51
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Nasello C, Poppi LA, Wu J, Kowalski TF, Thackray JK, Wang R, Persaud A, Mahboob M, Lin S, Spaseska R, Johnson CK, Gordon D, Tissir F, Heiman GA, Tischfield JA, Bocarsly M, Tischfield MA. Human mutations in high-confidence Tourette disorder genes affect sensorimotor behavior, reward learning, and striatal dopamine in mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.28.569034. [PMID: 38077033 PMCID: PMC10705456 DOI: 10.1101/2023.11.28.569034] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2024]
Abstract
Tourette disorder (TD) is poorly understood, despite affecting 1/160 children. A lack of animal models possessing construct, face, and predictive validity hinders progress in the field. We used CRISPR/Cas9 genome editing to generate mice with mutations orthologous to human de novo variants in two high-confidence Tourette genes, CELSR3 and WWC1 . Mice with human mutations in Celsr3 and Wwc1 exhibit cognitive and/or sensorimotor behavioral phenotypes consistent with TD. Sensorimotor gating deficits, as measured by acoustic prepulse inhibition, occur in both male and female Celsr3 TD models. Wwc1 mice show reduced prepulse inhibition only in females. Repetitive motor behaviors, common to Celsr3 mice and more pronounced in females, include vertical rearing and grooming. Sensorimotor gating deficits and rearing are attenuated by aripiprazole, a partial agonist at dopamine type II receptors. Unsupervised machine learning reveals numerous changes to spontaneous motor behavior and less predictable patterns of movement. Continuous fixed-ratio reinforcement shows Celsr3 TD mice have enhanced motor responding and reward learning. Electrically evoked striatal dopamine release, tested in one model, is greater. Brain development is otherwise grossly normal without signs of striatal interneuron loss. Altogether, mice expressing human mutations in high-confidence TD genes exhibit face and predictive validity. Reduced prepulse inhibition and repetitive motor behaviors are core behavioral phenotypes and are responsive to aripiprazole. Enhanced reward learning and motor responding occurs alongside greater evoked dopamine release. Phenotypes can also vary by sex and show stronger affection in females, an unexpected finding considering males are more frequently affected in TD. Significance Statement We generated mouse models that express mutations in high-confidence genes linked to Tourette disorder (TD). These models show sensorimotor and cognitive behavioral phenotypes resembling TD-like behaviors. Sensorimotor gating deficits and repetitive motor behaviors are attenuated by drugs that act on dopamine. Reward learning and striatal dopamine is enhanced. Brain development is grossly normal, including cortical layering and patterning of major axon tracts. Further, no signs of striatal interneuron loss are detected. Interestingly, behavioral phenotypes in affected females can be more pronounced than in males, despite male sex bias in the diagnosis of TD. These novel mouse models with construct, face, and predictive validity provide a new resource to study neural substrates that cause tics and related behavioral phenotypes in TD.
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52
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Knight A, Gschwind T, Galer P, Worrell GA, Litt B, Soltesz I, Beniczky S. Artificial intelligence in epilepsy phenotyping. Epilepsia 2023:10.1111/epi.17833. [PMID: 37983589 PMCID: PMC11102939 DOI: 10.1111/epi.17833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Accepted: 11/17/2023] [Indexed: 11/22/2023]
Abstract
Artificial intelligence (AI) allows data analysis and integration at an unprecedented granularity and scale. Here we review the technological advances, challenges, and future perspectives of using AI for electro-clinical phenotyping of animal models and patients with epilepsy. In translational research, AI models accurately identify behavioral states in animal models of epilepsy, allowing identification of correlations between neural activity and interictal and ictal behavior. Clinical applications of AI-based automated and semi-automated analysis of audio and video recordings of people with epilepsy, allow significant data reduction and reliable detection and classification of major motor seizures. AI models can accurately identify electrographic biomarkers of epilepsy, such as spikes, high-frequency oscillations, and seizure patterns. Integrating AI analysis of electroencephalographic, clinical, and behavioral data will contribute to optimizing therapy for patients with epilepsy.
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Affiliation(s)
| | - Tilo Gschwind
- Department of Neurosurgery, Stanford University, Stanford, USA
| | - Peter Galer
- Center for Neuroengineering and Therapeutics; Department of Bioengineering; Department of Neurology, Perelman School of Medicine, University of Pennsylvania, USA
| | | | - Brian Litt
- Center for Neuroengineering and Therapeutics; Department of Bioengineering; Department of Neurology, Perelman School of Medicine, University of Pennsylvania, USA
| | - Ivan Soltesz
- Department of Neurosurgery, Stanford University, Stanford, USA
| | - Sándor Beniczky
- Danish Epilepsy Centre Filadelfia, Dianalund, Aarhus University Hospital and Aarhus University, Aarhus, Denmark
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53
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Yang S, Chen ZY, Liang KW, Qin CJ, Yang Y, Fan WX, Jie CL, Ma XB. BARN: Behavior-Aware Relation Network for multi-label behavior detection in socially housed macaques. Zool Res 2023; 44:1026-1038. [PMID: 37804114 PMCID: PMC10802107 DOI: 10.24272/j.issn.2095-8137.2022.485] [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: 03/23/2023] [Accepted: 09/11/2023] [Indexed: 10/08/2023] Open
Abstract
Quantification of behaviors in macaques provides crucial support for various scientific disciplines, including pharmacology, neuroscience, and ethology. Despite recent advancements in the analysis of macaque behavior, research on multi-label behavior detection in socially housed macaques, including consideration of interactions among them, remains scarce. Given the lack of relevant approaches and datasets, we developed the Behavior-Aware Relation Network (BARN) for multi-label behavior detection of socially housed macaques. Our approach models the relationship of behavioral similarity between macaques, guided by a behavior-aware module and novel behavior classifier, which is suitable for multi-label classification. We also constructed a behavior dataset of rhesus macaques using ordinary RGB cameras mounted outside their cages. The dataset included 65 913 labels for 19 behaviors and 60 367 proposals, including identities and locations of the macaques. Experimental results showed that BARN significantly improved the baseline SlowFast network and outperformed existing relation networks. In conclusion, we successfully achieved multi-label behavior detection of socially housed macaques with both economic efficiency and high accuracy.
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Affiliation(s)
- Sen Yang
- College of Medicine and Biological Information Engineering, Northeastern University, Shenyang, Liaoning 110169, China
- MAIS, State Key Laboratory of Multimodal Artificial Intelligence Systems, Institute of Automation, Chinese Academy of Sciences, Beijing 100190, China
- School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhi-Yuan Chen
- MAIS, State Key Laboratory of Multimodal Artificial Intelligence Systems, Institute of Automation, Chinese Academy of Sciences, Beijing 100190, China
- School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ke-Wei Liang
- MAIS, State Key Laboratory of Multimodal Artificial Intelligence Systems, Institute of Automation, Chinese Academy of Sciences, Beijing 100190, China
- School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Cai-Jie Qin
- MAIS, State Key Laboratory of Multimodal Artificial Intelligence Systems, Institute of Automation, Chinese Academy of Sciences, Beijing 100190, China
- School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yang Yang
- MAIS, State Key Laboratory of Multimodal Artificial Intelligence Systems, Institute of Automation, Chinese Academy of Sciences, Beijing 100190, China
- School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wen-Xuan Fan
- College of Medicine and Biological Information Engineering, Northeastern University, Shenyang, Liaoning 110169, China
- MAIS, State Key Laboratory of Multimodal Artificial Intelligence Systems, Institute of Automation, Chinese Academy of Sciences, Beijing 100190, China
- School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chen-Lu Jie
- MAIS, State Key Laboratory of Multimodal Artificial Intelligence Systems, Institute of Automation, Chinese Academy of Sciences, Beijing 100190, China
- School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, 100049, China
- School of Automation, Harbin University of Science and Technology, Harbin, Heilongjiang 150080, China
| | - Xi-Bo Ma
- College of Medicine and Biological Information Engineering, Northeastern University, Shenyang, Liaoning 110169, China
- MAIS, State Key Laboratory of Multimodal Artificial Intelligence Systems, Institute of Automation, Chinese Academy of Sciences, Beijing 100190, China
- School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, 100049, China. E-mail:
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54
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Calhoun AJ, El Hady A. Everyone knows what behavior is but they just don't agree on it. iScience 2023; 26:108210. [PMID: 37953955 PMCID: PMC10638025 DOI: 10.1016/j.isci.2023.108210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 03/08/2023] [Accepted: 10/11/2023] [Indexed: 11/14/2023] Open
Abstract
Studying "behavior" lies at the heart of many disciplines. Nevertheless, academics rarely provide an explicit definition of what "behavior" actually is. What range of definitions do people use, and how does that vary across disciplines? To answer these questions, we have developed a survey to probe what constitutes "behavior." We find that academics adopt different definitions of behavior according to their academic discipline, animal model that they work with, and level of academic seniority. Using hierarchical clustering, we identify at least six distinct types of "behavior" which are used in seven distinct operational archetypes of "behavior." Individual respondents have clear consistent definitions of behavior, but these definitions are not consistent across the population. Our study is a call for academics to clarify what they mean by "behavior" wherever they study it, with the hope that this will foster interdisciplinary studies that will improve our understanding of behavioral phenomena.
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Affiliation(s)
- Adam J. Calhoun
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
| | - Ahmed El Hady
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
- Cluster for Advanced Study of Collective Behavior, University of Konstanz, Konstanz, Germany
- Max Planck Institute of Animal Behavior, Konstanz, Germany
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55
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Hope J, Beckerle T, Cheng PH, Viavattine Z, Feldkamp M, Fausner S, Saxena K, Ko E, Hryb I, Carter R, Ebner T, Kodandaramaiah S. Brain-wide neural recordings in mice navigating physical spaces enabled by a cranial exoskeleton. RESEARCH SQUARE 2023:rs.3.rs-3491330. [PMID: 38014260 PMCID: PMC10680923 DOI: 10.21203/rs.3.rs-3491330/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Complex behaviors are mediated by neural computations occurring throughout the brain. In recent years, tremendous progress has been made in developing technologies that can record neural activity at cellular resolution at multiple spatial and temporal scales. However, these technologies are primarily designed for studying the mammalian brain during head fixation - wherein the behavior of the animal is highly constrained. Miniaturized devices for studying neural activity in freely behaving animals are largely confined to recording from small brain regions owing to performance limitations. We present a cranial exoskeleton that assists mice in maneuvering neural recording headstages that are orders of magnitude larger and heavier than the mice, while they navigate physical behavioral environments. Force sensors embedded within the headstage are used to detect the mouse's milli-Newton scale cranial forces which then control the x, y, and yaw motion of the exoskeleton via an admittance controller. We discovered optimal controller tuning parameters that enable mice to locomote at physiologically realistic velocities and accelerations while maintaining natural walking gait. Mice maneuvering headstages weighing up to 1.5 kg can make turns, navigate 2D arenas, and perform a navigational decision-making task with the same performance as when freely behaving. We designed an imaging headstage and an electrophysiology headstage for the cranial exoskeleton to record brain-wide neural activity in mice navigating 2D arenas. The imaging headstage enabled recordings of Ca2+ activity of 1000s of neurons distributed across the dorsal cortex. The electrophysiology headstage supported independent control of up to 4 silicon probes, enabling simultaneous recordings from 100s of neurons across multiple brain regions and multiple days. Cranial exoskeletons provide flexible platforms for largescale neural recording during the exploration of physical spaces, a critical new paradigm for unraveling the brain-wide neural mechanisms that control complex behavior.
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Affiliation(s)
- James Hope
- Department of Mechanical Engineering, University of Minnesota, Twin Cities
| | - Travis Beckerle
- Department of Mechanical Engineering, University of Minnesota, Twin Cities
| | - Pin-Hao Cheng
- Department of Mechanical Engineering, University of Minnesota, Twin Cities
| | - Zoey Viavattine
- Department of Mechanical Engineering, University of Minnesota, Twin Cities
| | - Michael Feldkamp
- Department of Mechanical Engineering, University of Minnesota, Twin Cities
| | - Skylar Fausner
- Department of Mechanical Engineering, University of Minnesota, Twin Cities
| | - Kapil Saxena
- Department of Mechanical Engineering, University of Minnesota, Twin Cities
| | - Eunsong Ko
- Department of Mechanical Engineering, University of Minnesota, Twin Cities
| | - Ihor Hryb
- Department of Mechanical Engineering, University of Minnesota, Twin Cities
- Department of Neuroscience, University of Minnesota, Twin Cities
| | - Russell Carter
- Department of Biomedical Engineering, University of Minnesota, Twin Cities
| | - Timothy Ebner
- Department of Biomedical Engineering, University of Minnesota, Twin Cities
| | - Suhasa Kodandaramaiah
- Department of Mechanical Engineering, University of Minnesota, Twin Cities
- Department of Biomedical Engineering, University of Minnesota, Twin Cities
- Department of Neuroscience, University of Minnesota, Twin Cities
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56
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Jones H, Willis JA, Firth LC, Giachello CNG, Gilestro GF. A reductionist paradigm for high-throughput behavioural fingerprinting in Drosophila melanogaster. eLife 2023; 12:RP86695. [PMID: 37938101 PMCID: PMC10631757 DOI: 10.7554/elife.86695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2023] Open
Abstract
Understanding how the brain encodes behaviour is the ultimate goal of neuroscience and the ability to objectively and reproducibly describe and quantify behaviour is a necessary milestone on this path. Recent technological progresses in machine learning and computational power have boosted the development and adoption of systems leveraging on high-resolution video recording to track an animal pose and describe behaviour in all four dimensions. However, the high temporal and spatial resolution that these systems offer must come as a compromise with their throughput and accessibility. Here, we describe coccinella, an open-source reductionist framework combining high-throughput analysis of behaviour using real-time tracking on a distributed mesh of microcomputers (ethoscopes) with resource-lean statistical learning (HCTSA/Catch22). Coccinella is a reductionist system, yet outperforms state-of-the-art alternatives when exploring the pharmacobehaviour in Drosophila melanogaster.
