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Reemst K, Shahin H, Shahar OD. Learning and memory formation in zebrafish: Protein dynamics and molecular tools. Front Cell Dev Biol 2023; 11:1120984. [PMID: 36968211 PMCID: PMC10034119 DOI: 10.3389/fcell.2023.1120984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 02/20/2023] [Indexed: 03/12/2023] Open
Abstract
Research on learning and memory formation at the level of neural networks, as well as at the molecular level, is challenging due to the immense complexity of the brain. The zebrafish as a genetically tractable model organism can overcome many of the current challenges of studying molecular mechanisms of learning and memory formation. Zebrafish have a translucent, smaller and more accessible brain than that of mammals, allowing imaging of the entire brain during behavioral manipulations. Recent years have seen an extensive increase in published brain research describing the use of zebrafish for the study of learning and memory. Nevertheless, due to the complexity of the brain comprising many neural cell types that are difficult to isolate, it has been difficult to elucidate neural networks and molecular mechanisms involved in memory formation in an unbiased manner, even in zebrafish larvae. Therefore, data regarding the identity, location, and intensity of nascent proteins during memory formation is still sparse and our understanding of the molecular networks remains limited, indicating a need for new techniques. Here, we review recent progress in establishing learning paradigms for zebrafish and the development of methods to elucidate neural and molecular networks of learning. We describe various types of learning and highlight directions for future studies, focusing on molecular mechanisms of long-term memory formation and promising state-of-the-art techniques such as cell-type-specific metabolic labeling.
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Affiliation(s)
- Kitty Reemst
- Migal—Galilee Research Institute, Kiryat Shmona, Israel
- Department of Biotechnology, Tel-Hai College, Kiryat Shmona, Israel
| | - Heba Shahin
- Migal—Galilee Research Institute, Kiryat Shmona, Israel
- Department of Biotechnology, Tel-Hai College, Kiryat Shmona, Israel
| | - Or David Shahar
- Migal—Galilee Research Institute, Kiryat Shmona, Israel
- Department of Biotechnology, Tel-Hai College, Kiryat Shmona, Israel
- *Correspondence: Or David Shahar,
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Feng C, Nita-Lazar M, González-Montalbán N, Wang J, Mancini J, Wang S, Ravindran C, Ahmed H, Vasta GR. Manipulating Galectin Expression in Zebrafish (Danio rerio). Methods Mol Biol 2022; 2442:425-443. [PMID: 35320539 DOI: 10.1007/978-1-0716-2055-7_23] [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: 06/14/2023]
Abstract
Techniques for disrupting gene expression are invaluable tools for the analysis of the biological role of a gene product. Because of its genetic tractability and multiple advantages over conventional mammalian models, the zebrafish (Danio rerio) is recognized as a powerful system for gaining new insight into diverse aspects of human health and disease. Among the multiple mammalian gene families for which the zebrafish has shown promise as an invaluable model for functional studies, the galectins have attracted great interest due to their participation in early development, regulation of immune homeostasis, and recognition of microbial pathogens. Galectins are β-galactosyl-binding lectins with a characteristic sequence motif in their carbohydrate recognition domains (CRDs), that constitute an evolutionary conserved family ubiquitous in eukaryotic taxa. Galectins are emerging as key players in the modulation of many important pathological processes, which include acute and chronic inflammatory diseases, autoimmunity and cancer, thus making them potential molecular targets for innovative drug discovery. Here, we provide a review of the current methods available for the manipulation of gene expression in the zebrafish, with a focus on gene knockdown [morpholino (MO)-derived antisense oligonucleotides] and knockout (CRISPR-Cas) technologies.
