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Caioni G, Merola C, Perugini M, Angelozzi G, Amorena M, Benedetti E, Lucon-Xiccato T, Bertolucci C. Sodium valproate effects on the morphological and neurobehavioral phenotype of zebrafish. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2024; 110:104500. [PMID: 38977114 DOI: 10.1016/j.etap.2024.104500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 06/21/2024] [Accepted: 07/04/2024] [Indexed: 07/10/2024]
Abstract
The anticonvulsant sodium valproate (SV) is frequently administered as a medicament but bears several negative effects in case of exposure during development. We analyzed extensively these early development effects of using the zebrafish model. Zebrafish embryos were exposed as eggs to two sublethal concentrations of SV, 10 and 25 mg/L. A general embryo toxicity analysis revealed extended anomalies in the cardiovascular system, and in the craniofacial and the spinal skeleton, as well as high mortality, in the embryos exposed to SV. The teratogenic potential of SV was confirmed in hacthed larvae by morphometric and cartilage profile analysis. Last, neurobehavioral impairments due to SV were highlighted in subjects' activity, anxiety, response to stimulations, habituation learning, and daily synchronization of locomotor activity, overall mirroring typical phenotypes associated with autistic spectrum disorders. In conclusion, our results confirmed the presence of extended and multifaced impacts of exposure to SV during development.
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Affiliation(s)
- Giulia Caioni
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila 67100, Italy; Department of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Italy
| | - Carmine Merola
- Department of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Italy
| | - Monia Perugini
- Department of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Italy.
| | - Giovanni Angelozzi
- Department of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Italy
| | - Michele Amorena
- Department of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Italy
| | - Elisabetta Benedetti
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila 67100, Italy
| | - Tyrone Lucon-Xiccato
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Cristiano Bertolucci
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
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2
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Varma A, Udupa S, Sengupta M, Ghosh PK, Thirumalai V. A machine-learning tool to identify bistable states from calcium imaging data. J Physiol 2024; 602:1243-1271. [PMID: 38482722 DOI: 10.1113/jp284373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 02/09/2024] [Indexed: 04/04/2024] Open
Abstract
Mapping neuronal activation using calcium imaging in vivo during behavioural tasks has advanced our understanding of nervous system function. In almost all of these studies, calcium imaging is used to infer spike probabilities because action potentials activate voltage-gated calcium channels and increase intracellular calcium levels. However, neurons not only fire action potentials, but also convey information via intrinsic dynamics such as by generating bistable membrane potential states. Although a number of tools for spike inference have been developed and are currently being used, no tool exists for converting calcium imaging signals to maps of cellular state in bistable neurons. Purkinje neurons in the larval zebrafish cerebellum exhibit membrane potential bistability, firing either tonically or in bursts. Several studies have implicated the role of a population code in cerebellar function, with bistability adding an extra layer of complexity to this code. In the present study, we develop a tool, CaMLSort, which uses convolutional recurrent neural networks to classify calcium imaging traces as arising from either tonic or bursting cells. We validate this classifier using a number of different methods and find that it performs well on simulated event rasters as well as real biological data that it had not previously seen. Moreover, we find that CaMLsort generalizes to other bistable neurons, such as dopaminergic neurons in the ventral tegmental area of mice. Thus, this tool offers a new way of analysing calcium imaging data from bistable neurons to understand how they participate in network computation and natural behaviours. KEY POINTS: Calcium imaging, compriising the gold standard of inferring neuronal activity, does not report cellular state in neurons that are bistable, such as Purkinje neurons in the cerebellum of larval zebrafish. We model the relationship between Purkinje neuron electrical activity and its corresponding calcium signal to compile a dataset of state-labelled simulated calcium signals. We apply machine-learning methods to this dataset to develop a tool that can classify the state of a Purkinje neuron using only its calcium signal, which works well on real data even though it was trained only on simulated data. CaMLsort (Calcium imaging and Machine Learning based tool to sort intracellular state) also generalizes well to bistable neurons in a different brain region (ventral tegmental area) in a different model organism (mouse). This tool can facilitate our understanding of how these neurons carry out their functions in a circuit.
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Affiliation(s)
- Aalok Varma
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
| | - Sathvik Udupa
- Department of Electrical Engineering, Indian Institute of Science, Bangalore, India
| | - Mohini Sengupta
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
| | - Prasanta Kumar Ghosh
- Department of Electrical Engineering, Indian Institute of Science, Bangalore, India
| | - Vatsala Thirumalai
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
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3
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Luu P, Fraser SE, Schneider F. More than double the fun with two-photon excitation microscopy. Commun Biol 2024; 7:364. [PMID: 38531976 DOI: 10.1038/s42003-024-06057-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 03/15/2024] [Indexed: 03/28/2024] Open
Abstract
For generations researchers have been observing the dynamic processes of life through the lens of a microscope. This has offered tremendous insights into biological phenomena that span multiple orders of time- and length-scales ranging from the pure magic of molecular reorganization at the membrane of immune cells, to cell migration and differentiation during development or wound healing. Standard fluorescence microscopy techniques offer glimpses at such processes in vitro, however, when applied in intact systems, they are challenged by reduced signal strengths and signal-to-noise ratios that result from deeper imaging. As a remedy, two-photon excitation (TPE) microscopy takes a special place, because it allows us to investigate processes in vivo, in their natural environment, even in a living animal. Here, we review the fundamental principles underlying TPE aimed at basic and advanced microscopy users interested in adopting TPE for intravital imaging. We focus on applications in neurobiology, present current trends towards faster, wider and deeper imaging, discuss the combination with photon counting technologies for metabolic imaging and spectroscopy, as well as highlight outstanding issues and drawbacks in development and application of these methodologies.
