adopted zebrafish as a tractable model for studying brain development, defining neural circuits and performing chemical screens. Here we discuss strengths and limitations of using the zebrafish system to model neurological disorders. The underlying premise for many disease models is the high degree of homology between human and zebrafish genes, coupled with the conserved vertebrate Bauplan and repertoire of neurochemical signaling molecules. Yet, we caution that important evolutionary divergences often limit the extent to which human symptoms can be modeled meaningfully in zebrafish. We outline advances in genetic technologies that allow human mutations to be reproduced faithfully in zebrafish. Together with methods that visualize the development and function of neuronal pathways at the single cell level, there is now an unprecedented opportunity to understand how disease-associated genetic changes disrupt neural circuits, a level of analysis that is ideally suited to uncovering pathogenic changes in human brain disorders.
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Affiliation(s)
- Harold A Burgess
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, 20892, USA
| | - Edward A Burton
- Pittsburgh Institute for Neurodegenerative Diseases, University of Pittsburgh, Pittsburgh, PA, 15260, USA
- Department of Neurology, University of Pittsburgh, Pittsburgh, PA,15260, USA
- Geriatric Research, Education, and Clinical Center, Pittsburgh VA Healthcare System, Pittsburgh, PA, 15240, USA
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32
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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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33
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Thomson EE, Harfouche M, Kim K, Konda PC, Seitz CW, Cooke C, Xu S, Jacobs WS, Blazing R, Chen Y, Sharma S, Dunn TW, Park J, Horstmeyer RW, Naumann EA. Gigapixel imaging with a novel multi-camera array microscope. eLife 2022; 11:e74988. [PMID: 36515989 PMCID: PMC9917455 DOI: 10.7554/elife.74988] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 11/23/2022] [Indexed: 12/15/2022] Open
Abstract
The dynamics of living organisms are organized across many spatial scales. However, current cost-effective imaging systems can measure only a subset of these scales at once. We have created a scalable multi-camera array microscope (MCAM) that enables comprehensive high-resolution recording from multiple spatial scales simultaneously, ranging from structures that approach the cellular scale to large-group behavioral dynamics. By collecting data from up to 96 cameras, we computationally generate gigapixel-scale images and movies with a field of view over hundreds of square centimeters at an optical resolution of 18 µm. This allows us to observe the behavior and fine anatomical features of numerous freely moving model organisms on multiple spatial scales, including larval zebrafish, fruit flies, nematodes, carpenter ants, and slime mold. Further, the MCAM architecture allows stereoscopic tracking of the z-position of organisms using the overlapping field of view from adjacent cameras. Overall, by removing the bottlenecks imposed by single-camera image acquisition systems, the MCAM provides a powerful platform for investigating detailed biological features and behavioral processes of small model organisms across a wide range of spatial scales.
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Affiliation(s)
- Eric E Thomson
- Department of Neurobiology, Duke School of MedicineDurhamUnited States
| | | | - Kanghyun Kim
- Biomedical Engineering, Duke UniversityDurhamUnited States
| | - Pavan C Konda
- Biomedical Engineering, Duke UniversityDurhamUnited States
| | - Catherine W Seitz
- Department of Neurobiology, Duke School of MedicineDurhamUnited States
| | - Colin Cooke
- Biomedical Engineering, Duke UniversityDurhamUnited States
| | - Shiqi Xu
- Biomedical Engineering, Duke UniversityDurhamUnited States
| | - Whitney S Jacobs
- Department of Neurobiology, Duke School of MedicineDurhamUnited States
| | - Robin Blazing
- Department of Neurobiology, Duke School of MedicineDurhamUnited States
| | - Yang Chen
- Department of Neurobiology, Duke School of MedicineDurhamUnited States
| | | | - Timothy W Dunn
- Biomedical Engineering, Duke UniversityDurhamUnited States
| | | | - Roarke W Horstmeyer
- Ramona Optics IncDurhamUnited States
- Biomedical Engineering, Duke UniversityDurhamUnited States
| | - Eva A Naumann
- Department of Neurobiology, Duke School of MedicineDurhamUnited States
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34
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Alexander E, Cai LT, Fuchs S, Hladnik TC, Zhang Y, Subramanian V, Guilbeault NC, Vijayakumar C, Arunachalam M, Juntti SA, Thiele TR, Arrenberg AB, Cooper EA. Optic flow in the natural habitats of zebrafish supports spatial biases in visual self-motion estimation. Curr Biol 2022; 32:5008-5021.e8. [PMID: 36327979 PMCID: PMC9729457 DOI: 10.1016/j.cub.2022.10.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 08/15/2022] [Accepted: 10/05/2022] [Indexed: 12/12/2022]
Abstract
Animals benefit from knowing if and how they are moving. Across the animal kingdom, sensory information in the form of optic flow over the visual field is used to estimate self-motion. However, different species exhibit strong spatial biases in how they use optic flow. Here, we show computationally that noisy natural environments favor visual systems that extract spatially biased samples of optic flow when estimating self-motion. The performance associated with these biases, however, depends on interactions between the environment and the animal's brain and behavior. Using the larval zebrafish as a model, we recorded natural optic flow associated with swimming trajectories in the animal's habitat with an omnidirectional camera mounted on a mechanical arm. An analysis of these flow fields suggests that lateral regions of the lower visual field are most informative about swimming speed. This pattern is consistent with the recent findings that zebrafish optomotor responses are preferentially driven by optic flow in the lateral lower visual field, which we extend with behavioral results from a high-resolution spherical arena. Spatial biases in optic-flow sampling are likely pervasive because they are an effective strategy for determining self-motion in noisy natural environments.