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Affiliation(s)
- Hannah Jones
- Department of Life Sciences, Imperial College LondonLondonUnited Kingdom
| | - Jenny A Willis
- Syngenta, Jealott’s Hill International Research CentreBracknellUnited Kingdom
| | - Lucy C Firth
- Syngenta, Jealott’s Hill International Research CentreBracknellUnited Kingdom
| | - Carlo NG Giachello
- Syngenta, Jealott’s Hill International Research CentreBracknellUnited Kingdom
| | - Giorgio F Gilestro
- Department of Life Sciences, Imperial College LondonLondonUnited Kingdom
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57
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Lovelace JW, Ma J, Yadav S, Chhabria K, Shen H, Pang Z, Qi T, Sehgal R, Zhang Y, Bali T, Vaissiere T, Tan S, Liu Y, Rumbaugh G, Ye L, Kleinfeld D, Stringer C, Augustine V. Vagal sensory neurons mediate the Bezold-Jarisch reflex and induce syncope. Nature 2023; 623:387-396. [PMID: 37914931 PMCID: PMC10632149 DOI: 10.1038/s41586-023-06680-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 09/26/2023] [Indexed: 11/03/2023]
Abstract
Visceral sensory pathways mediate homeostatic reflexes, the dysfunction of which leads to many neurological disorders1. The Bezold-Jarisch reflex (BJR), first described2,3 in 1867, is a cardioinhibitory reflex that is speculated to be mediated by vagal sensory neurons (VSNs) that also triggers syncope. However, the molecular identity, anatomical organization, physiological characteristics and behavioural influence of cardiac VSNs remain mostly unknown. Here we leveraged single-cell RNA-sequencing data and HYBRiD tissue clearing4 to show that VSNs that express neuropeptide Y receptor Y2 (NPY2R) predominately connect the heart ventricular wall to the area postrema. Optogenetic activation of NPY2R VSNs elicits the classic triad of BJR responses-hypotension, bradycardia and suppressed respiration-and causes an animal to faint. Photostimulation during high-resolution echocardiography and laser Doppler flowmetry with behavioural observation revealed a range of phenotypes reflected in clinical syncope, including reduced cardiac output, cerebral hypoperfusion, pupil dilation and eye-roll. Large-scale Neuropixels brain recordings and machine-learning-based modelling showed that this manipulation causes the suppression of activity across a large distributed neuronal population that is not explained by changes in spontaneous behavioural movements. Additionally, bidirectional manipulation of the periventricular zone had a push-pull effect, with inhibition leading to longer syncope periods and activation inducing arousal. Finally, ablating NPY2R VSNs specifically abolished the BJR. Combined, these results demonstrate a genetically defined cardiac reflex that recapitulates characteristics of human syncope at physiological, behavioural and neural network levels.
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Affiliation(s)
- Jonathan W Lovelace
- Department of Neurobiology, University of California, San Diego, CA, USA
- Department of Neuroscience, Scripps Research, La Jolla, CA, USA
| | - Jingrui Ma
- Department of Neurobiology, University of California, San Diego, CA, USA
- Department of Neuroscience, Scripps Research, La Jolla, CA, USA
| | - Saurabh Yadav
- Department of Neurobiology, University of California, San Diego, CA, USA
- Department of Neuroscience, Scripps Research, La Jolla, CA, USA
| | | | - Hanbing Shen
- Department of Neuroscience, Scripps Research, La Jolla, CA, USA
| | - Zhengyuan Pang
- Department of Neuroscience, Scripps Research, La Jolla, CA, USA
| | - Tianbo Qi
- Department of Neuroscience, Scripps Research, La Jolla, CA, USA
| | - Ruchi Sehgal
- Department of Neuroscience, Scripps Research, La Jolla, CA, USA
| | - Yunxiao Zhang
- Department of Neuroscience, Scripps Research, La Jolla, CA, USA
| | - Tushar Bali
- Department of Neuroscience, Scripps Research, La Jolla, CA, USA
| | - Thomas Vaissiere
- University of Florida-Scripps Biomedical Research, Jupiter, FL, USA
| | - Shawn Tan
- Department of Neuroscience, Scripps Research, La Jolla, CA, USA
| | - Yuejia Liu
- Department of Neuroscience, Scripps Research, La Jolla, CA, USA
| | - Gavin Rumbaugh
- University of Florida-Scripps Biomedical Research, Jupiter, FL, USA
| | - Li Ye
- Department of Neuroscience, Scripps Research, La Jolla, CA, USA
| | - David Kleinfeld
- Department of Neurobiology, University of California, San Diego, CA, USA
- Department of Physics, University of California, San Diego, CA, USA
| | | | - Vineet Augustine
- Department of Neurobiology, University of California, San Diego, CA, USA.
- Department of Neuroscience, Scripps Research, La Jolla, CA, USA.
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58
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Tseng YT, Schaefke B, Wei P, Wang L. Defensive responses: behaviour, the brain and the body. Nat Rev Neurosci 2023; 24:655-671. [PMID: 37730910 DOI: 10.1038/s41583-023-00736-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/11/2023] [Indexed: 09/22/2023]
Abstract
Most animals live under constant threat from predators, and predation has been a major selective force in shaping animal behaviour. Nevertheless, defence responses against predatory threats need to be balanced against other adaptive behaviours such as foraging, mating and recovering from infection. This behavioural balance in ethologically relevant contexts requires adequate integration of internal and external signals in a complex interplay between the brain and the body. Despite this complexity, research has often considered defensive behaviour as entirely mediated by the brain processing threat-related information obtained via perception of the external environment. However, accumulating evidence suggests that the endocrine, immune, gastrointestinal and reproductive systems have important roles in modulating behavioural responses to threat. In this Review, we focus on how predatory threat defence responses are shaped by threat imminence and review the circuitry between subcortical brain regions involved in mediating defensive behaviours. Then, we discuss the intersection of peripheral systems involved in internal states related to infection, hunger and mating with the neurocircuits that underlie defence responses against predatory threat. Through this process, we aim to elucidate the interconnections between the brain and body as an integrated network that facilitates appropriate defensive responses to threat and to discuss the implications for future behavioural research.
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Affiliation(s)
- Yu-Ting Tseng
- CAS Key Laboratory of Brain Connectome and Manipulation, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Guangdong Provincial Key Laboratory of Brain Connectome and Behaviour, the Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Bernhard Schaefke
- CAS Key Laboratory of Brain Connectome and Manipulation, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Pengfei Wei
- CAS Key Laboratory of Brain Connectome and Manipulation, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Liping Wang
- CAS Key Laboratory of Brain Connectome and Manipulation, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
- Guangdong Provincial Key Laboratory of Brain Connectome and Behaviour, the Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
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59
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Talluri BC, Kang I, Lazere A, Quinn KR, Kaliss N, Yates JL, Butts DA, Nienborg H. Activity in primate visual cortex is minimally driven by spontaneous movements. Nat Neurosci 2023; 26:1953-1959. [PMID: 37828227 PMCID: PMC10620084 DOI: 10.1038/s41593-023-01459-5] [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: 07/19/2022] [Accepted: 09/08/2023] [Indexed: 10/14/2023]
Abstract
Organisms process sensory information in the context of their own moving bodies, an idea referred to as embodiment. This idea is important for developmental neuroscience, robotics and systems neuroscience. The mechanisms supporting embodiment are unknown, but a manifestation could be the observation in mice of brain-wide neuromodulation, including in the primary visual cortex, driven by task-irrelevant spontaneous body movements. We tested this hypothesis in macaque monkeys (Macaca mulatta), a primate model for human vision, by simultaneously recording visual cortex activity and facial and body movements. We also sought a direct comparison using an analogous approach to those used in mouse studies. Here we found that activity in the primate visual cortex (V1, V2 and V3/V3A) was associated with the animals' own movements, but this modulation was largely explained by the impact of the movements on the retinal image, that is, by changes in visual input. These results indicate that visual cortex in primates is minimally driven by spontaneous movements and may reflect species-specific sensorimotor strategies.
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Affiliation(s)
- Bharath Chandra Talluri
- Laboratory of Sensorimotor Research, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Incheol Kang
- Laboratory of Sensorimotor Research, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Adam Lazere
- Laboratory of Sensorimotor Research, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Katrina R Quinn
- Center for Integrative Neuroscience, University of Tübingen, Tübingen, Germany
| | - Nicholas Kaliss
- Laboratory of Sensorimotor Research, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jacob L Yates
- Herbert Wertheim School of Optometry & Vision Science, University of California, Berkeley, Berkeley, CA, USA
- Department of Biology and Program in Neuroscience and Cognitive Science, University of Maryland, College Park, MD, USA
| | - Daniel A Butts
- Department of Biology and Program in Neuroscience and Cognitive Science, University of Maryland, College Park, MD, USA
| | - Hendrikje Nienborg
- Laboratory of Sensorimotor Research, National Eye Institute, National Institutes of Health, Bethesda, MD, USA.
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Brickson L, Zhang L, Vollrath F, Douglas-Hamilton I, Titus AJ. Elephants and algorithms: a review of the current and future role of AI in elephant monitoring. J R Soc Interface 2023; 20:20230367. [PMID: 37963556 PMCID: PMC10645515 DOI: 10.1098/rsif.2023.0367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 10/23/2023] [Indexed: 11/16/2023] Open
Abstract
Artificial intelligence (AI) and machine learning (ML) present revolutionary opportunities to enhance our understanding of animal behaviour and conservation strategies. Using elephants, a crucial species in Africa and Asia's protected areas, as our focal point, we delve into the role of AI and ML in their conservation. Given the increasing amounts of data gathered from a variety of sensors like cameras, microphones, geophones, drones and satellites, the challenge lies in managing and interpreting this vast data. New AI and ML techniques offer solutions to streamline this process, helping us extract vital information that might otherwise be overlooked. This paper focuses on the different AI-driven monitoring methods and their potential for improving elephant conservation. Collaborative efforts between AI experts and ecological researchers are essential in leveraging these innovative technologies for enhanced wildlife conservation, setting a precedent for numerous other species.
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Affiliation(s)
| | | | - Fritz Vollrath
- Save the Elephants, Nairobi, Kenya
- Department of Biology, University of Oxford, Oxford, UK
| | | | - Alexander J. Titus
- Colossal Biosciences, Dallas, TX, USA
- Information Sciences Institute, University of Southern California, Los Angeles, USA
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61
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Costa AC, Vergassola M. Fluctuating landscapes and heavy tails in animal behavior. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.03.522580. [PMID: 36747746 PMCID: PMC9900741 DOI: 10.1101/2023.01.03.522580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Animal behavior is shaped by a myriad of mechanisms acting on a wide range of scales. This immense variability hampers quantitative reasoning and renders the identification of universal principles elusive. Through data analysis and theory, we here show that slow non-ergodic drives generally give rise to heavy-tailed statistics in behaving animals. We leverage high-resolution recordings of C. elegans locomotion to extract a self-consistent reduced order model for an inferred reaction coordinate, bridging from sub-second chaotic dynamics to long-lived stochastic transitions among metastable states. The slow mode dynamics exhibits heavy-tailed first passage time distributions and correlation functions, and we show that such heavy tails can be explained by dynamics on a time-dependent potential landscape. Inspired by these results, we introduce a generic model in which we separate faster mixing modes that evolve on a quasi-stationary potential, from slower non-ergodic modes that drive the potential landscape, and reflect slowly varying internal states. We show that, even for simple potential landscapes, heavy tails emerge when barrier heights fluctuate slowly and strongly enough. In particular, the distribution of first passage times and the correlation function can asymptote to a power law, with related exponents that depend on the strength and nature of the fluctuations. We support our theoretical findings through direct numerical simulations.
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Affiliation(s)
- Antonio Carlos Costa
- Laboratoire de Physique de l’Ecole normale supérieure, ENS, Université PSL, CNRS, Sorbonne Université, Université de Paris, F-75005 Paris, France
| | - Massimo Vergassola
- Laboratoire de Physique de l’Ecole normale supérieure, ENS, Université PSL, CNRS, Sorbonne Université, Université de Paris, F-75005 Paris, France
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62
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García MT, Tran DN, Peterson RE, Stegmann SK, Hanson SM, Reid CM, Xie Y, Vu S, Harwell CC. A developmentally defined population of neurons in the lateral septum controls responses to aversive stimuli. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.24.559205. [PMID: 37873286 PMCID: PMC10592641 DOI: 10.1101/2023.09.24.559205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
When interacting with their environment, animals must balance exploratory and defensive behavior to evaluate and respond to potential threats. The lateral septum (LS) is a structure in the ventral forebrain that calibrates the magnitude of behavioral responses to stress-related external stimuli, including the regulation of threat avoidance. The complex connectivity between the LS and other parts of the brain, together with its largely unexplored neuronal diversity, makes it difficult to understand how defined LS circuits control specific behaviors. Here, we describe a mouse model in which a population of neurons with a common developmental origin (Nkx2.1-lineage neurons) are absent from the LS. Using a combination of circuit tracing and behavioral analyses, we found that these neurons receive inputs from the perifornical area of the anterior hypothalamus (PeFAH) and are specifically activated in stressful contexts. Mice lacking Nkx2.1-lineage LS neurons display increased exploratory behavior even under stressful conditions. Our study extends the current knowledge about how defined neuronal populations within the LS can evaluate contextual information to select appropriate behavioral responses. This is a necessary step towards understanding the crucial role that the LS plays in neuropsychiatric conditions where defensive behavior is dysregulated, such as anxiety and aggression disorders.
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Affiliation(s)
- Miguel Turrero García
- Department of Neurology, University of California, San Francisco; San Francisco, CA
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research; San Francisco, CA
| | - Diana N. Tran
- Department of Neurobiology, Harvard Medical School; Boston, MA
| | | | | | - Sarah M. Hanson
- Department of Neurology, University of California, San Francisco; San Francisco, CA
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research; San Francisco, CA
| | - Christopher M. Reid
- Department of Neurology, University of California, San Francisco; San Francisco, CA
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research; San Francisco, CA
- Ph.D. Program in Neuroscience, Harvard University; Boston, MA
| | - Yajun Xie
- Department of Neurology, University of California, San Francisco; San Francisco, CA
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research; San Francisco, CA
| | - Steve Vu
- Department of Neurobiology, Harvard Medical School; Boston, MA
| | - Corey C. Harwell
- Department of Neurology, University of California, San Francisco; San Francisco, CA
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research; San Francisco, CA
- Chan Zuckerberg Biohub San Francisco; San Francisco, CA
- Lead contact
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63
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Lim SC, Fusi S, Hen R. Ventral CA1 Population Codes for Anxiety. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.25.559358. [PMID: 37808689 PMCID: PMC10557595 DOI: 10.1101/2023.09.25.559358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
The ventral hippocampus is a critical node in the distributed brain network that controls anxiety. Using miniature microscopy and calcium imaging, we recorded ventral CA1 (vCA1) neurons in freely moving mice as they explored variants of classic behavioral assays for anxiety. Unsupervised behavioral segmentation revealed clusters of behavioral motifs that corresponded to exploratory and vigilance-like states. We discovered multiple vCA1 population codes that represented the anxiogenic features of the environment, such as bright light and openness, as well as the moment-to-moment anxiety state of the animals. These population codes possessed distinct generalization properties: neural representations of anxiogenic features were different for open field and elevated plus/zero maze tasks, while neural representations of moment-to-moment anxiety state were similar across both experimental contexts. Our results suggest that anxiety is not tied to the aversive compartments of these mazes but is rather defined by a behavioral state and its corresponding population code that generalizes across environments.
