1
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Perry LJ, Perez BE, Wahba LR, Nikhil KL, Lenzen WC, Jones JR. A circadian behavioral analysis suite for real-time classification of daily rhythms in complex behaviors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.23.581778. [PMID: 39149294 PMCID: PMC11326128 DOI: 10.1101/2024.02.23.581778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Measuring animal behavior over long timescales has been traditionally limited to behaviors that are easily measurable with real-time sensors. More complex behaviors have been measured over time, but these approaches are considerably more challenging due to the intensive manual effort required for scoring behaviors. Recent advances in machine learning have introduced automated behavior analysis methods, but these often overlook long-term behavioral patterns and struggle with classification in varying environmental conditions. To address this, we developed a pipeline that enables continuous, parallel recording and acquisition of animal behavior for an indefinite duration. As part of this pipeline, we applied a recent breakthrough self-supervised computer vision model to reduce training bias and overfitting and to ensure classification robustness. Our system automatically classifies animal behaviors with a performance approaching that of expert-level human labelers. Critically, classification occurs continuously, across multiple animals, and in real time. As a proof-of-concept, we used our system to record behavior from 97 mice over two weeks to test the hypothesis that sex and estrogen influence circadian rhythms in nine distinct home cage behaviors. We discovered novel sex- and estrogen-dependent differences in circadian properties of several behaviors including digging and nesting rhythms. We present a generalized version of our pipeline and novel classification model, the "circadian behavioral analysis suite," (CBAS) as a user-friendly, open-source software package that allows researchers to automatically acquire and analyze behavioral rhythms with a throughput that rivals sensor-based methods, allowing for the temporal and circadian analysis of behaviors that were previously difficult or impossible to observe.
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Affiliation(s)
- Logan J Perry
- Department of Biology, Texas A&M University, College Station, TX
| | - Blanca E Perez
- Department of Biology, Texas A&M University, College Station, TX
| | - Larissa Rays Wahba
- Department of Biology, Washington University in St. Louis, St. Louis, MO
| | - K L Nikhil
- Department of Biology, Washington University in St. Louis, St. Louis, MO
| | - William C Lenzen
- Department of Biology, Texas A&M University, College Station, TX
| | - Jeff R Jones
- Department of Biology, Texas A&M University, College Station, TX
- Institute for Neuroscience, Texas A&M University, College Station, TX
- Center for Biological Clocks Research, Texas A&M University, College Station, TX
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2
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Salem G, Cope N, Garmendia M, Pu A, Somenhalli A, Krynitsky J, Cubert N, Jones T, Dold G, Fletcher A, Kravitz A, Pohida T, Dennis J. MouseVUER: video based open-source system for laboratory mouse home-cage monitoring. Sci Rep 2024; 14:2662. [PMID: 38302573 PMCID: PMC10834510 DOI: 10.1038/s41598-024-52788-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 01/23/2024] [Indexed: 02/03/2024] Open
Abstract
Video monitoring of mice in the home-cage reveals behavior profiles without the disruptions caused by specialized test setups and makes it possible to quantify changes in behavior patterns continually over long time frames. Several commercial home-cage monitoring systems are available with varying costs and capabilities; however there are currently no open-source systems for home-cage monitoring. We present an open-source system for top-down video monitoring of research mice in a slightly modified home-cage. The system is designed for integration with Allentown NexGen ventilated racks and allows unobstructed view of up to three mice, but can also be operated outside the rack. The system has an easy to duplicate and assemble home-cage design along with a video acquisition solution. The system utilizes a depth video camera, and we demonstrate the robustness of depth video for home-cage mice monitoring. For researchers without access to Allentown NexGen ventilated racks, we provide designs and assembly instructions for a standalone non-ventilated rack solution that holds three systems for more compact and efficient housing. We make all the design files, along with detailed assembly and installation instructions, available on the project webpage ( https://github.com/NIH-CIT-OIR-SPIS/MouseVUER ).
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Affiliation(s)
- Ghadi Salem
- Instrumentation Development and Engineering Application Solutions, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA.
| | - Niall Cope
- Oak Ridge Institute for Science and Education (ORISE), US Department of Energy, Oak Ridge, TN, USA
| | - Marcial Garmendia
- Instrumentation Development and Engineering Application Solutions, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
| | - Alex Pu
- Oak Ridge Institute for Science and Education (ORISE), US Department of Energy, Oak Ridge, TN, USA
| | - Abhishek Somenhalli
- Instrumentation Development and Engineering Application Solutions, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
| | - Jonathan Krynitsky
- Instrumentation Development and Engineering Application Solutions, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
| | - Noah Cubert
- Instrumentation Development and Engineering Application Solutions, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
| | - Thomas Jones
- Instrumentation Development and Engineering Application Solutions, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
| | - George Dold
- Section On Instrumentation, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
| | - Anthony Fletcher
- Scientific Information Office, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Alexxai Kravitz
- Dept of Psychiatry, Washington University in St Louis, St Louis, MO, USA
| | - Thomas Pohida
- Instrumentation Development and Engineering Application Solutions, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
| | - John Dennis
- Division of Veterinary Services, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA
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3
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Le VA, Sterley TL, Cheng N, Bains JS, Murari K. Markerless Mouse Tracking for Social Experiments. eNeuro 2024; 11:ENEURO.0154-22.2023. [PMID: 38233144 PMCID: PMC10901195 DOI: 10.1523/eneuro.0154-22.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 09/18/2023] [Accepted: 10/31/2023] [Indexed: 01/19/2024] Open
Abstract
Automated behavior quantification in socially interacting animals requires accurate tracking. While many methods have been very successful and highly generalizable to different settings, issues of mistaken identities and lost information on key anatomical features are common, although they can be alleviated by increased human effort in training or post-processing. We propose a markerless video-based tool to simultaneously track two interacting mice of the same appearance in controlled settings for quantifying behaviors such as different types of sniffing, touching, and locomotion to improve tracking accuracy under these settings without increased human effort. It incorporates conventional handcrafted tracking and deep-learning-based techniques. The tool is trained on a small number of manually annotated images from a basic experimental setup and outputs body masks and coordinates of the snout and tail-base for each mouse. The method was tested on several commonly used experimental conditions including bedding in the cage and fiberoptic or headstage implants on the mice. Results obtained without any human corrections after the automated analysis showed a near elimination of identities switches and a ∼15% improvement in tracking accuracy over pure deep-learning-based pose estimation tracking approaches. Our approach can be optionally ensembled with such techniques for further improvement. Finally, we demonstrated an application of this approach in studies of social behavior of mice by quantifying and comparing interactions between pairs of mice in which some lack olfaction. Together, these results suggest that our approach could be valuable for studying group behaviors in rodents, such as social interactions.
