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Zhou M, Wu B, Jeong H, Burke DA, Namboodiri VMK. An open-source behavior controller for associative learning and memory (B-CALM). Behav Res Methods 2024; 56:2695-2710. [PMID: 37464151 PMCID: PMC10898869 DOI: 10.3758/s13428-023-02182-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/23/2023] [Indexed: 07/20/2023]
Abstract
Associative learning and memory, i.e., learning and remembering the associations between environmental stimuli, self-generated actions, and outcomes such as rewards or punishments, are critical for the well-being of animals. Hence, the neural mechanisms underlying these processes are extensively studied using behavioral tasks in laboratory animals. Traditionally, these tasks have been controlled using commercial hardware and software, which limits scalability and accessibility due to their cost. More recently, due to the revolution in microcontrollers or microcomputers, several general-purpose and open-source solutions have been advanced for controlling neuroscientific behavioral tasks. While these solutions have great strength due to their flexibility and general-purpose nature, for the same reasons, they suffer from some disadvantages including the need for considerable programming expertise, limited online visualization, or slower than optimal response latencies for any specific task. Here, to mitigate these concerns, we present an open-source behavior controller for associative learning and memory (B-CALM). B-CALM provides an integrated suite that can control a host of associative learning and memory behaviors. As proof of principle for its applicability, we show data from head-fixed mice learning Pavlovian conditioning, operant conditioning, discrimination learning, as well as a timing task and a choice task. These can be run directly from a user-friendly graphical user interface (GUI) written in MATLAB that controls many independently running Arduino Mega microcontrollers in parallel (one per behavior box). In sum, B-CALM will enable researchers to execute a wide variety of associative learning and memory tasks in a scalable, accurate, and user-friendly manner.
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Affiliation(s)
- Mingkang Zhou
- Department of Neurology, University of California, San Francisco, CA, USA
- Neuroscience Graduate Program, University of California, San Francisco, CA, USA
| | - Brenda Wu
- Department of Neurology, University of California, San Francisco, CA, USA
| | - Huijeong Jeong
- Department of Neurology, University of California, San Francisco, CA, USA
| | - Dennis A Burke
- Department of Neurology, University of California, San Francisco, CA, USA
| | - Vijay Mohan K Namboodiri
- Department of Neurology, University of California, San Francisco, CA, USA.
- Neuroscience Graduate Program, University of California, San Francisco, CA, USA.
- Weill Institute for Neuroscience, Kavli Institute for Fundamental Neuroscience, Center for Integrative Neuroscience, University of California, San Francisco, CA, USA.
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De La Crompe B, Schneck M, Steenbergen F, Schneider A, Diester I. FreiBox: A Versatile Open-Source Behavioral Setup for Investigating the Neuronal Correlates of Behavioral Flexibility via 1-Photon Imaging in Freely Moving Mice. eNeuro 2023; 10:10/4/ENEURO.0469-22.2023. [PMID: 37105720 PMCID: PMC10166259 DOI: 10.1523/eneuro.0469-22.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 03/16/2023] [Accepted: 03/20/2023] [Indexed: 04/29/2023] Open
Abstract
To survive in a complex and changing environment, animals must adapt their behavior. This ability is called behavioral flexibility and is classically evaluated by a reversal learning paradigm. During such a paradigm, the animals adapt their behavior according to a change of the reward contingencies. To study these complex cognitive functions (from outcome evaluation to motor adaptation), we developed a versatile, low-cost, open-source platform, allowing us to investigate the neuronal correlates of behavioral flexibility with 1-photon calcium imaging. This platform consists of FreiBox, a novel low-cost Arduino behavioral setup, as well as further open-source tools, which we developed and integrated into our framework. FreiBox is controlled by a custom Python interface and integrates a new licking sensor (strain gauge lickometer) for controlling spatial licking behavioral tasks. In addition to allowing both discriminative and serial reversal learning, the Arduino can track mouse licking behavior in real time to control task events in a submillisecond timescale. To complete our setup, we also developed and validated an affordable commutator, which is crucial for recording calcium imaging with the Miniscope V4 in freely moving mice. Further, we demonstrated that FreiBox can be associated with 1-photon imaging and other open-source initiatives (e.g., Open Ephys) to form a versatile platform for exploring the neuronal substrates of licking-based behavioral flexibility in mice. The combination of the FreiBox behavioral setup and our low-cost commutator represents a highly competitive and complementary addition to the recently emerging battery of open-source initiatives.
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Affiliation(s)
- Brice De La Crompe
- Optophysiology-Optogenetics and Neurophysiology, University of Freiburg, 79110 Freiburg, Germany
- Institute of Biology III, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
- Intelligent Machine-Brain Interfacing Technology (IMBIT)-BrainLinks-BrainTools, University of Freiburg, 79110 Freiburg, Germany
| | - Megan Schneck
- Optophysiology-Optogenetics and Neurophysiology, University of Freiburg, 79110 Freiburg, Germany
- Institute of Biology III, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
- Intelligent Machine-Brain Interfacing Technology (IMBIT)-BrainLinks-BrainTools, University of Freiburg, 79110 Freiburg, Germany
| | - Florian Steenbergen
- Optophysiology-Optogenetics and Neurophysiology, University of Freiburg, 79110 Freiburg, Germany
- Institute of Biology III, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
- Intelligent Machine-Brain Interfacing Technology (IMBIT)-BrainLinks-BrainTools, University of Freiburg, 79110 Freiburg, Germany
| | - Artur Schneider
- Optophysiology-Optogenetics and Neurophysiology, University of Freiburg, 79110 Freiburg, Germany
- Institute of Biology III, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
- Intelligent Machine-Brain Interfacing Technology (IMBIT)-BrainLinks-BrainTools, University of Freiburg, 79110 Freiburg, Germany
| | - Ilka Diester
- Optophysiology-Optogenetics and Neurophysiology, University of Freiburg, 79110 Freiburg, Germany
- Institute of Biology III, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
- Intelligent Machine-Brain Interfacing Technology (IMBIT)-BrainLinks-BrainTools, University of Freiburg, 79110 Freiburg, Germany
- Bernstein Center for Computational Neuroscience, University of Freiburg, 79104 Freiburg, Germany
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Peng Y, Schöneberg N, Esposito MS, Geiger JRP, Sharott A, Tovote P. Current approaches to characterize micro- and macroscale circuit mechanisms of Parkinson's disease in rodent models. Exp Neurol 2022; 351:114008. [PMID: 35149118 PMCID: PMC7612860 DOI: 10.1016/j.expneurol.2022.114008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 01/17/2022] [Accepted: 02/04/2022] [Indexed: 11/24/2022]
Abstract
Accelerating technological progress in experimental neuroscience is increasing the scale as well as specificity of both observational and perturbational approaches to study circuit physiology. While these techniques have also been used to study disease mechanisms, a wider adoption of these approaches in the field of experimental neurology would greatly facilitate our understanding of neurological dysfunctions and their potential treatments at cellular and circuit level. In this review, we will introduce classic and novel methods ranging from single-cell electrophysiological recordings to state-of-the-art calcium imaging and cell-type specific optogenetic or chemogenetic stimulation. We will focus on their application in rodent models of Parkinson’s disease while also presenting their use in the context of motor control and basal ganglia function. By highlighting the scope and limitations of each method, we will discuss how they can be used to study pathophysiological mechanisms at local and global circuit levels and how novel frameworks can help to bridge these scales.
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Affiliation(s)
- Yangfan Peng
- Institute of Neurophysiology, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt Universität zu Berlin, Charitéplatz 1, 10117 Berlin, Germany; Department of Neurology, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt Universität zu Berlin, Charitéplatz 1, 10117 Berlin, Germany; MRC Brain Network Dynamics Unit, University of Oxford, Mansfield Road, Oxford OX1 3TH, United Kingdom.
| | - Nina Schöneberg
- Institute of Clinical Neurobiology, University Hospital Wuerzburg, Versbacher Str. 5, 97078 Wuerzburg, Germany
| | - Maria Soledad Esposito
- Medical Physics Department, Centro Atomico Bariloche, Comision Nacional de Energia Atomica (CNEA), Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Av. E. Bustillo 9500, R8402AGP San Carlos de Bariloche, Rio Negro, Argentina
| | - Jörg R P Geiger
- Institute of Neurophysiology, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt Universität zu Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Andrew Sharott
- MRC Brain Network Dynamics Unit, University of Oxford, Mansfield Road, Oxford OX1 3TH, United Kingdom
| | - Philip Tovote
- Institute of Clinical Neurobiology, University Hospital Wuerzburg, Versbacher Str. 5, 97078 Wuerzburg, Germany; Center for Mental Health, University of Wuerzburg, Margarete-Höppel-Platz 1, 97080 Wuerzburg, Germany.
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Inoue T, Terada S, Matsuzaki M, Izawa J. A small-scale robotic manipulandum for motor control study with rodents. Adv Robot 2021. [DOI: 10.1080/01691864.2021.1912637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Takahisa Inoue
- Empowerment Informatics, University of Tsukuba, Tsukuba, Japan
| | - Shin Terada
- Department of Physiology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Masanori Matsuzaki
- Department of Physiology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Brain Functional Dynamics Collaboration Laboratory, RIKEN Center for Brain Science, Wako, Japan
| | - Jun Izawa
- Faculty of Engineering, Information and Systems, University of Tsukuba, Tsukuba, Japan
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Latchoumane CFV, Barany DA, Karumbaiah L, Singh T. Neurostimulation and Reach-to-Grasp Function Recovery Following Acquired Brain Injury: Insight From Pre-clinical Rodent Models and Human Applications. Front Neurol 2020; 11:835. [PMID: 32849253 PMCID: PMC7396659 DOI: 10.3389/fneur.2020.00835] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 07/06/2020] [Indexed: 12/26/2022] Open
Abstract
Reach-to-grasp is an evolutionarily conserved motor function that is adversely impacted following stroke and traumatic brain injury (TBI). Non-invasive brain stimulation (NIBS) methods, such as transcranial magnetic stimulation and transcranial direct current stimulation, are promising tools that could enhance functional recovery of reach-to-grasp post-brain injury. Though the rodent literature provides a causal understanding of post-injury recovery mechanisms, it has had a limited impact on NIBS protocols in human research. The high degree of homology in reach-to-grasp circuitry between humans and rodents further implies that the application of NIBS to brain injury could be better informed by findings from pre-clinical rodent models and neurorehabilitation research. Here, we provide an overview of the advantages and limitations of using rodent models to advance our current understanding of human reach-to-grasp function, cortical circuitry, and reorganization. We propose that a cross-species comparison of reach-to-grasp recovery could provide a mechanistic framework for clinically efficacious NIBS treatments that could elicit better functional outcomes for patients.
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Affiliation(s)
- Charles-Francois V. Latchoumane
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, United States
- Regenerative Bioscience Center, University of Georgia, Athens, GA, United States
| | - Deborah A. Barany
- Department of Kinesiology, University of Georgia, Athens, GA, United States
| | - Lohitash Karumbaiah
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, United States
- Regenerative Bioscience Center, University of Georgia, Athens, GA, United States
| | - Tarkeshwar Singh
- Regenerative Bioscience Center, University of Georgia, Athens, GA, United States
- Department of Kinesiology, University of Georgia, Athens, GA, United States
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