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Affiliation(s)
- Chiguang Feng
- Department of Microbiology and Immunology, Institute of Marine and Environmental Technology, University of Maryland Baltimore, Baltimore, MD, USA
| | - Mihai Nita-Lazar
- Department of Microbiology and Immunology, Institute of Marine and Environmental Technology, University of Maryland Baltimore, Baltimore, MD, USA
| | - Nuria González-Montalbán
- Department of Microbiology and Immunology, Institute of Marine and Environmental Technology, University of Maryland Baltimore, Baltimore, MD, USA
| | - Jingyu Wang
- Department of Microbiology and Immunology, Institute of Marine and Environmental Technology, University of Maryland Baltimore, Baltimore, MD, USA
| | - Justin Mancini
- Department of Microbiology and Immunology, Institute of Marine and Environmental Technology, University of Maryland Baltimore, Baltimore, MD, USA
| | - Sheng Wang
- Department of Microbiology and Immunology, Institute of Marine and Environmental Technology, University of Maryland Baltimore, Baltimore, MD, USA
- State Key Laboratory for Biocontrol, School of Marine Sciences, Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Chinnarajan Ravindran
- Department of Microbiology and Immunology, Institute of Marine and Environmental Technology, University of Maryland Baltimore, Baltimore, MD, USA
- Department of Marine Biotechnology, National Institute of Oceanography (CSIR), Dona Paula, Goa, India
| | - Hafiz Ahmed
- Department of Biochemistry, School of Medicine, Institute of Marine and Environmental Technology, University of Maryland Baltimore, Baltimore, MD, USA
| | - Gerardo R Vasta
- Department of Microbiology and Immunology, Institute of Marine and Environmental Technology, University of Maryland Baltimore, Baltimore, MD, USA.
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Zebrafish automatic monitoring system for conditioning and behavioral analysis. Sci Rep 2021; 11:9330. [PMID: 33927213 PMCID: PMC8085222 DOI: 10.1038/s41598-021-87502-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 03/24/2021] [Indexed: 11/09/2022] Open
Abstract
Studies using zebrafish (Danio rerio) in neuro-behavioural research are growing. Measuring fish behavior by computational methods is one of the most efficient ways to avoid human bias in experimental analyses, extending them to various approaches. Sometimes, thorough analyses are difficult to do, as fish can behave unpredictably during an experimental strategy. However, the analyses can be implemented in an automated way, using an online strategy and video processing for a complete assessment of the zebrafish behavior, based on the detection and tracking of fish during an activity. Here, a fully automatic conditioning and detailed analysis of zebrafish behavior is presented. Microcontrolled components were used to control the delivery of visual and sound stimuli, in addition to the concise amounts of food after conditioned stimuli for adult zebrafish groups in a conventional tank. The images were captured and processed for automatic detection of the fish, and the training of the fish was done in two evaluation strategies: simple and complex. In simple conditioning, the zebrafish showed significant responses from the second attempt, learning that the conditioned stimulus was a predictor of food presentation in a specific space of the tank, where the food was dumped. When the fish were subjected to two stimuli for decision-making in the food reward, the zebrafish obtained better responses to red light stimuli in relation to vibration. The behavior change was clear in stimulated fish in relation to the control group, thus, the distances traveled and the speed were greater, while the polarization was lower in stimulated fish. This automated system allows for the conditioning and assessment of zebrafish behavior online, with greater stability in experiments, and in the analysis of the behavior of individual fish or fish schools, including learning and memory studies.
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Barreiros MDO, Dantas DDO, Silva LCDO, Ribeiro S, Barros AK. Zebrafish tracking using YOLOv2 and Kalman filter. Sci Rep 2021; 11:3219. [PMID: 33547349 PMCID: PMC7865020 DOI: 10.1038/s41598-021-81997-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 01/13/2021] [Indexed: 11/09/2022] Open
Abstract
Fish show rapid movements in various behavioral activities or associated with the presence of food. However, in periods of rapid movement, the rate at which occlusion occurs among the fish is quite high, causing inconsistency in the detection and tracking of fish, hindering the fish's identity and behavioral trajectory over a long period of time. Although some algorithms have been proposed to solve these problems, most of their applications were made in groups of fish that swim in shallow water and calm behavior, with few sudden movements. To solve these problems, a convolutional network of object recognition, YOLOv2, was used to delimit the region of the fish heads to optimize individual fish detection. In the tracking phase, the Kalman filter was used to estimate the best state of the fish's head position in each frame and, subsequently, the trajectories of each fish were connected among the frames. The results of the algorithm show adequate performances in the trajectories of groups of zebrafish that exhibited rapid movements.