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Affiliation(s)
- Van Anh Le
- Electrical and Software Engineering, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Toni-Lee Sterley
- Hotchkiss Brain Institute, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Ning Cheng
- Hotchkiss Brain Institute, University of Calgary, Calgary, AB T2N 1N4, Canada
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Jaideep S Bains
- Hotchkiss Brain Institute, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Kartikeya Murari
- Electrical and Software Engineering, University of Calgary, Calgary, AB T2N 1N4, Canada
- Hotchkiss Brain Institute, University of Calgary, Calgary, AB T2N 1N4, Canada
- Biomedical Engineering, University of Calgary, Calgary, AB T2N 1N4, Canada
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4
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Nwokedi EI, Bains RS, Bidaut L, Ye X, Wells S, Brown JM. Dual-Stream Spatiotemporal Networks with Feature Sharing for Monitoring Animals in the Home Cage. SENSORS (BASEL, SWITZERLAND) 2023; 23:9532. [PMID: 38067907 PMCID: PMC10708582 DOI: 10.3390/s23239532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 11/15/2023] [Accepted: 11/24/2023] [Indexed: 12/18/2023]
Abstract
This paper presents a spatiotemporal deep learning approach for mouse behavioral classification in the home-cage. Using a series of dual-stream architectures with assorted modifications for optimal performance, we introduce a novel feature sharing approach that jointly processes the streams at regular intervals throughout the network. The dataset in focus is an annotated, publicly available dataset of a singly-housed mouse. We achieved even better classification accuracy by ensembling the best performing models; an Inception-based network and an attention-based network, both of which utilize this feature sharing attribute. Furthermore, we demonstrate through ablation studies that for all models, the feature sharing architectures consistently outperform the conventional dual-stream having standalone streams. In particular, the inception-based architectures showed higher feature sharing gains with their increase in accuracy anywhere between 6.59% and 15.19%. The best-performing models were also further evaluated on other mouse behavioral datasets.
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Affiliation(s)
- Ezechukwu Israel Nwokedi
- School of Computer Science, College of Science, University of Lincoln, Brayford Pool, Lincoln LN6 7TS, UK (J.M.B.)
| | | | - Luc Bidaut
- Independent Researcher, Lincoln LN6 7TS, UK
| | - Xujiong Ye
- School of Computer Science, College of Science, University of Lincoln, Brayford Pool, Lincoln LN6 7TS, UK (J.M.B.)
| | - Sara Wells
- Mary Lyon Centre at MRC Harwell, Oxfordshire OX11 0RD, UK
| | - James M. Brown
- School of Computer Science, College of Science, University of Lincoln, Brayford Pool, Lincoln LN6 7TS, UK (J.M.B.)
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5
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Mösch L, Kunczik J, Breuer L, Merhof D, Gass P, Potschka H, Zechner D, Vollmar B, Tolba R, Häger C, Bleich A, Czaplik M, Pereira CB. Towards substitution of invasive telemetry: An integrated home cage concept for unobtrusive monitoring of objective physiological parameters in rodents. PLoS One 2023; 18:e0286230. [PMID: 37676867 PMCID: PMC10484458 DOI: 10.1371/journal.pone.0286230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 08/14/2023] [Indexed: 09/09/2023] Open
Abstract
This study presents a novel concept for a smart home cage design, tools, and software used to monitor the physiological parameters of mice and rats in animal-based experiments. The proposed system focuses on monitoring key clinical parameters, including heart rate, respiratory rate, and body temperature, and can also assess activity and circadian rhythm. As the basis of the smart home cage system, an in-depth analysis of the requirements was performed, including camera positioning, imaging system types, resolution, frame rates, external illumination, video acquisition, data storage, and synchronization. Two different camera perspectives were considered, and specific camera models, including two near-infrared and two thermal cameras, were selected to meet the requirements. The developed specifications, hardware models, and software are freely available via GitHub. During the first testing phase, the system demonstrated the potential of extracting vital parameters such as respiratory and heart rate. This technology has the potential to reduce the need for implantable sensors while providing reliable and accurate physiological data, leading to refinement and improvement in laboratory animal care.
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Affiliation(s)
- Lucas Mösch
- Department of Anaesthesiology, Faculty of Medicine, RWTH Aachen University, Aachen, North Rhine-Westphalia, Germany
| | - Janosch Kunczik
- Department of Anaesthesiology, Faculty of Medicine, RWTH Aachen University, Aachen, North Rhine-Westphalia, Germany
| | - Lukas Breuer
- Department of Anaesthesiology, Faculty of Medicine, RWTH Aachen University, Aachen, North Rhine-Westphalia, Germany
| | - Dorit Merhof
- Chair of Image Processing, Faculty of Computer and Data Science, Universität Regensburg, Regensburg, Bavaria, Germany
| | - Peter Gass
- Research Group Animal Models in Psychiatry, Department of Psychiatry and Psychotherapy, Central Institute of Mental Health Mannheim, Medical Faculty Mannheim, University of Heidelberg, Heidelberg, Baden Württemberg, Germany
| | - Heidrun Potschka
- Institute of Pharmacology, Toxicology, and Pharmacy, Ludwig-Maximilians-University, Munich, Bavaria, Germany
| | - Dietmar Zechner
- Rudolf-Zenker-Institute of Experimental Surgery, University Medical Centre Rostock, Rostock, Mecklenburg-Western Pomerania, Germany
| | - Brigitte Vollmar
- Rudolf-Zenker-Institute of Experimental Surgery, University Medical Centre Rostock, Rostock, Mecklenburg-Western Pomerania, Germany
| | - René Tolba
- Institute of Laboratory Animal Science, Faculty of Medicine, RWTH Aachen University, Aachen, North Rhine-Westphalia, Germany
| | - Christine Häger
- Institute for Laboratory Animal Science, Hannover Medical School, Hannover, Lower Saxony, Germany
| | - André Bleich
- Institute for Laboratory Animal Science, Hannover Medical School, Hannover, Lower Saxony, Germany
| | - Michael Czaplik
- Department of Anaesthesiology, Faculty of Medicine, RWTH Aachen University, Aachen, North Rhine-Westphalia, Germany
| | - Carina Barbosa Pereira
- Department of Anaesthesiology, Faculty of Medicine, RWTH Aachen University, Aachen, North Rhine-Westphalia, Germany
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6
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Benedict J, Cudmore RH. PiE: an open-source pipeline for home cage behavioral analysis. Front Neurosci 2023; 17:1222644. [PMID: 37583418 PMCID: PMC10423934 DOI: 10.3389/fnins.2023.1222644] [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: 05/15/2023] [Accepted: 07/13/2023] [Indexed: 08/17/2023] Open
Abstract
Over the last two decades a growing number of neuroscience labs are conducting behavioral assays in rodents. The equipment used to collect this behavioral data must effectively limit environmental and experimenter disruptions, to avoid confounding behavior data. Proprietary behavior boxes are expensive, offer limited compatible sensors, and constrain analysis with closed-source hardware and software. Here, we introduce PiE, an open-source, end-to-end, user-configurable, scalable, and inexpensive behavior assay system. The PiE system includes the custom-built behavior box to hold a home cage, as well as software enabling continuous video recording and individual behavior box environmental control. To limit experimental disruptions, the PiE system allows the control and monitoring of all aspects of a behavioral experiment using a remote web browser, including real-time video feeds. To allow experiments to scale up, the PiE system provides a web interface where any number of boxes can be controlled, and video data easily synchronized to a remote location. For the scoring of behavior video data, the PiE system includes a standalone desktop application that streamlines the blinded manual scoring of large datasets with a focus on quality control and assay flexibility. The PiE system is ideal for all types of behavior assays in which video is recorded. Users are free to use individual components of this setup independently, or to use the entire pipeline from data collection to analysis. Alpha testers have included scientists without prior coding experience. An example pipeline is demonstrated with the PiE system enabling the user to record home cage maternal behavior assays, synchronize the resulting data, conduct blinded scoring, and import the data into R for data visualization and analysis.