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Affiliation(s)
- Emma Alexander
- Herbert Wertheim School of Optometry & Vision Science, University of California, Berkeley, Berkeley, CA 94720, USA,Present address: Department of Computer Science, Northwestern University, Evanston, IL 60208, USA,Lead contact,Correspondence:
| | - Lanya T. Cai
- Herbert Wertheim School of Optometry & Vision Science, University of California, Berkeley, Berkeley, CA 94720, USA,Present address: Department of Radiology and Biomedical Imaging, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Sabrina Fuchs
- Werner Reichardt Centre for Integrative Neuroscience, Institute of Neurobiology, University of Tubingen, 72076 Tubingen, Germany
| | - Tim C. Hladnik
- Werner Reichardt Centre for Integrative Neuroscience, Institute of Neurobiology, University of Tubingen, 72076 Tubingen, Germany,Graduate Training Centre for Neuroscience, University of Tubingen, 72074 Tubingen, Germany
| | - Yue Zhang
- Werner Reichardt Centre for Integrative Neuroscience, Institute of Neurobiology, University of Tubingen, 72076 Tubingen, Germany,Graduate Training Centre for Neuroscience, University of Tubingen, 72074 Tubingen, Germany,Present address: Department of Cellular and Systems Neurobiology, Max Planck Institute for Biological Intelligence in Foundation, 82152 Martinsried, Germany
| | - Venkatesh Subramanian
- Department of Biological Sciences, University of Toronto Scarborough, Toronto M1C 1A4, Canada
| | - Nicholas C. Guilbeault
- Department of Biological Sciences, University of Toronto Scarborough, Toronto M1C 1A4, Canada,Department of Cell and Systems Biology, University of Toronto, Toronto M5S 3G5, Canada
| | - Chinnian Vijayakumar
- Department of Zoology, St. Andrew’s College, Gorakhpur, Uttar Pradesh 273001, India
| | - Muthukumarasamy Arunachalam
- Department of Zoology, School of Biological Sciences, Central University of Kerala, Kerala 671316, India,Present address: Centre for Inland Fishes and Conservation, St. Andrew’s College, Gorakhpur, Uttar Pradesh 273001, India
| | - Scott A. Juntti
- Department of Biology, University of Maryland, College Park, MD 20742, USA
| | - Tod R. Thiele
- Department of Biological Sciences, University of Toronto Scarborough, Toronto M1C 1A4, Canada,Department of Cell and Systems Biology, University of Toronto, Toronto M5S 3G5, Canada
| | - Aristides B. Arrenberg
- Werner Reichardt Centre for Integrative Neuroscience, Institute of Neurobiology, University of Tubingen, 72076 Tubingen, Germany
| | - Emily A. Cooper
- Herbert Wertheim School of Optometry & Vision Science, University of California, Berkeley, Berkeley, CA 94720, USA,Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA 94720, USA
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35
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Rajan G, Debregeas G, Orger MB, Del Bene F. An analysis pipeline to compare explorative locomotion across fish species. STAR Protoc 2022; 3:101850. [PMID: 36595960 PMCID: PMC9679675 DOI: 10.1016/j.xpro.2022.101850] [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: 06/01/2022] [Revised: 09/23/2022] [Accepted: 10/22/2022] [Indexed: 11/21/2022] Open
Abstract
Recently, we introduced a powerful approach that leverages differences in swimming behaviors of two closely related fish species to identify previously unreported locomotion-related neuronal correlates. Here, we present this analysis approach applicable for any species of fish to compare their short and long timescale swimming kinematics. We describe steps for data collection and cleaning, followed by the calculation of short timescale kinematics using half tail beats and the analysis of long timescale kinematics using mean square displacement and heading decorrelation. For complete details on the use and execution of this protocol, please refer to Rajan et al. (2022).1.