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64
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Voloh B, Maisson DJN, Cervera RL, Conover I, Zambre M, Hayden B, Zimmermann J. Hierarchical action encoding in prefrontal cortex of freely moving macaques. Cell Rep 2023; 42:113091. [PMID: 37656619 PMCID: PMC10591875 DOI: 10.1016/j.celrep.2023.113091] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 06/23/2023] [Accepted: 08/18/2023] [Indexed: 09/03/2023] Open
Abstract
Our natural behavioral repertoires include coordinated actions of characteristic types. To better understand how neural activity relates to the expression of actions and action switches, we studied macaques performing a freely moving foraging task in an open environment. We developed a novel analysis pipeline that can identify meaningful units of behavior, corresponding to recognizable actions such as sitting, walking, jumping, and climbing. On the basis of transition probabilities between these actions, we found that behavior is organized in a modular and hierarchical fashion. We found that, after regressing out many potential confounders, actions are associated with specific patterns of firing in each of six prefrontal brain regions and that, overall, encoding of action category is progressively stronger in more dorsal and more caudal prefrontal regions. Together, these results establish a link between selection of units of primate behavior on one hand and neuronal activity in prefrontal regions on the other.
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Affiliation(s)
- Benjamin Voloh
- Department of Neuroscience, University of Minnesota, Minneapolis, MN 55455, USA
| | - David J-N Maisson
- Department of Neuroscience, University of Minnesota, Minneapolis, MN 55455, USA
| | | | - Indirah Conover
- Department of Neuroscience, University of Minnesota, Minneapolis, MN 55455, USA
| | - Mrunal Zambre
- Department of Neuroscience, University of Minnesota, Minneapolis, MN 55455, USA
| | - Benjamin Hayden
- Department of Neuroscience, University of Minnesota, Minneapolis, MN 55455, USA; Department of Neurosurgery, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jan Zimmermann
- Department of Neuroscience, University of Minnesota, Minneapolis, MN 55455, USA; Center for Magnetic Resonance Research, University of Minnesota, Minneapolis, MN 55455, USA.
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65
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Butler DJ, Keim AP, Ray S, Azim E. Large-scale capture of hidden fluorescent labels for training generalizable markerless motion capture models. Nat Commun 2023; 14:5866. [PMID: 37752123 PMCID: PMC10522643 DOI: 10.1038/s41467-023-41565-3] [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: 05/30/2022] [Accepted: 09/08/2023] [Indexed: 09/28/2023] Open
Abstract
Deep learning-based markerless tracking has revolutionized studies of animal behavior. Yet the generalizability of trained models tends to be limited, as new training data typically needs to be generated manually for each setup or visual environment. With each model trained from scratch, researchers track distinct landmarks and analyze the resulting kinematic data in idiosyncratic ways. Moreover, due to inherent limitations in manual annotation, only a sparse set of landmarks are typically labeled. To address these issues, we developed an approach, which we term GlowTrack, for generating orders of magnitude more training data, enabling models that generalize across experimental contexts. We describe: a) a high-throughput approach for producing hidden labels using fluorescent markers; b) a multi-camera, multi-light setup for simulating diverse visual conditions; and c) a technique for labeling many landmarks in parallel, enabling dense tracking. These advances lay a foundation for standardized behavioral pipelines and more complete scrutiny of movement.
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Affiliation(s)
- Daniel J Butler
- Molecular Neurobiology Laboratory, Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Alexander P Keim
- Molecular Neurobiology Laboratory, Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Shantanu Ray
- Molecular Neurobiology Laboratory, Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Eiman Azim
- Molecular Neurobiology Laboratory, Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA, 92037, USA.
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Lang B, Kahnau P, Hohlbaum K, Mieske P, Andresen NP, Boon MN, Thöne-Reineke C, Lewejohann L, Diederich K. Challenges and advanced concepts for the assessment of learning and memory function in mice. Front Behav Neurosci 2023; 17:1230082. [PMID: 37809039 PMCID: PMC10551171 DOI: 10.3389/fnbeh.2023.1230082] [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: 05/28/2023] [Accepted: 09/05/2023] [Indexed: 10/10/2023] Open
Abstract
The mechanisms underlying the formation and retrieval of memories are still an active area of research and discussion. Manifold models have been proposed and refined over the years, with most assuming a dichotomy between memory processes involving non-conscious and conscious mechanisms. Despite our incomplete understanding of the underlying mechanisms, tests of memory and learning count among the most performed behavioral experiments. Here, we will discuss available protocols for testing learning and memory using the example of the most prevalent animal species in research, the laboratory mouse. A wide range of protocols has been developed in mice to test, e.g., object recognition, spatial learning, procedural memory, sequential problem solving, operant- and fear conditioning, and social recognition. Those assays are carried out with individual subjects in apparatuses such as arenas and mazes, which allow for a high degree of standardization across laboratories and straightforward data interpretation but are not without caveats and limitations. In animal research, there is growing concern about the translatability of study results and animal welfare, leading to novel approaches beyond established protocols. Here, we present some of the more recent developments and more advanced concepts in learning and memory testing, such as multi-step sequential lockboxes, assays involving groups of animals, as well as home cage-based assays supported by automated tracking solutions; and weight their potential and limitations against those of established paradigms. Shifting the focus of learning tests from the classical experimental chamber to settings which are more natural for rodents comes with a new set of challenges for behavioral researchers, but also offers the opportunity to understand memory formation and retrieval in a more conclusive way than has been attainable with conventional test protocols. We predict and embrace an increase in studies relying on methods involving a higher degree of automatization, more naturalistic- and home cage-based experimental setting as well as more integrated learning tasks in the future. We are confident these trends are suited to alleviate the burden on animal subjects and improve study designs in memory research.
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Affiliation(s)
- Benjamin Lang
- Animal Behavior and Laboratory Animal Science, Department of Veterinary Medicine, Institute for Animal Welfare, Free University of Berlin, Berlin, Germany
- Science of Intelligence, Research Cluster of Excellence, Berlin, Germany
| | - Pia Kahnau
- Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Katharina Hohlbaum
- Science of Intelligence, Research Cluster of Excellence, Berlin, Germany
- Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Paul Mieske
- Animal Behavior and Laboratory Animal Science, Department of Veterinary Medicine, Institute for Animal Welfare, Free University of Berlin, Berlin, Germany
- Science of Intelligence, Research Cluster of Excellence, Berlin, Germany
- Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Niek P. Andresen
- Science of Intelligence, Research Cluster of Excellence, Berlin, Germany
- Computer Vision and Remote Sensing, Technical University Berlin, Berlin, Germany
| | - Marcus N. Boon
- Science of Intelligence, Research Cluster of Excellence, Berlin, Germany
- Modeling of Cognitive Processes, Technical University of Berlin, Berlin, Germany
| | - Christa Thöne-Reineke
- Animal Behavior and Laboratory Animal Science, Department of Veterinary Medicine, Institute for Animal Welfare, Free University of Berlin, Berlin, Germany
- Science of Intelligence, Research Cluster of Excellence, Berlin, Germany
| | - Lars Lewejohann
- Animal Behavior and Laboratory Animal Science, Department of Veterinary Medicine, Institute for Animal Welfare, Free University of Berlin, Berlin, Germany
- Science of Intelligence, Research Cluster of Excellence, Berlin, Germany
- Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Kai Diederich
- Federal Institute for Risk Assessment (BfR), Berlin, Germany
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67
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MacDonald DI, Chesler AT. Painspotting. Neuron 2023; 111:2773-2774. [PMID: 37734319 DOI: 10.1016/j.neuron.2023.08.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 08/24/2023] [Accepted: 08/24/2023] [Indexed: 09/23/2023]
Abstract
How do we know an animal is feeling pain? In this issue of Neuron, Bohic et al.1 develop computational methods to detect pain in mice, shining a light on the behavioral changes that occur during pain, its relief, and recovery.
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Affiliation(s)
- Donald Iain MacDonald
- National Center for Complementary and Integrative Health, National Institutes of Health, Bethesda, MD, USA.
| | - Alexander T Chesler
- National Center for Complementary and Integrative Health, National Institutes of Health, Bethesda, MD, USA; National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
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68
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Bohic M, Pattison LA, Jhumka ZA, Rossi H, Thackray JK, Ricci M, Mossazghi N, Foster W, Ogundare S, Twomey CR, Hilton H, Arnold J, Tischfield MA, Yttri EA, St John Smith E, Abdus-Saboor I, Abraira VE. Mapping the neuroethological signatures of pain, analgesia, and recovery in mice. Neuron 2023; 111:2811-2830.e8. [PMID: 37442132 PMCID: PMC10697150 DOI: 10.1016/j.neuron.2023.06.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 12/16/2022] [Accepted: 06/16/2023] [Indexed: 07/15/2023]
Abstract
Ongoing pain is driven by the activation and modulation of pain-sensing neurons, affecting physiology, motor function, and motivation to engage in certain behaviors. The complexity of the pain state has evaded a comprehensive definition, especially in non-verbal animals. Here, in mice, we used site-specific electrophysiology to define key time points corresponding to peripheral sensitivity in acute paw inflammation and chronic knee pain models. Using supervised and unsupervised machine learning tools, we uncovered sensory-evoked coping postures unique to each model. Through 3D pose analytics, we identified movement sequences that robustly represent different pain states and found that commonly used analgesics do not return an animal's behavior to a pre-injury state. Instead, these analgesics induce a novel set of spontaneous behaviors that are maintained even after resolution of evoked pain behaviors. Together, these findings reveal previously unidentified neuroethological signatures of pain and analgesia at heightened pain states and during recovery.
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Affiliation(s)
- Manon Bohic
- Cell Biology and Neuroscience Department, Rutgers University, The State University of New Jersey, Piscataway, NJ, USA; W.M. Keck Center for Collaborative Neuroscience, Rutgers University, The State University of New Jersey, Piscataway, NJ, USA
| | - Luke A Pattison
- Department of Pharmacology, University of Cambridge, Cambridge, UK
| | - Z Anissa Jhumka
- Zuckerman Mind Brain Behavior Institute and Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Heather Rossi
- Zuckerman Mind Brain Behavior Institute and Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Joshua K Thackray
- Human Genetics Institute of New Jersey, Rutgers University, The State University of New Jersey, Piscataway, NJ, USA; Tourette International Collaborative Genetics Study (TIC Genetics), Piscataway, NJ, USA
| | - Matthew Ricci
- Data Science Initiative, Brown University, Providence, RI, USA; School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Nahom Mossazghi
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA, USA; Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA
| | - William Foster
- Zuckerman Mind Brain Behavior Institute and Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Simon Ogundare
- Zuckerman Mind Brain Behavior Institute and Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Colin R Twomey
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Helen Hilton
- Department of Pharmacology, University of Cambridge, Cambridge, UK
| | - Justin Arnold
- Zuckerman Mind Brain Behavior Institute and Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Max A Tischfield
- Cell Biology and Neuroscience Department, Rutgers University, The State University of New Jersey, Piscataway, NJ, USA; Child Health Institute of New Jersey, Robert Wood Johnson Medical School, New Brunswick, NJ, USA; Human Genetics Institute of New Jersey, Rutgers University, The State University of New Jersey, Piscataway, NJ, USA; Tourette International Collaborative Genetics Study (TIC Genetics), Piscataway, NJ, USA
| | - Eric A Yttri
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA, USA; Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA
| | | | - Ishmail Abdus-Saboor
- Zuckerman Mind Brain Behavior Institute and Department of Biological Sciences, Columbia University, New York, NY, USA.
| | - Victoria E Abraira
- Cell Biology and Neuroscience Department, Rutgers University, The State University of New Jersey, Piscataway, NJ, USA; W.M. Keck Center for Collaborative Neuroscience, Rutgers University, The State University of New Jersey, Piscataway, NJ, USA.
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69
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Gundersen BB, O'Brien WT, Schaffler MD, Schultz MN, Tsukahara T, Lorenzo SM, Nalesso V, Luo Clayton AH, Abel T, Crawley JN, Datta SR, Herault Y. Towards Preclinical Validation of Arbaclofen (R-baclofen) Treatment for 16p11.2 Deletion Syndrome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.01.538987. [PMID: 37745360 PMCID: PMC10515778 DOI: 10.1101/2023.05.01.538987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
A microdeletion on human chromosome 16p11.2 is one of the most common copy number variants associated with autism spectrum disorder and other neurodevelopmental disabilities. Arbaclofen, a GABA(B) receptor agonist, is a component of racemic baclofen, which is FDA-approved for treating spasticity, and has been shown to alleviate behavioral phenotypes, including recognition memory deficits, in animal models of 16p11.2 deletion. Given the lack of reproducibility sometimes observed in mouse behavioral studies, we brought together a consortium of four laboratories to study the effects of arbaclofen on behavior in three different mouse lines with deletions in the mouse region syntenic to human 16p11.2 to test the robustness of these findings. Arbaclofen rescued cognitive deficits seen in two 16p11.2 deletion mouse lines in traditional recognition memory paradigms. Using an unsupervised machine-learning approach to analyze behavior, one lab found that arbaclofen also rescued differences in exploratory behavior in the open field in 16p11.2 deletion mice. Arbaclofen was not sedating and had modest off-target behavioral effects at the doses tested. Our studies show that arbaclofen consistently rescues behavioral phenotypes in 16p11.2 deletion mice, providing support for clinical trials of arbaclofen in humans with this deletion.
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Affiliation(s)
| | | | - Melanie D Schaffler
- MIND Institute, University of California Davis School of Medicine, Sacramento, CA
| | - Maria N Schultz
- MIND Institute, University of California Davis School of Medicine, Sacramento, CA
| | | | - Sandra Martin Lorenzo
- Université de Strasbourg, CNRS UMR7104, INSERM U1258, Institut de Genetique et de Biologie Moleculaire et Cellulaire (IGBMC), Illkirch cedex, France
| | - Valerie Nalesso
- Université de Strasbourg, CNRS UMR7104, INSERM U1258, Institut de Genetique et de Biologie Moleculaire et Cellulaire (IGBMC), Illkirch cedex, France
| | | | - Ted Abel
- University of Iowa, Iowa City, IA
| | - Jacqueline N Crawley
- MIND Institute, University of California Davis School of Medicine, Sacramento, CA
| | | | - Yann Herault
- Université de Strasbourg, CNRS UMR7104, INSERM U1258, Institut de Genetique et de Biologie Moleculaire et Cellulaire (IGBMC), Illkirch cedex, France
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70
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Newman JP, Zhang J, Cuevas-López A, Miller NJ, Honda T, van der Goes MSH, Leighton AH, Carvalho F, Lopes G, Lakunina A, Siegle JH, Harnett MT, Wilson MA, Voigts J. A unified open-source platform for multimodal neural recording and perturbation during naturalistic behavior. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.30.554672. [PMID: 37693443 PMCID: PMC10491150 DOI: 10.1101/2023.08.30.554672] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Behavioral neuroscience faces two conflicting demands: long-duration recordings from large neural populations and unimpeded animal behavior. To meet this challenge, we developed ONIX, an open-source data acquisition system with high data throughput (2GB/sec) and low closed-loop latencies (<1ms) that uses a novel 0.3 mm thin tether to minimize behavioral impact. Head position and rotation are tracked in 3D and used to drive active commutation without torque measurements. ONIX can acquire from combinations of passive electrodes, Neuropixels probes, head-mounted microscopes, cameras, 3D-trackers, and other data sources. We used ONIX to perform uninterrupted, long (~7 hours) neural recordings in mice as they traversed complex 3-dimensional terrain. ONIX allowed exploration with similar mobility as non-implanted animals, in contrast to conventional tethered systems which restricted movement. By combining long recordings with full mobility, our technology will enable new progress on questions that require high-quality neural recordings during ethologically grounded behaviors.