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Affiliation(s)
- Jessie Benedict
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Robert H. Cudmore
- Department of Physiology and Membrane Biology, University of California-Davis School of Medicine, Davis, CA, United States
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7
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Luxem K, Sun JJ, Bradley SP, Krishnan K, Yttri E, Zimmermann J, Pereira TD, Laubach M. Open-source tools for behavioral video analysis: Setup, methods, and best practices. eLife 2023; 12:e79305. [PMID: 36951911 PMCID: PMC10036114 DOI: 10.7554/elife.79305] [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: 04/07/2022] [Accepted: 03/03/2023] [Indexed: 03/24/2023] Open
Abstract
Recently developed methods for video analysis, especially models for pose estimation and behavior classification, are transforming behavioral quantification to be more precise, scalable, and reproducible in fields such as neuroscience and ethology. These tools overcome long-standing limitations of manual scoring of video frames and traditional 'center of mass' tracking algorithms to enable video analysis at scale. The expansion of open-source tools for video acquisition and analysis has led to new experimental approaches to understand behavior. Here, we review currently available open-source tools for video analysis and discuss how to set up these methods for labs new to video recording. We also discuss best practices for developing and using video analysis methods, including community-wide standards and critical needs for the open sharing of datasets and code, more widespread comparisons of video analysis methods, and better documentation for these methods especially for new users. We encourage broader adoption and continued development of these tools, which have tremendous potential for accelerating scientific progress in understanding the brain and behavior.
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Affiliation(s)
- Kevin Luxem
- Cellular Neuroscience, Leibniz Institute for NeurobiologyMagdeburgGermany
| | - Jennifer J Sun
- Department of Computing and Mathematical Sciences, California Institute of TechnologyPasadenaUnited States
| | - Sean P Bradley
- Rodent Behavioral Core, National Institute of Mental Health, National Institutes of HealthBethesdaUnited States
| | - Keerthi Krishnan
- Department of Biochemistry and Cellular & Molecular Biology, University of TennesseeKnoxvilleUnited States
| | - Eric Yttri
- Department of Biological Sciences, Carnegie Mellon UniversityPittsburghUnited States
| | - Jan Zimmermann
- Department of Neuroscience, University of MinnesotaMinneapolisUnited States
| | - Talmo D Pereira
- The Salk Institute of Biological StudiesLa JollaUnited States
| | - Mark Laubach
- Department of Neuroscience, American UniversityWashington D.C.United States
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8
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Klein CJMI, Budiman T, Homberg JR, Verma D, Keijer J, van Schothorst EM. Measuring Locomotor Activity and Behavioral Aspects of Rodents Living in the Home-Cage. Front Behav Neurosci 2022; 16:877323. [PMID: 35464142 PMCID: PMC9021872 DOI: 10.3389/fnbeh.2022.877323] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 03/14/2022] [Indexed: 11/13/2022] Open
Abstract
Automatization and technological advances have led to a larger number of methods and systems to monitor and measure locomotor activity and more specific behavior of a wide variety of animal species in various environmental conditions in laboratory settings. In rodents, the majority of these systems require the animals to be temporarily taken away from their home-cage into separate observation cage environments which requires manual handling and consequently evokes distress for the animal and may alter behavioral responses. An automated high-throughput approach can overcome this problem. Therefore, this review describes existing automated methods and technologies which enable the measurement of locomotor activity and behavioral aspects of rodents in their most meaningful and stress-free laboratory environment: the home-cage. In line with the Directive 2010/63/EU and the 3R principles (replacement, reduction, refinement), this review furthermore assesses their suitability and potential for group-housed conditions as a refinement strategy, highlighting their current technological and practical limitations. It covers electrical capacitance technology and radio-frequency identification (RFID), which focus mainly on voluntary locomotor activity in both single and multiple rodents, respectively. Infrared beams and force plates expand the detection beyond locomotor activity toward basic behavioral traits but discover their full potential in individually housed rodents only. Despite the great premises of these approaches in terms of behavioral pattern recognition, more sophisticated methods, such as (RFID-assisted) video tracking technology need to be applied to enable the automated analysis of advanced behavioral aspects of individual animals in social housing conditions.
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Affiliation(s)
- Christian J. M. I. Klein
- Human and Animal Physiology, Wageningen University and Research, Wageningen, Netherlands
- TSE Systems GmbH, Berlin, Germany
| | | | - Judith R. Homberg
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, Netherlands
| | | | - Jaap Keijer
- Human and Animal Physiology, Wageningen University and Research, Wageningen, Netherlands
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9
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Tran T, Mach J, Gemikonakli G, Wu H, Allore H, Howlett SE, Little CB, Hilmer SN. Male-Female Differences In The Effects Of Age On Performance Measures Recorded For 23 Hours In Mice. J Gerontol A Biol Sci Med Sci 2021; 76:2141-2146. [PMID: 34171083 DOI: 10.1093/gerona/glab182] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Indexed: 11/13/2022] Open
Abstract
Functional independence is an important aspect of successful aging and differs with age and by sex in humans. Physical performance often declines earlier than other age-associated functional impairments. Rodent models are used to study pharmacological/toxicological effects of human therapies. However, physical outcomes in mice are usually assessed for short periods, with limited information on the influence of age and sex. Here, we investigated how age and sex affected murine physical performance over 23 hours of continuous observation. Young (3 months) and old (22 months) C57BL/6JArc male and female mice were assessed using the Laboratory Animal Behavior Observation, Registration, and Analysis System. Mice were individually housed for recording of distance travelled, mean gait speed, and durations of different physical activities. Compared to young mice of the same sex, old mice travelled significantly shorter distances with slower gait speeds, shorter durations of locomotion, rearing, climbing and immobility. Older mice groomed significantly more than young mice. Old females reared more during the light cycle than old males. Young females climbed substantially more than young males. Significant age*sex interactions were detected for rearing and climbing, whereby an age-related decline was greater in males than females. Our results suggest that old age reduces exploratory activities and increases grooming in mice. Age-related declines vary between sexes and tend to be greater in males. This non-invasive assessment can be applied to investigate how different interventions affect rodents of different ages and sexes, through the day-night cycle.