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Affiliation(s)
- Gokul Rajan
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 75012 Paris, France,Institut Curie, PSL Research University, INSERM U934, CNRS UMR3215, Paris, France,Champalimaud Research, Champalimaud Centre for the Unknown, Avenida Brasilia, Doca de Pedroucos, 1400-038 Lisboa, Portugal,Corresponding author
| | - Georges Debregeas
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP), 75005 Paris, France
| | - Michael B. Orger
- Champalimaud Research, Champalimaud Centre for the Unknown, Avenida Brasilia, Doca de Pedroucos, 1400-038 Lisboa, Portugal
| | - Filippo Del Bene
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 75012 Paris, France,Institut Curie, PSL Research University, INSERM U934, CNRS UMR3215, Paris, France,Corresponding author
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36
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Hossainian D, Shao E, Jiao B, Ilin VA, Parris RS, Zhou Y, Bai Q, Burton EA. Quantification of functional recovery in a larval zebrafish model of spinal cord injury. J Neurosci Res 2022; 100:2044-2054. [PMID: 35986577 PMCID: PMC10695274 DOI: 10.1002/jnr.25118] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 07/19/2022] [Accepted: 08/01/2022] [Indexed: 11/12/2023]
Abstract
Human spinal cord injury (SCI) is characterized by permanent loss of damaged axons, resulting in chronic disability. In contrast, zebrafish can regenerate axonal projections following central nervous system injury and re-establish synaptic contacts with distant targets; elucidation of the underlying molecular events is an important goal with translational potential for improving outcomes in SCI patients. We generated transgenic zebrafish with GFP-labeled axons and transected their spinal cords at 10 days post-fertilization. Intravital confocal microscopy revealed robust axonal regeneration following the procedure, with abundant axons bridging the transection site by 48 h post-injury. In order to analyze neurological function in this model, we developed and validated new open-source software to measure zebrafish lateral trunk curvature during propulsive and turning movements at high temporal resolution. Immediately following spinal cord transection, axial movements were dramatically decreased caudal to the lesion site, but preserved rostral to the injury, suggesting the induction of motor paralysis below the transection level. Over the subsequent 96 h, the magnitude of movements caudal to the lesion recovered to baseline, but the rate of change of truncal curvature did not fully recover, suggesting incomplete restoration of caudal strength over this time course. Quantification of both morphological and functional recovery following SCI will be important for the analysis of axonal regeneration and downstream events necessary for restoration of motor function. An extensive array of genetic and pharmacological interventions can be deployed in the larval zebrafish model to investigate the underlying molecular mechanisms.
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Affiliation(s)
- Darius Hossainian
- Department of Neurology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
- Pittsburgh Institute for Neurodegenerative Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
| | - Enhua Shao
- Department of Neurology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
- Pittsburgh Institute for Neurodegenerative Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
- Tsinghua University Medical School, Beijing, China
| | - Binxuan Jiao
- Department of Neurology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
- Pittsburgh Institute for Neurodegenerative Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
- Tsinghua University Medical School, Beijing, China
| | - Vladimir A. Ilin
- Department of Neurology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
- Pittsburgh Institute for Neurodegenerative Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
| | - Ritika S. Parris
- Department of Neurology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
- Pittsburgh Institute for Neurodegenerative Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
| | - Yangzhong Zhou
- Department of Neurology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
- Pittsburgh Institute for Neurodegenerative Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
- Tsinghua University Medical School, Beijing, China
| | - Qing Bai
- Department of Neurology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
- Pittsburgh Institute for Neurodegenerative Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
| | - Edward A. Burton
- Department of Neurology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
- Pittsburgh Institute for Neurodegenerative Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
- Geriatric Research, Education and Clinical Center, Pittsburgh VA Healthcare System, Pittsburgh, PA, 15213, USA
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37
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York RA, Brezovec LE, Coughlan J, Herbst S, Krieger A, Lee SY, Pratt B, Smart AD, Song E, Suvorov A, Matute DR, Tuthill JC, Clandinin TR. The evolutionary trajectory of drosophilid walking. Curr Biol 2022; 32:3005-3015.e6. [PMID: 35671756 PMCID: PMC9329251 DOI: 10.1016/j.cub.2022.05.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 03/03/2022] [Accepted: 05/13/2022] [Indexed: 11/26/2022]
Abstract
Neural circuits must both execute the behavioral repertoire of individuals and account for behavioral variation across species. Understanding how this variation emerges over evolutionary time requires large-scale phylogenetic comparisons of behavioral repertoires. Here, we describe the evolution of walking in fruit flies by capturing high-resolution, unconstrained movement from 13 species and 15 strains of drosophilids. We find that walking can be captured in a universal behavior space, the structure of which is evolutionarily conserved. However, the occurrence of and transitions between specific movements have evolved rapidly, resulting in repeated convergent evolution in the temporal structure of locomotion. Moreover, a meta-analysis demonstrates that many behaviors evolve more rapidly than other traits. Thus, the architecture and physiology of locomotor circuits can execute precise individual movements in one species and simultaneously support rapid evolutionary changes in the temporal ordering of these modular elements across clades.
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Affiliation(s)
- Ryan A York
- Department of Neurobiology, Stanford University, Stanford, CA 94305, USA.
| | - Luke E Brezovec
- Department of Neurobiology, Stanford University, Stanford, CA 94305, USA
| | - Jenn Coughlan
- Biology Department, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Steven Herbst
- Department of Neurobiology, Stanford University, Stanford, CA 94305, USA
| | - Avery Krieger
- Department of Neurobiology, Stanford University, Stanford, CA 94305, USA
| | - Su-Yee Lee
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195, USA
| | - Brandon Pratt
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195, USA
| | - Ashley D Smart
- Department of Neurobiology, Stanford University, Stanford, CA 94305, USA
| | - Eugene Song
- Department of Neurobiology, Stanford University, Stanford, CA 94305, USA
| | - Anton Suvorov
- Biology Department, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Daniel R Matute
- Biology Department, University of North Carolina, Chapel Hill, NC 27599, USA
| | - John C Tuthill
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195, USA
| | - Thomas R Clandinin
- Department of Neurobiology, Stanford University, Stanford, CA 94305, USA.