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Affiliation(s)
- Jonathan P Newman
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
- Picower Institute for Learning and Memory, MIT, Cambridge, MA, USA
- Open Ephys Inc. Atlanta, GA, USA
| | - Jie Zhang
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
- Picower Institute for Learning and Memory, MIT, Cambridge, MA, USA
| | - Aarón Cuevas-López
- Open Ephys Inc. Atlanta, GA, USA
- Dept. of Electrical Engineering, Polytechnic University of Valencia, Valencia, Spain
- Open Ephys Production Site, Lisbon, Portugal
| | - Nicholas J Miller
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
- McGovern Institute for Brain Research, MIT, Cambridge, MA, USA
| | - Takato Honda
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
- Picower Institute for Learning and Memory, MIT, Cambridge, MA, USA
| | - Marie-Sophie H van der Goes
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
- McGovern Institute for Brain Research, MIT, Cambridge, MA, USA
| | | | | | | | - Anna Lakunina
- Allen Institute for Neural Dynamics, Seattle, Washington, USA
| | - Joshua H Siegle
- Allen Institute for Neural Dynamics, Seattle, Washington, USA
| | - Mark T Harnett
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
- McGovern Institute for Brain Research, MIT, Cambridge, MA, USA
| | - Matthew A Wilson
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
- Picower Institute for Learning and Memory, MIT, Cambridge, MA, USA
| | - Jakob Voigts
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
- Open Ephys Inc. Atlanta, GA, USA
- McGovern Institute for Brain Research, MIT, Cambridge, MA, USA
- HHMI Janelia Research Campus, Ashburn, VA, USA
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Chelini G, Trombetta EM, Fortunato-Asquini T, Ollari O, Pecchia T, Bozzi Y. Automated Segmentation of the Mouse Body Language to Study Stimulus-Evoked Emotional Behaviors. eNeuro 2023; 10:ENEURO.0514-22.2023. [PMID: 37648448 PMCID: PMC10496135 DOI: 10.1523/eneuro.0514-22.2023] [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: 12/27/2022] [Revised: 07/15/2023] [Accepted: 07/24/2023] [Indexed: 09/01/2023] Open
Abstract
Understanding the neural basis of emotions is a critical step to uncover the biological substrates of neuropsychiatric disorders. To study this aspect in freely behaving mice, neuroscientists have relied on the observation of ethologically relevant bodily cues to infer the affective content of the subject, both in neutral conditions or in response to a stimulus. The best example of that is the widespread assessment of freezing in experiments testing both conditioned and unconditioned fear responses. While robust and powerful, these approaches come at a cost: they are usually confined within selected time windows, accounting for only a limited portion of the complexity of emotional fluctuation. Moreover, they often rely on visual inspection and subjective judgment, resulting in inconsistency across experiments and questionable result interpretations. To overcome these limitations, novel tools are arising, fostering a new avenue in the study of the mouse naturalistic behavior. In this work we developed a computational tool [stimulus-evoked behavioral tracking in 3D for rodents (SEB3R)] to automate and standardize an ethologically driven observation of freely moving mice. Using a combination of machine learning-based behavioral tracking and unsupervised cluster analysis, we identified statistically meaningful postures that could be used for empirical inference on a subsecond scale. We validated the efficacy of this tool in a stimulus-driven test, the whisker nuisance (WN) task, where mice are challenged with a prolonged and invasive whisker stimulation, showing that identified postures can be reliably used as a proxy for stimulus-driven fearful and explorative behaviors.
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Affiliation(s)
- Gabriele Chelini
- Center for Mind/Brain Sciences (CIMeC), University of Trento, Rovereto 38068, Italy
| | | | - Tommaso Fortunato-Asquini
- Department of Cellular, Computational, and Integrative Biology (CIBIO), University of Trento, Trento 38123, Italy
| | - Ottavia Ollari
- Center for Mind/Brain Sciences (CIMeC), University of Trento, Rovereto 38068, Italy
| | - Tommaso Pecchia
- Center for Mind/Brain Sciences (CIMeC), University of Trento, Rovereto 38068, Italy
| | - Yuri Bozzi
- Center for Mind/Brain Sciences (CIMeC), University of Trento, Rovereto 38068, Italy
- Consiglio Nazionale delle Ricerche (National Council of Research) Neuroscience Institute, Pisa 56124, Italy
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Voskobiynyk Y, Paz JT. AI-nalyzing Mouse Behavior to Combat Epilepsy. Epilepsy Curr 2023; 23:315-317. [PMID: 37901783 PMCID: PMC10601027 DOI: 10.1177/15357597231185215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2023] Open
Abstract
Hidden Behavioral Fingerprints in Epilepsy Gschwind T, Zeine A, Raikov I, Markowitz JE, Gillis WF, Felong S, Isom LL, Datta SR, Soltesz I. Neuron . 2023;111(9):1440-1452.e5. doi:10.1016/j.neuron.2023.02.003 . PMID: 36841241; PMCID: PMC10164063 Epilepsy is a major disorder affecting millions of people. Although modern electrophysiological and imaging approaches provide high-resolution access to the multi-scale brain circuit malfunctions in epilepsy, our understanding of how behavior changes with epilepsy has remained rudimentary. As a result, screening for new therapies for children and adults with devastating epilepsies still relies on the inherently subjective, semi-quantitative assessment of a handful of pre-selected behavioral signs of epilepsy in animal models. Here, we use machine learning-assisted 3D video analysis to reveal hidden behavioral phenotypes in mice with acquired and genetic epilepsies and track their alterations during post-insult epileptogenesis and in response to anti-epileptic drugs. These results show the persistent reconfiguration of behavioral fingerprints in epilepsy and indicate that they can be employed for rapid, automated anti-epileptic drug testing at scale.
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Affiliation(s)
| | - Jeanne T Paz
- Gladstone Institute of Neurological Disease, University of California, San Francisco, Department of Neurology, Weill Institute, Kavli Institute for Fundamental Neuroscience
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73
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Maselli A, Gordon J, Eluchans M, Lancia GL, Thiery T, Moretti R, Cisek P, Pezzulo G. Beyond simple laboratory studies: Developing sophisticated models to study rich behavior. Phys Life Rev 2023; 46:220-244. [PMID: 37499620 DOI: 10.1016/j.plrev.2023.07.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 07/06/2023] [Indexed: 07/29/2023]
Abstract
Psychology and neuroscience are concerned with the study of behavior, of internal cognitive processes, and their neural foundations. However, most laboratory studies use constrained experimental settings that greatly limit the range of behaviors that can be expressed. While focusing on restricted settings ensures methodological control, it risks impoverishing the object of study: by restricting behavior, we might miss key aspects of cognitive and neural functions. In this article, we argue that psychology and neuroscience should increasingly adopt innovative experimental designs, measurement methods, analysis techniques and sophisticated computational models to probe rich, ecologically valid forms of behavior, including social behavior. We discuss the challenges of studying rich forms of behavior as well as the novel opportunities offered by state-of-the-art methodologies and new sensing technologies, and we highlight the importance of developing sophisticated formal models. We exemplify our arguments by reviewing some recent streams of research in psychology, neuroscience and other fields (e.g., sports analytics, ethology and robotics) that have addressed rich forms of behavior in a model-based manner. We hope that these "success cases" will encourage psychologists and neuroscientists to extend their toolbox of techniques with sophisticated behavioral models - and to use them to study rich forms of behavior as well as the cognitive and neural processes that they engage.
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Affiliation(s)
- Antonella Maselli
- Institute of Cognitive Sciences and Technologies, National Research Council, Rome, Italy
| | - Jeremy Gordon
- University of California, Berkeley, Berkeley, CA, 94704, United States
| | - Mattia Eluchans
- Institute of Cognitive Sciences and Technologies, National Research Council, Rome, Italy; University of Rome "La Sapienza", Rome, Italy
| | - Gian Luca Lancia
- Institute of Cognitive Sciences and Technologies, National Research Council, Rome, Italy; University of Rome "La Sapienza", Rome, Italy
| | - Thomas Thiery
- Department of Psychology, University of Montréal, Montréal, Québec, Canada
| | - Riccardo Moretti
- Institute of Cognitive Sciences and Technologies, National Research Council, Rome, Italy; University of Rome "La Sapienza", Rome, Italy
| | - Paul Cisek
- Department of Neuroscience, University of Montréal, Montréal, Québec, Canada
| | - Giovanni Pezzulo
- Institute of Cognitive Sciences and Technologies, National Research Council, Rome, Italy.
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Phadke RA, Wetzel AM, Fournier LA, Sha M, Padró-Luna NM, Cruz-Martín A. REVEALS: An Open Source Multi Camera GUI For Rodent Behavior Acquisition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.22.554365. [PMID: 37662188 PMCID: PMC10473639 DOI: 10.1101/2023.08.22.554365] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Understanding the rich behavioral data generated by mice is essential for deciphering the function of the healthy and diseased brain. However, the current landscape lacks effective, affordable, and accessible methods for acquiring such data, especially when employing multiple cameras simultaneously. We have developed REVEALS (Rodent BEhaVior Multi-camErA Laboratory AcquiSition), a graphical user interface (GUI) written in python for acquiring rodent behavioral data via commonly used USB3 cameras. REVEALS allows for user-friendly control of recording from one or multiple cameras simultaneously while streamlining the data acquisition process, enabling researchers to collect and analyze large datasets efficiently. We release this software package as a stand-alone, open-source framework for researchers to use and modify according to their needs. We describe the details of the GUI implementation, including the camera control software and the video recording functionality. We validate results demonstrating the GUI's stability, reliability, and accuracy for capturing and analyzing rodent behavior using DeepLabCut pose estimation in both an object and social interaction assay. REVEALS can also be incorporated into other custom pipelines to analyze complex behavior, such as MoSeq. In summary, REVEALS provides an interface for collecting behavioral data from one or multiple perspectives that, combined with deep learning algorithms, will allow the scientific community to discover and characterize complex behavioral phenotypes to understand brain function better.
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Affiliation(s)
- Rhushikesh A. Phadke
- Molecular Biology, Cell Biology and Biochemistry Program, Boston University, Boston, MA, USA
| | - Austin M. Wetzel
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Luke A. Fournier
- Neurobiology Section in the Department of Biology, Boston University, Boston, MA, USA
| | - Mingqi Sha
- Neurobiology Section in the Department of Biology, Boston University, Boston, MA, USA
| | - Nicole M. Padró-Luna
- Summer Undergraduate Research Fellowship Program, Boston University, Boston, MA, USA
- College of Natural Sciences, Río Piedras Campus, University of Puerto Rico, Río Piedras, PR
| | - Alberto Cruz-Martín
- Neurobiology Section in the Department of Biology, Boston University, Boston, MA, USA
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75
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Hu B, Seybold B, Yang S, Sud A, Liu Y, Barron K, Cha P, Cosino M, Karlsson E, Kite J, Kolumam G, Preciado J, Zavala-Solorio J, Zhang C, Zhang X, Voorbach M, Tovcimak AE, Ruby JG, Ross DA. 3D mouse pose from single-view video and a new dataset. Sci Rep 2023; 13:13554. [PMID: 37604955 PMCID: PMC10442417 DOI: 10.1038/s41598-023-40738-w] [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: 11/25/2022] [Accepted: 08/16/2023] [Indexed: 08/23/2023] Open
Abstract
We present a method to infer the 3D pose of mice, including the limbs and feet, from monocular videos. Many human clinical conditions and their corresponding animal models result in abnormal motion, and accurately measuring 3D motion at scale offers insights into health. The 3D poses improve classification of health-related attributes over 2D representations. The inferred poses are accurate enough to estimate stride length even when the feet are mostly occluded. This method could be applied as part of a continuous monitoring system to non-invasively measure animal health, as demonstrated by its use in successfully classifying animals based on age and genotype. We introduce the Mouse Pose Analysis Dataset, the first large scale video dataset of lab mice in their home cage with ground truth keypoint and behavior labels. The dataset also contains high resolution mouse CT scans, which we use to build the shape models for 3D pose reconstruction.
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Affiliation(s)
- Bo Hu
- Google, 1600 Amphitheatre Parkway, Mountain View, CA, 94043, USA.
| | - Bryan Seybold
- Google, 1600 Amphitheatre Parkway, Mountain View, CA, 94043, USA
| | - Shan Yang
- Google, 1600 Amphitheatre Parkway, Mountain View, CA, 94043, USA
| | - Avneesh Sud
- Google, 1600 Amphitheatre Parkway, Mountain View, CA, 94043, USA
| | - Yi Liu
- Calico Life Sciences LLC, 1170 Veterans Blvd., South San Francisco, CA, 94080, USA
| | - Karla Barron
- Calico Life Sciences LLC, 1170 Veterans Blvd., South San Francisco, CA, 94080, USA
| | - Paulyn Cha
- Calico Life Sciences LLC, 1170 Veterans Blvd., South San Francisco, CA, 94080, USA
| | - Marcelo Cosino
- Calico Life Sciences LLC, 1170 Veterans Blvd., South San Francisco, CA, 94080, USA
| | - Ellie Karlsson
- Calico Life Sciences LLC, 1170 Veterans Blvd., South San Francisco, CA, 94080, USA
| | - Janessa Kite
- Calico Life Sciences LLC, 1170 Veterans Blvd., South San Francisco, CA, 94080, USA
| | - Ganesh Kolumam
- Calico Life Sciences LLC, 1170 Veterans Blvd., South San Francisco, CA, 94080, USA
| | - Joseph Preciado
- Calico Life Sciences LLC, 1170 Veterans Blvd., South San Francisco, CA, 94080, USA
| | - José Zavala-Solorio
- Calico Life Sciences LLC, 1170 Veterans Blvd., South San Francisco, CA, 94080, USA
| | - Chunlian Zhang
- Calico Life Sciences LLC, 1170 Veterans Blvd., South San Francisco, CA, 94080, USA
| | - Xiaomeng Zhang
- Translational Imaging, Neuroscience Discovery, Abbvie, 1 N. Waukegan Rd., North Chicago, IL, 60064-1802, USA
| | - Martin Voorbach
- Translational Imaging, Neuroscience Discovery, Abbvie, 1 N. Waukegan Rd., North Chicago, IL, 60064-1802, USA
| | - Ann E Tovcimak
- Translational Imaging, Neuroscience Discovery, Abbvie, 1 N. Waukegan Rd., North Chicago, IL, 60064-1802, USA
| | - J Graham Ruby
- Calico Life Sciences LLC, 1170 Veterans Blvd., South San Francisco, CA, 94080, USA
| | - David A Ross
- Google, 1600 Amphitheatre Parkway, Mountain View, CA, 94043, USA
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Cao S, Wu Y, Gao Z, Tang J, Xiong L, Hu J, Li C. Automated phenotyping of postoperative delirium-like behaviour in mice reveals the therapeutic efficacy of dexmedetomidine. Commun Biol 2023; 6:807. [PMID: 37532767 PMCID: PMC10397202 DOI: 10.1038/s42003-023-05149-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 07/17/2023] [Indexed: 08/04/2023] Open
Abstract
Postoperative delirium (POD) is a complicated and harmful clinical syndrome. Traditional behaviour analysis mostly focuses on static parameters. However, animal behaviour is a bottom-up and hierarchical organizational structure composed of time-varying posture dynamics. Spontaneous and task-driven behaviours are used to conduct comprehensive profiling of behavioural data of various aspects of model animals. A machine-learning based method is used to assess the effect of dexmedetomidine. Fourteen statistically different spontaneous behaviours are used to distinguish the non-POD group from the POD group. In the task-driven behaviour, the non-POD group has greater deep versus shallow investigation preference, with no significant preference in the POD group. Hyperactive and hypoactive subtypes can be distinguished through pose evaluation. Dexmedetomidine at a dose of 25 μg kg-1 reduces the severity and incidence of POD. Here we propose a multi-scaled clustering analysis framework that includes pose, behaviour and action sequence evaluation. This may represent the hierarchical dynamics of delirium-like behaviours.