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Affiliation(s)
- Marta de Oliveira Barreiros
- Department of Electrical Engineering, Laboratory for Biological Information Processing (PIB), Federal University of Maranhão (UFMA), Av. dos Portugueses, 1966, Vila Bacanga, São Luís, MA, 65080-805, Brazil.
| | - Diego de Oliveira Dantas
- Department of Electrical Engineering, Laboratory for Biological Information Processing (PIB), Federal University of Maranhão (UFMA), Av. dos Portugueses, 1966, Vila Bacanga, São Luís, MA, 65080-805, Brazil.,Department of Computational Engineering, Federal University of Maranhão (UFMA), Av. dos Portugueses, 1966, Vila Bacanga, São Luís, MA, Brazil
| | - Luís Claudio de Oliveira Silva
- Department of Electrical Engineering, Laboratory for Biological Information Processing (PIB), Federal University of Maranhão (UFMA), Av. dos Portugueses, 1966, Vila Bacanga, São Luís, MA, 65080-805, Brazil.,Department of Computational Engineering, Federal University of Maranhão (UFMA), Av. dos Portugueses, 1966, Vila Bacanga, São Luís, MA, Brazil
| | - Sidarta Ribeiro
- Brain Institute, Federal University of Rio Grande do Norte (UFRN), Av. Sen. Salgado Filho, 3000 Candelária, Natal, RN, Brazil
| | - Allan Kardec Barros
- Department of Electrical Engineering, Laboratory for Biological Information Processing (PIB), Federal University of Maranhão (UFMA), Av. dos Portugueses, 1966, Vila Bacanga, São Luís, MA, 65080-805, Brazil
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Buatois A, Gerlai R. Elemental and Configural Associative Learning in Spatial Tasks: Could Zebrafish be Used to Advance Our Knowledge? Front Behav Neurosci 2020; 14:570704. [PMID: 33390911 PMCID: PMC7773606 DOI: 10.3389/fnbeh.2020.570704] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 11/26/2020] [Indexed: 12/13/2022] Open
Abstract
Spatial learning and memory have been studied for several decades. Analyses of these processes pose fundamental scientific questions but are also relevant from a biomedical perspective. The cellular, synaptic and molecular mechanisms underlying spatial learning have been intensively investigated, yet the behavioral mechanisms/strategies in a spatial task still pose unanswered questions. Spatial learning relies upon configural information about cues in the environment. However, each of these cues can also independently form part of an elemental association with the specific spatial position, and thus spatial tasks may be solved using elemental (single CS and US association) learning. Here, we first briefly review what we know about configural learning from studies with rodents. Subsequently, we discuss the pros and cons of employing a relatively novel laboratory organism, the zebrafish in such studies, providing some examples of methods with which both elemental and configural learning may be explored with this species. Last, we speculate about future research directions focusing on how zebrafish may advance our knowledge. We argue that zebrafish strikes a reasonable compromise between system complexity and practical simplicity and that adding this species to the studies with laboratory rodents will allow us to gain a better understanding of both the evolution of and the mechanisms underlying spatial learning. We conclude that zebrafish research will enhance the translational relevance of our findings.
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Affiliation(s)
- Alexis Buatois
- Department of Psychology, University of Toronto Mississauga, Mississauga, ON, Canada
| | - Robert Gerlai
- Department of Psychology, University of Toronto Mississauga, Mississauga, ON, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
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Kuroda T, Gilroy SP, Cançado CR, Podlesnik CA. Effects of punishing target response during extinction on resurgence and renewal in zebrafish (Danio rerio). Behav Processes 2020; 178:104191. [DOI: 10.1016/j.beproc.2020.104191] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 07/01/2020] [Accepted: 07/01/2020] [Indexed: 12/13/2022]
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Manabe K, Dooling RJ. A psychophysical approach to measuring the threshold for acoustic stimulation in zebrafish (Danio rerio). THE JOURNAL OF THE ACOUSTICAL SOCIETY OF AMERICA 2020; 147:1059. [PMID: 32113261 DOI: 10.1121/10.0000722] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 01/24/2020] [Indexed: 06/10/2023]
Abstract
Zebrafish are a popular vertebrate animal model for biomedical research including investigations of the auditory system. Responses to acoustic stimulation have been a challenge to carefully measure in zebrafish. Here, the authors have developed a procedure for measuring hearing sensitivity in adult zebrafish using an appetitive automated Go/No Go task. In this task, a trial is initiated when a fish passes through an observing gate. In a sound trial, the fish is reinforced by an automated food delivery system when it enters the reinforcement compartment. If the fish enters the reinforcement compartment during a no-sound trial, a timeout is implemented. Zebrafish successfully learned this task in a median of about ten days of daily training. Zebrafish were most sensitive at a frequency of 800 Hz, which corresponds well with sensitivity reported from physiological methods. As far as the authors know, the present study is the first to provide hearing thresholds for zebrafish using a conventional combination of operant conditioning and psychophysical procedures. This could open the door to other kinds of tests using acoustic stimuli as are commonly conducted in many other laboratory animals.