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38
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Visual recognition of social signals by a tectothalamic neural circuit. Nature 2022; 608:146-152. [PMID: 35831500 PMCID: PMC9352588 DOI: 10.1038/s41586-022-04925-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 06/02/2022] [Indexed: 12/23/2022]
Abstract
Social affiliation emerges from individual-level behavioural rules that are driven by conspecific signals1-5. Long-distance attraction and short-distance repulsion, for example, are rules that jointly set a preferred interanimal distance in swarms6-8. However, little is known about their perceptual mechanisms and executive neural circuits3. Here we trace the neuronal response to self-like biological motion9,10, a visual trigger for affiliation in developing zebrafish2,11. Unbiased activity mapping and targeted volumetric two-photon calcium imaging revealed 21 activity hotspots distributed throughout the brain as well as clustered biological-motion-tuned neurons in a multimodal, socially activated nucleus of the dorsal thalamus. Individual dorsal thalamus neurons encode local acceleration of visual stimuli mimicking typical fish kinetics but are insensitive to global or continuous motion. Electron microscopic reconstruction of dorsal thalamus neurons revealed synaptic input from the optic tectum and projections into hypothalamic areas with conserved social function12-14. Ablation of the optic tectum or dorsal thalamus selectively disrupted social attraction without affecting short-distance repulsion. This tectothalamic pathway thus serves visual recognition of conspecifics, and dissociates neuronal control of attraction from repulsion during social affiliation, revealing a circuit underpinning collective behaviour.
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39
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Mazzucato L. Neural mechanisms underlying the temporal organization of naturalistic animal behavior. eLife 2022; 11:76577. [PMID: 35792884 PMCID: PMC9259028 DOI: 10.7554/elife.76577] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 06/07/2022] [Indexed: 12/17/2022] Open
Abstract
Naturalistic animal behavior exhibits a strikingly complex organization in the temporal domain, with variability arising from at least three sources: hierarchical, contextual, and stochastic. What neural mechanisms and computational principles underlie such intricate temporal features? In this review, we provide a critical assessment of the existing behavioral and neurophysiological evidence for these sources of temporal variability in naturalistic behavior. Recent research converges on an emergent mechanistic theory of temporal variability based on attractor neural networks and metastable dynamics, arising via coordinated interactions between mesoscopic neural circuits. We highlight the crucial role played by structural heterogeneities as well as noise from mesoscopic feedback loops in regulating flexible behavior. We assess the shortcomings and missing links in the current theoretical and experimental literature and propose new directions of investigation to fill these gaps.
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Affiliation(s)
- Luca Mazzucato
- Institute of Neuroscience, Departments of Biology, Mathematics and Physics, University of Oregon
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40
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Nelson JC, Granato M. Zebrafish behavior as a gateway to nervous system assembly and plasticity. Development 2022; 149:275367. [PMID: 35552393 PMCID: PMC9148562 DOI: 10.1242/dev.177998] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Nervous system assembly relies on a diversity of cellular processes ranging from dramatic tissue reorganization to local, subcellular changes all driven by precise molecular programs. Combined, these processes culminate in an animal's ability to plan and execute behaviors. Animal behavior can, therefore, serve as a functional readout of nervous system development. Benefitting from an expansive and growing set of molecular and imaging tools paired with an ever-growing number of assays of diverse behaviors, the zebrafish system has emerged as an outstanding platform at the intersection of nervous system assembly, plasticity and behavior. Here, we summarize recent advancements in the field, including how developing neural circuits are refined to shape complex behaviors and plasticity.
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Affiliation(s)
- Jessica C. Nelson
- Department of Cell and Developmental Biology, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045, USA,Department of Cell and Developmental Biology, University of Pennsylvania, Perelman School of Medicine, 421 Curie Blvd, Philadelphia, PA 19104, USA,Authors for correspondence (; )
| | - Michael Granato
- Department of Cell and Developmental Biology, University of Pennsylvania, Perelman School of Medicine, 421 Curie Blvd, Philadelphia, PA 19104, USA,Authors for correspondence (; )
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41
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Böhm UL, Kimura Y, Kawashima T, Ahrens MB, Higashijima SI, Engert F, Cohen AE. Voltage imaging identifies spinal circuits that modulate locomotor adaptation in zebrafish. Neuron 2022; 110:1211-1222.e4. [PMID: 35104451 PMCID: PMC8989672 DOI: 10.1016/j.neuron.2022.01.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 11/17/2021] [Accepted: 01/04/2022] [Indexed: 12/20/2022]
Abstract
Motor systems must continuously adapt their output to maintain a desired trajectory. While the spinal circuits underlying rhythmic locomotion are well described, little is known about how the network modulates its output strength. A major challenge has been the difficulty of recording from spinal neurons during behavior. Here, we use voltage imaging to map the membrane potential of large populations of glutamatergic neurons throughout the spinal cord of the larval zebrafish during fictive swimming in a virtual environment. We characterized a previously undescribed subpopulation of tonic-spiking ventral V3 neurons whose spike rate correlated with swimming strength and bout length. Optogenetic activation of V3 neurons led to stronger swimming and longer bouts but did not affect tail beat frequency. Genetic ablation of V3 neurons led to reduced locomotor adaptation. The power of voltage imaging allowed us to identify V3 neurons as a critical driver of locomotor adaptation in zebrafish.