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Affiliation(s)
- Silu Cao
- Department of Anesthesiology and Perioperative Medicine, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai, 200434, China
- Translational Research Institute of Brain and Brain-like Intelligence, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai, 200434, China
- Clinical Research Center for Anesthesiology and Perioperative Medicine, Tongji University, Shanghai, 200434, China
- Shanghai Key Laboratory of Anesthesiology and Brain Functional Modulation, Shanghai, 200434, China
| | - Yiling Wu
- School of Life Sciences and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Zilong Gao
- School of Life Sciences and Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, Westlake University, Hangzhou, 310024, China
- Chinese Institute for Brain Research, Beijing, 102206, China
| | - Jinxuan Tang
- Department of Anesthesiology and Perioperative Medicine, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai, 200434, China
- Translational Research Institute of Brain and Brain-like Intelligence, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai, 200434, China
- Clinical Research Center for Anesthesiology and Perioperative Medicine, Tongji University, Shanghai, 200434, China
- Shanghai Key Laboratory of Anesthesiology and Brain Functional Modulation, Shanghai, 200434, China
| | - Lize Xiong
- Department of Anesthesiology and Perioperative Medicine, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai, 200434, China
- Translational Research Institute of Brain and Brain-like Intelligence, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai, 200434, China
- Clinical Research Center for Anesthesiology and Perioperative Medicine, Tongji University, Shanghai, 200434, China
- Shanghai Key Laboratory of Anesthesiology and Brain Functional Modulation, Shanghai, 200434, China
| | - Ji Hu
- School of Life Sciences and Technology, ShanghaiTech University, Shanghai, 201210, China.
| | - Cheng Li
- Department of Anesthesiology and Perioperative Medicine, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai, 200434, China.
- Translational Research Institute of Brain and Brain-like Intelligence, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai, 200434, China.
- Clinical Research Center for Anesthesiology and Perioperative Medicine, Tongji University, Shanghai, 200434, China.
- Shanghai Key Laboratory of Anesthesiology and Brain Functional Modulation, Shanghai, 200434, China.
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77
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Bohic M, Upadhyay A, Eisdorfer JT, Keating J, Simon RC, Briones BA, Azadegan C, Nacht HD, Oputa O, Martinez AM, Bethell BN, Gradwell MA, Romanienko P, Ramer MS, Stuber GD, Abraira VE. A new Hoxb8FlpO mouse line for intersectional approaches to dissect developmentally defined adult sensorimotor circuits. Front Mol Neurosci 2023; 16:1176823. [PMID: 37603775 PMCID: PMC10437123 DOI: 10.3389/fnmol.2023.1176823] [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: 02/28/2023] [Accepted: 07/04/2023] [Indexed: 08/23/2023] Open
Abstract
Improvements in the speed and cost of expression profiling of neuronal tissues offer an unprecedented opportunity to define ever finer subgroups of neurons for functional studies. In the spinal cord, single cell RNA sequencing studies support decades of work on spinal cord lineage studies, offering a unique opportunity to probe adult function based on developmental lineage. While Cre/Flp recombinase intersectional strategies remain a powerful tool to manipulate spinal neurons, the field lacks genetic tools and strategies to restrict manipulations to the adult mouse spinal cord at the speed at which new tools develop. This study establishes a new workflow for intersectional mouse-viral strategies to dissect adult spinal function based on developmental lineages in a modular fashion. To restrict manipulations to the spinal cord, we generate a brain-sparing Hoxb8FlpO mouse line restricting Flp recombinase expression to caudal tissue. Recapitulating endogenous Hoxb8 gene expression, Flp-dependent reporter expression is present in the caudal embryo starting day 9.5. This expression restricts Flp activity in the adult to the caudal brainstem and below. Hoxb8FlpO heterozygous and homozygous mice do not develop any of the sensory or locomotor phenotypes evident in Hoxb8 heterozygous or mutant animals, suggesting normal developmental function of the Hoxb8 gene and protein in Hoxb8FlpO mice. Compared to the variability of brain recombination in available caudal Cre and Flp lines, Hoxb8FlpO activity is not present in the brain above the caudal brainstem, independent of mouse genetic background. Lastly, we combine the Hoxb8FlpO mouse line with dorsal horn developmental lineage Cre mouse lines to express GFP in developmentally determined dorsal horn populations. Using GFP-dependent Cre recombinase viruses and Cre recombinase-dependent inhibitory chemogenetics, we target developmentally defined lineages in the adult. We show how developmental knock-out versus transient adult silencing of the same ROR𝛃 lineage neurons affects adult sensorimotor behavior. In summary, this new mouse line and viral approach provides a blueprint to dissect adult somatosensory circuit function using Cre/Flp genetic tools to target spinal cord interneurons based on genetic lineage.
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Affiliation(s)
- Manon Bohic
- Cell Biology and Neuroscience Department, Rutgers University, The State University of New Jersey, Piscataway, NJ, United States
- W.M. Keck Center for Collaborative Neuroscience, Rutgers University, The State University of New Jersey, Piscataway, NJ, United States
| | - Aman Upadhyay
- Cell Biology and Neuroscience Department, Rutgers University, The State University of New Jersey, Piscataway, NJ, United States
- W.M. Keck Center for Collaborative Neuroscience, Rutgers University, The State University of New Jersey, Piscataway, NJ, United States
- Neuroscience PhD Program at Rutgers Robert Wood Johnson Medical School, Piscataway, NJ, United States
| | - Jaclyn T. Eisdorfer
- Cell Biology and Neuroscience Department, Rutgers University, The State University of New Jersey, Piscataway, NJ, United States
- W.M. Keck Center for Collaborative Neuroscience, Rutgers University, The State University of New Jersey, Piscataway, NJ, United States
| | - Jessica Keating
- Cell Biology and Neuroscience Department, Rutgers University, The State University of New Jersey, Piscataway, NJ, United States
- W.M. Keck Center for Collaborative Neuroscience, Rutgers University, The State University of New Jersey, Piscataway, NJ, United States
- School of Medicine, Oregon Health and Science University, Portland, OR, United States
- M.D./PhD Program in Neuroscience, School of Medicine, Oregon Health and Science University, Portland, OR, United States
| | - Rhiana C. Simon
- Center for the Neurobiology of Addiction, Pain, and Emotion, Department of Anesthesiology and Pain Medicine, Department of Pharmacology, University of Washington, Seattle, WA, United States
| | - Brandy A. Briones
- Center for the Neurobiology of Addiction, Pain, and Emotion, Department of Anesthesiology and Pain Medicine, Department of Pharmacology, University of Washington, Seattle, WA, United States
| | - Chloe Azadegan
- Cell Biology and Neuroscience Department, Rutgers University, The State University of New Jersey, Piscataway, NJ, United States
- W.M. Keck Center for Collaborative Neuroscience, Rutgers University, The State University of New Jersey, Piscataway, NJ, United States
| | - Hannah D. Nacht
- Cell Biology and Neuroscience Department, Rutgers University, The State University of New Jersey, Piscataway, NJ, United States
- W.M. Keck Center for Collaborative Neuroscience, Rutgers University, The State University of New Jersey, Piscataway, NJ, United States
| | - Olisemeka Oputa
- Cell Biology and Neuroscience Department, Rutgers University, The State University of New Jersey, Piscataway, NJ, United States
- W.M. Keck Center for Collaborative Neuroscience, Rutgers University, The State University of New Jersey, Piscataway, NJ, United States
| | - Alana M. Martinez
- Cell Biology and Neuroscience Department, Rutgers University, The State University of New Jersey, Piscataway, NJ, United States
- W.M. Keck Center for Collaborative Neuroscience, Rutgers University, The State University of New Jersey, Piscataway, NJ, United States
| | - Bridget N. Bethell
- International Collaboration on Repair Discoveries and Department of Zoology, The University of British Columbia, Vancouver, BC, Canada
| | - Mark A. Gradwell
- Cell Biology and Neuroscience Department, Rutgers University, The State University of New Jersey, Piscataway, NJ, United States
- W.M. Keck Center for Collaborative Neuroscience, Rutgers University, The State University of New Jersey, Piscataway, NJ, United States
| | - Peter Romanienko
- Genome Editing Shared Resource, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, United States
| | - Matt S. Ramer
- International Collaboration on Repair Discoveries and Department of Zoology, The University of British Columbia, Vancouver, BC, Canada
| | - Garret D. Stuber
- Center for the Neurobiology of Addiction, Pain, and Emotion, Department of Anesthesiology and Pain Medicine, Department of Pharmacology, University of Washington, Seattle, WA, United States
| | - Victoria E. Abraira
- Cell Biology and Neuroscience Department, Rutgers University, The State University of New Jersey, Piscataway, NJ, United States
- W.M. Keck Center for Collaborative Neuroscience, Rutgers University, The State University of New Jersey, Piscataway, NJ, United States
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78
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Bordes J, Miranda L, Reinhardt M, Narayan S, Hartmann J, Newman EL, Brix LM, van Doeselaar L, Engelhardt C, Dillmann L, Mitra S, Ressler KJ, Pütz B, Agakov F, Müller-Myhsok B, Schmidt MV. Automatically annotated motion tracking identifies a distinct social behavioral profile following chronic social defeat stress. Nat Commun 2023; 14:4319. [PMID: 37463994 PMCID: PMC10354203 DOI: 10.1038/s41467-023-40040-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 07/07/2023] [Indexed: 07/20/2023] Open
Abstract
Severe stress exposure increases the risk of stress-related disorders such as major depressive disorder (MDD). An essential characteristic of MDD is the impairment of social functioning and lack of social motivation. Chronic social defeat stress is an established animal model for MDD research, which induces a cascade of physiological and behavioral changes. Current markerless pose estimation tools allow for more complex and naturalistic behavioral tests. Here, we introduce the open-source tool DeepOF to investigate the individual and social behavioral profile in mice by providing supervised and unsupervised pipelines using DeepLabCut-annotated pose estimation data. Applying this tool to chronic social defeat in male mice, the DeepOF supervised and unsupervised pipelines detect a distinct stress-induced social behavioral pattern, which was particularly observed at the beginning of a novel social encounter and fades with time due to habituation. In addition, while the classical social avoidance task does identify the stress-induced social behavioral differences, both DeepOF behavioral pipelines provide a clearer and more detailed profile. Moreover, DeepOF aims to facilitate reproducibility and unification of behavioral classification by providing an open-source tool, which can advance the study of rodent individual and social behavior, thereby enabling biological insights and, for example, subsequent drug development for psychiatric disorders.
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Affiliation(s)
- Joeri Bordes
- Research Group Neurobiology of Stress Resilience, Max Planck Institute of Psychiatry, 80804, Munich, Germany
| | - Lucas Miranda
- Research Group Statistical Genetics, Max Planck Institute of Psychiatry, 80804, Munich, Germany
- International Max Planck Research School for Translational Psychiatry (IMPRS-TP), 80804, Munich, Germany
| | - Maya Reinhardt
- Research Group Neurobiology of Stress Resilience, Max Planck Institute of Psychiatry, 80804, Munich, Germany
| | - Sowmya Narayan
- Research Group Neurobiology of Stress Resilience, Max Planck Institute of Psychiatry, 80804, Munich, Germany
- International Max Planck Research School for Translational Psychiatry (IMPRS-TP), 80804, Munich, Germany
| | - Jakob Hartmann
- Department of Psychiatry, Harvard Medical School, McLean Hospital, Belmont, MA, 02478, USA
| | - Emily L Newman
- Department of Psychiatry, Harvard Medical School, McLean Hospital, Belmont, MA, 02478, USA
| | - Lea Maria Brix
- Research Group Neurobiology of Stress Resilience, Max Planck Institute of Psychiatry, 80804, Munich, Germany
- International Max Planck Research School for Translational Psychiatry (IMPRS-TP), 80804, Munich, Germany
| | - Lotte van Doeselaar
- Research Group Neurobiology of Stress Resilience, Max Planck Institute of Psychiatry, 80804, Munich, Germany
- International Max Planck Research School for Translational Psychiatry (IMPRS-TP), 80804, Munich, Germany
| | - Clara Engelhardt
- Research Group Neurobiology of Stress Resilience, Max Planck Institute of Psychiatry, 80804, Munich, Germany
| | - Larissa Dillmann
- Research Group Neurobiology of Stress Resilience, Max Planck Institute of Psychiatry, 80804, Munich, Germany
| | - Shiladitya Mitra
- Research Group Neurobiology of Stress Resilience, Max Planck Institute of Psychiatry, 80804, Munich, Germany
| | - Kerry J Ressler
- Department of Psychiatry, Harvard Medical School, McLean Hospital, Belmont, MA, 02478, USA
| | - Benno Pütz
- Research Group Statistical Genetics, Max Planck Institute of Psychiatry, 80804, Munich, Germany
| | - Felix Agakov
- Pharmatics Limited, Edinburgh, EH16 4UX, Scotland, UK
| | - Bertram Müller-Myhsok
- Research Group Statistical Genetics, Max Planck Institute of Psychiatry, 80804, Munich, Germany.
| | - Mathias V Schmidt
- Research Group Neurobiology of Stress Resilience, Max Planck Institute of Psychiatry, 80804, Munich, Germany.