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Affiliation(s)
- Peter Luu
- Translational Imaging Center, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA, 90089, USA
- Department of Biological Sciences, Division of Molecular and Computational Biology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Scott E Fraser
- Translational Imaging Center, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA, 90089, USA
- Department of Biological Sciences, Division of Molecular and Computational Biology, University of Southern California, Los Angeles, CA, 90089, USA
- Alfred Mann Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, 90089, USA
| | - Falk Schneider
- Translational Imaging Center, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA, 90089, USA.
- Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA, 90089, USA.
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4
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Doszyn O, Dulski T, Zmorzynska J. Diving into the zebrafish brain: exploring neuroscience frontiers with genetic tools, imaging techniques, and behavioral insights. Front Mol Neurosci 2024; 17:1358844. [PMID: 38533456 PMCID: PMC10963419 DOI: 10.3389/fnmol.2024.1358844] [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: 12/21/2023] [Accepted: 02/27/2024] [Indexed: 03/28/2024] Open
Abstract
The zebrafish (Danio rerio) is increasingly used in neuroscience research. Zebrafish are relatively easy to maintain, and their high fecundity makes them suitable for high-throughput experiments. Their small, transparent embryos and larvae allow for easy microscopic imaging of the developing brain. Zebrafish also share a high degree of genetic similarity with humans, and are amenable to genetic manipulation techniques, such as gene knockdown, knockout, or knock-in, which allows researchers to study the role of specific genes relevant to human brain development, function, and disease. Zebrafish can also serve as a model for behavioral studies, including locomotion, learning, and social interactions. In this review, we present state-of-the-art methods to study the brain function in zebrafish, including genetic tools for labeling single neurons and neuronal circuits, live imaging of neural activity, synaptic dynamics and protein interactions in the zebrafish brain, optogenetic manipulation, and the use of virtual reality technology for behavioral testing. We highlight the potential of zebrafish for neuroscience research, especially regarding brain development, neuronal circuits, and genetic-based disorders and discuss its certain limitations as a model.
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Affiliation(s)
| | | | - J. Zmorzynska
- Laboratory of Molecular and Cellular Neurobiology, International Institute of Molecular and Cell Biology in Warsaw (IIMCB), Warsaw, Poland
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5
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Frommelt J, Liu E, Bhaidani A, Hu B, Gao Y, Ye D, Lin F. Flat mount preparation for whole-mount fluorescent imaging of zebrafish embryos. Biol Open 2023; 12:bio060048. [PMID: 37746815 PMCID: PMC10373579 DOI: 10.1242/bio.060048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 06/23/2023] [Indexed: 09/26/2023] Open
Abstract
The zebrafish is a widely used model organism for biomedical research due to its ease of maintenance, external fertilization of embryos, rapid embryonic development, and availability of established genetic tools. One notable advantage of using zebrafish is the transparency of the embryos, which enables high-resolution imaging of specific cells, tissues, and structures through the use of transgenic and knock-in lines. However, as the embryo develops, multiple layers of tissue wrap around the lipid-enriched yolk, which can create a challenge to image tissues located deep within the embryo. While various methods are available, such as two-photon imaging, cryosectioning, vibratome sectioning, and micro-surgery, each of these has limitations. In this study, we present a novel deyolking method that allows for high-quality imaging of tissues that are obscured by other tissues and the yolk. Embryos are lightly fixed in 1% PFA to remove the yolk without damaging embryonic tissues and are then refixed in 4% PFA and mounted on custom-made bridged slides. This method offers a simple way to prepare imaging samples that can be subjected to further preparation, such as immunostaining. Furthermore, the bridged slides described in this study can be used for imaging tissue and organ preparations from various model organisms.
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Affiliation(s)
- Joseph Frommelt
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Emily Liu
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Afraz Bhaidani
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Bo Hu
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Yuanyuan Gao
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Ding Ye
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Fang Lin
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
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6
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Sree Kumar H, Wisner AS, Refsnider JM, Martyniuk CJ, Zubcevic J. Small fish, big discoveries: zebrafish shed light on microbial biomarkers for neuro-immune-cardiovascular health. Front Physiol 2023; 14:1186645. [PMID: 37324381 PMCID: PMC10267477 DOI: 10.3389/fphys.2023.1186645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 05/22/2023] [Indexed: 06/17/2023] Open
Abstract
Zebrafish (Danio rerio) have emerged as a powerful model to study the gut microbiome in the context of human conditions, including hypertension, cardiovascular disease, neurological disorders, and immune dysfunction. Here, we highlight zebrafish as a tool to bridge the gap in knowledge in linking the gut microbiome and physiological homeostasis of cardiovascular, neural, and immune systems, both independently and as an integrated axis. Drawing on zebrafish studies to date, we discuss challenges in microbiota transplant techniques and gnotobiotic husbandry practices. We present advantages and current limitations in zebrafish microbiome research and discuss the use of zebrafish in identification of microbial enterotypes in health and disease. We also highlight the versatility of zebrafish studies to further explore the function of human conditions relevant to gut dysbiosis and reveal novel therapeutic targets.