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Affiliation(s)
- Urs L Böhm
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Yukiko Kimura
- National Institutes of Natural Sciences, Okazaki Institute for Integrative Bioscience, National Institute for Physiological Sciences, Okazaki, Aichi 444-8787, Japan
| | - Takashi Kawashima
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Misha B Ahrens
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Shin-Ichi Higashijima
- National Institutes of Natural Sciences, Okazaki Institute for Integrative Bioscience, National Institute for Physiological Sciences, Okazaki, Aichi 444-8787, Japan
| | - Florian Engert
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Adam E Cohen
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Department of Physics, Harvard University, Cambridge, MA 02138, USA.
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42
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Parallel locomotor control strategies in mice and flies. Curr Opin Neurobiol 2022; 73:102516. [DOI: 10.1016/j.conb.2022.01.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 12/23/2021] [Accepted: 01/06/2022] [Indexed: 12/26/2022]
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43
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Rajan G, Lafaye J, Faini G, Carbo-Tano M, Duroure K, Tanese D, Panier T, Candelier R, Henninger J, Britz R, Judkewitz B, Gebhardt C, Emiliani V, Debregeas G, Wyart C, Del Bene F. Evolutionary divergence of locomotion in two related vertebrate species. Cell Rep 2022; 38:110585. [PMID: 35354040 DOI: 10.1016/j.celrep.2022.110585] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 12/15/2021] [Accepted: 03/08/2022] [Indexed: 11/27/2022] Open
Abstract
Locomotion exists in diverse forms in nature; however, little is known about how closely related species with similar neuronal circuitry can evolve different navigational strategies to explore their environments. Here, we investigate this question by comparing divergent swimming pattern in larval Danionella cerebrum (DC) and zebrafish (ZF). We show that DC displays long continuous swimming events when compared with the short burst-and-glide swimming in ZF. We reveal that mesencephalic locomotion maintenance neurons in the midbrain are sufficient to cause this increased swimming. Moreover, we propose that the availability of dissolved oxygen and timing of swim bladder inflation drive the observed differences in the swim pattern. Our findings uncover the neural substrate underlying the evolutionary divergence of locomotion and its adaptation to their environmental constraints.
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Affiliation(s)
- Gokul Rajan
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 75012 Paris, France; Institut Curie, PSL Research University, INSERM U934, CNRS UMR3215, Paris, France
| | - Julie Lafaye
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP), 75005 Paris, France
| | - Giulia Faini
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 75012 Paris, France
| | - Martin Carbo-Tano
- Institut du Cerveau (ICM), Sorbonne Universités, UPMC Univ Paris 06 CNRS UMR 7225, Inserm U1127, Hôpital Pitié-Salpêtrière, 75013 Paris, France
| | - Karine Duroure
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 75012 Paris, France; Institut Curie, PSL Research University, INSERM U934, CNRS UMR3215, Paris, France
| | - Dimitrii Tanese
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 75012 Paris, France
| | - Thomas Panier
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP), 75005 Paris, France
| | - Raphaël Candelier
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP), 75005 Paris, France
| | - Jörg Henninger
- Charité-Universitätsmedizin Berlin, Einstein Center for Neurosciences, NeuroCure Cluster of Excellence, 10117 Berlin, Germany
| | - Ralf Britz
- Senckenberg Naturhistorische Sammlungen Dresden, Museum für Zoologie, 01109 Dresden, Germany
| | - Benjamin Judkewitz
- Charité-Universitätsmedizin Berlin, Einstein Center for Neurosciences, NeuroCure Cluster of Excellence, 10117 Berlin, Germany
| | - Christoph Gebhardt
- Institut Curie, PSL Research University, INSERM U934, CNRS UMR3215, Paris, France
| | - Valentina Emiliani
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 75012 Paris, France
| | - Georges Debregeas
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP), 75005 Paris, France
| | - Claire Wyart
- Institut du Cerveau (ICM), Sorbonne Universités, UPMC Univ Paris 06 CNRS UMR 7225, Inserm U1127, Hôpital Pitié-Salpêtrière, 75013 Paris, France
| | - Filippo Del Bene
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 75012 Paris, France; Institut Curie, PSL Research University, INSERM U934, CNRS UMR3215, Paris, France.