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79
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Camilleri MPJ, Zhang L, Bains RS, Zisserman A, Williams CKI. Persistent animal identification leveraging non-visual markers. MACHINE VISION AND APPLICATIONS 2023; 34:68. [PMID: 37457592 PMCID: PMC10345053 DOI: 10.1007/s00138-023-01414-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 05/29/2023] [Accepted: 06/12/2023] [Indexed: 07/18/2023]
Abstract
Our objective is to locate and provide a unique identifier for each mouse in a cluttered home-cage environment through time, as a precursor to automated behaviour recognition for biological research. This is a very challenging problem due to (i) the lack of distinguishing visual features for each mouse, and (ii) the close confines of the scene with constant occlusion, making standard visual tracking approaches unusable. However, a coarse estimate of each mouse's location is available from a unique RFID implant, so there is the potential to optimally combine information from (weak) tracking with coarse information on identity. To achieve our objective, we make the following key contributions: (a) the formulation of the object identification problem as an assignment problem (solved using Integer Linear Programming), (b) a novel probabilistic model of the affinity between tracklets and RFID data, and (c) a curated dataset with per-frame BB and regularly spaced ground-truth annotations for evaluating the models. The latter is a crucial part of the model, as it provides a principled probabilistic treatment of object detections given coarse localisation. Our approach achieves 77% accuracy on this animal identification problem, and is able to reject spurious detections when the animals are hidden.
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Affiliation(s)
| | - Li Zhang
- School of Data Science, Fudan University, Shanghai, China
| | | | - Andrew Zisserman
- Department of Engineering Science, University of Oxford, Oxford, UK
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80
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Mimica B, Tombaz T, Battistin C, Fuglstad JG, Dunn BA, Whitlock JR. Behavioral decomposition reveals rich encoding structure employed across neocortex in rats. Nat Commun 2023; 14:3947. [PMID: 37402724 DOI: 10.1038/s41467-023-39520-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 06/16/2023] [Indexed: 07/06/2023] Open
Abstract
The cortical population code is pervaded by activity patterns evoked by movement, but it remains largely unknown how such signals relate to natural behavior or how they might support processing in sensory cortices where they have been observed. To address this we compared high-density neural recordings across four cortical regions (visual, auditory, somatosensory, motor) in relation to sensory modulation, posture, movement, and ethograms of freely foraging male rats. Momentary actions, such as rearing or turning, were represented ubiquitously and could be decoded from all sampled structures. However, more elementary and continuous features, such as pose and movement, followed region-specific organization, with neurons in visual and auditory cortices preferentially encoding mutually distinct head-orienting features in world-referenced coordinates, and somatosensory and motor cortices principally encoding the trunk and head in egocentric coordinates. The tuning properties of synaptically coupled cells also exhibited connection patterns suggestive of area-specific uses of pose and movement signals, particularly in visual and auditory regions. Together, our results indicate that ongoing behavior is encoded at multiple levels throughout the dorsal cortex, and that low-level features are differentially utilized by different regions to serve locally relevant computations.
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Affiliation(s)
- Bartul Mimica
- Princeton Neuroscience Institute, Princeton University, Washington Road, Princeton, 100190, NJ, USA.
| | - Tuçe Tombaz
- Kavli Institute for Systems Neuroscience, Norwegian University of Science and Technology, Olav Kyrres Gate 9, 7030, Trondheim, Norway
| | - Claudia Battistin
- Kavli Institute for Systems Neuroscience, Norwegian University of Science and Technology, Olav Kyrres Gate 9, 7030, Trondheim, Norway
- Department of Mathematical Sciences, Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Jingyi Guo Fuglstad
- Kavli Institute for Systems Neuroscience, Norwegian University of Science and Technology, Olav Kyrres Gate 9, 7030, Trondheim, Norway
| | - Benjamin A Dunn
- Kavli Institute for Systems Neuroscience, Norwegian University of Science and Technology, Olav Kyrres Gate 9, 7030, Trondheim, Norway
- Department of Mathematical Sciences, Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Jonathan R Whitlock
- Kavli Institute for Systems Neuroscience, Norwegian University of Science and Technology, Olav Kyrres Gate 9, 7030, Trondheim, Norway.
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81
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Voloh B, Eisenreich BR, Maisson DJN, Ebitz RB, Park HS, Hayden BY, Zimmermann J. Hierarchical organization of rhesus macaque behavior. OXFORD OPEN NEUROSCIENCE 2023; 2:kvad006. [PMID: 37577290 PMCID: PMC10421634 DOI: 10.1093/oons/kvad006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 06/11/2023] [Accepted: 06/12/2023] [Indexed: 08/15/2023]
Abstract
Primatologists, psychologists and neuroscientists have long hypothesized that primate behavior is highly structured. However, delineating that structure has been impossible due to the difficulties of precision behavioral tracking. Here we analyzed a dataset consisting of continuous measures of the 3D position of two male rhesus macaques (Macaca mulatta) performing three different tasks in a large unrestrained environment over several hours. Using an unsupervised embedding approach on the tracked joints, we identified commonly repeated pose patterns, which we call postures. We found that macaques' behavior is characterized by 49 distinct postures, lasting an average of 0.6 seconds. We found evidence that behavior is hierarchically organized, in that transitions between poses tend to occur within larger modules, which correspond to identifiable actions; these actions are further organized hierarchically. Our behavioral decomposition allows us to identify universal (cross-individual and cross-task) and unique (specific to each individual and task) principles of behavior. These results demonstrate the hierarchical nature of primate behavior, provide a method for the automated ethogramming of primate behavior, and provide important constraints on neural models of pose generation.
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Affiliation(s)
- Benjamin Voloh
- Department of Neuroscience, Center for Magnetic Resonance Research, Center for Neuroengineering, 1 Baylor Plaza, Houston, TX 77030
| | - Benjamin R Eisenreich
- Department of Neuroscience, Center for Magnetic Resonance Research, Center for Neuroengineering, 1 Baylor Plaza, Houston, TX 77030
| | - David J-N Maisson
- Department of Neuroscience, Center for Magnetic Resonance Research, Center for Neuroengineering, 1 Baylor Plaza, Houston, TX 77030
| | - R Becket Ebitz
- Department of Neuroscience, Center for Magnetic Resonance Research, Center for Neuroengineering, 1 Baylor Plaza, Houston, TX 77030
| | - Hyun Soo Park
- Department of Computer Science and Engineering, University of Minnesota, 40 Church St, Minneapolis, MN 55455, USA
| | - Benjamin Y Hayden
- Department of Neuroscience, Center for Magnetic Resonance Research, Center for Neuroengineering, 1 Baylor Plaza, Houston, TX 77030
| | - Jan Zimmermann
- Department of Neuroscience, Center for Magnetic Resonance Research, Center for Neuroengineering, 1 Baylor Plaza, Houston, TX 77030
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82
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Hope J, Beckerle T, Cheng PH, Viavattine Z, Feldkamp M, Fausner S, Saxena K, Ko E, Hryb I, Carter R, Ebner T, Kodandaramaiah S. Brain-wide neural recordings in mice navigating physical spaces enabled by a cranial exoskeleton. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.04.543578. [PMID: 37333228 PMCID: PMC10274744 DOI: 10.1101/2023.06.04.543578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Complex behaviors are mediated by neural computations occurring throughout the brain. In recent years, tremendous progress has been made in developing technologies that can record neural activity at cellular resolution at multiple spatial and temporal scales. However, these technologies are primarily designed for studying the mammalian brain during head fixation - wherein the behavior of the animal is highly constrained. Miniaturized devices for studying neural activity in freely behaving animals are largely confined to recording from small brain regions owing to performance limitations. We present a cranial exoskeleton that assists mice in maneuvering neural recording headstages that are orders of magnitude larger and heavier than the mice, while they navigate physical behavioral environments. Force sensors embedded within the headstage are used to detect the mouse's milli-Newton scale cranial forces which then control the x, y, and yaw motion of the exoskeleton via an admittance controller. We discovered optimal controller tuning parameters that enable mice to locomote at physiologically realistic velocities and accelerations while maintaining natural walking gait. Mice maneuvering headstages weighing up to 1.5 kg can make turns, navigate 2D arenas, and perform a navigational decision-making task with the same performance as when freely behaving. We designed an imaging headstage and an electrophysiology headstage for the cranial exoskeleton to record brain-wide neural activity in mice navigating 2D arenas. The imaging headstage enabled recordings of Ca2+ activity of 1000s of neurons distributed across the dorsal cortex. The electrophysiology headstage supported independent control of up to 4 silicon probes, enabling simultaneous recordings from 100s of neurons across multiple brain regions and multiple days. Cranial exoskeletons provide flexible platforms for largescale neural recording during the exploration of physical spaces, a critical new paradigm for unraveling the brain-wide neural mechanisms that control complex behavior.
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Affiliation(s)
- James Hope
- Department of Mechanical Engineering, University of Minnesota, Twin Cities
| | - Travis Beckerle
- Department of Mechanical Engineering, University of Minnesota, Twin Cities
| | - Pin-Hao Cheng
- Department of Mechanical Engineering, University of Minnesota, Twin Cities
| | - Zoey Viavattine
- Department of Mechanical Engineering, University of Minnesota, Twin Cities
| | - Michael Feldkamp
- Department of Mechanical Engineering, University of Minnesota, Twin Cities
| | - Skylar Fausner
- Department of Mechanical Engineering, University of Minnesota, Twin Cities
| | - Kapil Saxena
- Department of Mechanical Engineering, University of Minnesota, Twin Cities
| | - Eunsong Ko
- Department of Mechanical Engineering, University of Minnesota, Twin Cities
| | - Ihor Hryb
- Department of Mechanical Engineering, University of Minnesota, Twin Cities
- Department of Neuroscience, University of Minnesota, Twin Cities
| | - Russell Carter
- Department of Biomedical Engineering, University of Minnesota, Twin Cities
| | - Timothy Ebner
- Department of Biomedical Engineering, University of Minnesota, Twin Cities
| | - Suhasa Kodandaramaiah
- Department of Mechanical Engineering, University of Minnesota, Twin Cities
- Department of Biomedical Engineering, University of Minnesota, Twin Cities
- Department of Neuroscience, University of Minnesota, Twin Cities
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83
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Verpeut JL, Bergeler S, Kislin M, William Townes F, Klibaite U, Dhanerawala ZM, Hoag A, Janarthanan S, Jung C, Lee J, Pisano TJ, Seagraves KM, Shaevitz JW, Wang SSH. Cerebellar contributions to a brainwide network for flexible behavior in mice. Commun Biol 2023; 6:605. [PMID: 37277453 PMCID: PMC10241932 DOI: 10.1038/s42003-023-04920-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 05/05/2023] [Indexed: 06/07/2023] Open
Abstract
The cerebellum regulates nonmotor behavior, but the routes of influence are not well characterized. Here we report a necessary role for the posterior cerebellum in guiding a reversal learning task through a network of diencephalic and neocortical structures, and in flexibility of free behavior. After chemogenetic inhibition of lobule VI vermis or hemispheric crus I Purkinje cells, mice could learn a water Y-maze but were impaired in ability to reverse their initial choice. To map targets of perturbation, we imaged c-Fos activation in cleared whole brains using light-sheet microscopy. Reversal learning activated diencephalic and associative neocortical regions. Distinctive subsets of structures were altered by perturbation of lobule VI (including thalamus and habenula) and crus I (including hypothalamus and prelimbic/orbital cortex), and both perturbations influenced anterior cingulate and infralimbic cortex. To identify functional networks, we used correlated variation in c-Fos activation within each group. Lobule VI inactivation weakened within-thalamus correlations, while crus I inactivation divided neocortical activity into sensorimotor and associative subnetworks. In both groups, high-throughput automated analysis of whole-body movement revealed deficiencies in across-day behavioral habituation to an open-field environment. Taken together, these experiments reveal brainwide systems for cerebellar influence that affect multiple flexible responses.
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Affiliation(s)
- Jessica L Verpeut
- Neuroscience Institute, Princeton University, Washington Road, Princeton, NJ, 08544, USA.
| | - Silke Bergeler
- Neuroscience Institute, Princeton University, Washington Road, Princeton, NJ, 08544, USA
- Department of Physics, Princeton University, Princeton, NJ, 08544, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08544, USA
| | - Mikhail Kislin
- Neuroscience Institute, Princeton University, Washington Road, Princeton, NJ, 08544, USA
| | - F William Townes
- Department of Statistics and Data Science, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Ugne Klibaite
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 01451, USA
| | - Zahra M Dhanerawala
- Neuroscience Institute, Princeton University, Washington Road, Princeton, NJ, 08544, USA
| | - Austin Hoag
- Neuroscience Institute, Princeton University, Washington Road, Princeton, NJ, 08544, USA
| | - Sanjeev Janarthanan
- Neuroscience Institute, Princeton University, Washington Road, Princeton, NJ, 08544, USA
| | - Caroline Jung
- Neuroscience Institute, Princeton University, Washington Road, Princeton, NJ, 08544, USA
| | - Junuk Lee
- Neuroscience Institute, Princeton University, Washington Road, Princeton, NJ, 08544, USA
| | - Thomas J Pisano
- Neuroscience Institute, Princeton University, Washington Road, Princeton, NJ, 08544, USA
| | - Kelly M Seagraves
- Neuroscience Institute, Princeton University, Washington Road, Princeton, NJ, 08544, USA
| | - Joshua W Shaevitz
- Department of Physics, Princeton University, Princeton, NJ, 08544, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08544, USA
| | - Samuel S-H Wang
- Neuroscience Institute, Princeton University, Washington Road, Princeton, NJ, 08544, USA.
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84
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85
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Chen Z, Zhang R, Fang HS, Zhang YE, Bal A, Zhou H, Rock RR, Padilla-Coreano N, Keyes LR, Zhu H, Li YL, Komiyama T, Tye KM, Lu C. AlphaTracker: a multi-animal tracking and behavioral analysis tool. Front Behav Neurosci 2023; 17:1111908. [PMID: 37324523 PMCID: PMC10266280 DOI: 10.3389/fnbeh.2023.1111908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 02/21/2023] [Indexed: 06/17/2023] Open
Abstract
Computer vision has emerged as a powerful tool to elevate behavioral research. This protocol describes a computer vision machine learning pipeline called AlphaTracker, which has minimal hardware requirements and produces reliable tracking of multiple unmarked animals, as well as behavioral clustering. AlphaTracker pairs a top-down pose-estimation software combined with unsupervised clustering to facilitate behavioral motif discovery that will accelerate behavioral research. All steps of the protocol are provided as open-source software with graphic user interfaces or implementable with command-line prompts. Users with a graphical processing unit (GPU) can model and analyze animal behaviors of interest in less than a day. AlphaTracker greatly facilitates the analysis of the mechanism of individual/social behavior and group dynamics.