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Affiliation(s)
- Hemaa Sree Kumar
- Department of Physiology and Pharmacology, University of Toledo, Toledo, OH, United States
- Department of Neuroscience and Neurological Disorders, University of Toledo, Toledo, OH, United States
| | - Alexander S. Wisner
- Department of Medicinal and Biological Chemistry, University of Toledo, Toledo, OH, United States
- Center for Drug Design and Development, College of Pharmacy and Pharmaceutical Sciences, University of Toledo, Toledo, OH, United States
| | - Jeanine M. Refsnider
- Department of Environmental Sciences, University of Toledo, Toledo, OH, United States
| | - Christopher J. Martyniuk
- Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, OH, United States
| | - Jasenka Zubcevic
- Department of Physiology and Pharmacology, University of Toledo, Toledo, OH, United States
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7
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Naija A, Yalcin HC. Evaluation of cadmium and mercury on cardiovascular and neurological systems: Effects on humans and fish. Toxicol Rep 2023; 10:498-508. [PMID: 37396852 PMCID: PMC10313869 DOI: 10.1016/j.toxrep.2023.04.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 04/09/2023] [Accepted: 04/17/2023] [Indexed: 07/04/2023] Open
Abstract
Chemicals are at the top of public health concerns and metals have received much attention in terms of toxicological studies. Cadmium (Cd) and mercury (Hg) are among the most toxic heavy metals and are widely distributed in the environment. They are considered important factors involved in several organ disturbances. Heart and brain tissues are not among the first exposure sites to Cd and Hg but they are directly affected and may manifest intoxication reactions leading to death. Many cases of human intoxication with Cd and Hg showed that these metals have potential cardiotoxic and neurotoxic effects. Human exposure to heavy metals is through fish consumption which is considered as an excellent source of human nutrients. In the current review, we will summarize the most known cases of human intoxication with Cd and Hg, highlight their toxic effects on fish, and investigate the common signal pathways of both Cd and Hg to affect heart and brain tissues. Also, we will present the most common biomarkers used in the assessment of cardiotoxicity and neurotoxicity using Zebrafish model.
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8
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Valle AF, Honnef R, Seelig JD. Automated long-term two-photon imaging in head-fixed walking Drosophila. J Neurosci Methods 2021; 368:109432. [PMID: 34861285 DOI: 10.1016/j.jneumeth.2021.109432] [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: 05/03/2021] [Revised: 11/24/2021] [Accepted: 11/26/2021] [Indexed: 10/19/2022]
Abstract
BACKGROUND The brain of Drosophila shows dynamics at multiple timescales, from the millisecond range of fast voltage or calcium transients to functional and structural changes occurring over multiple days. To relate such dynamics to behavior requires monitoring neural circuits across these multiple timescales in behaving animals. NEW METHOD Here, we develop a technique for automated long-term two-photon imaging in fruit flies, during wakefulness and extended bouts of immobility, as typically observed during sleep, navigating in virtual reality over up to seven days. The method is enabled by laser surgery, a microrobotic arm for controlling forceps for dissection assistance, an automated feeding robot, as well as volumetric, simultaneous multiplane imaging. RESULTS The approach is validated in the fly's head direction system and walking behavior as well a neural activity are recorded. The head direction system tracks the fly's walking direction over multiple days. COMPARISON WITH EXISTING METHODS In comparison with previous head-fixed preparations, the time span over which tethered behavior and neural activity can be recorded at the same time is extended from hours to days. Additionally, the reproducibility and ease of dissections are improved compared with manual approaches. Different from previous laser surgery approaches, only continuous wave lasers are required. Lastly, an automated feeding system allows continuously maintaining the fly for several days in the virtual reality setup without user intervention. CONCLUSIONS Imaging in behaving flies over multiple timescales will be useful for understanding circadian activity, learning and long-term memory, or sleep.
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Affiliation(s)
| | - Rolf Honnef
- Center of Advanced European Studies and Research (caesar), Bonn, Germany
| | - Johannes D Seelig
- Center of Advanced European Studies and Research (caesar), Bonn, Germany.
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9
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Cho ES, Han S, Lee KH, Kim CH, Yoon YG. 3DM: deep decomposition and deconvolution microscopy for rapid neural activity imaging. OPTICS EXPRESS 2021; 29:32700-32711. [PMID: 34615335 DOI: 10.1364/oe.439619] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 09/14/2021] [Indexed: 05/18/2023]
Abstract
We report the development of deep decomposition and deconvolution microscopy (3DM), a computational microscopy method for the volumetric imaging of neural activity. 3DM overcomes the major challenge of deconvolution microscopy, the ill-posed inverse problem. We take advantage of the temporal sparsity of neural activity to reformulate and solve the inverse problem using two neural networks which perform sparse decomposition and deconvolution. We demonstrate the capability of 3DM via in vivo imaging of the neural activity of a whole larval zebrafish brain with a field of view of 1040 µm × 400 µm × 235 µm and with estimated lateral and axial resolutions of 1.7 µm and 5.4 µm, respectively, at imaging rates of up to 4.2 volumes per second.