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Affiliation(s)
- Trang Tran
- Laboratory of Ageing and Pharmacology, Kolling Institute of Medical Research, Royal North Shore Hospital, University of Sydney, St Leonards, New South Wales, Australia.,Faculty of Medicine and Health, University of Sydney, New South Wales, Australia.,Departments of Clinical Pharmacology and Aged Care, Royal North Shore Hospital, St Leonards, New South Wales, Australia
| | - John Mach
- Laboratory of Ageing and Pharmacology, Kolling Institute of Medical Research, Royal North Shore Hospital, University of Sydney, St Leonards, New South Wales, Australia.,Faculty of Medicine and Health, University of Sydney, New South Wales, Australia.,Departments of Clinical Pharmacology and Aged Care, Royal North Shore Hospital, St Leonards, New South Wales, Australia
| | - Gizem Gemikonakli
- Laboratory of Ageing and Pharmacology, Kolling Institute of Medical Research, Royal North Shore Hospital, University of Sydney, St Leonards, New South Wales, Australia.,Faculty of Medicine and Health, University of Sydney, New South Wales, Australia.,Departments of Clinical Pharmacology and Aged Care, Royal North Shore Hospital, St Leonards, New South Wales, Australia
| | - Harry Wu
- Laboratory of Ageing and Pharmacology, Kolling Institute of Medical Research, Royal North Shore Hospital, University of Sydney, St Leonards, New South Wales, Australia.,Faculty of Medicine and Health, University of Sydney, New South Wales, Australia.,Departments of Clinical Pharmacology and Aged Care, Royal North Shore Hospital, St Leonards, New South Wales, Australia
| | - Heather Allore
- Department of Internal Medicine, Yale University, New Haven, Connecticut, United States.,Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut, United States
| | - Susan E Howlett
- Department of Pharmacology and Medicine (Geriatric Medicine), Dalhousie University, Halifax, Nova Scotia, Canada
| | - Christopher B Little
- Faculty of Medicine and Health, University of Sydney, New South Wales, Australia.,Raymond Purves Bone and Joint Research Laboratory, Kolling Institute of Medical Research, Institute of Bone and Joint Research, Royal North Shore Hospital, University of Sydney, St Leonards, New South Wales, Australia
| | - Sarah N Hilmer
- Laboratory of Ageing and Pharmacology, Kolling Institute of Medical Research, Royal North Shore Hospital, University of Sydney, St Leonards, New South Wales, Australia.,Faculty of Medicine and Health, University of Sydney, New South Wales, Australia.,Departments of Clinical Pharmacology and Aged Care, Royal North Shore Hospital, St Leonards, New South Wales, Australia
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10
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Matikainen-Ankney BA, Earnest T, Ali M, Casey E, Wang JG, Sutton AK, Legaria AA, Barclay KM, Murdaugh LB, Norris MR, Chang YH, Nguyen KP, Lin E, Reichenbach A, Clarke RE, Stark R, Conway SM, Carvalho F, Al-Hasani R, McCall JG, Creed MC, Cazares V, Buczynski MW, Krashes MJ, Andrews ZB, Kravitz AV. An open-source device for measuring food intake and operant behavior in rodent home-cages. eLife 2021; 10:66173. [PMID: 33779547 PMCID: PMC8075584 DOI: 10.7554/elife.66173] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 03/26/2021] [Indexed: 01/26/2023] Open
Abstract
Feeding is critical for survival, and disruption in the mechanisms that govern food intake underlies disorders such as obesity and anorexia nervosa. It is important to understand both food intake and food motivation to reveal mechanisms underlying feeding disorders. Operant behavioral testing can be used to measure the motivational component to feeding, but most food intake monitoring systems do not measure operant behavior. Here, we present a new solution for monitoring both food intake and motivation in rodent home-cages: the Feeding Experimentation Device version 3 (FED3). FED3 measures food intake and operant behavior in rodent home-cages, enabling longitudinal studies of feeding behavior with minimal experimenter intervention. It has a programmable output for synchronizing behavior with optogenetic stimulation or neural recordings. Finally, FED3 design files are open-source and freely available, allowing researchers to modify FED3 to suit their needs.
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Affiliation(s)
| | - Thomas Earnest
- Department of Psychiatry, Washington University in St. LouisSt. LouisUnited States
| | - Mohamed Ali
- National Institute of Diabetes and Digestive and Kidney DiseasesBethesdaUnited States,Department of Bioengineering, University of MarylandCollege ParkUnited States
| | - Eric Casey
- Department of Psychiatry, Washington University in St. LouisSt. LouisUnited States
| | - Justin G Wang
- Department of Neuroscience, Washington University in St. LouisSt. LouisUnited States
| | - Amy K Sutton
- National Institute of Diabetes and Digestive and Kidney DiseasesBethesdaUnited States
| | - Alex A Legaria
- Department of Neuroscience, Washington University in St. LouisSt. LouisUnited States
| | - Kia M Barclay
- Department of Neuroscience, Washington University in St. LouisSt. LouisUnited States
| | - Laura B Murdaugh
- Department of Neuroscience, Virginia Polytechnic and State UniversityBlacksburgUnited States
| | - Makenzie R Norris
- Department of Neuroscience, Washington University in St. LouisSt. LouisUnited States,Center for Clinical Pharmacology, University of Health Sciences and PharmacySt. LouisUnited States
| | - Yu-Hsuan Chang
- Department of Neuroscience, Washington University in St. LouisSt. LouisUnited States
| | - Katrina P Nguyen
- National Institute of Diabetes and Digestive and Kidney DiseasesBethesdaUnited States
| | - Eric Lin
- Department of Psychiatry, Washington University in St. LouisSt. LouisUnited States
| | | | | | - Romana Stark
- Department of Physiology, Monash UniversityClaytonAustralia
| | - Sineadh M Conway
- Center for Clinical Pharmacology, University of Health Sciences and PharmacySt. LouisUnited States,Department of Anesthesiology, Washington University in St. LouisSt. LouisUnited States
| | | | - Ream Al-Hasani
- Center for Clinical Pharmacology, University of Health Sciences and PharmacySt. LouisUnited States,Department of Anesthesiology, Washington University in St. LouisSt. LouisUnited States
| | - Jordan G McCall
- Center for Clinical Pharmacology, University of Health Sciences and PharmacySt. LouisUnited States,Department of Anesthesiology, Washington University in St. LouisSt. LouisUnited States
| | - Meaghan C Creed
- Department of Psychiatry, Washington University in St. LouisSt. LouisUnited States,Department of Neuroscience, Washington University in St. LouisSt. LouisUnited States,Department of Anesthesiology, Washington University in St. LouisSt. LouisUnited States
| | - Victor Cazares
- Department of Psychology, Williams CollegeWilliamstownUnited States
| | - Matthew W Buczynski
- Department of Neuroscience, Virginia Polytechnic and State UniversityBlacksburgUnited States
| | - Michael J Krashes
- National Institute of Diabetes and Digestive and Kidney DiseasesBethesdaUnited States
| | - Zane B Andrews
- Department of Physiology, Monash UniversityClaytonAustralia
| | - Alexxai V Kravitz
- Department of Psychiatry, Washington University in St. LouisSt. LouisUnited States,Department of Neuroscience, Washington University in St. LouisSt. LouisUnited States,Department of Anesthesiology, Washington University in St. LouisSt. LouisUnited States
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11
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Salem G, Krynitsky J, Cubert N, Pu A, Anfinrud S, Pedersen J, Lehman J, Kanuri A, Pohida T. Digital video recorder for Raspberry PI cameras with multi-camera synchronous acquisition. HARDWAREX 2020; 8:e00160. [PMID: 35498233 PMCID: PMC9041262 DOI: 10.1016/j.ohx.2020.e00160] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 11/04/2020] [Accepted: 11/21/2020] [Indexed: 06/14/2023]
Abstract
Video acquisition and analysis have become integral parts of scientific research. Two major components of a video acquisition system are the choice of camera and the acquisition software. A vast variety of cameras are available on the market. Turnkey multi-camera synchronous acquisition software, however, is not as widely available. For prototyping applications, the Raspberry Pi (RPi) has been widely utilized due to many factors, including cost. There are implementations for video acquisition and preview from a single RPi camera, including one implementation released by the RPi organization itself. However, there are no multi-camera acquisition solutions for the RPi. This paper presents an open-source digital video recorder (DVR) system for the popular RPi camera. The DVR is simple to setup and use for acquisition with a single camera or multiple cameras. In the case of multiple cameras, the acquisition is synchronized between cameras. The DVR comes with a graphical user interface (GUI) to allow previewing the camera streams, setting recording parameters, and associating "names" to cameras. The acquisition code as well as the DVR GUI are written in Python. The open-source software also includes a GUI for playback of recorded video. The versatility of the DVR is demonstrated with a life science research application involving high-throughput monitoring of fruit-flies.