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Affiliation(s)
- Kazuchika Manabe
- College of Bioresource Sciences, Nihon University, 1866, Kameino, Fujisawa, Kanagawa 252-0880, Japan
| | - R J Dooling
- University of Maryland, College Park, Maryland 20742, USA
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Kuroda T. A system for the real-time tracking of operant behavior as an application of 3D camera. J Exp Anal Behav 2018; 110:522-544. [PMID: 30230551 DOI: 10.1002/jeab.471] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Revised: 08/03/2018] [Accepted: 08/13/2018] [Indexed: 12/17/2022]
Abstract
The capacity of 3D cameras to measure many different aspects of behavior (e.g., velocity, pattern, and posture) could contribute to the understanding of behavior. The present article describes a system for the real-time tracking of operant behavior, which is applicable to other domains of behavioral science as well. Methods for real-time 3D tracking of animal behavior are described, along with sample C++ programs. A demonstration using one zebrafish as a subject indicated that the present system successfully tracked the 3D motion of the fish. Moreover, the acquisition of a target response (i.e., approach to a corner of the aquarium) was demonstrated with the arrangement of a reinforcement contingency at the corner in the absence of a traditional, salient operandum. The system offers the capacity to characterize more completely ongoing behavior in learning tasks across a range of species than simply performance of discrete operant responses. The system also is capable of tracking multiple individuals simultaneously so it is possible both to study social interactions and arrange contingencies for engaging in social behavior. Other possible applications of 3D cameras are discussed.
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Barretto AB, Maia CM, Alves NPC, Giaquinto PC. Water jet: a simple method for classical conditioning in fish. Acta Ethol 2018. [DOI: 10.1007/s10211-018-0297-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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10
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Kuroda T, Mizutani Y. Response acquisition by zebrafish (Danio rerio) with delayed reinforcement. J Exp Anal Behav 2018; 109:520-532. [PMID: 29624678 DOI: 10.1002/jeab.324] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 03/13/2018] [Indexed: 11/07/2022]
Abstract
Zebrafish (Danio rerio) is a common vertebrate animal model in biomedical research and is a promising species for studying how genes interact with environmental factors in determining behavior. The present study investigated how reinforcement parameters affect zebrafish behavior by assessing response acquisition with delayed reinforcement, which has been studied with other species (e.g., rats, pigeons, humans, etc.) but not with zebrafish. Twenty-four experimentally naïve subjects were exposed to a tandem fixed-ratio 1 differential-reinforcement-of-other-behavior x-s schedule of reinforcement, where x varied across subjects. There were six different delay-to-reinforcement durations and sets of four fish were assigned to each delay duration. All of the fish assigned to a 0-, 0.5-, or 1-s delay acquired responding. Two fish acquired responding with a 3-s delay and one fish appeared to have acquired it with a 6-s delay although the latter result was less clear. None acquired responding with a 12-s delay. These results suggest that zebrafish behavior is sensitive to delays to reinforcement and the time frame over which reinforcement is effective may be limited approximately to 6 s. This time frame is shorter than that found with other species. Practical and theoretical implications of the present finding are discussed.