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10
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Andreana M, Sturtzel C, Spielvogel CP, Papp L, Leitgeb R, Drexler W, Distel M, Unterhuber A. Toward Quantitative in vivo Label-Free Tracking of Lipid Distribution in a Zebrafish Cancer Model. Front Cell Dev Biol 2021; 9:675636. [PMID: 34277618 PMCID: PMC8280786 DOI: 10.3389/fcell.2021.675636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 05/04/2021] [Indexed: 11/26/2022] Open
Abstract
Cancer cells often adapt their lipid metabolism to accommodate the increased fatty acid demand for membrane biogenesis and energy production. Upregulation of fatty acid uptake from the environment of cancer cells has also been reported as an alternative mechanism. To investigate the role of lipids in tumor onset and progression and to identify potential diagnostic biomarkers, lipids are ideally imaged directly within the intact tumor tissue in a label-free way. In this study, we investigated lipid accumulation and distribution in living zebrafish larvae developing a tumor by means of coherent anti-Stokes Raman scattering microscopy. Quantitative textural features based on radiomics revealed higher lipid accumulation in oncogene-expressing larvae compared to healthy ones. This high lipid accumulation could reflect an altered lipid metabolism in the hyperproliferating oncogene-expressing cells.
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Affiliation(s)
- Marco Andreana
- Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, Vienna, Austria
| | - Caterina Sturtzel
- Innovative Cancer Models, St. Anna Children's Cancer Research Institute, Vienna, Austria.,Zebrafish Platform Austria for Preclinical Drug Screening (ZANDR), Vienna, Austria
| | - Clemens P Spielvogel
- Division of Nuclear Medicine, Department of Medical Imaging and Image-Guided Therapy, Medical University of Vienna, Vienna, Austria.,Christian Doppler Laboratory for Applied Metabolomics, Medical University of Vienna, Vienna, Austria
| | - Laszlo Papp
- Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, Vienna, Austria
| | - Rainer Leitgeb
- Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, Vienna, Austria.,Christian Doppler Laboratory OPTRAMED, Medical University of Vienna, Vienna, Austria
| | - Wolfgang Drexler
- Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, Vienna, Austria
| | - Martin Distel
- Innovative Cancer Models, St. Anna Children's Cancer Research Institute, Vienna, Austria.,Zebrafish Platform Austria for Preclinical Drug Screening (ZANDR), Vienna, Austria
| | - Angelika Unterhuber
- Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, Vienna, Austria
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11
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Lauri A, Fasano G, Venditti M, Dallapiccola B, Tartaglia M. In vivo Functional Genomics for Undiagnosed Patients: The Impact of Small GTPases Signaling Dysregulation at Pan-Embryo Developmental Scale. Front Cell Dev Biol 2021; 9:642235. [PMID: 34124035 PMCID: PMC8194860 DOI: 10.3389/fcell.2021.642235] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/12/2021] [Indexed: 12/24/2022] Open
Abstract
While individually rare, disorders affecting development collectively represent a substantial clinical, psychological, and socioeconomic burden to patients, families, and society. Insights into the molecular mechanisms underlying these disorders are required to speed up diagnosis, improve counseling, and optimize management toward targeted therapies. Genome sequencing is now unveiling previously unexplored genetic variations in undiagnosed patients, which require functional validation and mechanistic understanding, particularly when dealing with novel nosologic entities. Functional perturbations of key regulators acting on signals' intersections of evolutionarily conserved pathways in these pathological conditions hinder the fine balance between various developmental inputs governing morphogenesis and homeostasis. However, the distinct mechanisms by which these hubs orchestrate pathways to ensure the developmental coordinates are poorly understood. Integrative functional genomics implementing quantitative in vivo models of embryogenesis with subcellular precision in whole organisms contribute to answering these questions. Here, we review the current knowledge on genes and mechanisms critically involved in developmental syndromes and pediatric cancers, revealed by genomic sequencing and in vivo models such as insects, worms and fish. We focus on the monomeric GTPases of the RAS superfamily and their influence on crucial developmental signals and processes. We next discuss the effectiveness of exponentially growing functional assays employing tractable models to identify regulatory crossroads. Unprecedented sophistications are now possible in zebrafish, i.e., genome editing with single-nucleotide precision, nanoimaging, highly resolved recording of multiple small molecules activity, and simultaneous monitoring of brain circuits and complex behavioral response. These assets permit accurate real-time reporting of dynamic small GTPases-controlled processes in entire organisms, owning the potential to tackle rare disease mechanisms.