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Affiliation(s)
- Ghadi Salem
- Signal Processing and Instrumentation Section, Office of Intramural Research, Center for Information Technology, National Institutes of Health, USA
| | - Jonathan Krynitsky
- Signal Processing and Instrumentation Section, Office of Intramural Research, Center for Information Technology, National Institutes of Health, USA
| | - Noah Cubert
- Signal Processing and Instrumentation Section, Office of Intramural Research, Center for Information Technology, National Institutes of Health, USA
| | - Alex Pu
- Division of Veterinary Services, Center for Biologics Evaluation and Research, U. S. Food and Drug Administration, USA
| | - Simeon Anfinrud
- Signal Processing and Instrumentation Section, Office of Intramural Research, Center for Information Technology, National Institutes of Health, USA
| | - Jonathan Pedersen
- Signal Processing and Instrumentation Section, Office of Intramural Research, Center for Information Technology, National Institutes of Health, USA
| | - Joshua Lehman
- Signal Processing and Instrumentation Section, Office of Intramural Research, Center for Information Technology, National Institutes of Health, USA
| | - Ajith Kanuri
- Signal Processing and Instrumentation Section, Office of Intramural Research, Center for Information Technology, National Institutes of Health, USA
| | - Thomas Pohida
- Signal Processing and Instrumentation Section, Office of Intramural Research, Center for Information Technology, National Institutes of Health, USA
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12
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Yao H, Peterson AL, Li J, Xu H, Dennery PA. Heme Oxygenase 1 and 2 Differentially Regulate Glucose Metabolism and Adipose Tissue Mitochondrial Respiration: Implications for Metabolic Dysregulation. Int J Mol Sci 2020; 21:ijms21197123. [PMID: 32992485 PMCID: PMC7582259 DOI: 10.3390/ijms21197123] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 09/22/2020] [Accepted: 09/24/2020] [Indexed: 12/15/2022] Open
Abstract
Heme oxygenase (HO) consists of inducible (HO-1) and constitutive (HO-2) isoforms that are encoded by Hmox1 and Hmox2 genes, respectively. As an anti-inflammatory and antioxidant molecule, HO participates in the development of metabolic diseases. Whether Hmox deficiency causes metabolic abnormalities under basal conditions remains unclear. We hypothesized that HO-1 and HO-2 differentially affect global and adipose tissue metabolism. To test this hypothesis, we determined insulin sensitivity, glucose tolerance, energy expenditure, and respiratory exchange ratio in global Hmox1-/- and Hmox2-/- mice. Body weight was reduced in female but not male Hmox1-/- and Hmox2-/- mice. Reduced insulin sensitivity and physical activity were observed in Hmox1-/- but not Hmox2-/- mice. Deletion of either Hmox1 or Hmox2 had no effects on glucose tolerance, energy expenditure or respiratory exchange ratio. Mitochondrial respiration was unchanged in gonadal fat pads (white adipose tissue, WAT) of Hmox1-/- mice. Hmox2 deletion increased proton leak and glycolysis in gonadal, but not interscapular fat tissues (brown adipose tissue, BAT). Uncoupling protein and Hmox1 genes were unchanged in gonadal fat pads of Hmox2-/- mice. Conclusively, HO-1 maintains insulin sensitivity, while HO-2 represses glycolysis and proton leak in the WAT under basal condition. This suggests that HO-1 and HO-2 differentially modulate metabolism, which may impact the metabolic syndrome.
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Affiliation(s)
- Hongwei Yao
- Department of Molecular Biology, Cell Biology & Biochemistry, Division of Biology and Medicine, Brown University, Providence, RI 02860, USA; (H.Y.); (A.L.P.)
| | - Abigail L. Peterson
- Department of Molecular Biology, Cell Biology & Biochemistry, Division of Biology and Medicine, Brown University, Providence, RI 02860, USA; (H.Y.); (A.L.P.)
| | - Jie Li
- Department of Epidemiology, Brown University, Providence, RI 02860, USA; (J.L.); (H.X.)
| | - Haiyan Xu
- Department of Epidemiology, Brown University, Providence, RI 02860, USA; (J.L.); (H.X.)
| | - Phyllis A. Dennery
- Department of Molecular Biology, Cell Biology & Biochemistry, Division of Biology and Medicine, Brown University, Providence, RI 02860, USA; (H.Y.); (A.L.P.)
- Department of Pediatrics, Warren Alpert Medical School of Brown University, Providence, RI 02860, USA
- Correspondence: ; Tel.: +1-401-444-5648
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13
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Rodent Arena Tracker (RAT): A Machine Vision Rodent Tracking Camera and Closed Loop Control System. eNeuro 2020; 7:ENEURO.0485-19.2020. [PMID: 32284342 PMCID: PMC7221356 DOI: 10.1523/eneuro.0485-19.2020] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 03/30/2020] [Accepted: 03/31/2020] [Indexed: 11/21/2022] Open
Abstract
Video tracking is an essential tool in rodent research. Here, we demonstrate a machine vision rodent tracking camera based on a low-cost, open-source, machine vision camera, the OpenMV Cam M7. We call our device the rodent arena tracker (RAT), and it is a pocket-sized machine vision-based position tracker. The RAT does not require a tethered computer to operate and costs about $120 per device to build. These features make the RAT scalable to large installations and accessible to research institutions and educational settings where budgets may be limited. The RAT processes incoming video in real-time at 15 Hz and saves x and y positional information to an onboard microSD card. The RAT also provides a programmable multi-function input/output pin that can be used for controlling other equipment, transmitting tracking information in real time, or receiving data from other devices. Finally, the RAT includes a real-time clock (RTC) for accurate time stamping of data files. Real-time image processing averts the need to save video, greatly reducing storage, data handling, and communication requirements. To demonstrate the capabilities of the RAT, we performed three validation studies: (1) a 4-d experiment measuring circadian activity patterns; (2) logging of mouse positional information alongside status information from a pellet dispensing device; and (3) control of an optogenetic stimulation system for a real-time place preference (RTPP) brain stimulation reinforcement study. Our design files, build instructions, and code for the RAT implementation are open source and freely available online to facilitate dissemination and further development of the RAT.