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Affiliation(s)
- Zexin Chen
- Department of Computer Science, Shanghai Jiao Tong University, Shanghai, China
| | - Ruihan Zhang
- Zhiyuan College, Shanghai Jiao Tong University, Shanghai, China
- Media Arts and Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Hao-Shu Fang
- Department of Computer Science, Shanghai Jiao Tong University, Shanghai, China
| | - Yu E. Zhang
- Department of Neurobiology, Center for Neural Circuits and Behavior, University of California, San Diego, La Jolla, CA, United States
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, United States
| | - Aneesh Bal
- Department of Psychological and Brain Sciences, Johns Hopkins University, Baltimore, MD, United States
- Salk Institute for Biological Studies, La Jolla, CA, United States
| | - Haowen Zhou
- Zhiyuan College, Shanghai Jiao Tong University, Shanghai, China
| | - Rachel R. Rock
- Salk Institute for Biological Studies, La Jolla, CA, United States
| | - Nancy Padilla-Coreano
- Salk Institute for Biological Studies, La Jolla, CA, United States
- Department of Neuroscience, University of Florida, Gainesville, FL, United States
| | - Laurel R. Keyes
- Salk Institute for Biological Studies, La Jolla, CA, United States
- Howard Hughes Medical Institute, The Salk Institute, La Jolla, CA, United States
| | - Haoyi Zhu
- Department of Computer Science, Shanghai Jiao Tong University, Shanghai, China
| | - Yong-Lu Li
- Department of Computer Science, Shanghai Jiao Tong University, Shanghai, China
| | - Takaki Komiyama
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, United States
| | - Kay M. Tye
- Salk Institute for Biological Studies, La Jolla, CA, United States
- Howard Hughes Medical Institute, The Salk Institute, La Jolla, CA, United States
| | - Cewu Lu
- Department of Computer Science, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Artificial Intelligence Laboratory, Shanghai, China
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86
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Tseng YT, Zhao B, Ding H, Liang L, Schaefke B, Wang L. Systematic evaluation of a predator stress model of depression in mice using a hierarchical 3D-motion learning framework. Transl Psychiatry 2023; 13:178. [PMID: 37231005 DOI: 10.1038/s41398-023-02481-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/07/2023] [Accepted: 05/16/2023] [Indexed: 05/27/2023] Open
Abstract
Investigation of the neurobiology of depression in humans depends on animal models that attempt to mimic specific features of the human disorder. However, frequently-used paradigms based on social stress cannot be easily applied to female mice which has led to a large sex bias in preclinical studies of depression. Furthermore, most studies focus on one or only a few behavioral assessments, with time and practical considerations prohibiting a comprehensive evaluation. In this study, we demonstrate that predator stress effectively induced depression-like behaviors in both male and female mice. By comparing predator stress and social defeat models, we observed that the former elicited a higher level of behavioral despair and the latter elicited more robust social avoidance. Furthermore, the use of machine learning (ML)-based spontaneous behavioral classification can distinguish mice subjected to one type of stress from another, and from non-stressed mice. We show that related patterns of spontaneous behaviors correspond to depression status as measured by canonical depression-like behaviors, which illustrates that depression-like symptoms can be predicted by ML-classified behavior patterns. Overall, our study confirms that the predator stress induced phenotype in mice is a good reflection of several important aspects of depression in humans and illustrates that ML-supported analysis can simultaneously evaluate multiple behavioral alterations in different animal models of depression, providing a more unbiased and holistic approach for the study of neuropsychiatric disorders.
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Affiliation(s)
- Yu-Ting Tseng
- CAS Key Laboratory of Brain Connectome and Manipulation, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
- Guangdong Provincial Key Laboratory of Brain Connectome and Behavior, the Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
| | - Binghao Zhao
- CAS Key Laboratory of Brain Connectome and Manipulation, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- Guangdong Provincial Key Laboratory of Brain Connectome and Behavior, the Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Hui Ding
- CAS Key Laboratory of Brain Connectome and Manipulation, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- Guangdong Provincial Key Laboratory of Brain Connectome and Behavior, the Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Lisha Liang
- CAS Key Laboratory of Brain Connectome and Manipulation, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- Guangdong Provincial Key Laboratory of Brain Connectome and Behavior, the Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Bernhard Schaefke
- CAS Key Laboratory of Brain Connectome and Manipulation, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Liping Wang
- CAS Key Laboratory of Brain Connectome and Manipulation, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
- Guangdong Provincial Key Laboratory of Brain Connectome and Behavior, the Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
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87
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Ravens A, Stacher-Hörndli CN, Emery J, Steinwand S, Shepherd JD, Gregg C. Arc regulates a second-guessing cognitive bias during naturalistic foraging through effects on discrete behavior modules. iScience 2023; 26:106761. [PMID: 37216088 PMCID: PMC10196573 DOI: 10.1016/j.isci.2023.106761] [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: 08/04/2022] [Revised: 11/29/2022] [Accepted: 04/24/2023] [Indexed: 05/24/2023] Open
Abstract
Foraging in animals relies on innate decision-making heuristics that can result in suboptimal cognitive biases in some contexts. The mechanisms underlying these biases are not well understood, but likely involve strong genetic effects. To explore this, we studied fasted mice using a naturalistic foraging paradigm and discovered an innate cognitive bias called "second-guessing." This involves repeatedly investigating an empty former food patch instead of consuming available food, which hinders the mice from maximizing feeding benefits. The synaptic plasticity gene Arc is revealed to play a role in this bias, as Arc-deficient mice did not exhibit second-guessing and consumed more food. In addition, unsupervised machine learning decompositions of foraging identified specific behavior sequences, or "modules", that are affected by Arc. These findings highlight the genetic basis of cognitive biases in decision making, show links between behavior modules and cognitive bias, and provide insight into the ethological roles of Arc in naturalistic foraging.
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Affiliation(s)
- Alicia Ravens
- University of Utah, Department of Neurobiology, Salt Lake City, UT, USA
| | | | - Jared Emery
- Storyline Health Inc., Salt Lake City, UT, USA
| | - Susan Steinwand
- University of Utah, Department of Neurobiology, Salt Lake City, UT, USA
| | - Jason D. Shepherd
- University of Utah, Department of Neurobiology, Salt Lake City, UT, USA
- University of Utah, Department of Biochemistry School of Medicine, Salt Lake City, UT, USA
- University of Utah, Department of Ophthalmology & Visual Sciences, Salt Lake City, UT, USA
| | - Christopher Gregg
- University of Utah, Department of Neurobiology, Salt Lake City, UT, USA
- University of Utah, Department of Human Genetics, Salt Lake City, UT, USA
- Storyline Health Inc., Salt Lake City, UT, USA
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88
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Kucukdereli H, Amsalem O, Pottala T, Lim M, Potgieter L, Hasbrouck A, Lutas A, Andermann ML. Chronic stress triggers seeking of a starvation-like state in anxiety-prone female mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.16.541013. [PMID: 37292650 PMCID: PMC10245771 DOI: 10.1101/2023.05.16.541013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Elevated anxiety often precedes anorexia nervosa and persists after weight restoration. Patients with anorexia nervosa often describe hunger as pleasant, potentially because food restriction can be anxiolytic. Here, we tested whether chronic stress can cause animals to prefer a starvation-like state. We developed a virtual reality place preference paradigm in which head-fixed mice can voluntarily seek a starvation-like state induced by optogenetic stimulation of hypothalamic agouti-related peptide (AgRP) neurons. Prior to stress induction, male but not female mice showed mild aversion to AgRP stimulation. Strikingly, following chronic stress, a subset of females developed a strong preference for AgRP stimulation that was predicted by high baseline anxiety. Such stress-induced changes in preference were reflected in changes in facial expressions during AgRP stimulation. Our study suggests that stress may cause females predisposed to anxiety to seek a starvation state, and provides a powerful experimental framework for investigating the underlying neural mechanisms.
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89
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Gschwind T, Zeine A, Raikov I, Markowitz JE, Gillis WF, Felong S, Isom LL, Datta SR, Soltesz I. Hidden behavioral fingerprints in epilepsy. Neuron 2023; 111:1440-1452.e5. [PMID: 36841241 PMCID: PMC10164063 DOI: 10.1016/j.neuron.2023.02.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 11/11/2022] [Accepted: 02/01/2023] [Indexed: 02/27/2023]
Abstract
Epilepsy is a major disorder affecting millions of people. Although modern electrophysiological and imaging approaches provide high-resolution access to the multi-scale brain circuit malfunctions in epilepsy, our understanding of how behavior changes with epilepsy has remained rudimentary. As a result, screening for new therapies for children and adults with devastating epilepsies still relies on the inherently subjective, semi-quantitative assessment of a handful of pre-selected behavioral signs of epilepsy in animal models. Here, we use machine learning-assisted 3D video analysis to reveal hidden behavioral phenotypes in mice with acquired and genetic epilepsies and track their alterations during post-insult epileptogenesis and in response to anti-epileptic drugs. These results show the persistent reconfiguration of behavioral fingerprints in epilepsy and indicate that they can be employed for rapid, automated anti-epileptic drug testing at scale.
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Affiliation(s)
- Tilo Gschwind
- Department of Neurosurgery, Stanford University, Stanford, CA 94305, USA.
| | - Ayman Zeine
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Ivan Raikov
- Department of Neurosurgery, Stanford University, Stanford, CA 94305, USA
| | | | - Winthrop F Gillis
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Sylwia Felong
- Department of Neurosurgery, Stanford University, Stanford, CA 94305, USA
| | - Lori L Isom
- Department of Pharmacology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Ivan Soltesz
- Department of Neurosurgery, Stanford University, Stanford, CA 94305, USA
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90
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Sridhar VH, Davidson JD, Twomey CR, Sosna MMG, Nagy M, Couzin ID. Inferring social influence in animal groups across multiple timescales. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220062. [PMID: 36802787 PMCID: PMC9939267 DOI: 10.1098/rstb.2022.0062] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023] Open
Abstract
Many animal behaviours exhibit complex temporal dynamics, suggesting there are multiple timescales at which they should be studied. However, researchers often focus on behaviours that occur over relatively restricted temporal scales, typically ones that are more accessible to human observation. The situation becomes even more complex when considering multiple animals interacting, where behavioural coupling can introduce new timescales of importance. Here, we present a technique to study the time-varying nature of social influence in mobile animal groups across multiple temporal scales. As case studies, we analyse golden shiner fish and homing pigeons, which move in different media. By analysing pairwise interactions among individuals, we show that predictive power of the factors affecting social influence depends on the timescale of analysis. Over short timescales the relative position of a neighbour best predicts its influence and the distribution of influence across group members is relatively linear, with a small slope. At longer timescales, however, both relative position and kinematics are found to predict influence, and nonlinearity in the influence distribution increases, with a small number of individuals being disproportionately influential. Our results demonstrate that different interpretations of social influence arise from analysing behaviour at different timescales, highlighting the importance of considering its multiscale nature. This article is part of a discussion meeting issue 'Collective behaviour through time'.
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Affiliation(s)
- Vivek H. Sridhar
- Department of Biology, University of Konstanz, 78464 Konstanz, Germany,Centre for the Advanced Study of Collective Behaviour, University of Konstanz, 78464 Konstanz, Germany,Department of Collective Behaviour, Max Planck Institute of Animal Behavior, 78464 Konstanz, Germany,Department for the Ecology of Animal Societies, Max Planck Institute of Animal Behavior, 78467 Konstanz, Germany
| | - Jacob D. Davidson
- Department of Biology, University of Konstanz, 78464 Konstanz, Germany,Centre for the Advanced Study of Collective Behaviour, University of Konstanz, 78464 Konstanz, Germany,Department of Collective Behaviour, Max Planck Institute of Animal Behavior, 78464 Konstanz, Germany
| | - Colin R. Twomey
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA,Mind Center for Outreach, Research, and Education, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Matthew M. G. Sosna
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - Máté Nagy
- Department of Biology, University of Konstanz, 78464 Konstanz, Germany,Centre for the Advanced Study of Collective Behaviour, University of Konstanz, 78464 Konstanz, Germany,Department of Collective Behaviour, Max Planck Institute of Animal Behavior, 78464 Konstanz, Germany,MTA-ELTE Statistical and Biological Physics Research Group, Hungarian Academy of Sciences, Budapest 1117, Hungary,MTA-ELTE ‘Lendület’ Collective Behaviour Research Group, Hungarian Academy of Sciences, Eötvös Loránd University, Budapest 1117, Hungary,Department of Biological Physics, Eötvös Loránd University, Pázmány Péter sétány 1A, Budapest 1117, Hungary
| | - Iain D. Couzin
- Department of Biology, University of Konstanz, 78464 Konstanz, Germany,Centre for the Advanced Study of Collective Behaviour, University of Konstanz, 78464 Konstanz, Germany,Department of Collective Behaviour, Max Planck Institute of Animal Behavior, 78464 Konstanz, Germany
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91
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Levy DR, Hunter N, Lin S, Robinson EM, Gillis W, Conlin EB, Anyoha R, Shansky RM, Datta SR. Mouse spontaneous behavior reflects individual variation rather than estrous state. Curr Biol 2023; 33:1358-1364.e4. [PMID: 36889318 PMCID: PMC10090034 DOI: 10.1016/j.cub.2023.02.035] [Citation(s) in RCA: 50] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 12/12/2022] [Accepted: 02/10/2023] [Indexed: 03/09/2023]
Abstract
Behavior is shaped by both the internal state of an animal and its individual behavioral biases. Rhythmic variation in gonadal hormones during the estrous cycle is a defining feature of the female internal state, one that regulates many aspects of sociosexual behavior. However, it remains unclear whether estrous state influences spontaneous behavior and, if so, how these effects might relate to individual behavioral variation. Here, we address this question by longitudinally characterizing the open-field behavior of female mice across different phases of the estrous cycle, using unsupervised machine learning to decompose spontaneous behavior into its constituent elements.1,2,3,4 We find that each female mouse exhibits a characteristic pattern of exploration that uniquely identifies it as an individual across many experimental sessions; by contrast, estrous state only negligibly impacts behavior, despite its known effects on neural circuits that regulate action selection and movement. Like female mice, male mice exhibit individual-specific patterns of behavior in the open field; however, the exploratory behavior of males is significantly more variable than that expressed by females both within and across individuals. These findings suggest underlying functional stability to the circuits that support exploration in female mice, reveal a surprising degree of specificity in individual behavior, and provide empirical support for the inclusion of both sexes in experiments querying spontaneous behaviors.
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Affiliation(s)
- Dana Rubi Levy
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Nigel Hunter
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Sherry Lin
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | | | - Winthrop Gillis
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | | | - Rockwell Anyoha
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
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92
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Yamada K, Toda K. Habit formation viewed as structural change in the behavioral network. Commun Biol 2023; 6:303. [PMID: 37016036 PMCID: PMC10073220 DOI: 10.1038/s42003-023-04500-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 01/18/2023] [Indexed: 04/06/2023] Open
Abstract
Habit formation is a process in which an action becomes involuntary. While goal-directed behavior is driven by its consequences, habits are elicited by a situation rather than its consequences. Existing theories have proposed that actions are controlled by corresponding two distinct systems. Although canonical theories based on such distinctions are starting to be challenged, there are a few theoretical frameworks that implement goal-directed behavior and habits within a single system. Here, we propose a novel theoretical framework by hypothesizing that behavior is a network composed of several responses. With this framework, we have shown that the transition of goal-directed actions to habits is caused by a change in a single network structure. Furthermore, we confirmed that the proposed network model behaves in a manner consistent with the existing experimental results reported in animal behavioral studies. Our results revealed that habit could be formed under the control of a single system rather than two distinct systems. By capturing the behavior as a single network change, this framework provides a new perspective on studying the structure of the behavior for experimental and theoretical research.
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Affiliation(s)
- Kota Yamada
- Department of Psychology, Keio University, Tokyo, Japan.