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Affiliation(s)
- Antonella Lauri
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | | | | | | | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
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12
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Fitzgerald JA, Könemann S, Krümpelmann L, Županič A, Vom Berg C. Approaches to Test the Neurotoxicity of Environmental Contaminants in the Zebrafish Model: From Behavior to Molecular Mechanisms. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2021; 40:989-1006. [PMID: 33270929 DOI: 10.1002/etc.4951] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 08/15/2020] [Accepted: 11/29/2020] [Indexed: 06/12/2023]
Abstract
The occurrence of neuroactive chemicals in the aquatic environment is on the rise and poses a potential threat to aquatic biota of currently unpredictable outcome. In particular, subtle changes caused by these chemicals to an organism's sensation or behavior are difficult to tackle with current test systems that focus on rodents or with in vitro test systems that omit whole-animal responses. In recent years, the zebrafish (Danio rerio) has become a popular model organism for toxicological studies and testing strategies, such as the standardized use of zebrafish early life stages in the Organisation for Economic Co-operation and Development's guideline 236. In terms of neurotoxicity, the zebrafish provides a powerful model to investigate changes to the nervous system from several different angles, offering the ability to tackle the mechanisms of action of chemicals in detail. The mechanistic understanding gained through the analysis of this model species provides a good basic knowledge of how neuroactive chemicals might interact with a teleost nervous system. Such information can help infer potential effects occurring to other species exposed to neuroactive chemicals in their aquatic environment and predicting potential risks of a chemical for the aquatic ecosystem. In the present article, we highlight approaches ranging from behavioral to structural, functional, and molecular analysis of the larval zebrafish nervous system, providing a holistic view of potential neurotoxic outcomes. Environ Toxicol Chem 2021;40:989-1006. © 2020 SETAC.
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Affiliation(s)
- Jennifer A Fitzgerald
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Sarah Könemann
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- EPF Lausanne, School of Architecture, Civil and Environmental Engineering, Lausanne, Switzerland
| | - Laura Krümpelmann
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Anže Županič
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- National Institute of Biology, Ljubljana, Slovenia
| | - Colette Vom Berg
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
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13
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Abu-Siniyeh A, Al-Zyoud W. Highlights on selected microscopy techniques to study zebrafish developmental biology. Lab Anim Res 2020; 36:12. [PMID: 32346532 PMCID: PMC7178987 DOI: 10.1186/s42826-020-00044-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 04/06/2020] [Indexed: 02/07/2023] Open
Abstract
Bio-imaging is a tedious task when it concerns exploring cell functions, developmental mechanisms, and other vital processes in vivo. Single-cell resolution is challenging due to different issues such as sample size, the scattering of intact and opaque tissue, pigmentation in untreated animals, the movement of living organs, and maintaining the sample under physiological conditions. These factors might lead researchers to implement microscopy techniques with a suitable animal model to mimic the nature of the living cells. Zebrafish acquired its prestigious reputation in the biomedical research field due to its transparency under advanced microscopes. Therefore, various microscopy techniques, including Multi-Photon, Light-Sheet Microscopy, and Second Harmonic Generation, simplify the discovery of different types of internal functions in zebrafish. In this review, we briefly discuss three recent microscopy techniques that are being utilized because they are non-invasive in investigating developmental events in zebrafish embryo and larvae.
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Affiliation(s)
- Ahmed Abu-Siniyeh
- 1Clinical Laboratory Sciences Department, College of Applied Medical Science, Taif University, Taif, Kingdom of Saudi Arabia
| | - Walid Al-Zyoud
- 2Department of Biomedical Engineering, School of Applied Medical Sciences, German Jordanian University, Amman, Jordan
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14
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Cerebellar Neurodynamics Predict Decision Timing and Outcome on the Single-Trial Level. Cell 2020; 180:536-551.e17. [PMID: 31955849 DOI: 10.1016/j.cell.2019.12.018] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 10/28/2019] [Accepted: 12/12/2019] [Indexed: 12/20/2022]
Abstract
Goal-directed behavior requires the interaction of multiple brain regions. How these regions and their interactions with brain-wide activity drive action selection is less understood. We have investigated this question by combining whole-brain volumetric calcium imaging using light-field microscopy and an operant-conditioning task in larval zebrafish. We find global, recurring dynamics of brain states to exhibit pre-motor bifurcations toward mutually exclusive decision outcomes. These dynamics arise from a distributed network displaying trial-by-trial functional connectivity changes, especially between cerebellum and habenula, which correlate with decision outcome. Within this network the cerebellum shows particularly strong and predictive pre-motor activity (>10 s before movement initiation), mainly within the granule cells. Turn directions are determined by the difference neuroactivity between the ipsilateral and contralateral hemispheres, while the rate of bi-hemispheric population ramping quantitatively predicts decision time on the trial-by-trial level. Our results highlight a cognitive role of the cerebellum and its importance in motor planning.