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14
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Hasenau JJ. Reproducibility and Comparative aspects of Terrestrial Housing Systems and Husbandry Procedures in Animal Research Facilities on Study Data. ILAR J 2020; 60:228-238. [DOI: 10.1093/ilar/ilz021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 08/30/2019] [Accepted: 10/08/2019] [Indexed: 01/03/2023] Open
Abstract
Abstract
As mentioned in other chapters, reproducibility of research data is very complicated and has numerous contributors for concerns. This chapter will discuss the animal housing systems and corresponding husbandry practices in regard to current practices and known and potential confounders in the research environment. This area has a very high impact for reproducibility and comparability of study data outcomes.
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15
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Salem G, Krynitsky J, Hayes M, Pohida T, Burgos-Artizzu X. Three-Dimensional Pose Estimation for Laboratory Mouse From Monocular Images. IEEE TRANSACTIONS ON IMAGE PROCESSING : A PUBLICATION OF THE IEEE SIGNAL PROCESSING SOCIETY 2019; 28:4273-4287. [PMID: 30946667 PMCID: PMC6677238 DOI: 10.1109/tip.2019.2908796] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Video-based activity and behavior analysis of mice has garnered wide attention in biomedical research. Animal facilities hold large numbers of mice housed in "home-cages" densely stored within ventilated racks. Automated analysis of mice activity in their home-cages can provide a new set of sensitive measures for detecting abnormalities and time-resolved deviation from the baseline behavior. Large-scale monitoring in animal facilities requires minimal footprint hardware that integrates seamlessly with the ventilated racks. The compactness of hardware imposes the use of fisheye lenses positioned in close proximity to the cage. In this paper, we propose a systematic approach to accurately estimate the 3D pose of the mouse from single-monocular fisheye-distorted images. Our approach employs a novel adaptation of a structured forest algorithm. We benchmark our algorithm against existing methods. We demonstrate the utility of the pose estimates in predicting mouse behavior in a continuous video.
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16
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Singh S, Bermudez-Contreras E, Nazari M, Sutherland RJ, Mohajerani MH. Low-cost solution for rodent home-cage behaviour monitoring. PLoS One 2019; 14:e0220751. [PMID: 31374097 PMCID: PMC6677321 DOI: 10.1371/journal.pone.0220751] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 07/22/2019] [Indexed: 11/18/2022] Open
Abstract
In the current research on measuring complex behaviours/phenotyping in rodents, most of the experimental design requires the experimenter to remove the animal from its home-cage environment and place it in an unfamiliar apparatus (novel environment). This interaction may influence behaviour, general well-being, and the metabolism of the animal, affecting the phenotypic outcome even if the data collection method is automated. Most of the commercially available solutions for home-cage monitoring are expensive and usually lack the flexibility to be incorporated with existing home-cages. Here we present a low-cost solution for monitoring home-cage behaviour of rodents that can be easily incorporated to practically any available rodent home-cage. To demonstrate the use of our system, we reliably predict the sleep/wake state of mice in their home-cage using only video. We validate these results using hippocampal local field potential (LFP) and electromyography (EMG) data. Our approach provides a low-cost flexible methodology for high-throughput studies of sleep, circadian rhythm and rodent behaviour with minimal experimenter interference.
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Affiliation(s)
- Surjeet Singh
- Canadian Centre for Behavioural Neuroscience, Department of Neuroscience, University of Lethbridge, Lethbridge, AB, Canada
| | - Edgar Bermudez-Contreras
- Canadian Centre for Behavioural Neuroscience, Department of Neuroscience, University of Lethbridge, Lethbridge, AB, Canada
| | - Mojtaba Nazari
- Canadian Centre for Behavioural Neuroscience, Department of Neuroscience, University of Lethbridge, Lethbridge, AB, Canada
| | - Robert J. Sutherland
- Canadian Centre for Behavioural Neuroscience, Department of Neuroscience, University of Lethbridge, Lethbridge, AB, Canada
- * E-mail: (RJS); (MHM)
| | - Majid H. Mohajerani
- Canadian Centre for Behavioural Neuroscience, Department of Neuroscience, University of Lethbridge, Lethbridge, AB, Canada
- * E-mail: (RJS); (MHM)
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17
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Ali MA, Kravitz AV. Challenges in quantifying food intake in rodents. Brain Res 2019; 1693:188-191. [PMID: 29903621 DOI: 10.1016/j.brainres.2018.02.040] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 02/04/2018] [Accepted: 02/24/2018] [Indexed: 01/13/2023]
Abstract
Feeding is a critical behavior that animals depend on for survival, and pathological alterations in food intake underlie disorders such as obesity and anorexia nervosa. To understand these disorders and their development in animal models, researchers must quantify food intake. Although conceptually straightforward, it remains a challenge to obtain accurate records of food intake in rodents. Several approaches have been used to accomplish this, each with benefits and drawbacks. In this article, we survey the four most common methods for measuring food intake in rodents: manual weighing of food, automated weighing scales, pellet dispensers, and video-based analyses. We highlight each method's benefits and drawbacks for use in feeding research, focusing on accuracy, potential sources of errors, affordability, and practical concerns relating to their use. Finally, we discuss the outlook for feeding devices and unmet challenges for measuring food intake in laboratory rodents.
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Affiliation(s)
- Mohamed A Ali
- National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA
| | - Alexxai V Kravitz
- National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA; National Institute on Drug Abuse, Baltimore, MD, USA.
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18
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Silva MJ, Eekhoff JD, Patel T, Kenney-Hunt JP, Brodt MD, Steger-May K, Scheller EL, Cheverud JM. Effects of High-Fat Diet and Body Mass on Bone Morphology and Mechanical Properties in 1100 Advanced Intercross Mice. J Bone Miner Res 2019; 34:711-725. [PMID: 30615803 PMCID: PMC6879418 DOI: 10.1002/jbmr.3648] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 11/09/2018] [Accepted: 11/19/2018] [Indexed: 01/19/2023]
Abstract
Obesity is generally protective against osteoporosis and bone fracture. However, recent studies indicate that the influence of obesity on the skeleton is complex and can be detrimental. We evaluated the effects of a high-fat, obesogenic diet on the femur and radius of 1100 mice (males and females) from the Large-by-Small advanced intercross line (F34 generation). At age 5 months, bone morphology was assessed by microCT and mechanical properties by three-point bending. Mice raised on a high-fat diet had modestly greater cortical area, bending stiffness, and strength. Size-independent material properties were unaffected by a high-fat diet, indicating that diet influenced bone quantity but not quality. Bone size and mechanical properties were strongly correlated with body mass. However, the increases in many bone traits per unit increase in body mass were less in high-fat diet mice than low-fat diet mice. Thus, although mice raised on a high-fat diet have, on average, bigger and stronger bones than low-fat-fed mice, a high-fat diet diminished the positive relationship between body mass and bone size and whole-bone strength. The findings support the concept that there are diminishing benefits to skeletal health with increasing obesity. © 2019 American Society for Bone and Mineral Research.
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Affiliation(s)
- Matthew J Silva
- Department of Orthopaedic Surgery, Washington University in Saint Louis, St. Louis, MO, USA.,Department of Biomedical Engineering, Washington University in Saint Louis, St. Louis, MO, USA
| | - Jeremy D Eekhoff
- Department of Biomedical Engineering, Washington University in Saint Louis, St. Louis, MO, USA
| | - Tarpit Patel
- Department of Orthopaedic Surgery, Washington University in Saint Louis, St. Louis, MO, USA
| | - Jane P Kenney-Hunt
- Department of Anatomy and Neurobiology, Washington University in Saint Louis, St. Louis, MO, USA
| | - Michael D Brodt
- Department of Orthopaedic Surgery, Washington University in Saint Louis, St. Louis, MO, USA
| | - Karen Steger-May
- Division of Biostatistics, Washington University in Saint Louis, St. Louis, MO, USA
| | - Erica L Scheller
- Division of Bone and Mineral Diseases, Department of Medicine, Washington University in Saint Louis, St. Louis, MO, USA
| | - James M Cheverud
- Department of Anatomy and Neurobiology, Washington University in Saint Louis, St. Louis, MO, USA.,Department of Biology, Loyola University Chicago, Chicago, IL, USA
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19
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Svenson KL, Paigen B. Recommended housing densities for research mice: filling the gap in data-driven alternatives. FASEB J 2019; 33:3097-3111. [PMID: 30521372 PMCID: PMC6404583 DOI: 10.1096/fj.201801972r] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 11/12/2018] [Indexed: 12/14/2022]
Abstract
Space recommendations for mice made in the Guide for Care and Use of Laboratory Animals have not changed since 1972, despite important improvements in husbandry and caging practices. The 1996 version of the Guide put forth a challenge to investigators to produce new data evaluating the effects of space allocation on the well-being of mice. In this review, we summarize many studies published in response to this challenge. We distinguish between studies using ventilated or nonventilated caging systems and those evaluating reproductive performance or general well-being of adult mice. We discuss how these studies might affect current housing density considerations in both production and research settings and consider gaps in mouse housing density research. Additionally, we discuss reliable methods used to monitor and quantify general well-being of research mice. Collectively, this large body of new data suggests that husbandry practices dictating optimal breeding schemes and space allocation per mouse can be reconsidered. Specifically, these data demonstrate that prewean culling of litters has no benefit, trio breeding is an effective production strategy without adversely affecting pup survival and well-being, and housing of adult mice at densities of up to twice current Guide recommendations does not compromise well-being for most strains.-Svenson, K. L., Paigen, B. Recommended housing densities for research mice: filling the gap in data-driven alternatives.
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20
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Anderson SJ, Lockhart JS, Estaki M, Quin C, Hirota SA, Alston L, Buret AG, Hancock TM, Petri B, Gibson DL, Morck DW. Effects of Azithromycin on Behavior, Pathologic Signs, and Changes in Cytokines, Chemokines, and Neutrophil Migration in C57BL/6 Mice Exposed to Dextran Sulfate Sodium. Comp Med 2019; 69:4-15. [PMID: 30545428 PMCID: PMC6382047 DOI: 10.30802/aalas-cm-18-000001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 02/08/2018] [Accepted: 07/13/2018] [Indexed: 12/16/2022]
Abstract
Here we characterized the murine dextran sulfate sodium (DSS) model of acute colitis. Specifically, we evaluated azithromycin and metronidazole treatment regimens to assess their effects on animal wellbeing, pathologic changes, barrier function, cytokine and chemokine profiles, and neutrophil migration in colon tissue. Azithromycin treatment significantly reduced the severity of colitis, as assessed through body weight change, water consumption, macroscopic lesions, and animal behaviors (activity level, climbing, and grooming), but did not alter food consumption or feeding behavior. Mucosal barrier function (evaluated by using FITC-labeled dextran) was decreased after DSS exposure; azithromycin did not significantly alter barrier function in mice with colitis, whereas metronidazole exacerbated the colitis-related deficit in barrier function. In addition, metronidazole appeared to exacerbate disease as assessed through water consumption and animal behaviors (overall activity, climbing, grooming, and drinking) but had no effect on weight loss, macroscopic lesions, or eating behavior. Pathologic changes were typical for DSS treatment. Antibiotic treatment resulted in reduced levels of proinflammatory cytokines and chemokines and decreased neutrophil adhesion and emigration in DSS-exposed mice. The results highlight the importance of clinical and behavioral assessments in addition to laboratory evaluation as tools to evaluate animal welfare and therapeutic efficacy in disease models. Data from this study suggest that azithromycin may convey some benefits in the mouse DSS colitis model through modulation of the immune response, including neutrophil migration into tissues, whereas metronidazole may exacerbate colitis.
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Affiliation(s)
- Stefanie J Anderson
- Animal Health Unit, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Joey S Lockhart
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Mehrbod Estaki
- Department of Biology, University of British Columbia, Okanagan, Kelowna, British Columbia, Canada
| | - Candice Quin
- Department of Biology, University of British Columbia, Okanagan, Kelowna, British Columbia, Canada
| | - Simon A Hirota
- Department of Microbiology, Immunology, and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Laurie Alston
- Department of Microbiology, Immunology, and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Andre G Buret
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Trina M Hancock
- Animal Health Unit, University of Calgary, Calgary, Alberta, Canada
| | - Björn Petri
- Department of Microbiology, Immunology, and Infectious Diseases, Department of Physiology and Pharmacology, Mouse Phenomics Resource Laboratory, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Deanna L Gibson
- Department of Biology, University of British Columbia, Okanagan, Kelowna, British Columbia, Canada
| | - Douglas W Morck
- Animal Health Unit, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Department of Biology, University of British Columbia, Okanagan, Kelowna, British Columbia, Department of Comparative Biology and Experimental Medicine, University of Calgary, Calgary, Alberta, Canada;,
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21
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Ahloy-Dallaire J, Klein JD, Davis JK, Garner JP. Automated monitoring of mouse feeding and body weight for continuous health assessment. Lab Anim 2018; 53:342-351. [PMID: 30286683 DOI: 10.1177/0023677218797974] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Routine health assessment of laboratory rodents can be improved using automated home cage monitoring. Continuous, non-stressful, objective assessment of rodents unaware that they are being watched, including during their active dark period, reveals behavioural and physiological changes otherwise invisible to human caretakers. We developed an automated feeder that tracks feed intake, body weight, and physical appearance of individual radio frequency identification-tagged mice in social home cages. Here, we experimentally induce illness via lipopolysaccharide challenge and show that this automated tracking apparatus reveals sickness behaviour (reduced food intake) as early as 2-4 hours after lipopolysaccharide injection, whereas human observers conducting routine health checks fail to detect a significant difference between sick mice and saline-injected controls. Continuous automated monitoring additionally reveals pronounced circadian rhythms in both feed intake and body weight. Automated home cage monitoring is a non-invasive, reliable mode of health surveillance allowing caretakers to more efficiently detect and respond to early signs of illness in laboratory rodent populations.