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44
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Vandevoorde K, Vollenkemper L, Schwan C, Kohlhase M, Schenck W. Using Artificial Intelligence for Assistance Systems to Bring Motor Learning Principles into Real World Motor Tasks. SENSORS 2022; 22:s22072481. [PMID: 35408094 PMCID: PMC9002555 DOI: 10.3390/s22072481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/18/2022] [Accepted: 03/20/2022] [Indexed: 11/03/2022]
Abstract
Humans learn movements naturally, but it takes a lot of time and training to achieve expert performance in motor skills. In this review, we show how modern technologies can support people in learning new motor skills. First, we introduce important concepts in motor control, motor learning and motor skill learning. We also give an overview about the rapid expansion of machine learning algorithms and sensor technologies for human motion analysis. The integration between motor learning principles, machine learning algorithms and recent sensor technologies has the potential to develop AI-guided assistance systems for motor skill training. We give our perspective on this integration of different fields to transition from motor learning research in laboratory settings to real world environments and real world motor tasks and propose a stepwise approach to facilitate this transition.
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45
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Chen Y, Li W, Xiang L, Mi X, Duan M, Wu C. Fish personality affects their exposure to microplastics. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 233:113301. [PMID: 35176674 DOI: 10.1016/j.ecoenv.2022.113301] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 01/07/2022] [Accepted: 02/08/2022] [Indexed: 06/14/2023]
Abstract
Microplastics (MPs) have been found in nearly half of the fish samples collected from the field worldwide. There are feeding behavior differences caused by animal personality among fish individuals. However, how personality affects the exposure of fish to microplastics is unclear. In this study, adult zebrafish were used as a model to study the effects of fish personality (boldness) on MPs exposure. Experiment showed that zebrafish captured MPs actively when MPs were added to the system but spit part of the MPs out after capturing. Bold zebrafish had higher feeding activities, captured MPs more frequently and swallowed more MPs than shy zebrafish. Zebrafish ingested brine shrimp preferentially when both brine shrimp and MPs were provided at the same time, and less MPs were swallowed in co-ingestion situation. Spearman correlation analysis indicated that there is a significantly positive correlation between boldness and feeding MPs frequency. Results of this work demonstrate that zebrafish mistake MPs as food and capture them actively but can discriminate MPs as inedible substances after ingestion and spit part of the MPs out. Bold zebrafish have a higher MP exposure burden than shy zebrafish due to their difference in feeding behaviors. The influence of fish personality needs to be considered for future toxicity studies and risk assessment of fish exposed to MPs.
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Affiliation(s)
- Yuling Chen
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Weiwei Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Lingli Xiang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; China West Normal University, Sichuan 637002, China
| | - Xiangyuan Mi
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Ming Duan
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
| | - Chenxi Wu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
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46
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Reddy G, Desban L, Tanaka H, Roussel J, Mirat O, Wyart C. A lexical approach for identifying behavioural action sequences. PLoS Comput Biol 2022; 18:e1009672. [PMID: 35007275 PMCID: PMC8782473 DOI: 10.1371/journal.pcbi.1009672] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 01/21/2022] [Accepted: 11/16/2021] [Indexed: 12/14/2022] Open
Abstract
Animals display characteristic behavioural patterns when performing a task, such as the spiraling of a soaring bird or the surge-and-cast of a male moth searching for a female. Identifying such recurring sequences occurring rarely in noisy behavioural data is key to understanding the behavioural response to a distributed stimulus in unrestrained animals. Existing models seek to describe the dynamics of behaviour or segment individual locomotor episodes rather than to identify the rare and transient sequences of locomotor episodes that make up the behavioural response. To fill this gap, we develop a lexical, hierarchical model of behaviour. We designed an unsupervised algorithm called "BASS" to efficiently identify and segment recurring behavioural action sequences transiently occurring in long behavioural recordings. When applied to navigating larval zebrafish, BASS extracts a dictionary of remarkably long, non-Markovian sequences consisting of repeats and mixtures of slow forward and turn bouts. Applied to a novel chemotaxis assay, BASS uncovers chemotactic strategies deployed by zebrafish to avoid aversive cues consisting of sequences of fast large-angle turns and burst swims. In a simulated dataset of soaring gliders climbing thermals, BASS finds the spiraling patterns characteristic of soaring behaviour. In both cases, BASS succeeds in identifying rare action sequences in the behaviour deployed by freely moving animals. BASS can be easily incorporated into the pipelines of existing behavioural analyses across diverse species, and even more broadly used as a generic algorithm for pattern recognition in low-dimensional sequential data.
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Affiliation(s)
- Gautam Reddy
- NSF-Simons Center for Mathematical & Statistical Analysis of Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Laura Desban
- Sorbonne Université, Institut du Cerveau (ICM), Inserm U 1127, CNRS UMR 7225, Paris, France
| | - Hidenori Tanaka
- Physics & Informatics Laboratories, NTT Research, Inc., East Palo Alto, California, United States of America
- Department of Applied Physics, Stanford University, Stanford, California, United States of America
| | - Julian Roussel
- Sorbonne Université, Institut du Cerveau (ICM), Inserm U 1127, CNRS UMR 7225, Paris, France
| | - Olivier Mirat
- Sorbonne Université, Institut du Cerveau (ICM), Inserm U 1127, CNRS UMR 7225, Paris, France
| | - Claire Wyart
- Sorbonne Université, Institut du Cerveau (ICM), Inserm U 1127, CNRS UMR 7225, Paris, France
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Harpaz R, Nguyen MN, Bahl A, Engert F. Precise visuomotor transformations underlying collective behavior in larval zebrafish. Nat Commun 2021; 12:6578. [PMID: 34772934 PMCID: PMC8590009 DOI: 10.1038/s41467-021-26748-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 10/19/2021] [Indexed: 12/21/2022] Open
Abstract
Complex schooling behaviors result from local interactions among individuals. Yet, how sensory signals from neighbors are analyzed in the visuomotor stream of animals is poorly understood. Here, we studied aggregation behavior in larval zebrafish and found that over development larvae transition from overdispersed groups to tight shoals. Using a virtual reality assay, we characterized the algorithms fish use to transform visual inputs from neighbors into movement decisions. We found that young larvae turn away from virtual neighbors by integrating and averaging retina-wide visual occupancy within each eye, and by using a winner-take-all strategy for binocular integration. As fish mature, their responses expand to include attraction to virtual neighbors, which is based on similar algorithms of visual integration. Using model simulations, we show that the observed algorithms accurately predict group structure over development. These findings allow us to make testable predictions regarding the neuronal circuits underlying collective behavior in zebrafish.
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Affiliation(s)
- Roy Harpaz
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, 02138, USA.
- Center for Brain Science, Harvard University, Cambridge, MA, 02138, USA.
| | - Minh Nguyet Nguyen
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Armin Bahl
- Centre for the Advanced Study of Collective Behaviour, University of Konstanz, Konstanz, 78464, Germany
| | - Florian Engert
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, 02138, USA
- Center for Brain Science, Harvard University, Cambridge, MA, 02138, USA
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48
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Fuss T. Mate Choice, Sex Roles and Sexual Cognition: Neuronal Prerequisites Supporting Cognitive Mate Choice. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.749499] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Across taxa, mate choice is a highly selective process involving both intra- and intersexual selection processes aiming to pass on one’s genes, making mate choice a pivotal tool of sexual selection. Individuals adapt mate choice behavior dynamically in response to environmental and social changes. These changes are perceived sensorily and integrated on a neuronal level, which ultimately leads to an adequate behavioral response. Along with perception and prior to an appropriate behavioral response, the choosing sex has (1) to recognize and discriminate between the prospective mates and (2) to be able to assess and compare their performance in order to make an informed decision. To do so, cognitive processes allow for the simultaneous processing of multiple information from the (in-) animate environment as well as from a variety of both sexual and social (but non-sexual) conspecific cues. Although many behavioral aspects of cognition on one side and of mate choice displays on the other are well understood, the interplay of neuronal mechanisms governing both determinants, i.e., governing cognitive mate choice have been described only vaguely. This review aimed to throw a spotlight on neuronal prerequisites, networks and processes supporting the interaction between mate choice, sex roles and sexual cognition, hence, supporting cognitive mate choice. How does neuronal activity differ between males and females regarding social cognition? Does sex or the respective sex role within the prevailing mating system mirror at a neuronal level? How does cognitive competence affect mate choice? Conversely, how does mate choice affect the cognitive abilities of both sexes? Benefitting from studies using different neuroanatomical techniques such as neuronal activity markers, differential coexpression or candidate gene analyses, modulatory effects of neurotransmitters and hormones, or imaging techniques such as fMRI, there is ample evidence pointing to a reflection of sex and the respective sex role at the neuronal level, at least in individual brain regions. Moreover, this review aims to summarize evidence for cognitive abilities influencing mate choice and vice versa. At the same time, new questions arise centering the complex relationship between neurobiology, cognition and mate choice, which we will perhaps be able to answer with new experimental techniques.