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15
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Vaz R, Hofmeister W, Lindstrand A. Zebrafish Models of Neurodevelopmental Disorders: Limitations and Benefits of Current Tools and Techniques. Int J Mol Sci 2019; 20:ijms20061296. [PMID: 30875831 PMCID: PMC6471844 DOI: 10.3390/ijms20061296] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 02/26/2019] [Accepted: 03/11/2019] [Indexed: 12/13/2022] Open
Abstract
For the past few years there has been an exponential increase in the use of animal models to confirm the pathogenicity of candidate disease-causing genetic variants found in patients. One such animal model is the zebrafish. Despite being a non-mammalian animal, the zebrafish model has proven its potential in recapitulating the phenotypes of many different human genetic disorders. This review will focus on recent advances in the modeling of neurodevelopmental disorders in zebrafish, covering aspects from early brain development to techniques used for modulating gene expression, as well as how to best characterize the resulting phenotypes. We also review other existing models of neurodevelopmental disorders, and the current efforts in developing and testing compounds with potential therapeutic value.
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Affiliation(s)
- Raquel Vaz
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden.
| | - Wolfgang Hofmeister
- Laboratory of Molecular and Cellular Cardiology, Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, 5000 Odense, Denmark and the Novo Nordisk Foundation for Stem cell Biology (Danstem), University of Copenhagen, 2200 Copenhagen, Denmark.
| | - Anna Lindstrand
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine and Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, 171 76 Stockholm, Sweden.
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16
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Bercier V, Rosello M, Del Bene F, Revenu C. Zebrafish as a Model for the Study of Live in vivo Processive Transport in Neurons. Front Cell Dev Biol 2019; 7:17. [PMID: 30838208 PMCID: PMC6389722 DOI: 10.3389/fcell.2019.00017] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 02/01/2019] [Indexed: 12/13/2022] Open
Abstract
Motor proteins are responsible for transport of vesicles and organelles within the cell cytoplasm. They interact with the actin cytoskeleton and with microtubules to ensure communication and supply throughout the cell. Much work has been done in vitro and in silico to unravel the key players, including the dynein motor complex, the kinesin and myosin superfamilies, and their interacting regulatory complexes, but there is a clear need for in vivo data as recent evidence suggests previous models might not recapitulate physiological conditions. The zebrafish embryo provides an excellent system to study these processes in intact animals due to the ease of genetic manipulation and the optical transparency allowing live imaging. We present here the advantages of the zebrafish embryo as a system to study live in vivo processive transport in neurons and provide technical recommendations for successful analysis.
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Affiliation(s)
- Valérie Bercier
- Institut Curie, PSL Research University, Inserm U934, CNRS UMR3215, Paris, France.,Laboratory of Neurobiology, Center for Brain and Disease Research, Research Group Experimental Neurology, Department of Neurosciences, VIB-KU Leuven, Leuven, Belgium
| | - Marion Rosello
- Institut Curie, PSL Research University, Inserm U934, CNRS UMR3215, Paris, France
| | - Filippo Del Bene
- Institut Curie, PSL Research University, Inserm U934, CNRS UMR3215, Paris, France
| | - Céline Revenu
- Institut Curie, PSL Research University, Inserm U934, CNRS UMR3215, Paris, France
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17
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Manipulating Neuronal Activity in the Developing Zebrafish Spinal Cord to Investigate Adaptive Myelination. Methods Mol Biol 2019; 1936:211-225. [PMID: 30820901 DOI: 10.1007/978-1-4939-9072-6_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
In the central nervous system, oligodendrocyte-lineage cells and myelination can adapt to physiological brain activity. Since myelin can in turn regulate neuronal function, such "adaptive" myelination has been proposed as a form of nervous system plasticity, implicated in learning and cognition. The molecular and cellular mechanisms underlying adaptive myelination and its functional consequences remain to be fully defined, partly because it remains challenging to manipulate activity and monitor myelination over time in vivo at single-cell resolution, in a model that would also allow examination of the functional output of individual neurons and circuits. Here, we describe a workflow to manipulate neuronal activity and to assess oligodendrocyte-lineage cell dynamics and myelination in larval zebrafish, a vertebrate animal model that is ideal for live imaging and amenable to genetic discovery, and that has well-characterized neuronal circuits with myelinated axons.
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18
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Wanner AA, Vishwanathan A. Methods for Mapping Neuronal Activity to Synaptic Connectivity: Lessons From Larval Zebrafish. Front Neural Circuits 2018; 12:89. [PMID: 30410437 PMCID: PMC6209671 DOI: 10.3389/fncir.2018.00089] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 09/28/2018] [Indexed: 12/29/2022] Open
Abstract
For a mechanistic understanding of neuronal circuits in the brain, a detailed description of information flow is necessary. Thereby it is crucial to link neuron function to the underlying circuit structure. Multiphoton calcium imaging is the standard technique to record the activity of hundreds of neurons simultaneously. Similarly, recent advances in high-throughput electron microscopy techniques allow for the reconstruction of synaptic resolution wiring diagrams. These two methods can be combined to study both function and structure in the same specimen. Due to its small size and optical transparency, the larval zebrafish brain is one of the very few vertebrate systems where both, activity and connectivity of all neurons from entire, anatomically defined brain regions, can be analyzed. Here, we describe different methods and the tools required for combining multiphoton microscopy with dense circuit reconstruction from electron microscopy stacks of entire brain regions in the larval zebrafish.