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Affiliation(s)
| | - Jon D Klein
- 2 Department of Animal Sciences, Purdue University, United States
| | - Jerry K Davis
- 3 Department of Comparative Pathobiology, Purdue University, United States
| | - Joseph P Garner
- 1 Department of Comparative Medicine, Stanford University, United States.,4 Department of Psychiatry and Behavioral Sciences, Stanford University, United States
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22
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Hillar C, Onnis G, Rhea D, Tecott L. Active State Organization of Spontaneous Behavioral Patterns. Sci Rep 2018; 8:1064. [PMID: 29348406 PMCID: PMC5773533 DOI: 10.1038/s41598-017-18276-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 12/06/2017] [Indexed: 11/16/2022] Open
Abstract
We report the development and validation of a principled analytical approach to reveal the manner in which diverse mouse home cage behaviors are organized. We define and automate detection of two mutually-exclusive low-dimensional spatiotemporal units of behavior: “Active” and “Inactive” States. Analyses of these features using a large multimodal 16-strain behavioral dataset provide a series of novel insights into how feeding, drinking, and movement behaviors are coordinately expressed in Mus Musculus. Moreover, we find that patterns of Active State expression are exquisitely sensitive to strain, and classical supervised machine learning incorporating these features provides 99% cross-validated accuracy in genotyping animals using behavioral data alone. Altogether, these findings advance understanding of the organization of spontaneous behavior and provide a high-throughput phenotyping strategy with wide applicability to behavioral neuroscience and animal models of disease.
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Affiliation(s)
- C Hillar
- University of California, San Francisco Department of Psychiatry, 1550 4th Street, San Francisco, CA, 94158, USA
| | - G Onnis
- University of California, San Francisco Department of Psychiatry, 1550 4th Street, San Francisco, CA, 94158, USA
| | - D Rhea
- University of California, San Francisco Department of Psychiatry, 1550 4th Street, San Francisco, CA, 94158, USA
| | - L Tecott
- University of California, San Francisco Department of Psychiatry, 1550 4th Street, San Francisco, CA, 94158, USA.
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23
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Bains RS, Wells S, Sillito RR, Armstrong JD, Cater HL, Banks G, Nolan PM. Assessing mouse behaviour throughout the light/dark cycle using automated in-cage analysis tools. J Neurosci Methods 2017; 300:37-47. [PMID: 28456660 PMCID: PMC5909039 DOI: 10.1016/j.jneumeth.2017.04.014] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 04/21/2017] [Accepted: 04/22/2017] [Indexed: 12/15/2022]
Abstract
Automated assessment of mouse home-cage behaviour is robust and reliable. Analysis over multiple light/dark cycles improves ability to classify behaviours. Combined RFID and video analysis enables home-cage analysis in group housed animals.
An important factor in reducing variability in mouse test outcomes has been to develop assays that can be used for continuous automated home cage assessment. Our experience has shown that this has been most evidenced in long-term assessment of wheel-running activity in mice. Historically, wheel-running in mice and other rodents have been used as a robust assay to determine, with precision, the inherent period of circadian rhythms in mice. Furthermore, this assay has been instrumental in dissecting the molecular genetic basis of mammalian circadian rhythms. In teasing out the elements of this test that have determined its robustness – automated assessment of an unforced behaviour in the home cage over long time intervals – we and others have been investigating whether similar test apparatus could be used to accurately discriminate differences in distinct behavioural parameters in mice. Firstly, using these systems, we explored behaviours in a number of mouse inbred strains to determine whether we could extract biologically meaningful differences. Secondly, we tested a number of relevant mutant lines to determine how discriminative these parameters were. Our findings show that, when compared to conventional out-of-cage phenotyping, a far deeper understanding of mouse mutant phenotype can be established by monitoring behaviour in the home cage over one or more light:dark cycles.
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Affiliation(s)
- Rasneer S Bains
- Mary Lyon Centre, MRC Harwell Institute, Harwell Science Campus, Oxfordshire, UK
| | - Sara Wells
- Mary Lyon Centre, MRC Harwell Institute, Harwell Science Campus, Oxfordshire, UK
| | | | - J Douglas Armstrong
- Actual Analytics Ltd., Edinburgh, UK; School of Informatics, University of Edinburgh, Edinburgh, UK
| | - Heather L Cater
- Mary Lyon Centre, MRC Harwell Institute, Harwell Science Campus, Oxfordshire, UK
| | - Gareth Banks
- Mammalian Genetics Unit, MRC Harwell Institute, Harwell Science Campus, Oxfordshire, UK
| | - Patrick M Nolan
- Mammalian Genetics Unit, MRC Harwell Institute, Harwell Science Campus, Oxfordshire, UK.
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Allen MJ, Hankenson KD, Goodrich L, Boivin GP, von Rechenberg B. Ethical use of animal models in musculoskeletal research. J Orthop Res 2017; 35:740-751. [PMID: 27864887 DOI: 10.1002/jor.23485] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 11/16/2016] [Indexed: 02/04/2023]
Abstract
The use of animals in research is under increasing scrutiny from the general public, funding agencies, and regulatory authorities. Our ability to continue to perform in-vivo studies in laboratory animals will be critically determined by how researchers respond to this new reality. This Perspectives article summarizes recent and ongoing initiatives within ORS and allied organizations to ensure that musculoskeletal research is performed to the highest ethical standards. It goes on to present an overview of the practical application of the 3Rs (reduction, refinement, and replacement) into experimental design and execution, and discusses recent guidance with regard to improvements in the way in which animal data are reported in publications. The overarching goal of this review is to challenge the status quo, to highlight the absolute interdependence between animal welfare and rigorous science, and to provide practical recommendations and resources to allow clinicians and scientists to optimize the ways in which they undertake preclinical studies involving animals. © 2016 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 35:740-751, 2017.
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Affiliation(s)
- Matthew J Allen
- Department of Veterinary Medicine, Surgical Discovery Centre, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, United Kingdom
| | | | | | - Gregory P Boivin
- Wright State University, Dayton, 45435, Ohio.,Veterans Affairs Medical Center, Cincinnati, 45220, Ohio
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Dougherty JP, Springer DA, Gershengorn MC. The Treadmill Fatigue Test: A Simple, High-throughput Assay of Fatigue-like Behavior for the Mouse. J Vis Exp 2016. [PMID: 27286034 DOI: 10.3791/54052] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Fatigue is a prominent symptom in many diseases and disorders and reduces quality of life for many people. The lack of clear pathogenesis and failure of current interventions to adequately treat fatigue in all patients leaves a need for new treatment options. Despite the therapeutic need and importance of preclinical research in helping identify promising novel treatments, few preclinical assays of fatigue are available. Moreover, the most common preclinical assay used to assess fatigue-like behavior, voluntary wheel running, is not suitable for use with some strains of mice, may not be sensitive to drugs that reduce fatigue, and has relatively low throughput. The current protocol describes a novel, non-voluntary preclinical assay of fatigue-like behavior, the treadmill fatigue test, and provides evidence of its efficacy in detecting fatigue-like behavior in mice treated with a chemotherapy drug known to cause fatigue in humans and fatigue-like behavior in animals. This assay may be a beneficial alternative to wheel running, as fatigue-like behavior and potential interventions can be assessed in a greater number of mice over a shorter time frame, thus permitting faster discovery of new therapeutic options.
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Affiliation(s)
- John P Dougherty
- Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health
| | - Danielle A Springer
- Murine Phenotyping Core, National Heart, Lung, and Blood Institute, National Institutes of Health
| | - Marvin C Gershengorn
- Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health;
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