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Madden ME, Suminaite D, Ortiz E, Early JJ, Koudelka S, Livesey MR, Bianco IH, Granato M, Lyons DA. CNS Hypomyelination Disrupts Axonal Conduction and Behavior in Larval Zebrafish. J Neurosci 2021; 41:9099-9111. [PMID: 34544838 PMCID: PMC8570833 DOI: 10.1523/jneurosci.0842-21.2021] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 08/11/2021] [Accepted: 08/16/2021] [Indexed: 11/21/2022] Open
Abstract
Myelination is essential for central nervous system (CNS) formation, health and function. As a model organism, larval zebrafish have been extensively employed to investigate the molecular and cellular basis of CNS myelination, because of their genetic tractability and suitability for non-invasive live cell imaging. However, it has not been assessed to what extent CNS myelination affects neural circuit function in zebrafish larvae, prohibiting the integration of molecular and cellular analyses of myelination with concomitant network maturation. To test whether larval zebrafish might serve as a suitable platform with which to study the effects of CNS myelination and its dysregulation on circuit function, we generated zebrafish myelin regulatory factor (myrf) mutants with CNS-specific hypomyelination and investigated how this affected their axonal conduction properties and behavior. We found that myrf mutant larvae exhibited increased latency to perform startle responses following defined acoustic stimuli. Furthermore, we found that hypomyelinated animals often selected an impaired response to acoustic stimuli, exhibiting a bias toward reorientation behavior instead of the stimulus-appropriate startle response. To begin to study how myelination affected the underlying circuitry, we established electrophysiological protocols to assess various conduction properties along single axons. We found that the hypomyelinated myrf mutants exhibited reduced action potential conduction velocity and an impaired ability to sustain high-frequency action potential firing. This study indicates that larval zebrafish can be used to bridge molecular and cellular investigation of CNS myelination with multiscale assessment of neural circuit function.SIGNIFICANCE STATEMENT Myelination of CNS axons is essential for their health and function, and it is now clear that myelination is a dynamic life-long process subject to modulation by neuronal activity. However, it remains unclear precisely how changes to myelination affects animal behavior and underlying action potential conduction along axons in intact neural circuits. In recent years, zebrafish have been employed to study cellular and molecular mechanisms of myelination, because of their relatively simple, optically transparent, experimentally tractable vertebrate nervous system. Here we find that changes to myelination alter the behavior of young zebrafish and action potential conduction along individual axons, providing a platform to integrate molecular, cellular, and circuit level analyses of myelination using this model.
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Affiliation(s)
- M E Madden
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, United Kingdom
| | - D Suminaite
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, United Kingdom
| | - E Ortiz
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - J J Early
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, United Kingdom
| | - S Koudelka
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, United Kingdom
| | - M R Livesey
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, United Kingdom
- Sheffield Institute for Translational Neuroscience, Department of Neuroscience, The University of Sheffield, Sheffield S10 2HQ, United Kingdom
| | - I H Bianco
- Neuroscience, Physiology and Pharmacology, University College London, London WC1E 6BT, United Kingdom
| | - M Granato
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - D A Lyons
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, United Kingdom
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Mancienne T, Marquez-Legorreta E, Wilde M, Piber M, Favre-Bulle I, Vanwalleghem G, Scott EK. Contributions of Luminance and Motion to Visual Escape and Habituation in Larval Zebrafish. Front Neural Circuits 2021; 15:748535. [PMID: 34744637 PMCID: PMC8568047 DOI: 10.3389/fncir.2021.748535] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 09/24/2021] [Indexed: 11/13/2022] Open
Abstract
Animals from insects to humans perform visual escape behavior in response to looming stimuli, and these responses habituate if looms are presented repeatedly without consequence. While the basic visual processing and motor pathways involved in this behavior have been described, many of the nuances of predator perception and sensorimotor gating have not. Here, we have performed both behavioral analyses and brain-wide cellular-resolution calcium imaging in larval zebrafish while presenting them with visual loom stimuli or stimuli that selectively deliver either the movement or the dimming properties of full loom stimuli. Behaviorally, we find that, while responses to repeated loom stimuli habituate, no such habituation occurs when repeated movement stimuli (in the absence of luminance changes) are presented. Dim stimuli seldom elicit escape responses, and therefore cannot habituate. Neither repeated movement stimuli nor repeated dimming stimuli habituate the responses to subsequent full loom stimuli, suggesting that full looms are required for habituation. Our calcium imaging reveals that motion-sensitive neurons are abundant in the brain, that dim-sensitive neurons are present but more rare, and that neurons responsive to both stimuli (and to full loom stimuli) are concentrated in the tectum. Neurons selective to full loom stimuli (but not to movement or dimming) were not evident. Finally, we explored whether movement- or dim-sensitive neurons have characteristic response profiles during habituation to full looms. Such functional links between baseline responsiveness and habituation rate could suggest a specific role in the brain-wide habituation network, but no such relationships were found in our data. Overall, our results suggest that, while both movement- and dim-sensitive neurons contribute to predator escape behavior, neither plays a specific role in brain-wide visual habituation networks or in behavioral habituation.
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Affiliation(s)
- Tessa Mancienne
- The Queensland Brain Institute, The University of Queensland, Saint Lucia, QLD, Australia
| | | | - Maya Wilde
- The Queensland Brain Institute, The University of Queensland, Saint Lucia, QLD, Australia
| | - Marielle Piber
- School of Medicine, Medical Sciences, and Nutrition, University of Aberdeen, Aberdeen, United Kingdom
| | - Itia Favre-Bulle
- The Queensland Brain Institute, The University of Queensland, Saint Lucia, QLD, Australia
- School of Mathematics and Physics, The University of Queensland, Saint Lucia, QLD, Australia
| | - Gilles Vanwalleghem
- The Queensland Brain Institute, The University of Queensland, Saint Lucia, QLD, Australia
| | - Ethan K. Scott
- The Queensland Brain Institute, The University of Queensland, Saint Lucia, QLD, Australia
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