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Affiliation(s)
- Adrian A Wanner
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, United States
| | - Ashwin Vishwanathan
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, United States
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19
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Rich A. Improved Imaging of Zebrafish Motility. Neurogastroenterol Motil 2018; 30:e13435. [PMID: 30240125 PMCID: PMC6152886 DOI: 10.1111/nmo.13435] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 07/06/2018] [Accepted: 06/30/2018] [Indexed: 12/12/2022]
Abstract
Zebrafish larvae are transparent and the entire gastrointestinal (GI) tract is easily visualized. Application of a new image analysis technique is reported in this issue of Neurogastroenterology and Motility (Neurogastroenterol Motil., 2018, volume 30, e13351). The technique quantifies movement in images collected in a timed sequence, and characterizes smooth muscle contractions based on contraction distance and frequency. The technique also reports the contraction amplitude, or the distance moved. This technique, and current spatiotemporal mapping techniques, are essential tools enabling characterization of GI motility patterns in intact physiological settings. Advances and development of transgenic zebrafish that lack pigmentation, with calcium reporters expressed in specific cell types, or with inactivation of specific genes contribute to our understanding of the generation, and regulation of GI motility at the molecular, cellular, and systemic level. Finally, development of chambers that immobilize zebrafish larvae for long-duration imaging will contribute to our technique toolbox, and will provide an increased experimental throughput.
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Affiliation(s)
- Adam Rich
- The College at Brockport, SUNY, 350 New Campus Drive, Brockport, NY 14420 USA, Telephone: 585-395-5740
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20
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Integrative whole-brain neuroscience in larval zebrafish. Curr Opin Neurobiol 2018; 50:136-145. [PMID: 29486425 DOI: 10.1016/j.conb.2018.02.004] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 01/23/2018] [Accepted: 02/04/2018] [Indexed: 11/22/2022]
Abstract
Due to their small size and transparency, zebrafish larvae are amenable to a range of fluorescence microscopy techniques. With the development of sensitive genetically encoded calcium indicators, this has extended to the whole-brain imaging of neural activity with cellular resolution. This technique has been used to study brain-wide population dynamics accompanying sensory processing and sensorimotor transformations, and has spurred the development of innovative closed-loop behavioral paradigms in which stimulus-response relationships can be studied. More recently, microscopes have been developed that allow whole-brain calcium imaging in freely swimming and behaving larvae. In this review, we highlight the technologies underlying whole-brain functional imaging in zebrafish, provide examples of the sensory and motor processes that have been studied with this technique, and discuss the need to merge data from whole-brain functional imaging studies with neurochemical and anatomical information to develop holistic models of functional neural circuits.
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21
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Legradi JB, Di Paolo C, Kraak MHS, van der Geest HG, Schymanski EL, Williams AJ, Dingemans MML, Massei R, Brack W, Cousin X, Begout ML, van der Oost R, Carion A, Suarez-Ulloa V, Silvestre F, Escher BI, Engwall M, Nilén G, Keiter SH, Pollet D, Waldmann P, Kienle C, Werner I, Haigis AC, Knapen D, Vergauwen L, Spehr M, Schulz W, Busch W, Leuthold D, Scholz S, vom Berg CM, Basu N, Murphy CA, Lampert A, Kuckelkorn J, Grummt T, Hollert H. An ecotoxicological view on neurotoxicity assessment. ENVIRONMENTAL SCIENCES EUROPE 2018; 30:46. [PMID: 30595996 PMCID: PMC6292971 DOI: 10.1186/s12302-018-0173-x] [Citation(s) in RCA: 139] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 10/31/2018] [Indexed: 05/04/2023]
Abstract
The numbers of potential neurotoxicants in the environment are raising and pose a great risk for humans and the environment. Currently neurotoxicity assessment is mostly performed to predict and prevent harm to human populations. Despite all the efforts invested in the last years in developing novel in vitro or in silico test systems, in vivo tests with rodents are still the only accepted test for neurotoxicity risk assessment in Europe. Despite an increasing number of reports of species showing altered behaviour, neurotoxicity assessment for species in the environment is not required and therefore mostly not performed. Considering the increasing numbers of environmental contaminants with potential neurotoxic potential, eco-neurotoxicity should be also considered in risk assessment. In order to do so novel test systems are needed that can cope with species differences within ecosystems. In the field, online-biomonitoring systems using behavioural information could be used to detect neurotoxic effects and effect-directed analyses could be applied to identify the neurotoxicants causing the effect. Additionally, toxic pressure calculations in combination with mixture modelling could use environmental chemical monitoring data to predict adverse effects and prioritize pollutants for laboratory testing. Cheminformatics based on computational toxicological data from in vitro and in vivo studies could help to identify potential neurotoxicants. An array of in vitro assays covering different modes of action could be applied to screen compounds for neurotoxicity. The selection of in vitro assays could be guided by AOPs relevant for eco-neurotoxicity. In order to be able to perform risk assessment for eco-neurotoxicity, methods need to focus on the most sensitive species in an ecosystem. A test battery using species from different trophic levels might be the best approach. To implement eco-neurotoxicity assessment into European risk assessment, cheminformatics and in vitro screening tests could be used as first approach to identify eco-neurotoxic pollutants. In a second step, a small species test battery could be applied to assess the risks of ecosystems.