- Japan Society for Promotion of Science, Tokyo, Japan.
| | - Koji Toda
- Department of Psychology, Keio University, Tokyo, Japan
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93
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Zeraati R, Shi YL, Steinmetz NA, Gieselmann MA, Thiele A, Moore T, Levina A, Engel TA. Intrinsic timescales in the visual cortex change with selective attention and reflect spatial connectivity. Nat Commun 2023; 14:1858. [PMID: 37012299 PMCID: PMC10070246 DOI: 10.1038/s41467-023-37613-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 03/24/2023] [Indexed: 04/05/2023] Open
Abstract
Intrinsic timescales characterize dynamics of endogenous fluctuations in neural activity. Variation of intrinsic timescales across the neocortex reflects functional specialization of cortical areas, but less is known about how intrinsic timescales change during cognitive tasks. We measured intrinsic timescales of local spiking activity within columns of area V4 in male monkeys performing spatial attention tasks. The ongoing spiking activity unfolded across at least two distinct timescales, fast and slow. The slow timescale increased when monkeys attended to the receptive fields location and correlated with reaction times. By evaluating predictions of several network models, we found that spatiotemporal correlations in V4 activity were best explained by the model in which multiple timescales arise from recurrent interactions shaped by spatially arranged connectivity, and attentional modulation of timescales results from an increase in the efficacy of recurrent interactions. Our results suggest that multiple timescales may arise from the spatial connectivity in the visual cortex and flexibly change with the cognitive state due to dynamic effective interactions between neurons.
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Affiliation(s)
- Roxana Zeraati
- International Max Planck Research School for the Mechanisms of Mental Function and Dysfunction, University of Tübingen, Tübingen, Germany
- Max Planck Institute for Biological Cybernetics, Tübingen, Germany
| | - Yan-Liang Shi
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
| | | | - Marc A Gieselmann
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Alexander Thiele
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Tirin Moore
- Department of Neurobiology and Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Anna Levina
- Max Planck Institute for Biological Cybernetics, Tübingen, Germany.
- Department of Computer Science, University of Tübingen, Tübingen, Germany.
- Bernstein Center for Computational Neuroscience Tübingen, Tübingen, Germany.
| | - Tatiana A Engel
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA.
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94
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Couzin ID, Heins C. Emerging technologies for behavioral research in changing environments. Trends Ecol Evol 2023; 38:346-354. [PMID: 36509561 DOI: 10.1016/j.tree.2022.11.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 11/14/2022] [Accepted: 11/21/2022] [Indexed: 12/13/2022]
Abstract
The first response exhibited by animals to changing environments is typically behavioral. Behavior is thus central to predicting, and mitigating, the impacts that natural and anthropogenic environmental changes will have on populations and, consequently, ecosystems. Yet the inherently multiscale nature of behavior, as well as the complexities associated with inferring how animals perceive their world, and make decisions, has constrained the scope of behavioral research. Major technological advances in electronics and in machine learning, however, provide increasingly powerful means to see, analyze, and interpret behavior in its natural complexity. We argue that these disruptive technologies will foster new approaches that will allow us to move beyond quantitative descriptions and reveal the underlying generative processes that give rise to behavior.
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Affiliation(s)
- Iain D Couzin
- Department of Collective Behaviour, Max Planck Institute of Animal Behavior, Konstanz, Germany; Centre for the Advanced Study of Collective Behaviour & Department of Biology, University of Konstanz, Germany.
| | - Conor Heins
- Department of Collective Behaviour, Max Planck Institute of Animal Behavior, Konstanz, Germany; Centre for the Advanced Study of Collective Behaviour & Department of Biology, University of Konstanz, Germany
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95
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Hu Y, Ferrario CR, Maitland AD, Ionides RB, Ghimire A, Watson B, Iwasaki K, White H, Xi Y, Zhou J, Ye B. LabGym: Quantification of user-defined animal behaviors using learning-based holistic assessment. CELL REPORTS METHODS 2023; 3:100415. [PMID: 37056376 PMCID: PMC10088092 DOI: 10.1016/j.crmeth.2023.100415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 10/19/2022] [Accepted: 02/01/2023] [Indexed: 03/09/2023]
Abstract
Quantifying animal behavior is important for biological research. Identifying behaviors is the prerequisite of quantifying them. Current computational tools for behavioral quantification typically use high-level properties such as body poses to identify the behaviors, which constrains the information available for a holistic assessment. Here we report LabGym, an open-source computational tool for quantifying animal behaviors without this constraint. In LabGym, we introduce "pattern image" to represent the animal's motion pattern, in addition to "animation" that shows all spatiotemporal details of a behavior. These two pieces of information are assessed holistically by customizable deep neural networks for accurate behavior identifications. The quantitative measurements of each behavior are then calculated. LabGym is applicable for experiments involving multiple animals, requires little programming knowledge to use, and provides visualizations of behavioral datasets. We demonstrate its efficacy in capturing subtle behavioral changes in diverse animal species.
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Affiliation(s)
- Yujia Hu
- Life Sciences Institute and Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Carrie R. Ferrario
- Department of Pharmacology and Psychology Department (Biopsychology), University of Michigan, Ann Arbor, MI 48109, USA
| | - Alexander D. Maitland
- Department of Pharmacology and Psychology Department (Biopsychology), University of Michigan, Ann Arbor, MI 48109, USA
| | - Rita B. Ionides
- Department of Pharmacology and Psychology Department (Biopsychology), University of Michigan, Ann Arbor, MI 48109, USA
| | - Anjesh Ghimire
- Department of Psychiatry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Brendon Watson
- Department of Psychiatry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Kenichi Iwasaki
- Life Sciences Institute and Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Hope White
- Life Sciences Institute and Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yitao Xi
- Life Sciences Institute and Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jie Zhou
- Department of Computer Science, Northern Illinois University, DeKalb, IL 60115, USA
| | - Bing Ye
- Life Sciences Institute and Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
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96
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Reznikova Z. Information Theory Opens New Dimensions in Experimental Studies of Animal Behaviour and Communication. Animals (Basel) 2023; 13:ani13071174. [PMID: 37048430 PMCID: PMC10093743 DOI: 10.3390/ani13071174] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/15/2023] [Accepted: 03/24/2023] [Indexed: 03/29/2023] Open
Abstract
Over the last 40–50 years, ethology has become increasingly quantitative and computational. However, when analysing animal behavioural sequences, researchers often need help finding an adequate model to assess certain characteristics of these sequences while using a relatively small number of parameters. In this review, I demonstrate that the information theory approaches based on Shannon entropy and Kolmogorov complexity can furnish effective tools to analyse and compare animal natural behaviours. In addition to a comparative analysis of stereotypic behavioural sequences, information theory can provide ideas for particular experiments on sophisticated animal communications. In particular, it has made it possible to discover the existence of a developed symbolic “language” in leader-scouting ant species based on the ability of these ants to transfer abstract information about remote events.
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97
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Sanders LM, Scott RT, Yang JH, Qutub AA, Garcia Martin H, Berrios DC, Hastings JJA, Rask J, Mackintosh G, Hoarfrost AL, Chalk S, Kalantari J, Khezeli K, Antonsen EL, Babdor J, Barker R, Baranzini SE, Beheshti A, Delgado-Aparicio GM, Glicksberg BS, Greene CS, Haendel M, Hamid AA, Heller P, Jamieson D, Jarvis KJ, Komarova SV, Komorowski M, Kothiyal P, Mahabal A, Manor U, Mason CE, Matar M, Mias GI, Miller J, Myers JG, Nelson C, Oribello J, Park SM, Parsons-Wingerter P, Prabhu RK, Reynolds RJ, Saravia-Butler A, Saria S, Sawyer A, Singh NK, Snyder M, Soboczenski F, Soman K, Theriot CA, Van Valen D, Venkateswaran K, Warren L, Worthey L, Zitnik M, Costes SV. Biological research and self-driving labs in deep space supported by artificial intelligence. NAT MACH INTELL 2023. [DOI: 10.1038/s42256-023-00618-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2023]
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98
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Petzold A, van den Munkhof HE, Figge-Schlensok R, Korotkova T. Complementary lateral hypothalamic populations resist hunger pressure to balance nutritional and social needs. Cell Metab 2023; 35:456-471.e6. [PMID: 36827985 PMCID: PMC10028225 DOI: 10.1016/j.cmet.2023.02.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 05/03/2022] [Accepted: 02/08/2023] [Indexed: 02/25/2023]
Abstract
Animals continuously weigh hunger and thirst against competing needs, such as social contact and mating, according to state and opportunity. Yet neuronal mechanisms of sensing and ranking nutritional needs remain poorly understood. Here, combining calcium imaging in freely behaving mice, optogenetics, and chemogenetics, we show that two neuronal populations of the lateral hypothalamus (LH) guide increasingly hungry animals through behavioral choices between nutritional and social rewards. While increased food consumption was marked by increasing inhibition of a leptin receptor-expressing (LepRLH) subpopulation at a fast timescale, LepRLH neurons limited feeding or drinking and promoted social interaction despite hunger or thirst. Conversely, neurotensin-expressing LH neurons preferentially encoded water despite hunger pressure and promoted water seeking, while relegating social needs. Thus, hunger and thirst gate both LH populations in a complementary manner to enable the flexible fulfillment of multiple essential needs.
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Affiliation(s)
- Anne Petzold
- Institute for Systems Physiology, Faculty of Medicine, University of Cologne and University Clinic Cologne, Cologne 50931, Germany; Max Planck Institute for Metabolism Research, Cologne 50931, Germany
| | - Hanna Elin van den Munkhof
- Institute for Systems Physiology, Faculty of Medicine, University of Cologne and University Clinic Cologne, Cologne 50931, Germany; Max Planck Institute for Metabolism Research, Cologne 50931, Germany
| | - Rebecca Figge-Schlensok
- Institute for Systems Physiology, Faculty of Medicine, University of Cologne and University Clinic Cologne, Cologne 50931, Germany; Max Planck Institute for Metabolism Research, Cologne 50931, Germany
| | - Tatiana Korotkova
- Institute for Systems Physiology, Faculty of Medicine, University of Cologne and University Clinic Cologne, Cologne 50931, Germany; Max Planck Institute for Metabolism Research, Cologne 50931, Germany; Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD) and Center of Molecular Medicine Cologne (CMMC), University of Cologne, Cologne 50931, Germany.
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99
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Shemesh Y, Chen A. A paradigm shift in translational psychiatry through rodent neuroethology. Mol Psychiatry 2023; 28:993-1003. [PMID: 36635579 PMCID: PMC10005947 DOI: 10.1038/s41380-022-01913-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 12/05/2022] [Accepted: 12/07/2022] [Indexed: 01/14/2023]
Abstract
Mental disorders are a significant cause of disability worldwide. They profoundly affect individuals' well-being and impose a substantial financial burden on societies and governments. However, despite decades of extensive research, the effectiveness of current therapeutics for mental disorders is often not satisfactory or well tolerated by the patient. Moreover, most novel therapeutic candidates fail in clinical testing during the most expensive phases (II and III), which results in the withdrawal of pharma companies from investing in the field. It also brings into question the effectiveness of using animal models in preclinical studies to discover new therapeutic agents and predict their potential for treating mental illnesses in humans. Here, we focus on rodents as animal models and propose that they are essential for preclinical investigations of candidate therapeutic agents' mechanisms of action and for testing their safety and efficiency. Nevertheless, we argue that there is a need for a paradigm shift in the methodologies used to measure animal behavior in laboratory settings. Specifically, behavioral readouts obtained from short, highly controlled tests in impoverished environments and social contexts as proxies for complex human behavioral disorders might be of limited face validity. Conversely, animal models that are monitored in more naturalistic environments over long periods display complex and ethologically relevant behaviors that reflect evolutionarily conserved endophenotypes of translational value. We present how semi-natural setups in which groups of mice are individually tagged, and video recorded continuously can be attainable and affordable. Moreover, novel open-source machine-learning techniques for pose estimation enable continuous and automatic tracking of individual body parts in groups of rodents over long periods. The trajectories of each individual animal can further be subjected to supervised machine learning algorithms for automatic detection of specific behaviors (e.g., chasing, biting, or fleeing) or unsupervised automatic detection of behavioral motifs (e.g., stereotypical movements that might be harder to name or label manually). Compared to studies of animals in the wild, semi-natural environments are more compatible with neural and genetic manipulation techniques. As such, they can be used to study the neurobiological mechanisms underlying naturalistic behavior. Hence, we suggest that such a paradigm possesses the best out of classical ethology and the reductive behaviorist approach and may provide a breakthrough in discovering new efficient therapies for mental illnesses.
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Affiliation(s)
- Yair Shemesh
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Alon Chen
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel.
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, 7610001, Israel.
- Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, 80804, Munich, Germany.
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100
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Westlin C, Theriault JE, Katsumi Y, Nieto-Castanon A, Kucyi A, Ruf SF, Brown SM, Pavel M, Erdogmus D, Brooks DH, Quigley KS, Whitfield-Gabrieli S, Barrett LF. Improving the study of brain-behavior relationships by revisiting basic assumptions. Trends Cogn Sci 2023; 27:246-257. [PMID: 36739181 PMCID: PMC10012342 DOI: 10.1016/j.tics.2022.12.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/23/2022] [Accepted: 12/29/2022] [Indexed: 02/05/2023]
Abstract
Neuroimaging research has been at the forefront of concerns regarding the failure of experimental findings to replicate. In the study of brain-behavior relationships, past failures to find replicable and robust effects have been attributed to methodological shortcomings. Methodological rigor is important, but there are other overlooked possibilities: most published studies share three foundational assumptions, often implicitly, that may be faulty. In this paper, we consider the empirical evidence from human brain imaging and the study of non-human animals that calls each foundational assumption into question. We then consider the opportunities for a robust science of brain-behavior relationships that await if scientists ground their research efforts in revised assumptions supported by current empirical evidence.
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Affiliation(s)
| | - Jordan E Theriault
- Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Yuta Katsumi
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Alfonso Nieto-Castanon
- Department of Speech, Language, and Hearing Sciences, Boston University, Boston, MA, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Aaron Kucyi
- Department of Psychological and Brain Sciences, Drexel University, Philadelphia, PA, USA
| | - Sebastian F Ruf
- Department of Civil and Environmental Engineering, Northeastern University, Boston, MA, USA
| | - Sarah M Brown
- Department of Computer Science and Statistics, University of Rhode Island, Kingston, RI, USA
| | - Misha Pavel
- Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA; Bouvé College of Health Sciences, Northeastern University, Boston, MA, USA
| | - Deniz Erdogmus
- Department of Electrical and Computer Engineering, Northeastern University, Boston, MA, USA
| | - Dana H Brooks
- Department of Electrical and Computer Engineering, Northeastern University, Boston, MA, USA
| | - Karen S Quigley
- Department of Psychology, Northeastern University, Boston, MA, USA
| | | | - Lisa Feldman Barrett
- Department of Psychology, Northeastern University, Boston, MA, USA; A.A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, USA; Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
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