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Kuroda T, Mizutani Y, Cançado CR, Podlesnik CA. Reversal learning and resurgence of operant behavior in zebrafish ( Danio rerio ). Behav Processes 2017. [DOI: 10.1016/j.beproc.2017.06.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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12
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Operant models of relapse in zebrafish ( Danio rerio ): Resurgence, renewal, and reinstatement. Behav Brain Res 2017; 335:215-222. [DOI: 10.1016/j.bbr.2017.08.023] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 08/03/2017] [Accepted: 08/14/2017] [Indexed: 12/11/2022]
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13
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Doyle JM, Merovitch N, Wyeth RC, Stoyek MR, Schmidt M, Wilfart F, Fine A, Croll RP. A simple automated system for appetitive conditioning of zebrafish in their home tanks. Behav Brain Res 2016; 317:444-452. [PMID: 27659557 DOI: 10.1016/j.bbr.2016.09.044] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 09/16/2016] [Accepted: 09/18/2016] [Indexed: 11/16/2022]
Abstract
We describe here an automated apparatus that permits rapid conditioning paradigms for zebrafish. Arduino microprocessors were used to control the delivery of auditory or visual stimuli to groups of adult or juvenile zebrafish in their home tanks in a conventional zebrafish facility. An automatic feeder dispensed precise amounts of food immediately after the conditioned stimuli, or at variable delays for controls. Responses were recorded using inexpensive cameras, with the video sequences analysed with ImageJ or Matlab. Fish showed significant conditioned responses in as few as 5 trials, learning that the conditioned stimulus was a predictor of food presentation at the water surface and at the end of the tank where the food was dispensed. Memories of these conditioned associations persisted for at least 2days after training when fish were tested either as groups or as individuals. Control fish, for which the auditory or visual stimuli were specifically unpaired with food, showed no comparable responses. This simple, low-cost, automated system permits scalable conditioning of zebrafish with minimal human intervention, greatly reducing both variability and labour-intensiveness. It will be useful for studies of the neural basis of learning and memory, and for high-throughput screening of compounds modifying those processes.
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Affiliation(s)
- Jillian M Doyle
- Department of Physiology & Biophysics, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Neil Merovitch
- Department of Physiology & Biophysics, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Russell C Wyeth
- Department of Biology, St. Francis Xavier University, Antigonish, NS B2G 2W5, Canada
| | - Matthew R Stoyek
- Department of Medical Neuroscience, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Michael Schmidt
- Department of Anesthesia, Pain Management and Perioperative Medicine, Dalhousie University, Halifax, NS B3H 4R2, Canada; School of Biomedical Engineering, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Florentin Wilfart
- Department of Anesthesia, Pain Management and Perioperative Medicine, Dalhousie University, Halifax, NS B3H 4R2, Canada; School of Biomedical Engineering, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Alan Fine
- Department of Physiology & Biophysics, Dalhousie University, Halifax, NS B3H 4R2, Canada; School of Biomedical Engineering, Dalhousie University, Halifax, NS B3H 4R2, Canada.
| | - Roger P Croll
- Department of Physiology & Biophysics, Dalhousie University, Halifax, NS B3H 4R2, Canada.
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15
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Feng C, Nita-Lazar M, González-Montalbán N, Wang J, Mancini J, Ravindran C, Ahmed H, Vasta GR. Manipulating galectin expression in zebrafish (Danio rerio). Methods Mol Biol 2015; 1207:327-41. [PMID: 25253151 DOI: 10.1007/978-1-4939-1396-1_22] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Techniques for disrupting gene expression are invaluable tools for the analysis of the biological role(s) of a gene product. Because of its genetic tractability and multiple advantages over conventional mammalian models, the zebrafish (Danio rerio) is recognized as a powerful system for gaining new insight into diverse aspects of human health and disease. Among the multiple mammalian gene families for which the zebrafish has shown promise as an invaluable model for functional studies, the galectins have attracted great interest due to their participation in early development, regulation of immune homeostasis, and recognition of microbial pathogens. Galectins are β-galactosyl-binding lectins with a characteristic sequence motif in their carbohydrate recognition domains (CRDs), which comprise an evolutionary conserved family ubiquitous in eukaryotic taxa. Galectins are emerging as key players in the modulation of many important pathological processes, which include acute and chronic inflammatory diseases, autoimmunity and cancer, thus making them potential molecular targets for innovative drug discovery. Here, we provide a review of the current methods available for the manipulation of gene expression in the zebrafish, with a focus on gene knockdown [morpholino (MO)-derived antisense oligonucleotides] and knockout (CRISPR-Cas) technologies.
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Affiliation(s)
- Chiguang Feng
- Department of Microbiology and Immunology, School of Medicine, University of Maryland, Baltimore, MD, USA
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