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Affiliation(s)
- J. B. Legradi
- Institute for Environmental Research, Department of Ecosystem Analysis, ABBt–Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
- Environment and Health, VU University, 1081 HV Amsterdam, The Netherlands
| | - C. Di Paolo
- Institute for Environmental Research, Department of Ecosystem Analysis, ABBt–Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - M. H. S. Kraak
- FAME-Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, P.O. Box 94248, 1090 GE Amsterdam, The Netherlands
| | - H. G. van der Geest
- FAME-Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, P.O. Box 94248, 1090 GE Amsterdam, The Netherlands
| | - E. L. Schymanski
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6 Avenue du Swing, 4367 Belvaux, Luxembourg
| | - A. J. Williams
- National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency, 109 T.W. Alexander Dr., Research Triangle Park, NC 27711 USA
| | - M. M. L. Dingemans
- KWR Watercycle Research Institute, Groningenhaven 7, 3433 PE Nieuwegein, The Netherlands
| | - R. Massei
- Department Effect-Directed Analysis, Helmholtz Centre for Environmental Research-UFZ, Permoserstr. 15, Leipzig, Germany
| | - W. Brack
- Department Effect-Directed Analysis, Helmholtz Centre for Environmental Research-UFZ, Permoserstr. 15, Leipzig, Germany
| | - X. Cousin
- Ifremer, UMR MARBEC, Laboratoire Adaptation et Adaptabilités des Animaux et des Systèmes, Route de Maguelone, 34250 Palavas-les-Flots, France
- INRA, UMR GABI, INRA, AgroParisTech, Domaine de Vilvert, Batiment 231, 78350 Jouy-en-Josas, France
| | - M.-L. Begout
- Ifremer, Laboratoire Ressources Halieutiques, Place Gaby Coll, 17137 L’Houmeau, France
| | - R. van der Oost
- Department of Technology, Research and Engineering, Waternet Institute for the Urban Water Cycle, Amsterdam, The Netherlands
| | - A. Carion
- Laboratory of Evolutionary and Adaptive Physiology, Institute of Life, Earth and Environment, University of Namur, 5000 Namur, Belgium
| | - V. Suarez-Ulloa
- Laboratory of Evolutionary and Adaptive Physiology, Institute of Life, Earth and Environment, University of Namur, 5000 Namur, Belgium
| | - F. Silvestre
- Laboratory of Evolutionary and Adaptive Physiology, Institute of Life, Earth and Environment, University of Namur, 5000 Namur, Belgium
| | - B. I. Escher
- Department of Cell Toxicology, Helmholtz Centre for Environmental Research-UFZ, Permoserstr. 15, 04318 Leipzig, Germany
- Eberhard Karls University Tübingen, Environmental Toxicology, Center for Applied Geosciences, 72074 Tübingen, Germany
| | - M. Engwall
- MTM Research Centre, School of Science and Technology, Örebro University, Fakultetsgatan 1, 70182 Örebro, Sweden
| | - G. Nilén
- MTM Research Centre, School of Science and Technology, Örebro University, Fakultetsgatan 1, 70182 Örebro, Sweden
| | - S. H. Keiter
- MTM Research Centre, School of Science and Technology, Örebro University, Fakultetsgatan 1, 70182 Örebro, Sweden
| | - D. Pollet
- Faculty of Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, Stephanstrasse 7, 64295 Darmstadt, Germany
| | - P. Waldmann
- Faculty of Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, Stephanstrasse 7, 64295 Darmstadt, Germany
| | - C. Kienle
- Swiss Centre for Applied Ecotoxicology Eawag-EPFL, Überlandstrasse 133, 8600 Dübendorf, Switzerland
| | - I. Werner
- Swiss Centre for Applied Ecotoxicology Eawag-EPFL, Überlandstrasse 133, 8600 Dübendorf, Switzerland
| | - A.-C. Haigis
- Institute for Environmental Research, Department of Ecosystem Analysis, ABBt–Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - D. Knapen
- Zebrafishlab, Veterinary Physiology and Biochemistry, University of Antwerp, Wilrijk, Belgium
| | - L. Vergauwen
- Zebrafishlab, Veterinary Physiology and Biochemistry, University of Antwerp, Wilrijk, Belgium
| | - M. Spehr
- Institute for Biology II, Department of Chemosensation, RWTH Aachen University, Aachen, Germany
| | - W. Schulz
- Zweckverband Landeswasserversorgung, Langenau, Germany
| | - W. Busch
- Department of Bioanalytical Ecotoxicology, UFZ–Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - D. Leuthold
- Department of Bioanalytical Ecotoxicology, UFZ–Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - S. Scholz
- Department of Bioanalytical Ecotoxicology, UFZ–Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - C. M. vom Berg
- Department of Environmental Toxicology, Swiss Federal Institute of Aquatic Science and Technology, Eawag, Dübendorf, 8600 Switzerland
| | - N. Basu
- Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, Canada
| | - C. A. Murphy
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, USA
| | - A. Lampert
- Institute of Physiology (Neurophysiology), Aachen, Germany
| | - J. Kuckelkorn
- Section Toxicology of Drinking Water and Swimming Pool Water, Federal Environment Agency (UBA), