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Bénichou A, Masson JB, Vestergaard CL. Compression-based inference of network motif sets. PLoS Comput Biol 2024; 20:e1012460. [PMID: 39388477 DOI: 10.1371/journal.pcbi.1012460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 09/04/2024] [Indexed: 10/12/2024] Open
Abstract
Physical and functional constraints on biological networks lead to complex topological patterns across multiple scales in their organization. A particular type of higher-order network feature that has received considerable interest is network motifs, defined as statistically regular subgraphs. These may implement fundamental logical and computational circuits and are referred to as "building blocks of complex networks". Their well-defined structures and small sizes also enable the testing of their functions in synthetic and natural biological experiments. Here, we develop a framework for motif mining based on lossless network compression using subgraph contractions. This provides an alternative definition of motif significance which allows us to compare different motifs and select the collectively most significant set of motifs as well as other prominent network features in terms of their combined compression of the network. Our approach inherently accounts for multiple testing and correlations between subgraphs and does not rely on a priori specification of an appropriate null model. It thus overcomes common problems in hypothesis testing-based motif analysis and guarantees robust statistical inference. We validate our methodology on numerical data and then apply it on synaptic-resolution biological neural networks, as a medium for comparative connectomics, by evaluating their respective compressibility and characterize their inferred circuit motifs.
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Affiliation(s)
- Alexis Bénichou
- Institut Pasteur, Université Paris Cité, CNRS UMR 3751, Decision and Bayesian Computation, Paris, France
- Epiméthée, Inria, Paris, France
| | - Jean-Baptiste Masson
- Institut Pasteur, Université Paris Cité, CNRS UMR 3751, Decision and Bayesian Computation, Paris, France
- Epiméthée, Inria, Paris, France
| | - Christian L Vestergaard
- Institut Pasteur, Université Paris Cité, CNRS UMR 3751, Decision and Bayesian Computation, Paris, France
- Epiméthée, Inria, Paris, France
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2
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Bukwich M, Campbell MG, Zoltowski D, Kingsbury L, Tomov MS, Stern J, Kim HR, Drugowitsch J, Linderman SW, Uchida N. Competitive integration of time and reward explains value-sensitive foraging decisions and frontal cortex ramping dynamics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.05.556267. [PMID: 37732217 PMCID: PMC10508756 DOI: 10.1101/2023.09.05.556267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
Patch foraging presents a ubiquitous decision-making process in which animals decide when to abandon a resource patch of diminishing value to pursue an alternative. We developed a virtual foraging task in which mouse behavior varied systematically with patch value. Mouse behavior could be explained by a model integrating time and rewards antagonistically, scaled by a latent patience state. The model accounted for deviations from predictions of optimal foraging theory. Neural recordings throughout frontal areas revealed encoding of decision variables from the integrator model, most robustly in frontal cortex. Regression modeling followed by unsupervised clustering identified a subset of ramping neurons. These neurons' firing rates ramped up gradually (up to tens of seconds), were inhibited by rewards, and were better described as a continuous ramp than a discrete stepping process. Together, these results identify integration via frontal cortex ramping dynamics as a candidate mechanism for solving patch foraging problems.
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Affiliation(s)
- Michael Bukwich
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, 02138
- Center for Brain Science, Harvard University, Cambridge, MA, 02138
- Current address: Sainsbury Wellcome Centre, University College London, London, W1T 4JG, UK
| | - Malcolm G Campbell
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, 02138
- Center for Brain Science, Harvard University, Cambridge, MA, 02138
| | - David Zoltowski
- Department of Statistics, Stanford University, Stanford, CA, 94305
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA 94305
| | - Lyle Kingsbury
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, 02138
- Center for Brain Science, Harvard University, Cambridge, MA, 02138
| | - Momchil S Tomov
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, 02138
- Center for Brain Science, Harvard University, Cambridge, MA, 02138
- Current address: Motional AD LLC, Boston, MA 02210
| | - Joshua Stern
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, 02138
- Center for Brain Science, Harvard University, Cambridge, MA, 02138
| | - HyungGoo R Kim
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, 02138
- Center for Brain Science, Harvard University, Cambridge, MA, 02138
- Center for Neuroscience Imaging Research, Institute for Basic Science, Suwon 16419, Republic of Korea
- Department of Biomedical Engineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Jan Drugowitsch
- Department of Neurobiology, Harvard Medical School, Boston, MA, 02115
| | - Scott W Linderman
- Department of Statistics, Stanford University, Stanford, CA, 94305
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA 94305
| | - Naoshige Uchida
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, 02138
- Center for Brain Science, Harvard University, Cambridge, MA, 02138
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3
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Lebovich L, Alisch T, Redhead ES, Parker MO, Loewenstein Y, Couzin ID, de Bivort BL. Spatiotemporal dynamics of locomotor decisions in Drosophila melanogaster. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.04.611038. [PMID: 39282352 PMCID: PMC11398310 DOI: 10.1101/2024.09.04.611038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/11/2024]
Abstract
Decision-making in animals often involves choosing actions while navigating the environment, a process markedly different from static decision paradigms commonly studied in laboratory settings. Even in decision-making assays in which animals can freely locomote, decision outcomes are often interpreted as happening at single points in space and single moments in time, a simplification that potentially glosses over important spatiotemporal dynamics. We investigated locomotor decision-making in Drosophila melanogaster in Y-shaped mazes, measuring the extent to which their future choices could be predicted through space and time. We demonstrate that turn-decisions can be reliably predicted from flies' locomotor dynamics, with distinct predictability phases emerging as flies progress through maze regions. We show that these predictability dynamics are not merely the result of maze geometry or wall-following tendencies, but instead reflect the capacity of flies to move in ways that depend on sustained locomotor signatures, suggesting an active, working memory-like process. Additionally, we demonstrate that fly mutants known to have sensory and information-processing deficits exhibit altered spatial predictability patterns, highlighting the role of visual, mechanosensory, and dopaminergic signaling in locomotor decision-making. Finally, highlighting the broad applicability of our analyses, we generalize our findings to other species and tasks. We show that human participants in a virtual Y-maze exhibited similar decision predictability dynamics as flies. This study advances our understanding of decision-making processes, emphasizing the importance of spatial and temporal dynamics of locomotor behavior in the lead-up to discrete choice outcomes.
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Affiliation(s)
- Lior Lebovich
- Department of Collective Behaviour, Max Planck Institute of Animal Behavior, Konstanz, Germany
- Centre for the Advanced Study of Collective Behaviour, University of Konstanz, Universitätsstraße 10, 78464, Konstanz, Germany
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Tom Alisch
- Department of Organismic & Evolutionary Biology & Center for Brain Science, Harvard University, Cambridge, Massachusetts, U.S.A
| | | | | | - Yonatan Loewenstein
- The Edmond and Lily Safra Center for Brain Sciences, The Alexander Silberman Institute of Life Sciences, Dept. of Cognitive and Brain Sciences and The Federmann Center for the Study of Rationality, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Iain D Couzin
- Department of Collective Behaviour, Max Planck Institute of Animal Behavior, Konstanz, Germany
- Centre for the Advanced Study of Collective Behaviour, University of Konstanz, Universitätsstraße 10, 78464, Konstanz, Germany
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Benjamin L de Bivort
- Department of Organismic & Evolutionary Biology & Center for Brain Science, Harvard University, Cambridge, Massachusetts, U.S.A
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4
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Rafiei F, Shekhar M, Rahnev D. The neural network RTNet exhibits the signatures of human perceptual decision-making. Nat Hum Behav 2024; 8:1752-1770. [PMID: 38997452 DOI: 10.1038/s41562-024-01914-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 05/13/2024] [Indexed: 07/14/2024]
Abstract
Convolutional neural networks show promise as models of biological vision. However, their decision behaviour, including the facts that they are deterministic and use equal numbers of computations for easy and difficult stimuli, differs markedly from human decision-making, thus limiting their applicability as models of human perceptual behaviour. Here we develop a new neural network, RTNet, that generates stochastic decisions and human-like response time (RT) distributions. We further performed comprehensive tests that showed RTNet reproduces all foundational features of human accuracy, RT and confidence and does so better than all current alternatives. To test RTNet's ability to predict human behaviour on novel images, we collected accuracy, RT and confidence data from 60 human participants performing a digit discrimination task. We found that the accuracy, RT and confidence produced by RTNet for individual novel images correlated with the same quantities produced by human participants. Critically, human participants who were more similar to the average human performance were also found to be closer to RTNet's predictions, suggesting that RTNet successfully captured average human behaviour. Overall, RTNet is a promising model of human RTs that exhibits the critical signatures of perceptual decision-making.
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Affiliation(s)
- Farshad Rafiei
- School of Psychology, Georgia Institute of Technology, Atlanta, GA, USA.
| | - Medha Shekhar
- School of Psychology, Georgia Institute of Technology, Atlanta, GA, USA
| | - Dobromir Rahnev
- School of Psychology, Georgia Institute of Technology, Atlanta, GA, USA
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5
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Harpaz R, Phillips M, Goel R, Fishman MC, Engert F. Experience-dependent modulation of collective behavior in larval zebrafish. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.02.606403. [PMID: 39149341 PMCID: PMC11326175 DOI: 10.1101/2024.08.02.606403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Complex group behavior can emerge from simple inter-individual interactions. Commonly, these interactions are considered static and hardwired and little is known about how experience and learning affect collective group behavior. Young larvae use well described visuomotor transformations to guide interindividual interactions and collective group structure. Here, we use naturalistic and virtual-reality (VR) experiments to impose persistent changes in population density and measure their effects on future visually evoked turning behavior and the resulting changes in group structure. We find that neighbor distances decrease after exposure to higher population densities, and increase after the experience of lower densities. These adaptations develop slowly and gradually, over tens of minutes and remain stable over many hours. Mechanistically, we find that larvae estimate their current group density by tracking the frequency of neighbor-evoked looming events on the retina and couple the strength of their future interactions to that estimate. A time-varying state-space model that modulates agents' social interactions based on their previous visual-social experiences, accurately describes our behavioral observations and predicts novel aspects of behavior. These findings provide concrete evidence that inter-individual interactions are not static, but rather continuously evolve based on past experience and current environmental demands. The underlying neurobiological mechanisms of experience dependent modulation can now be explored in this small and transparent model organism.
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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 02138, USA
| | - Morgan Phillips
- Department of Molecular and Cellular Biology, Harvard University, Cambridge 02138, USA
- Center for Brain Science, Harvard University, Cambridge 02138, USA
| | - Ronan Goel
- Department of Molecular and Cellular Biology, Harvard University, Cambridge 02138, USA
- Center for Brain Science, Harvard University, Cambridge 02138, USA
| | - Mark C Fishman
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Florian Engert
- Department of Molecular and Cellular Biology, Harvard University, Cambridge 02138, USA
- Center for Brain Science, Harvard University, Cambridge 02138, USA
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6
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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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7
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Vohra SK, Harth P, Isoe Y, Bahl A, Fotowat H, Engert F, Hege HC, Baum D. A Visual Interface for Exploring Hypotheses About Neural Circuits. IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS 2024; 30:3945-3958. [PMID: 37022819 PMCID: PMC11252567 DOI: 10.1109/tvcg.2023.3243668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
One of the fundamental problems in neurobiological research is to understand how neural circuits generate behaviors in response to sensory stimuli. Elucidating such neural circuits requires anatomical and functional information about the neurons that are active during the processing of the sensory information and generation of the respective response, as well as an identification of the connections between these neurons. With modern imaging techniques, both morphological properties of individual neurons as well as functional information related to sensory processing, information integration and behavior can be obtained. Given the resulting information, neurobiologists are faced with the task of identifying the anatomical structures down to individual neurons that are linked to the studied behavior and the processing of the respective sensory stimuli. Here, we present a novel interactive tool that assists neurobiologists in the aforementioned tasks by allowing them to extract hypothetical neural circuits constrained by anatomical and functional data. Our approach is based on two types of structural data: brain regions that are anatomically or functionally defined, and morphologies of individual neurons. Both types of structural data are interlinked and augmented with additional information. The presented tool allows the expert user to identify neurons using Boolean queries. The interactive formulation of these queries is supported by linked views, using, among other things, two novel 2D abstractions of neural circuits. The approach was validated in two case studies investigating the neural basis of vision-based behavioral responses in zebrafish larvae. Despite this particular application, we believe that the presented tool will be of general interest for exploring hypotheses about neural circuits in other species, genera and taxa.
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8
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Wilde M, Poulsen RE, Qin W, Arnold J, Favre-Bulle IA, Mattingley JB, Scott EK, Stednitz SJ. EVIDENCE FOR AUDITORY STIMULUS-SPECIFIC ADAPTATION BUT NOT DEVIANCE DETECTION IN LARVAL ZEBRAFISH BRAINS. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.14.597058. [PMID: 38915708 PMCID: PMC11195219 DOI: 10.1101/2024.06.14.597058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Animals receive a constant stream of sensory input, and detecting changes in this sensory landscape is critical to their survival. One signature of change detection in humans is the auditory mismatch negativity (MMN), a neural response to unexpected stimuli that deviate from a predictable sequence. This process requires the auditory system to adapt to specific repeated stimuli while remaining sensitive to novel input (stimulus-specific adaptation). MMN was originally described in humans, and equivalent responses have been found in other mammals and birds, but it is not known to what extent this deviance detection circuitry is evolutionarily conserved. Here we present the first evidence for stimulus-specific adaptation in the brain of a teleost fish, using whole-brain calcium imaging of larval zebrafish at single-neuron resolution with selective plane illumination microscopy. We found frequency-specific responses across the brain with variable response amplitudes for frequencies of the same volume, and created a loudness curve to model this effect. We presented an auditory 'oddball' stimulus in an otherwise predictable train of pure tone stimuli, and did not find a population of neurons with specific responses to deviant tones that were not otherwise explained by stimulus-specific adaptation. Further, we observed no deviance responses to an unexpected omission of a sound in a repetitive sequence of white noise bursts. These findings extend the known scope of auditory adaptation and deviance responses across the evolutionary tree, and lay groundwork for future studies to describe the circuitry underlying auditory adaptation at the level of individual neurons.
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Affiliation(s)
- Maya Wilde
- Queensland Brain Institute, University of Queensland
- Department of Anatomy and Physiology, University of Melbourne
| | - Rebecca E Poulsen
- Department of Linguistics, Faculty of Medicine, Health and Human Sciences, Macquarie University
| | - Wei Qin
- Department of Anatomy and Physiology, University of Melbourne
| | - Joshua Arnold
- Queensland Brain Institute, University of Queensland
| | - Itia A Favre-Bulle
- Queensland Brain Institute, University of Queensland
- School of Mathematics and Physics, University of Queensland
| | - Jason B Mattingley
- Queensland Brain Institute, University of Queensland
- School of Psychology, University of Queensland
| | - Ethan K Scott
- Queensland Brain Institute, University of Queensland
- Department of Anatomy and Physiology, University of Melbourne
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9
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Chen AB, Duque M, Wang VM, Dhanasekar M, Mi X, Rymbek A, Tocquer L, Narayan S, Prober D, Yu G, Wyart C, Engert F, Ahrens MB. Norepinephrine changes behavioral state via astroglial purinergic signaling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.23.595576. [PMID: 38826423 PMCID: PMC11142163 DOI: 10.1101/2024.05.23.595576] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Both neurons and glia communicate via diffusible neuromodulatory substances, but the substrates of computation in such neuromodulatory networks are unclear. During behavioral transitions in the larval zebrafish, the neuromodulator norepinephrine drives fast excitation and delayed inhibition of behavior and circuit activity. We find that the inhibitory arm of this feedforward motif is implemented by astroglial purinergic signaling. Neuromodulator imaging, behavioral pharmacology, and perturbations of neurons and astroglia reveal that norepinephrine triggers astroglial release of adenosine triphosphate, extracellular conversion into adenosine, and behavioral suppression through activation of hindbrain neuronal adenosine receptors. This work, along with a companion piece by Lefton and colleagues demonstrating an analogous pathway mediating the effect of norepinephrine on synaptic connectivity in mice, identifies a computational and behavioral role for an evolutionarily conserved astroglial purinergic signaling axis in norepinephrine-mediated behavioral and brain state transitions.
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Affiliation(s)
- Alex B. Chen
- Janelia Research Campus, Howard Hughes Medical Institute; Ashburn, VA 20147, USA
- Department of Molecular and Cellular Biology, Harvard University; Cambridge, MA 02138, USA
- Graduate Program in Neuroscience, Harvard Medical School; Boston, MA 02115, USA
| | - Marc Duque
- Department of Molecular and Cellular Biology, Harvard University; Cambridge, MA 02138, USA
- Graduate Program in Neuroscience, Harvard Medical School; Boston, MA 02115, USA
| | - Vickie M. Wang
- Department of Molecular and Cellular Biology, Harvard University; Cambridge, MA 02138, USA
- Graduate Program in Neuroscience, Harvard Medical School; Boston, MA 02115, USA
| | - Mahalakshmi Dhanasekar
- Sorbonne Université, Paris Brain Institute (Institut du Cerveau, ICM), Institut National de la Santé et de la Recherche Médicale U1127, Centre National de la Recherche Scientifique Unité Mixte de Recherche 7225, Assistance Publique–Hôpitaux de Paris, Campus Hospitalier Pitié-Salpêtrière, Paris, France
| | - Xuelong Mi
- Bradley Department of Electrical and Computer Engineering; Virginia Polytechnic Institute and State University; Arlington, VA 22203, USA
| | - Altyn Rymbek
- Tianqiao and Chrissy Chen Institute for Neuroscience, Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Loeva Tocquer
- Sorbonne Université, Paris Brain Institute (Institut du Cerveau, ICM), Institut National de la Santé et de la Recherche Médicale U1127, Centre National de la Recherche Scientifique Unité Mixte de Recherche 7225, Assistance Publique–Hôpitaux de Paris, Campus Hospitalier Pitié-Salpêtrière, Paris, France
| | - Sujatha Narayan
- Janelia Research Campus, Howard Hughes Medical Institute; Ashburn, VA 20147, USA
- Present address: Allen Institute for Neural Dynamics; Seattle, WA 98109, USA
| | - David Prober
- Tianqiao and Chrissy Chen Institute for Neuroscience, Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Guoqiang Yu
- Department of Automation, Tsinghua University; Beijing 100084, P.R. China
| | - Claire Wyart
- Sorbonne Université, Paris Brain Institute (Institut du Cerveau, ICM), Institut National de la Santé et de la Recherche Médicale U1127, Centre National de la Recherche Scientifique Unité Mixte de Recherche 7225, Assistance Publique–Hôpitaux de Paris, Campus Hospitalier Pitié-Salpêtrière, Paris, France
| | - Florian Engert
- Department of Molecular and Cellular Biology, Harvard University; Cambridge, MA 02138, USA
| | - Misha B. Ahrens
- Janelia Research Campus, Howard Hughes Medical Institute; Ashburn, VA 20147, USA
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10
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Hughes S, Hessel EVS. Zebrafish and nematodes as whole organism models to measure developmental neurotoxicity. Crit Rev Toxicol 2024; 54:330-343. [PMID: 38832580 DOI: 10.1080/10408444.2024.2342448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 04/05/2024] [Indexed: 06/05/2024]
Abstract
Despite the growing epidemiological evidence of an association between toxin exposure and developmental neurotoxicity (DNT), systematic testing of DNT is not mandatory in international regulations for admission of pharmaceuticals or industrial chemicals. However, to date around 200 compounds, ranging from pesticides, pharmaceuticals and industrial chemicals, have been tested for DNT in the current OECD test guidelines (TG-443 or TG-426). There are calls for the development of new approach methodologies (NAMs) for DNT, which has resulted in a DNT testing battery using in vitro human cell-based assays. These assays provide a means to elucidate the molecular mechanisms of toxicity in humans which is lacking in animal-based toxicity tests. However, cell-based assays do not represent all steps of the complex process leading to DNT. Validated models with a multi-organ network of pathways that interact at the molecular, cellular and tissue level at very specific timepoints in a life cycle are currently missing. Consequently, whole model organisms are being developed to screen for, and causally link, new molecular targets of DNT compounds and how they affect whole brain development and neurobehavioral endpoints. Given the practical and ethical restraints associated with vertebrate testing, lower animal models that qualify as 3 R (reduce, refine and replace) models, including the nematode (Caenorhabditis elegans) and the zebrafish (Danio rerio) will prove particularly valuable for unravelling toxicity pathways leading to DNT. Although not as complex as the human brain, these 3 R-models develop a complete functioning brain with numerous neurodevelopmental processes overlapping with human brain development. Importantly, the main signalling pathways relating to (neuro)development, metabolism and growth are highly conserved in these models. We propose the use of whole model organisms specifically zebrafish and C. elegans for DNT relevant endpoints.
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Affiliation(s)
- Samantha Hughes
- Department of Environmental Health and Toxicology, A-LIFE, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Ellen V S Hessel
- Centre for Health Protection, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
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11
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Collins EMS, Hessel EVS, Hughes S. How neurobehavior and brain development in alternative whole-organism models can contribute to prediction of developmental neurotoxicity. Neurotoxicology 2024; 102:48-57. [PMID: 38552718 PMCID: PMC11139590 DOI: 10.1016/j.neuro.2024.03.005] [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: 12/22/2023] [Revised: 03/01/2024] [Accepted: 03/23/2024] [Indexed: 04/12/2024]
Abstract
Developmental neurotoxicity (DNT) is not routinely evaluated in chemical risk assessment because current test paradigms for DNT require the use of mammalian models which are ethically controversial, expensive, and resource demanding. Consequently, efforts have focused on revolutionizing DNT testing through affordable novel alternative methods for risk assessment. The goal is to develop a DNT in vitro test battery amenable to high-throughput screening (HTS). Currently, the DNT in vitro test battery consists primarily of human cell-based assays because of their immediate relevance to human health. However, such cell-based assays alone are unable to capture the complexity of a developing nervous system. Whole organismal systems that qualify as 3 R (Replace, Reduce and Refine) models are urgently needed to complement cell-based DNT testing. These models can provide the necessary organismal context and be used to explore the impact of chemicals on brain function by linking molecular and/or cellular changes to behavioural readouts. The nematode Caenorhabditis elegans, the planarian Dugesia japonica, and embryos of the zebrafish Danio rerio are all suited to low-cost HTS and each has unique strengths for DNT testing. Here, we review the strengths and the complementarity of these organisms in a novel, integrative context and highlight how they can augment current cell-based assays for more comprehensive and robust DNT screening of chemicals. Considering the limitations of all in vitro test systems, we discuss how a smart combinatory use of these systems will contribute to a better human relevant risk assessment of chemicals that considers the complexity of the developing brain.
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Affiliation(s)
- Eva-Maria S Collins
- Swarthmore College, Biology, 500 College Avenue, Swarthmore, PA 19081, USA; Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Center of Excellence in Environmental Toxicology, University of Pennsylvania, Philadelphia, PA, USA.
| | - Ellen V S Hessel
- Centre for Health Protection, National Institute for Public Health and the Environment (RIVM), Antonie van Leeuwenhoeklaan 9, Bilthoven, 3721 MA, the Netherlands
| | - Samantha Hughes
- Department of Environmental Health and Toxicology, A-LIFE, Vrije Universiteit Amsterdam, de Boelelaan 1085, Amsterdam, 1081 HV, the Netherlands.
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12
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Lewis CM, Wunderle T, Fries P. Top-down modulation of visual cortical stimulus encoding and gamma independent of firing rates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.11.589006. [PMID: 38645050 PMCID: PMC11030389 DOI: 10.1101/2024.04.11.589006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Neurons in primary visual cortex integrate sensory input with signals reflecting the animal's internal state to support flexible behavior. Internal variables, such as expectation, attention, or current goals, are imposed in a top-down manner via extensive feedback projections from higher-order areas. We optogenetically activated a high-order visual area, area 21a, in the lightly anesthetized cat (OptoTD), while recording from neuronal populations in V1. OptoTD induced strong, up to several fold, changes in gamma-band synchronization together with much smaller changes in firing rate, and the two effects showed no correlation. OptoTD effects showed specificity for the features of the simultaneously presented visual stimuli. OptoTD-induced changes in gamma synchronization, but not firing rates, were predictive of simultaneous changes in the amount of encoded stimulus information. Our findings suggest that one important role of top-down signals is to modulate synchronization and the information encoded by populations of sensory neurons.
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13
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Zaupa M, Nagaraj N, Sylenko A, Baier H, Sawamiphak S, Filosa A. The Calmodulin-interacting peptide Pcp4a regulates feeding state-dependent behavioral choice in zebrafish. Neuron 2024; 112:1150-1164.e6. [PMID: 38295792 DOI: 10.1016/j.neuron.2024.01.001] [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: 03/01/2023] [Revised: 10/06/2023] [Accepted: 01/02/2024] [Indexed: 04/06/2024]
Abstract
Animals constantly need to judge the valence of an object in their environment: is it potential food or a threat? The brain makes fundamental decisions on the appropriate behavioral strategy by integrating external information from sensory organs and internal signals related to physiological needs. For example, a hungry animal may take more risks than a satiated one when deciding to approach or avoid an object. Using a proteomic profiling approach, we identified the Calmodulin-interacting peptide Pcp4a as a key regulator of foraging-related decisions. Food intake reduced abundance of protein and mRNA of pcp4a via dopamine D2-like receptor-mediated repression of adenylate cyclase. Accordingly, deleting the pcp4a gene made zebrafish larvae more risk averse in a binary decision assay. Strikingly, neurons in the tectum became less responsive to prey-like visual stimuli in pcp4a mutants, thus biasing the behavior toward avoidance. This study pinpoints a molecular mechanism modulating behavioral choice according to internal state.
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Affiliation(s)
- Margherita Zaupa
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13092 Berlin, Germany; Freie Universität Berlin, Institute for Biology, 14195 Berlin, Germany
| | - Nagarjuna Nagaraj
- Biochemistry Core Facility, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Anna Sylenko
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13092 Berlin, Germany; Freie Universität Berlin, Institute for Biology, 14195 Berlin, Germany
| | - Herwig Baier
- Max Planck Institute for Biological Intelligence, 82152 Martinsried, Germany
| | - Suphansa Sawamiphak
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13092 Berlin, Germany
| | - Alessandro Filosa
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13092 Berlin, Germany.
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14
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Félix R, Markov DA, Renninger SL, Tomás AR, Laborde A, Carey MR, Orger MB, Portugues R. Structural and Functional Organization of Visual Responses in the Inferior Olive of Larval Zebrafish. J Neurosci 2024; 44:e2352212023. [PMID: 38195508 PMCID: PMC10883660 DOI: 10.1523/jneurosci.2352-21.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 11/22/2023] [Accepted: 12/01/2023] [Indexed: 01/11/2024] Open
Abstract
The olivo-cerebellar system plays an important role in vertebrate sensorimotor control. Here, we investigate sensory representations in the inferior olive (IO) of larval zebrafish and their spatial organization. Using single-cell labeling of genetically identified IO neurons, we find that they can be divided into at least two distinct groups based on their spatial location, dendritic morphology, and axonal projection patterns. In the same genetically targeted population, we recorded calcium activity in response to a set of visual stimuli using two-photon imaging. We found that most IO neurons showed direction-selective and binocular responses to visual stimuli and that the functional properties were spatially organized within the IO. Light-sheet functional imaging that allowed for simultaneous activity recordings at the soma and axonal level revealed tight coupling between functional properties, soma location, and axonal projection patterns of IO neurons. Taken together, our results suggest that anatomically defined classes of IO neurons correspond to distinct functional types, and that topographic connections between IO and cerebellum contribute to organization of the cerebellum into distinct functional zones.
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Affiliation(s)
- Rita Félix
- Champalimaud Research, Champalimaud Centre for the Unknown, Lisbon 1400-038, Portugal
| | - Daniil A Markov
- Max Planck Institute of Neurobiology, Sensorimotor Control Research Group, 82152 Martinsried, Germany
| | - Sabine L Renninger
- Champalimaud Research, Champalimaud Centre for the Unknown, Lisbon 1400-038, Portugal
| | - Ana Raquel Tomás
- Champalimaud Research, Champalimaud Centre for the Unknown, Lisbon 1400-038, Portugal
| | - Alexandre Laborde
- Champalimaud Research, Champalimaud Centre for the Unknown, Lisbon 1400-038, Portugal
| | - Megan R Carey
- Champalimaud Research, Champalimaud Centre for the Unknown, Lisbon 1400-038, Portugal
| | - Michael B Orger
- Champalimaud Research, Champalimaud Centre for the Unknown, Lisbon 1400-038, Portugal
| | - Ruben Portugues
- Max Planck Institute of Neurobiology, Sensorimotor Control Research Group, 82152 Martinsried, Germany
- Institute of Neuroscience, Technical University of Munich, 80802 Munich, Germany
- Munich Cluster of Systems Neurology (SyNergy), 81377 Munich, Germany
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15
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Barabási DL, Schuhknecht GFP, Engert F. Functional neuronal circuits emerge in the absence of developmental activity. Nat Commun 2024; 15:364. [PMID: 38191595 PMCID: PMC10774424 DOI: 10.1038/s41467-023-44681-2] [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: 05/19/2023] [Accepted: 12/29/2023] [Indexed: 01/10/2024] Open
Abstract
The complex neuronal circuitry of the brain develops from limited information contained in the genome. After the genetic code instructs the birth of neurons, the emergence of brain regions, and the formation of axon tracts, it is believed that temporally structured spiking activity shapes circuits for behavior. Here, we challenge the learning-dominated assumption that spiking activity is required for circuit formation by quantifying its contribution to the development of visually-guided swimming in the larval zebrafish. We found that visual experience had no effect on the emergence of the optomotor response (OMR) in dark-reared zebrafish. We then raised animals while pharmacologically silencing action potentials with the sodium channel blocker tricaine. After washout of the anesthetic, fish could swim and performed with 75-90% accuracy in the OMR paradigm. Brain-wide imaging confirmed that neuronal circuits came 'online' fully tuned, without requiring activity-dependent plasticity. Thus, complex sensory-guided behaviors can emerge through activity-independent developmental mechanisms.
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Affiliation(s)
- Dániel L Barabási
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA.
- Biophysics Program, Harvard University, Cambridge, MA, USA.
| | | | - Florian Engert
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
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16
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Narayanan S, Varma A, Thirumalai V. Predictive neural computations in the cerebellum contribute to motor planning and faster behavioral responses in larval zebrafish. SCIENCE ADVANCES 2024; 10:eadi6470. [PMID: 38170763 PMCID: PMC10775999 DOI: 10.1126/sciadv.adi6470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 12/01/2023] [Indexed: 01/05/2024]
Abstract
The ability to predict the future based on past experience lies at the core of the brain's ability to adapt behavior. However, the neural mechanisms that participate in generating and updating predictions are not clearly understood. Further, the evolutionary antecedents and the prevalence of predictive processing among vertebrates are even less explored. Here, we show evidence of predictive processing via the involvement of cerebellar circuits in larval zebrafish. We presented stereotyped optic flow stimuli to larval zebrafish to evoke swims and discovered that lesioning the cerebellum abolished prediction-dependent modulation of swim latency. When expectations of optic flow direction did not match with reality, error signals arrive at Purkinje cells via the olivary climbing fibers, whereas granule cells and Purkinje cells encode signals of expectation. Strong neural representations of expectation correlate with faster swim responses and vice versa. In sum, our results show evidence for predictive processing in nonmammalian vertebrates with the involvement of cerebellum, an evolutionarily conserved brain structure.
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17
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Dong K, Liu WC, Su Y, Lyu Y, Huang H, Zheng N, Rogers JA, Nan K. Scalable Electrophysiology of Millimeter-Scale Animals with Electrode Devices. BME FRONTIERS 2023; 4:0034. [PMID: 38435343 PMCID: PMC10907027 DOI: 10.34133/bmef.0034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 11/08/2023] [Indexed: 03/05/2024] Open
Abstract
Millimeter-scale animals such as Caenorhabditis elegans, Drosophila larvae, zebrafish, and bees serve as powerful model organisms in the fields of neurobiology and neuroethology. Various methods exist for recording large-scale electrophysiological signals from these animals. Existing approaches often lack, however, real-time, uninterrupted investigations due to their rigid constructs, geometric constraints, and mechanical mismatch in integration with soft organisms. The recent research establishes the foundations for 3-dimensional flexible bioelectronic interfaces that incorporate microfabricated components and nanoelectronic function with adjustable mechanical properties and multidimensional variability, offering unique capabilities for chronic, stable interrogation and stimulation of millimeter-scale animals and miniature tissue constructs. This review summarizes the most advanced technologies for electrophysiological studies, based on methods of 3-dimensional flexible bioelectronics. A concluding section addresses the challenges of these devices in achieving freestanding, robust, and multifunctional biointerfaces.
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Affiliation(s)
- Kairu Dong
- College of Pharmaceutical Sciences,
Zhejiang University, Hangzhou 310058, China
- National Key Laboratory of Advanced Drug Delivery and Release Systems,
Zhejiang University, Hangzhou 310058, China
- College of Biomedical Engineering & Instrument Science,
Zhejiang University, Hangzhou, 310027, China
| | - Wen-Che Liu
- College of Pharmaceutical Sciences,
Zhejiang University, Hangzhou 310058, China
- National Key Laboratory of Advanced Drug Delivery and Release Systems,
Zhejiang University, Hangzhou 310058, China
| | - Yuyan Su
- College of Pharmaceutical Sciences,
Zhejiang University, Hangzhou 310058, China
- Department of Gastroenterology, Brigham and Women’s Hospital,
Harvard Medical School, Boston, MA 02115, USA
| | - Yidan Lyu
- College of Pharmaceutical Sciences,
Zhejiang University, Hangzhou 310058, China
| | - Hao Huang
- College of Pharmaceutical Sciences,
Zhejiang University, Hangzhou 310058, China
- College of Chemical and Biological Engineering,
Zhejiang University, Hangzhou 310058, China
| | - Nenggan Zheng
- Qiushi Academy for Advanced Studies,
Zhejiang University, Hangzhou 310027, China
- College of Computer Science and Technology,
Zhejiang University, Hangzhou 310027, China
- State Key Lab of Brain-Machine Intelligence,
Zhejiang University, Hangzhou 310058, China
- CCAI by MOE and Zhejiang Provincial Government (ZJU), Hangzhou 310027, China
| | - John A. Rogers
- Querrey Simpson Institute for Bioelectronics,
Northwestern University, Evanston, IL 60208, USA
- Department of Biomedical Engineering,
Northwestern University, Evanston, IL 60208, USA
- Department of Materials Science and Engineering,
Northwestern University, Evanston, IL 60208, USA
- Department of Mechanical Engineering,
Northwestern University, Evanston, IL 60208, USA
| | - Kewang Nan
- College of Pharmaceutical Sciences,
Zhejiang University, Hangzhou 310058, China
- National Key Laboratory of Advanced Drug Delivery and Release Systems,
Zhejiang University, Hangzhou 310058, China
- Jinhua Institute of Zhejiang University, Jinhua 321299, China
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18
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Légaré A, Lemieux M, Desrosiers P, De Koninck P. Zebrafish brain atlases: a collective effort for a tiny vertebrate brain. NEUROPHOTONICS 2023; 10:044409. [PMID: 37786400 PMCID: PMC10541682 DOI: 10.1117/1.nph.10.4.044409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 09/03/2023] [Accepted: 09/13/2023] [Indexed: 10/04/2023]
Abstract
In the past two decades, digital brain atlases have emerged as essential tools for sharing and integrating complex neuroscience datasets. Concurrently, the larval zebrafish has become a prominent vertebrate model offering a strategic compromise for brain size, complexity, transparency, optogenetic access, and behavior. We provide a brief overview of digital atlases recently developed for the larval zebrafish brain, intersecting neuroanatomical information, gene expression patterns, and connectivity. These atlases are becoming pivotal by centralizing large datasets while supporting the generation of circuit hypotheses as functional measurements can be registered into an atlas' standard coordinate system to interrogate its structural database. As challenges persist in mapping neural circuits and incorporating functional measurements into zebrafish atlases, we emphasize the importance of collaborative efforts and standardized protocols to expand these resources to crack the complex codes of neuronal activity guiding behavior in this tiny vertebrate brain.
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Affiliation(s)
| | - Mado Lemieux
- CERVO Brain Research Center, Québec, Québec, Canada
| | - Patrick Desrosiers
- CERVO Brain Research Center, Québec, Québec, Canada
- Université Laval, Department of Physics, Engineering Physics and Optics, Québec, Québec, Canada
| | - Paul De Koninck
- CERVO Brain Research Center, Québec, Québec, Canada
- Université Laval, Department of Biochemistry, Microbiology and Bio-informatics, Québec, Québec, Canada
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19
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Evans CG, Barry MA, Perkins MH, Jing J, Weiss KR, Cropper EC. Variable task switching in the feeding network of Aplysia is a function of differential command input. J Neurophysiol 2023; 130:941-952. [PMID: 37671445 PMCID: PMC10648941 DOI: 10.1152/jn.00190.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 08/09/2023] [Accepted: 08/31/2023] [Indexed: 09/07/2023] Open
Abstract
Command systems integrate sensory information and then activate the interneurons and motor neurons that mediate behavior. Much research has established that the higher-order projection neurons that constitute these systems can play a key role in specifying the nature of the motor activity induced, or determining its parametric features. To a large extent, these insights have been obtained by contrasting activity induced by stimulating one neuron (or set of neurons) to activity induced by stimulating a different neuron (or set of neurons). The focus of our work differs. We study one type of motor program, ingestive feeding in the mollusc Aplysia californica, which can either be triggered when a single projection neuron (CBI-2) is repeatedly stimulated or can be triggered by projection neuron coactivation (e.g., activation of CBI-2 and CBI-3). We ask why this might be an advantageous arrangement. The cellular/molecular mechanisms that configure motor activity are different in the two situations because the released neurotransmitters differ. We focus on an important consequence of this arrangement, the fact that a persistent state can be induced with repeated CBI-2 stimulation that is not necessarily induced by CBI-2/3 coactivation. We show that this difference can have consequences for the ability of the system to switch from one type of activity to another.NEW & NOTEWORTHY We study a type of motor program that can be induced either by stimulating a higher-order projection neuron that induces a persistent state, or by coactivating projection neurons that configure activity but do not produce a state change. We show that when an activity is configured without a state change, it is possible to immediately return to an intermediate state that subsequently can be converted to any type of motor program.
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Affiliation(s)
- Colin G Evans
- Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States
| | - Michael A Barry
- Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States
| | - Matthew H Perkins
- Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States
| | - Jian Jing
- Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States
- State Key Laboratory of Pharmaceutical Biotechnology, Institute for Brain Sciences, Chemistry and Biomedicine Innovation Center, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Advanced Institute for Life Sciences, School of Life Sciences, Nanjing University, Nanjing, China
| | - Klaudiusz R Weiss
- Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States
| | - Elizabeth C Cropper
- Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States
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20
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Ortiz EA, Campbell PD, Nelson JC, Granato M. A single base pair substitution on Chromosome 25 in zebrafish distinguishes between development and acute regulation of behavioral thresholds. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.25.554673. [PMID: 37662318 PMCID: PMC10473726 DOI: 10.1101/2023.08.25.554673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Behavioral thresholds define the lowest stimulus intensities sufficient to elicit a behavioral response. Establishment of baseline behavioral thresholds during development is critical for proper responses throughout the animal's life. Despite the relevance of such innate thresholds, the molecular mechanisms critical to establishing behavioral thresholds during development are not well understood. The acoustic startle response is a conserved behavior whose threshold is established during development yet is subsequently acutely regulated. We have previously identified a zebrafish mutant line ( escapist ) that displays a decreased baseline or innate acoustic startle threshold. Here, we identify a single base pair substitution on Chromosome 25 located within the coding sequence of the synaptotagmin 7a ( syt7a ) gene that is tightly linked to the escapist acoustic hypersensitivity phenotype. By generating animals in which we deleted the syt7a open reading frame, and subsequent complementation testing with the escapist line, we demonstrate that loss of syt7a function is not the cause of the escapist behavioral phenotype. Nonetheless, escapist mutants provide a powerful tool to decipher the overlap between acute and developmental regulation of behavioral thresholds. Extensive behavioral analyses reveal that in escapist mutants the establishment of the innate acoustic startle threshold is impaired, while regulation of its acute threshold remains intact. Moreover, our behavioral analyses reveal a deficit in baseline responses to visual stimuli, but not in the acute regulation of responses to visual stimuli. Together, this work eliminates loss of syt7a as causative for the escapist phenotype and suggests that mechanisms that regulate the establishment of behavioral thresholds in escapist larvae can operate largely independently from those regulating acute threshold regulation.
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21
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Cai LT, Krishna VS, Hladnik TC, Guilbeault NC, Vijayakumar C, Arunachalam M, Juntti SA, Arrenberg AB, Thiele TR, Cooper EA. Spatiotemporal visual statistics of aquatic environments in the natural habitats of zebrafish. Sci Rep 2023; 13:12028. [PMID: 37491571 PMCID: PMC10368656 DOI: 10.1038/s41598-023-36099-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 05/29/2023] [Indexed: 07/27/2023] Open
Abstract
Animal sensory systems are tightly adapted to the demands of their environment. In the visual domain, research has shown that many species have circuits and systems that exploit statistical regularities in natural visual signals. The zebrafish is a popular model animal in visual neuroscience, but relatively little quantitative data is available about the visual properties of the aquatic habitats where zebrafish reside, as compared to terrestrial environments. Improving our understanding of the visual demands of the aquatic habitats of zebrafish can enhance the insights about sensory neuroscience yielded by this model system. We analyzed a video dataset of zebrafish habitats captured by a stationary camera and compared this dataset to videos of terrestrial scenes in the same geographic area. Our analysis of the spatiotemporal structure in these videos suggests that zebrafish habitats are characterized by low visual contrast and strong motion when compared to terrestrial environments. Similar to terrestrial environments, zebrafish habitats tended to be dominated by dark contrasts, particularly in the lower visual field. We discuss how these properties of the visual environment can inform the study of zebrafish visual behavior and neural processing and, by extension, can inform our understanding of the vertebrate brain.
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Affiliation(s)
- Lanya T Cai
- Herbert Wertheim School of Optometry & Vision Science, University of California, Berkeley, CA, USA
| | - Venkatesh S Krishna
- Department of Biological Sciences, University of Toronto, Scarborough, ON, Canada
| | - Tim C Hladnik
- Werner Reichardt Centre for Integrative Neuroscience, Institute of Neurobiology, University of Tübingen, Tübingen, Germany
- Graduate Training Centre for Neuroscience, University of Tübingen, Tübingen, Germany
| | - Nicholas C Guilbeault
- Department of Biological Sciences, University of Toronto, Scarborough, ON, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada
| | - Chinnian Vijayakumar
- Department of Zoology, Department of Zoology, St. Andrew's College, Gorakhpur, Uttar Pradesh, India
| | - Muthukumarasamy Arunachalam
- Department of Zoology, School of Biological Sciences, Central University of Kerala, Kasaragod, Kerala, India
- Centre for Inland Fishes and Conservation, St. Andrew's College, Gorakhpur, Uttar Pradesh, India
| | - Scott A Juntti
- Department of Biology, University of Maryland, College Park, MD, USA
| | - Aristides B Arrenberg
- Werner Reichardt Centre for Integrative Neuroscience, Institute of Neurobiology, University of Tübingen, Tübingen, Germany
| | - Tod R Thiele
- Department of Biological Sciences, University of Toronto, Scarborough, ON, Canada.
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada.
| | - Emily A Cooper
- Herbert Wertheim School of Optometry & Vision Science, University of California, Berkeley, CA, USA.
- Helen Wills Neuroscience Institute, University of California, Berkeley, CA, USA.
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22
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Vijayan V, Wang F, Wang K, Chakravorty A, Adachi A, Akhlaghpour H, Dickson BJ, Maimon G. A rise-to-threshold process for a relative-value decision. Nature 2023; 619:563-571. [PMID: 37407812 PMCID: PMC10356611 DOI: 10.1038/s41586-023-06271-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 05/26/2023] [Indexed: 07/07/2023]
Abstract
Whereas progress has been made in the identification of neural signals related to rapid, cued decisions1-3, less is known about how brains guide and terminate more ethologically relevant decisions in which an animal's own behaviour governs the options experienced over minutes4-6. Drosophila search for many seconds to minutes for egg-laying sites with high relative value7,8 and have neurons, called oviDNs, whose activity fulfills necessity and sufficiency criteria for initiating the egg-deposition motor programme9. Here we show that oviDNs express a calcium signal that (1) dips when an egg is internally prepared (ovulated), (2) drifts up and down over seconds to minutes-in a manner influenced by the relative value of substrates-as a fly determines whether to lay an egg and (3) reaches a consistent peak level just before the abdomen bend for egg deposition. This signal is apparent in the cell bodies of oviDNs in the brain and it probably reflects a behaviourally relevant rise-to-threshold process in the ventral nerve cord, where the synaptic terminals of oviDNs are located and where their output can influence behaviour. We provide perturbational evidence that the egg-deposition motor programme is initiated once this process hits a threshold and that subthreshold variation in this process regulates the time spent considering options and, ultimately, the choice taken. Finally, we identify a small recurrent circuit that feeds into oviDNs and show that activity in each of its constituent cell types is required for laying an egg. These results argue that a rise-to-threshold process regulates a relative-value, self-paced decision and provide initial insight into the underlying circuit mechanism for building this process.
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Affiliation(s)
- Vikram Vijayan
- Laboratory of Integrative Brain Function and Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA.
| | - Fei Wang
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Kaiyu Wang
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Lingang Laboratory, Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, China
| | - Arun Chakravorty
- Laboratory of Integrative Brain Function and Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Atsuko Adachi
- Laboratory of Integrative Brain Function and Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - Hessameddin Akhlaghpour
- Laboratory of Integrative Brain Function and Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
| | - Barry J Dickson
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Queensland Brain Institute, University of Queensland, St Lucia, Queensland, Australia
| | - Gaby Maimon
- Laboratory of Integrative Brain Function and Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA.
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23
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Jacobs EAK, Ryu S. Larval zebrafish as a model for studying individual variability in translational neuroscience research. Front Behav Neurosci 2023; 17:1143391. [PMID: 37424749 PMCID: PMC10328419 DOI: 10.3389/fnbeh.2023.1143391] [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: 01/12/2023] [Accepted: 05/22/2023] [Indexed: 07/11/2023] Open
Abstract
The larval zebrafish is a popular model for translational research into neurological and psychiatric disorders due to its conserved vertebrate brain structures, ease of genetic and experimental manipulation and small size and scalability to large numbers. The possibility of obtaining in vivo whole-brain cellular resolution neural data is contributing important advances into our understanding of neural circuit function and their relation to behavior. Here we argue that the larval zebrafish is ideally poised to push our understanding of how neural circuit function relates to behavior to the next level by including considerations of individual differences. Understanding variability across individuals is particularly relevant for tackling the variable presentations that neuropsychiatric conditions frequently show, and it is equally elemental if we are to achieve personalized medicine in the future. We provide a blueprint for investigating variability by covering examples from humans and other model organisms as well as existing examples from larval zebrafish. We highlight recent studies where variability may be hiding in plain sight and suggest how future studies can take advantage of existing paradigms for further exploring individual variability. We conclude with an outlook on how the field can harness the unique strengths of the zebrafish model to advance this important impending translational question.
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Affiliation(s)
- Elina A. K. Jacobs
- Institute of Human Genetics, University Medical Center of Johannes Gutenberg University Mainz, Mainz, Germany
| | - Soojin Ryu
- Institute of Human Genetics, University Medical Center of Johannes Gutenberg University Mainz, Mainz, Germany
- Living Systems Institute, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
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24
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Parvez S, Brandt ZJ, Peterson RT. Large-scale F0 CRISPR screens in vivo using MIC-Drop. Nat Protoc 2023; 18:1841-1865. [PMID: 37069311 PMCID: PMC10419324 DOI: 10.1038/s41596-023-00821-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 01/26/2023] [Indexed: 04/19/2023]
Abstract
The zebrafish is a powerful model system for studying animal development, for modeling genetic diseases, and for large-scale in vivo functional genetics. Because of its ease of use and its high efficiency in targeted gene perturbation, CRISPR-Cas9 has recently gained prominence as the tool of choice for genetic manipulation in zebrafish. However, scaling up the technique for high-throughput in vivo functional genetics has been a challenge. We recently developed a method, Multiplexed Intermixed CRISPR Droplets (MIC-Drop), that makes large-scale CRISPR screening in zebrafish possible. Here, we outline the step-by-step protocol for performing functional genetic screens in zebrafish by using MIC-Drop. MIC-Drop uses multiplexed single-guide RNAs to generate biallelic mutations in injected zebrafish embryos, allowing genetic screens to be performed in F0 animals. Combining microfluidics and DNA barcoding enables simultaneous targeting of tens to hundreds of genes from a single injection needle, while also enabling retrospective and rapid identification of the genotype responsible for an observed phenotype. The primary target audiences for MIC-Drop are developmental biologists, zebrafish geneticists, and researchers interested in performing in vivo functional genetic screens in a vertebrate model system. MIC-Drop will also prove useful in the hands of chemical biologists seeking to identify targets of small molecules that cause phenotypic changes in zebrafish. By using MIC-Drop, a typical screen of 100 genes can be conducted within 2-3 weeks by a single user.
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Affiliation(s)
- Saba Parvez
- Department of Pharmacology & Toxicology, College of Pharmacy, University of Utah, Salt Lake City, UT, USA
| | - Zachary J Brandt
- Department of Pharmacology & Toxicology, College of Pharmacy, University of Utah, Salt Lake City, UT, USA
| | - Randall T Peterson
- Department of Pharmacology & Toxicology, College of Pharmacy, University of Utah, Salt Lake City, UT, USA.
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25
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Lee CJ, Lee HY, Yu YS, Ryu KB, Lee H, Kim K, Shin SY, Gil YC, Cho SJ. Brain compartmentalization based on transcriptome analyses and its gene expression in Octopus minor. Brain Struct Funct 2023:10.1007/s00429-023-02647-6. [PMID: 37138199 DOI: 10.1007/s00429-023-02647-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 04/17/2023] [Indexed: 05/05/2023]
Abstract
Coleoid cephalopods have a high intelligence, complex structures, and large brain. The cephalopod brain is divided into supraesophageal mass, subesophageal mass and optic lobe. Although much is known about the structural organization and connections of various lobes of octopus brain, there are few studies on the brain of cephalopod at the molecular level. In this study, we demonstrated the structure of an adult Octopus minor brain by histomorphological analyses. Through visualization of neuronal and proliferation markers, we found that adult neurogenesis occurred in the vL and posterior svL. We also obtained specific 1015 genes by transcriptome of O. minor brain and selected OLFM3, NPY, GnRH, and GDF8 genes. The expression of genes in the central brain showed the possibility of using NPY and GDF8 as molecular marker of compartmentation in the central brain. This study will provide useful information for establishing a molecular atlas of cephalopod brain.
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Affiliation(s)
- Chan-Jun Lee
- Department of Biological Sciences and Biotechnology, College of Natural Sciences, Chungbuk National University, Cheongju, Chungbuk, 28644, Republic of Korea
| | - Hae-Youn Lee
- Department of Biological Sciences and Biotechnology, College of Natural Sciences, Chungbuk National University, Cheongju, Chungbuk, 28644, Republic of Korea
| | - Yun-Sang Yu
- Department of Biological Sciences and Biotechnology, College of Natural Sciences, Chungbuk National University, Cheongju, Chungbuk, 28644, Republic of Korea
| | - Kyoung-Bin Ryu
- Clinical Research Division, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju, Chungbuk, 28159, Republic of Korea
| | - Hyerim Lee
- Department of Biological Sciences and Biotechnology, College of Natural Sciences, Chungbuk National University, Cheongju, Chungbuk, 28644, Republic of Korea
| | - Kyunghwan Kim
- Department of Biological Sciences and Biotechnology, College of Natural Sciences, Chungbuk National University, Cheongju, Chungbuk, 28644, Republic of Korea
| | - Song Yub Shin
- Department of Cellular and Molecular Medicine, School of Medicine, Chosun University, Gwangju, 61452, Republic of Korea.
| | - Young-Chun Gil
- Department of Anatomy, College of Medicine, Chungbuk National University, Cheongju, 28644, Republic of Korea.
| | - Sung-Jin Cho
- Department of Biological Sciences and Biotechnology, College of Natural Sciences, Chungbuk National University, Cheongju, Chungbuk, 28644, Republic of Korea.
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26
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Ji P, Wang Y, Peron T, Li C, Nagler J, Du J. Structure and function in artificial, zebrafish and human neural networks. Phys Life Rev 2023; 45:74-111. [PMID: 37182376 DOI: 10.1016/j.plrev.2023.04.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 04/20/2023] [Indexed: 05/16/2023]
Abstract
Network science provides a set of tools for the characterization of the structure and functional behavior of complex systems. Yet a major problem is to quantify how the structural domain is related to the dynamical one. In other words, how the diversity of dynamical states of a system can be predicted from the static network structure? Or the reverse problem: starting from a set of signals derived from experimental recordings, how can one discover the network connections or the causal relations behind the observed dynamics? Despite the advances achieved over the last two decades, many challenges remain concerning the study of the structure-dynamics interplay of complex systems. In neuroscience, progress is typically constrained by the low spatio-temporal resolution of experiments and by the lack of a universal inferring framework for empirical systems. To address these issues, applications of network science and artificial intelligence to neural data have been rapidly growing. In this article, we review important recent applications of methods from those fields to the study of the interplay between structure and functional dynamics of human and zebrafish brain. We cover the selection of topological features for the characterization of brain networks, inference of functional connections, dynamical modeling, and close with applications to both the human and zebrafish brain. This review is intended to neuroscientists who want to become acquainted with techniques from network science, as well as to researchers from the latter field who are interested in exploring novel application scenarios in neuroscience.
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Affiliation(s)
- Peng Ji
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai 200433, China; Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, Ministry of Education, Shanghai 200433, China; MOE Frontiers Center for Brain Science, Fudan University, Shanghai 200433, China
| | - Yufan Wang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China
| | - Thomas Peron
- Institute of Mathematics and Computer Science, University of São Paulo, São Carlos 13566-590, São Paulo, Brazil.
| | - Chunhe Li
- Shanghai Center for Mathematical Sciences and School of Mathematical Sciences, Fudan University, Shanghai 200433, China; Institute of Science and Technology for Brain-Inspired Intelligence and MOE Frontiers Center for Brain Science, Fudan University, Shanghai 200433, China.
| | - Jan Nagler
- Deep Dynamics, Frankfurt School of Finance & Management, Frankfurt, Germany; Centre for Human and Machine Intelligence, Frankfurt School of Finance & Management, Frankfurt, Germany
| | - Jiulin Du
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China.
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27
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Barabási DL, Beynon T, Katona Á, Perez-Nieves N. Complex computation from developmental priors. Nat Commun 2023; 14:2226. [PMID: 37076523 PMCID: PMC10115783 DOI: 10.1038/s41467-023-37980-1] [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: 11/04/2022] [Accepted: 04/07/2023] [Indexed: 04/21/2023] Open
Abstract
Machine learning (ML) models have long overlooked innateness: how strong pressures for survival lead to the encoding of complex behaviors in the nascent wiring of a brain. Here, we derive a neurodevelopmental encoding of artificial neural networks that considers the weight matrix of a neural network to be emergent from well-studied rules of neuronal compatibility. Rather than updating the network's weights directly, we improve task fitness by updating the neurons' wiring rules, thereby mirroring evolutionary selection on brain development. We find that our model (1) provides sufficient representational power for high accuracy on ML benchmarks while also compressing parameter count, and (2) can act as a regularizer, selecting simple circuits that provide stable and adaptive performance on metalearning tasks. In summary, by introducing neurodevelopmental considerations into ML frameworks, we not only model the emergence of innate behaviors, but also define a discovery process for structures that promote complex computations.
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Affiliation(s)
| | | | - Ádám Katona
- Electrical and Electronic Engineering, Imperial College London, London, UK
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28
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Winding M, Pedigo BD, Barnes CL, Patsolic HG, Park Y, Kazimiers T, Fushiki A, Andrade IV, Khandelwal A, Valdes-Aleman J, Li F, Randel N, Barsotti E, Correia A, Fetter RD, Hartenstein V, Priebe CE, Vogelstein JT, Cardona A, Zlatic M. The connectome of an insect brain. Science 2023; 379:eadd9330. [PMID: 36893230 PMCID: PMC7614541 DOI: 10.1126/science.add9330] [Citation(s) in RCA: 89] [Impact Index Per Article: 89.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 02/07/2023] [Indexed: 03/11/2023]
Abstract
Brains contain networks of interconnected neurons and so knowing the network architecture is essential for understanding brain function. We therefore mapped the synaptic-resolution connectome of an entire insect brain (Drosophila larva) with rich behavior, including learning, value computation, and action selection, comprising 3016 neurons and 548,000 synapses. We characterized neuron types, hubs, feedforward and feedback pathways, as well as cross-hemisphere and brain-nerve cord interactions. We found pervasive multisensory and interhemispheric integration, highly recurrent architecture, abundant feedback from descending neurons, and multiple novel circuit motifs. The brain's most recurrent circuits comprised the input and output neurons of the learning center. Some structural features, including multilayer shortcuts and nested recurrent loops, resembled state-of-the-art deep learning architectures. The identified brain architecture provides a basis for future experimental and theoretical studies of neural circuits.
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Affiliation(s)
- Michael Winding
- University of Cambridge, Department of Zoology, Cambridge, UK
- MRC Laboratory of Molecular Biology, Neurobiology Division, Cambridge, UK
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Benjamin D. Pedigo
- Johns Hopkins University, Department of Biomedical Engineering, Baltimore, MD, USA
| | - Christopher L. Barnes
- MRC Laboratory of Molecular Biology, Neurobiology Division, Cambridge, UK
- University of Cambridge, Department of Physiology, Development, and Neuroscience, Cambridge, UK
| | - Heather G. Patsolic
- Johns Hopkins University, Department of Applied Mathematics and Statistics, Baltimore, MD, USA
- Accenture, Arlington, VA, USA
| | - Youngser Park
- Johns Hopkins University, Center for Imaging Science, Baltimore, MD, USA
| | - Tom Kazimiers
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- kazmos GmbH, Dresden, Germany
| | - Akira Fushiki
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - Ingrid V. Andrade
- University of California Los Angeles, Department of Molecular, Cell and Developmental Biology, Los Angeles, CA, USA
| | - Avinash Khandelwal
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Javier Valdes-Aleman
- University of Cambridge, Department of Zoology, Cambridge, UK
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Feng Li
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Nadine Randel
- University of Cambridge, Department of Zoology, Cambridge, UK
- MRC Laboratory of Molecular Biology, Neurobiology Division, Cambridge, UK
| | - Elizabeth Barsotti
- MRC Laboratory of Molecular Biology, Neurobiology Division, Cambridge, UK
- University of Cambridge, Department of Physiology, Development, and Neuroscience, Cambridge, UK
| | - Ana Correia
- MRC Laboratory of Molecular Biology, Neurobiology Division, Cambridge, UK
- University of Cambridge, Department of Physiology, Development, and Neuroscience, Cambridge, UK
| | - Richard D. Fetter
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Stanford University, Stanford, CA, USA
| | - Volker Hartenstein
- University of California Los Angeles, Department of Molecular, Cell and Developmental Biology, Los Angeles, CA, USA
| | - Carey E. Priebe
- Johns Hopkins University, Department of Applied Mathematics and Statistics, Baltimore, MD, USA
- Johns Hopkins University, Center for Imaging Science, Baltimore, MD, USA
| | - Joshua T. Vogelstein
- Johns Hopkins University, Department of Biomedical Engineering, Baltimore, MD, USA
- Johns Hopkins University, Center for Imaging Science, Baltimore, MD, USA
| | - Albert Cardona
- MRC Laboratory of Molecular Biology, Neurobiology Division, Cambridge, UK
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- University of Cambridge, Department of Physiology, Development, and Neuroscience, Cambridge, UK
| | - Marta Zlatic
- University of Cambridge, Department of Zoology, Cambridge, UK
- MRC Laboratory of Molecular Biology, Neurobiology Division, Cambridge, UK
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
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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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Sy SKH, Chan DCW, Chan RCH, Lyu J, Li Z, Wong KKY, Choi CHJ, Mok VCT, Lai HM, Randlett O, Hu Y, Ko H. An optofluidic platform for interrogating chemosensory behavior and brainwide neural representation in larval zebrafish. Nat Commun 2023; 14:227. [PMID: 36641479 PMCID: PMC9840631 DOI: 10.1038/s41467-023-35836-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 01/03/2023] [Indexed: 01/15/2023] Open
Abstract
Studying chemosensory processing desires precise chemical cue presentation, behavioral response monitoring, and large-scale neuronal activity recording. Here we present Fish-on-Chips, a set of optofluidic tools for highly-controlled chemical delivery while simultaneously imaging behavioral outputs and whole-brain neuronal activities at cellular resolution in larval zebrafish. These include a fluidics-based swimming arena and an integrated microfluidics-light sheet fluorescence microscopy (µfluidics-LSFM) system, both of which utilize laminar fluid flows to achieve spatiotemporally precise chemical cue presentation. To demonstrate the strengths of the platform, we used the navigation arena to reveal binasal input-dependent behavioral strategies that larval zebrafish adopt to evade cadaverine, a death-associated odor. The µfluidics-LSFM system enables sequential presentation of odor stimuli to individual or both nasal cavities separated by only ~100 µm. This allowed us to uncover brainwide neural representations of cadaverine sensing and binasal input summation in the vertebrate model. Fish-on-Chips is readily generalizable and will empower the investigation of neural coding in the chemical senses.
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Affiliation(s)
- Samuel K H Sy
- Division of Neurology, Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Department of Biomedical Engineering, Faculty of Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Department of Electrical and Electronic Engineering, Faculty of Engineering, The University of Hong Kong, Pok Fu Lam, Hong Kong Island, Hong Kong SAR, China
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong SAR, China
| | - Danny C W Chan
- Division of Neurology, Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Department of Anaesthesia and Intensive Care, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Peter Hung Pain Research Institute, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Roy C H Chan
- Division of Neurology, Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Jing Lyu
- Division of Neurology, Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Zhongqi Li
- Division of Neurology, Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Kenneth K Y Wong
- Department of Electrical and Electronic Engineering, Faculty of Engineering, The University of Hong Kong, Pok Fu Lam, Hong Kong Island, Hong Kong SAR, China
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong SAR, China
| | - Chung Hang Jonathan Choi
- Department of Biomedical Engineering, Faculty of Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Peter Hung Pain Research Institute, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Chow Yuk Ho Technology Centre for Innovative Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Vincent C T Mok
- Division of Neurology, Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Margaret K. L. Cheung Research Centre for Management of Parkinsonism, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Gerald Choa Neuroscience Institute, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Hei-Ming Lai
- Division of Neurology, Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Margaret K. L. Cheung Research Centre for Management of Parkinsonism, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Gerald Choa Neuroscience Institute, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Department of Psychiatry, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Owen Randlett
- Institut national de la santé et de la recherche médicale, Université Claude Bernard Lyon 1, Lyon, France
| | - Yu Hu
- Department of Mathematics and Division of Life Science, Faculty of Science, Hong Kong University of Science and Technology, Clear Water Bay, New Territories, Hong Kong SAR, China
| | - Ho Ko
- Division of Neurology, Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.
- Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.
- Peter Hung Pain Research Institute, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.
- Chow Yuk Ho Technology Centre for Innovative Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.
- Margaret K. L. Cheung Research Centre for Management of Parkinsonism, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.
- Gerald Choa Neuroscience Institute, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.
- Department of Psychiatry, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.
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31
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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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32
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Thurley K. Naturalistic neuroscience and virtual reality. Front Syst Neurosci 2022; 16:896251. [PMID: 36467978 PMCID: PMC9712202 DOI: 10.3389/fnsys.2022.896251] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 10/31/2022] [Indexed: 04/04/2024] Open
Abstract
Virtual reality (VR) is one of the techniques that became particularly popular in neuroscience over the past few decades. VR experiments feature a closed-loop between sensory stimulation and behavior. Participants interact with the stimuli and not just passively perceive them. Several senses can be stimulated at once, large-scale environments can be simulated as well as social interactions. All of this makes VR experiences more natural than those in traditional lab paradigms. Compared to the situation in field research, a VR simulation is highly controllable and reproducible, as required of a laboratory technique used in the search for neural correlates of perception and behavior. VR is therefore considered a middle ground between ecological validity and experimental control. In this review, I explore the potential of VR in eliciting naturalistic perception and behavior in humans and non-human animals. In this context, I give an overview of recent virtual reality approaches used in neuroscientific research.
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Affiliation(s)
- Kay Thurley
- Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
- Bernstein Center for Computational Neuroscience Munich, Munich, Germany
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33
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A Mini-Review Regarding the Modalities to Study Neurodevelopmental Disorders-Like Impairments in Zebrafish—Focussing on Neurobehavioural and Psychological Responses. Brain Sci 2022; 12:brainsci12091147. [PMID: 36138883 PMCID: PMC9496774 DOI: 10.3390/brainsci12091147] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 08/24/2022] [Accepted: 08/24/2022] [Indexed: 11/17/2022] Open
Abstract
Neurodevelopmental disorders (NDDs) are complex disorders which can be associated with many comorbidities and exhibit multifactorial-dependent phenotypes. An important characteristic is represented by the early onset of the symptoms, during childhood or young adulthood, with a great impact on the socio-cognitive functioning of the affected individuals. Thus, the aim of our review is to describe and to argue the necessity of early developmental stages zebrafish models, focusing on NDDs, especially autism spectrum disorders (ASD) and also on schizophrenia. The utility of the animal models in NDDs or schizophrenia research remains quite controversial. Relevant discussions can be opened regarding the specific characteristics of the animal models and the relationship with the etiologies, physiopathology, and development of these disorders. The zebrafish models behaviors displayed as early as during the pre-hatching embryo stage (locomotor activity prone to repetitive behavior), and post-hatching embryo stage, such as memory, perception, affective-like, and social behaviors can be relevant in ASD and schizophrenia research. The neurophysiological processes impaired in both ASD and schizophrenia are generally highly conserved across all vertebrates. However, the relatively late individual development and conscious social behavior exhibited later in the larval stage are some of the most important limitations of these model animal species.
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34
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Im J, Eom HJ, Choi J. Effect of Early-Life Exposure of Polystyrene Microplastics on Behavior and DNA Methylation in Later Life Stage of Zebrafish. ARCHIVES OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2022; 82:558-568. [PMID: 35469368 DOI: 10.1007/s00244-022-00924-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 03/09/2022] [Indexed: 06/14/2023]
Abstract
Microplastic contamination has received increasing attention in recent years, and concern regarding the toxicity of microplastics to the environment and humans has increased. In this study, we investigated the neurodevelopmental toxicity of polystyrene microplastics (PSMPs) in the zebrafish Danio rerio under different exposure scenarios. Zebrafish were exposed to PSMPs during embryonic stage and then allowed the fish to recover. The neurodevelopmental toxic responses were investigated using fish behavior and behavior-related gene expression. Early-life exposure to PSMPs did not alter fish behavior at the early stage; however, it led to hyperactivity later life stage. Generally, oxidative stress (i.e., sod2 and nrf2a)- and nervous system (i.e., slc6a4b, npy, and nrbf2)-related gene expression increased in all PSMPs-exposed fish. DNA hypomethylation was observed in fish challenged for a second time using the same PSMPs. Taken together, the current results imply that PSMPs have neurodevelopmental toxic potential when introduced early in life.
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Affiliation(s)
- Jeongeun Im
- School of Environmental Engineering, University of Seoul, 163 Siripdaero, Dongdaemun-gu, Seoul, 02504, Republic of Korea
| | - Hyun-Jeong Eom
- School of Environmental Engineering, University of Seoul, 163 Siripdaero, Dongdaemun-gu, Seoul, 02504, Republic of Korea
| | - Jinhee Choi
- School of Environmental Engineering, University of Seoul, 163 Siripdaero, Dongdaemun-gu, Seoul, 02504, Republic of Korea.
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35
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Lin A, Witvliet D, Hernandez-Nunez L, Linderman SW, Samuel ADT, Venkatachalam V. Imaging whole-brain activity to understand behavior. NATURE REVIEWS. PHYSICS 2022; 4:292-305. [PMID: 37409001 PMCID: PMC10320740 DOI: 10.1038/s42254-022-00430-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 01/25/2022] [Indexed: 07/07/2023]
Abstract
The brain evolved to produce behaviors that help an animal inhabit the natural world. During natural behaviors, the brain is engaged in many levels of activity from the detection of sensory inputs to decision-making to motor planning and execution. To date, most brain studies have focused on small numbers of neurons that interact in limited circuits. This allows analyzing individual computations or steps of neural processing. During behavior, however, brain activity must integrate multiple circuits in different brain regions. The activities of different brain regions are not isolated, but may be contingent on one another. Coordinated and concurrent activity within and across brain areas is organized by (1) sensory information from the environment, (2) the animal's internal behavioral state, and (3) recurrent networks of synaptic and non-synaptic connectivity. Whole-brain recording with cellular resolution provides a new opportunity to dissect the neural basis of behavior, but whole-brain activity is also mutually contingent on behavior itself. This is especially true for natural behaviors like navigation, mating, or hunting, which require dynamic interaction between the animal, its environment, and other animals. In such behaviors, the sensory experience of an unrestrained animal is actively shaped by its movements and decisions. Many of the signaling and feedback pathways that an animal uses to guide behavior only occur in freely moving animals. Recent technological advances have enabled whole-brain recording in small behaving animals including nematodes, flies, and zebrafish. These whole-brain experiments capture neural activity with cellular resolution spanning sensory, decision-making, and motor circuits, and thereby demand new theoretical approaches that integrate brain dynamics with behavioral dynamics. Here, we review the experimental and theoretical methods that are being employed to understand animal behavior and whole-brain activity, and the opportunities for physics to contribute to this emerging field of systems neuroscience.
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Affiliation(s)
- Albert Lin
- Department of Physics, Harvard University, Cambridge, MA, USA
- Center for Brain Science, Harvard University, Cambridge, MA, USA
- Center for the Physics of Biological Function, Princeton University, Princeton, NJ, USA
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
| | - Daniel Witvliet
- Department of Physics, Harvard University, Cambridge, MA, USA
- Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Luis Hernandez-Nunez
- Center for Brain Science, Harvard University, Cambridge, MA, USA
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Scott W Linderman
- Department of Statistics, Stanford University, Stanford, CA, USA
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
| | - Aravinthan D T Samuel
- Department of Physics, Harvard University, Cambridge, MA, USA
- Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Vivek Venkatachalam
- Center for Brain Science, Harvard University, Cambridge, MA, USA
- Department of Physics, Northeastern University, Boston, MA, USA
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Derosiere G, Thura D, Cisek P, Duque J. Hasty sensorimotor decisions rely on an overlap of broad and selective changes in motor activity. PLoS Biol 2022; 20:e3001598. [PMID: 35389982 PMCID: PMC9017893 DOI: 10.1371/journal.pbio.3001598] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 04/19/2022] [Accepted: 03/10/2022] [Indexed: 12/27/2022] Open
Abstract
Humans and other animals are able to adjust their speed–accuracy trade-off (SAT) at will depending on the urge to act, favoring either cautious or hasty decision policies in different contexts. An emerging view is that SAT regulation relies on influences exerting broad changes on the motor system, tuning its activity up globally when hastiness is at premium. The present study aimed to test this hypothesis. A total of 50 participants performed a task involving choices between left and right index fingers, in which incorrect choices led either to a high or to a low penalty in 2 contexts, inciting them to emphasize either cautious or hasty policies. We applied transcranial magnetic stimulation (TMS) on multiple motor representations, eliciting motor-evoked potentials (MEPs) in 9 finger and leg muscles. MEP amplitudes allowed us to probe activity changes in the corresponding finger and leg representations, while participants were deliberating about which index to choose. Our data indicate that hastiness entails a broad amplification of motor activity, although this amplification was limited to the chosen side. On top of this effect, we identified a local suppression of motor activity, surrounding the chosen index representation. Hence, a decision policy favoring speed over accuracy appears to rely on overlapping processes producing a broad (but not global) amplification and a surround suppression of motor activity. The latter effect may help to increase the signal-to-noise ratio of the chosen representation, as supported by single-trial correlation analyses indicating a stronger differentiation of activity changes in finger representations in the hasty context. Many have argued that the regulation of the speed-accuracy tradeoff relies on an urgency signal, which implements "collapsing decision thresholds" by tuning neural activity in a global manner in decision-related structures. This study indicates that the reality is more subtle, with several aspects of "urgency" being specifically targeted to particular corticospinal populations within the motor system.
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Affiliation(s)
- Gerard Derosiere
- Institute of Neuroscience, Laboratory of Neurophysiology, Université Catholique de Louvain, Brussels, Belgium
- * E-mail:
| | - David Thura
- Lyon Neuroscience Research Center–Impact Team, Inserm U1028, CNRS UMR5292, Lyon 1 University, Bron, France
| | - Paul Cisek
- Department of Neuroscience, Université de Montréal, Montréal, Canada
| | - Julie Duque
- Institute of Neuroscience, Laboratory of Neurophysiology, Université Catholique de Louvain, Brussels, Belgium
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Tang M, Duan X, Yang A, He S, Zhou Y, Liu Y, Zhang L, Luo X, Shi P, Li H, Lin X. Fish Capsules: A System for High-Throughput Screening of Combinatorial Drugs. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2104449. [PMID: 35088577 PMCID: PMC8948576 DOI: 10.1002/advs.202104449] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 12/13/2021] [Indexed: 06/14/2023]
Abstract
Large-scale screening of molecules heavily relies on phenotyping of small living organisms during preclinical development. However, deep profiling candidate therapeutics on whole animals typically requires laborious manipulations and anesthetic treatment using traditional techniques or automated tools. Here, a novel fish capsule system that combines automated zebrafish encapsulating technology and droplet microarray strategy for in vivo functional screening of mono/polytherapies is described. This platform enables automated, rapid zebrafish orientation and immobilization in agarose to generate large-scale fish capsules by using a microfluidic device. Based on the effect of discontinuous dewetting, the prompt trapping of fish capsules in the aqueous arrays is successfully demonstrate. This system provides the capability to integrate pharmaceutical treatments with real-time multispectral microscopic imaging in a simple, pipetting-free and highly parallel manner. Coupling with machine learning algorithms, a small library of compounds is screened and analyzed, and clues about how to exploit compound combinations as therapeutic candidates are obtained. It is believed that this proposed strategy can be readily applied to multiple fields and is especially useful in the exploration of combinatorial drugs with limited amounts of samples and resources to accelerate the identification of novel therapeutics for precision medicines.
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Affiliation(s)
- Minghui Tang
- Guangdong Provincial Key Laboratory of Sensor Technology and Biomedical InstrumentSchool of Biomedical EngineeringSun Yat‐Sen UniversityGuangzhou510006China
| | - Xin Duan
- Guangdong Provincial Key Laboratory of Sensor Technology and Biomedical InstrumentSchool of Biomedical EngineeringSun Yat‐Sen UniversityGuangzhou510006China
| | - Anqi Yang
- Guangdong Provincial Key Laboratory of Sensor Technology and Biomedical InstrumentSchool of Biomedical EngineeringSun Yat‐Sen UniversityGuangzhou510006China
| | - Shijie He
- Guangdong Provincial Key Laboratory of Sensor Technology and Biomedical InstrumentSchool of Biomedical EngineeringSun Yat‐Sen UniversityGuangzhou510006China
| | - Yajing Zhou
- Guangdong Provincial Key Laboratory of Sensor Technology and Biomedical InstrumentSchool of Biomedical EngineeringSun Yat‐Sen UniversityGuangzhou510006China
| | - Yuxin Liu
- Guangdong Provincial Key Laboratory of Sensor Technology and Biomedical InstrumentSchool of Biomedical EngineeringSun Yat‐Sen UniversityGuangzhou510006China
| | - Lu Zhang
- Guangdong Provincial Key Laboratory of Sensor Technology and Biomedical InstrumentSchool of Biomedical EngineeringSun Yat‐Sen UniversityGuangzhou510006China
| | - Xuan Luo
- Department of Biomedical EngineeringCity University of Hong KongKowloonHong Kong SAR999077China
- Shenzhen Research InstituteCity University of Hong KongShenzhenGuangdong523808China
| | - Peng Shi
- Department of Biomedical EngineeringCity University of Hong KongKowloonHong Kong SAR999077China
- Shenzhen Research InstituteCity University of Hong KongShenzhenGuangdong523808China
| | - Honglin Li
- State Key Laboratory of Bioreactor EngineeringShanghai Key Laboratory of New Drug DesignSchool of PharmacyEast China University of Science and TechnologyShanghai200237China
| | - Xudong Lin
- Guangdong Provincial Key Laboratory of Sensor Technology and Biomedical InstrumentSchool of Biomedical EngineeringSun Yat‐Sen UniversityGuangzhou510006China
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Sheardown E, Torres-Perez JV, Anagianni S, Fraser SE, Vallortigara G, Butterworth B, Miletto-Petrazzini ME, Brennan CH. Characterizing ontogeny of quantity discrimination in zebrafish. Proc Biol Sci 2022; 289:20212544. [PMID: 35135351 PMCID: PMC8826302 DOI: 10.1098/rspb.2021.2544] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 01/07/2022] [Indexed: 11/12/2022] Open
Abstract
A sense of non-symbolic numerical magnitudes is widespread in the animal kingdom and has been documented in adult zebrafish. Here, we investigated the ontogeny of this ability using a group size preference (GSP) task in juvenile zebrafish. Fish showed GSP from 21 days post-fertilization and reliably chose the larger group when presented with discriminations of between 1 versus 3, 2 versus 5 and 2 versus 3 conspecifics but not 2 versus 4 conspecifics. When the ratio between the number of conspecifics in each group was maintained at 1 : 2, fish could discriminate between 1 versus 2 individuals and 3 versus 6, but again, not when given a choice between 2 versus 4 individuals. These findings are in agreement with studies in other species, suggesting the systems involved in quantity representation do not operate separately from other cognitive mechanisms. Rather they suggest quantity processing in fishes may be the result of an interplay between attentional, cognitive and memory-related mechanisms as in humans and other animals. Our results emphasize the potential of the use of zebrafish to explore the genetic and neural processes underlying the ontogeny and function of number cognition.
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Affiliation(s)
- Eva Sheardown
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology and Neuroscience, Kings College London, New Hunt's House, Guy's Campus, London SE1 1UL, UK
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Jose Vicente Torres-Perez
- Departament de Biologia Cellular, Biologia Funcional i Antropologia física, Fac. de CC. Biològiques, Universitat de València, C/ Dr. Moliner 50, 46100 Burjassot (València), Spain
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Sofia Anagianni
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Scott E. Fraser
- Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, USA
| | | | - Brian Butterworth
- UCL Institute of Cognitive Neuroscience, 17 Queen Square, London WC1N 3AZ, UK
| | - Maria Elena Miletto-Petrazzini
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
- Department of General Psychology, University of Padova, 35131 Padova, Italy
| | - Caroline H. Brennan
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
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39
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Audiovisual integration in the Mauthner cell enhances escape probability and reduces response latency. Sci Rep 2022; 12:1097. [PMID: 35058502 PMCID: PMC8776867 DOI: 10.1038/s41598-022-04998-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 01/03/2022] [Indexed: 11/09/2022] Open
Abstract
AbstractFast and accurate threat detection is critical for animal survival. Reducing perceptual ambiguity by integrating multiple sources of sensory information can enhance perception and reduce response latency. However, studies addressing the link between behavioral correlates of multisensory integration and its underlying neural basis are rare. Fish that detect an urgent threat escape with an explosive behavior known as C-start. The C-start is driven by an identified neural circuit centered on the Mauthner cell, an identified neuron capable of triggering escapes in response to visual and auditory stimuli. Here we demonstrate that goldfish can integrate visual looms and brief auditory stimuli to increase C-start probability. This multisensory enhancement is inversely correlated to the salience of the stimuli, with weaker auditory cues producing a proportionally stronger multisensory effect. We also show that multisensory stimuli reduced C-start response latency, with most escapes locked to the presentation of the auditory cue. We make a direct link between behavioral data and its underlying neural mechanism by reproducing the behavioral data with an integrate-and-fire computational model of the Mauthner cell. This model of the Mauthner cell circuit suggests that excitatory inputs integrated at the soma are key elements in multisensory decision making during fast C-start escapes. This provides a simple but powerful mechanism to enhance threat detection and survival.
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40
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From decision to action: Detailed modelling of frog tadpoles reveals neuronal mechanisms of decision-making and reproduces unpredictable swimming movements in response to sensory signals. PLoS Comput Biol 2021; 17:e1009654. [PMID: 34898604 PMCID: PMC8699619 DOI: 10.1371/journal.pcbi.1009654] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 12/23/2021] [Accepted: 11/17/2021] [Indexed: 01/30/2023] Open
Abstract
How does the brain process sensory stimuli, and decide whether to initiate locomotor behaviour? To investigate this question we develop two whole body computer models of a tadpole. The "Central Nervous System" (CNS) model uses evidence from whole-cell recording to define 2300 neurons in 12 classes to study how sensory signals from the skin initiate and stop swimming. In response to skin stimulation, it generates realistic sensory pathway spiking and shows how hindbrain sensory memory populations on each side can compete to initiate reticulospinal neuron firing and start swimming. The 3-D "Virtual Tadpole" (VT) biomechanical model with realistic muscle innervation, body flexion, body-water interaction, and movement is then used to evaluate if motor nerve outputs from the CNS model can produce swimming-like movements in a volume of "water". We find that the whole tadpole VT model generates reliable and realistic swimming. Combining these two models opens new perspectives for experiments.
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41
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The geometry of decision-making in individuals and collectives. Proc Natl Acad Sci U S A 2021; 118:2102157118. [PMID: 34880130 PMCID: PMC8685676 DOI: 10.1073/pnas.2102157118] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/19/2021] [Indexed: 11/18/2022] Open
Abstract
Almost all animals must make decisions on the move. Here, employing an approach that integrates theory and high-throughput experiments (using state-of-the-art virtual reality), we reveal that there exist fundamental geometrical principles that result from the inherent interplay between movement and organisms’ internal representation of space. Specifically, we find that animals spontaneously reduce the world into a series of sequential binary decisions, a response that facilitates effective decision-making and is robust both to the number of options available and to context, such as whether options are static (e.g., refuges) or mobile (e.g., other animals). We present evidence that these same principles, hitherto overlooked, apply across scales of biological organization, from individual to collective decision-making. Choosing among spatially distributed options is a central challenge for animals, from deciding among alternative potential food sources or refuges to choosing with whom to associate. Using an integrated theoretical and experimental approach (employing immersive virtual reality), we consider the interplay between movement and vectorial integration during decision-making regarding two, or more, options in space. In computational models of this process, we reveal the occurrence of spontaneous and abrupt “critical” transitions (associated with specific geometrical relationships) whereby organisms spontaneously switch from averaging vectorial information among, to suddenly excluding one among, the remaining options. This bifurcation process repeats until only one option—the one ultimately selected—remains. Thus, we predict that the brain repeatedly breaks multichoice decisions into a series of binary decisions in space–time. Experiments with fruit flies, desert locusts, and larval zebrafish reveal that they exhibit these same bifurcations, demonstrating that across taxa and ecological contexts, there exist fundamental geometric principles that are essential to explain how, and why, animals move the way they do.
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42
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Kenney JW, Steadman PE, Young O, Shi MT, Polanco M, Dubaishi S, Covert K, Mueller T, Frankland PW. A 3D adult zebrafish brain atlas (AZBA) for the digital age. eLife 2021; 10:69988. [PMID: 34806976 PMCID: PMC8639146 DOI: 10.7554/elife.69988] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 11/21/2021] [Indexed: 01/19/2023] Open
Abstract
Zebrafish have made significant contributions to our understanding of the vertebrate brain and the neural basis of behavior, earning a place as one of the most widely used model organisms in neuroscience. Their appeal arises from the marriage of low cost, early life transparency, and ease of genetic manipulation with a behavioral repertoire that becomes more sophisticated as animals transition from larvae to adults. To further enhance the use of adult zebrafish, we created the first fully segmented three-dimensional digital adult zebrafish brain atlas (AZBA). AZBA was built by combining tissue clearing, light-sheet fluorescence microscopy, and three-dimensional image registration of nuclear and antibody stains. These images were used to guide segmentation of the atlas into over 200 neuroanatomical regions comprising the entirety of the adult zebrafish brain. As an open source, online (azba.wayne.edu), updatable digital resource, AZBA will significantly enhance the use of adult zebrafish in furthering our understanding of vertebrate brain function in both health and disease.
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Affiliation(s)
- Justin W Kenney
- Department of Biological Sciences, Wayne State University, Detroit, United States.,Program in Neurosciences and Mental Health, The Hospital for Sick Children, Toronto, Canada
| | - Patrick E Steadman
- Program in Neurosciences and Mental Health, The Hospital for Sick Children, Toronto, Canada
| | - Olivia Young
- Department of Biological Sciences, Wayne State University, Detroit, United States
| | - Meng Ting Shi
- Department of Biological Sciences, Wayne State University, Detroit, United States
| | - Maris Polanco
- Department of Biological Sciences, Wayne State University, Detroit, United States
| | - Saba Dubaishi
- Department of Biological Sciences, Wayne State University, Detroit, United States
| | - Kristopher Covert
- Department of Biological Sciences, Wayne State University, Detroit, United States
| | - Thomas Mueller
- Division of Biology, Kansas State University, Manhattan, United States
| | - Paul W Frankland
- Program in Neurosciences and Mental Health, The Hospital for Sick Children, Toronto, Canada.,Department of Physiology, University of Toronto, Toronto, Canada.,Institute of Medical Sciences, University of Toronto, Toronto, Canada.,Department of Psychology, University of Toronto, Toronto, Canada
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43
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Buerkle N, Jeanne JM. Decision making: An analogue implementation of a drift-diffusion computation in the Drosophila mushroom body. Curr Biol 2021; 31:R1479-R1482. [PMID: 34813753 DOI: 10.1016/j.cub.2021.09.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
A new study combines electrophysiology, optogenetics, and behavior to investigate a decision-making circuit in the fly brain, revealing all the major features predicted by drift-diffusion models. Strikingly, much of this computation takes place subthreshold, independent of action potentials.
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Affiliation(s)
- Nathan Buerkle
- Department of Neuroscience, Yale University, 333 Cedar Street, New Haven, CT 06510, USA.
| | - James M Jeanne
- Department of Neuroscience, Yale University, 333 Cedar Street, New Haven, CT 06510, USA.
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44
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Vrontou E, Groschner LN, Szydlowski S, Brain R, Krebbers A, Miesenböck G. Response competition between neurons and antineurons in the mushroom body. Curr Biol 2021; 31:4911-4922.e4. [PMID: 34610272 PMCID: PMC8612741 DOI: 10.1016/j.cub.2021.09.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 08/03/2021] [Accepted: 09/03/2021] [Indexed: 11/04/2022]
Abstract
The mushroom bodies of Drosophila contain circuitry compatible with race models of perceptual choice. When flies discriminate odor intensity differences, opponent pools of αβ core Kenyon cells (on and off αβc KCs) accumulate evidence for increases or decreases in odor concentration. These sensory neurons and “antineurons” connect to a layer of mushroom body output neurons (MBONs) which bias behavioral intent in opposite ways. All-to-all connectivity between the competing integrators and their MBON partners allows for correct and erroneous decisions; dopaminergic reinforcement sets choice probabilities via reciprocal changes to the efficacies of on and off KC synapses; and pooled inhibition between αβc KCs can establish equivalence with the drift-diffusion formalism known to describe behavioral performance. The response competition network gives tangible form to many features envisioned in theoretical models of mammalian decision making, but it differs from these models in one respect: the principal variables—the fill levels of the integrators and the strength of inhibition between them—are represented by graded potentials rather than spikes. In pursuit of similar computational goals, a small brain may thus prioritize the large information capacity of analog signals over the robustness and temporal processing span of pulsatile codes. Mushroom body output neurons respond with excitation to odor on- and offset On and off responses reflect the convergence of oppositely tuned Kenyon cells (KCs) Opponent KCs compete by eliciting inhibitory feedback from a common interneuron pool KCs and interneurons communicate through graded potentials rather than spikes
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Affiliation(s)
- Eleftheria Vrontou
- Centre for Neural Circuits and Behaviour, University of Oxford, Tinsley Building, Mansfield Road, Oxford OX1 3SR, UK
| | - Lukas N Groschner
- Centre for Neural Circuits and Behaviour, University of Oxford, Tinsley Building, Mansfield Road, Oxford OX1 3SR, UK
| | - Susanne Szydlowski
- Centre for Neural Circuits and Behaviour, University of Oxford, Tinsley Building, Mansfield Road, Oxford OX1 3SR, UK
| | - Ruth Brain
- Centre for Neural Circuits and Behaviour, University of Oxford, Tinsley Building, Mansfield Road, Oxford OX1 3SR, UK
| | - Alina Krebbers
- Centre for Neural Circuits and Behaviour, University of Oxford, Tinsley Building, Mansfield Road, Oxford OX1 3SR, UK
| | - Gero Miesenböck
- Centre for Neural Circuits and Behaviour, University of Oxford, Tinsley Building, Mansfield Road, Oxford OX1 3SR, UK.
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45
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Markov DA, Petrucco L, Kist AM, Portugues R. A cerebellar internal model calibrates a feedback controller involved in sensorimotor control. Nat Commun 2021; 12:6694. [PMID: 34795244 PMCID: PMC8602262 DOI: 10.1038/s41467-021-26988-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 10/28/2021] [Indexed: 11/18/2022] Open
Abstract
Animals must adapt their behavior to survive in a changing environment. Behavioral adaptations can be evoked by two mechanisms: feedback control and internal-model-based control. Feedback controllers can maintain the sensory state of the animal at a desired level under different environmental conditions. In contrast, internal models learn the relationship between the motor output and its sensory consequences and can be used to recalibrate behaviors. Here, we present multiple unpredictable perturbations in visual feedback to larval zebrafish performing the optomotor response and show that they react to these perturbations through a feedback control mechanism. In contrast, if a perturbation is long-lasting, fish adapt their behavior by updating a cerebellum-dependent internal model. We use modelling and functional imaging to show that the neuronal requirements for these mechanisms are met in the larval zebrafish brain. Our results illustrate the role of the cerebellum in encoding internal models and how these can calibrate neuronal circuits involved in reactive behaviors depending on the interactions between animal and environment.
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Affiliation(s)
- Daniil A Markov
- Sensorimotor Control Research Group, Max Planck Institute of Neurobiology, 82152, Martinsried, Germany
| | - Luigi Petrucco
- Sensorimotor Control Research Group, Max Planck Institute of Neurobiology, 82152, Martinsried, Germany
- Institute of Neuroscience, Technical University of Munich, 80802, Munich, Germany
| | - Andreas M Kist
- Sensorimotor Control Research Group, Max Planck Institute of Neurobiology, 82152, Martinsried, Germany
- Division of Phoniatrics and Pediatric Audiology, Department of Otorhinolaryngology, Head and Neck Surgery, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, 91054, Erlangen, Germany
| | - Ruben Portugues
- Sensorimotor Control Research Group, Max Planck Institute of Neurobiology, 82152, Martinsried, Germany.
- Institute of Neuroscience, Technical University of Munich, 80802, Munich, Germany.
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany.
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46
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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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47
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Harpaz R, Aspiras AC, Chambule S, Tseng S, Bind MA, Engert F, Fishman MC, Bahl A. Collective behavior emerges from genetically controlled simple behavioral motifs in zebrafish. SCIENCE ADVANCES 2021; 7:eabi7460. [PMID: 34613782 PMCID: PMC8494438 DOI: 10.1126/sciadv.abi7460] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 08/13/2021] [Indexed: 06/13/2023]
Abstract
It is not understood how changes in the genetic makeup of individuals alter the behavior of groups of animals. Here, we find that, even at early larval stages, zebrafish regulate their proximity and alignment with each other. Two simple visual responses, one that measures relative visual field occupancy and one that accounts for global visual motion, suffice to account for the group behavior that emerges. Mutations in genes known to affect social behavior in humans perturb these simple reflexes in individual larval zebrafish and change their emergent collective behaviors in the predicted fashion. Model simulations show that changes in these two responses in individual mutant animals predict well the distinctive collective patterns that emerge in a group. Hence, group behaviors reflect in part genetically defined primitive sensorimotor “motifs,” which are evident even in young larvae.
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Affiliation(s)
- Roy Harpaz
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
- Center for Brain Science, Harvard University, Cambridge, MA 02138, USA
| | - Ariel C. Aspiras
- Harvard Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Sydney Chambule
- Harvard Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Sierra Tseng
- Harvard Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Marie-Abèle Bind
- Biostatistics Center, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Florian Engert
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
- Center for Brain Science, Harvard University, Cambridge, MA 02138, USA
| | - Mark C. Fishman
- Harvard Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Armin Bahl
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
- Center for Brain Science, Harvard University, Cambridge, MA 02138, USA
- Centre for the Advanced Study of Collective Behaviour, University of Konstanz, Konstanz 78464, Germany
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48
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Schreiner DC, Yalcinbas EA, Gremel CM. A Push For Examining Subjective Experience in Value-Based Decision-Making. Curr Opin Behav Sci 2021; 41:45-49. [PMID: 34056054 PMCID: PMC8153361 DOI: 10.1016/j.cobeha.2021.03.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Subjective experience is a powerful contributor to value-based decision-making. Not every decision is the same, nor made in isolation. Rather, decision-making relies on historical information and internal states for adaptive control. Hence, it is inherently continuous with respect to time - one decision or action evolves into the next. However, forays into the neurobiological underpinnings of decision-making have too frequently ignored the contribution of such continuous subjective experience, instead tying circuit activity and brain area involvement to discrete averaged behaviors and task parameters. While much information has been gained through these investigations, recent works have demonstrated the potential for a greater understanding of neural mechanisms when the continuous, experiential nature of behavior is integrated into the investigation. Such integration has important implications for disease states with disordered decision-making such as addiction, where subjective experience is a large contributor to the disorder.
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Affiliation(s)
- Drew C. Schreiner
- The Department of Psychology, University of California San Diego, La Jolla, CA 92093, USA
| | - Ege A. Yalcinbas
- The Neurosciences Graduate Program, University of California San Diego, La Jolla, CA 92093, USA
| | - Christina M. Gremel
- The Department of Psychology, University of California San Diego, La Jolla, CA 92093, USA
- The Neurosciences Graduate Program, University of California San Diego, La Jolla, CA 92093, USA
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49
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Hein AM, Altshuler DL, Cade DE, Liao JC, Martin BT, Taylor GK. An Algorithmic Approach to Natural Behavior. Curr Biol 2021; 30:R663-R675. [PMID: 32516620 DOI: 10.1016/j.cub.2020.04.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Uncovering the mechanisms and implications of natural behavior is a goal that unites many fields of biology. Yet, the diversity, flexibility, and multi-scale nature of these behaviors often make understanding elusive. Here, we review studies of animal pursuit and evasion - two special classes of behavior where theory-driven experiments and new modeling techniques are beginning to uncover the general control principles underlying natural behavior. A key finding of these studies is that intricate sequences of pursuit and evasion behavior can often be constructed through simple, repeatable rules that link sensory input to motor output: we refer to these rules as behavioral algorithms. Identifying and mathematically characterizing these algorithms has led to important insights, including the discovery of guidance rules that attacking predators use to intercept mobile prey, and coordinated neural and biomechanical mechanisms that animals use to avoid impending collisions. Here, we argue that algorithms provide a good starting point for studies of natural behavior more generally. Rather than beginning at the neural or ecological levels of organization, we advocate starting in the middle, where the algorithms that link sensory input to behavioral output can provide a solid foundation from which to explore both the implementation and the ecological outcomes of behavior. We review insights that have been gained through such an algorithmic approach to pursuit and evasion behaviors. From these, we synthesize theoretical principles and lay out key modeling tools needed to apply an algorithmic approach to the study of other complex natural behaviors.
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Affiliation(s)
- Andrew M Hein
- Southwest Fisheries Science Center, National Oceanic and Atmospheric Administration, Santa Cruz, CA 95060, USA; Institute of Marine Sciences, University of California, Santa Cruz, CA 95060, USA; Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95060, USA.
| | - Douglas L Altshuler
- Department of Zoology, University of British Columbia, Vancouver, BC V6T1Z4, Canada
| | - David E Cade
- Institute of Marine Sciences, University of California, Santa Cruz, CA 95060, USA; Hopkins Marine Station, Department of Biology, Stanford University, Pacific Grove, CA 93950, USA
| | - James C Liao
- The Whitney Laboratory for Marine Bioscience, Department of Biology, University of Florida, 9505 Ocean Shore Blvd., St. Augustine, FL 32080, USA
| | - Benjamin T Martin
- Southwest Fisheries Science Center, National Oceanic and Atmospheric Administration, Santa Cruz, CA 95060, USA; Institute of Marine Sciences, University of California, Santa Cruz, CA 95060, USA; Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Graham K Taylor
- Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford OX1 3SZ, UK
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50
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Rodríguez F, Quintero B, Amores L, Madrid D, Salas-Peña C, Salas C. Spatial Cognition in Teleost Fish: Strategies and Mechanisms. Animals (Basel) 2021; 11:2271. [PMID: 34438729 PMCID: PMC8388456 DOI: 10.3390/ani11082271] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/20/2021] [Accepted: 07/28/2021] [Indexed: 01/25/2023] Open
Abstract
Teleost fish have been traditionally considered primitive vertebrates compared to mammals and birds in regard to brain complexity and behavioral functions. However, an increasing amount of evidence suggests that teleosts show advanced cognitive capabilities including spatial navigation skills that parallel those of land vertebrates. Teleost fish rely on a multiplicity of sensory cues and can use a variety of spatial strategies for navigation, ranging from relatively simple body-centered orientation responses to allocentric or "external world-centered" navigation, likely based on map-like relational memory representations of the environment. These distinct spatial strategies are based on separate brain mechanisms. For example, a crucial brain center for egocentric orientation in teleost fish is the optic tectum, which can be considered an essential hub in a wider brain network responsible for the generation of egocentrically referenced actions in space. In contrast, other brain centers, such as the dorsolateral telencephalic pallium of teleost fish, considered homologue to the hippocampal pallium of land vertebrates, seem to be crucial for allocentric navigation based on map-like spatial memory. Such hypothetical relational memory representations endow fish's spatial behavior with considerable navigational flexibility, allowing them, for example, to perform shortcuts and detours.
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Affiliation(s)
| | | | | | | | | | - Cosme Salas
- Laboratorio de Psicobiología, Universidad de Sevilla, 41018 Sevilla, Spain; (F.R.); (B.Q.); (L.A.); (D.M.); (C.S.-P.)
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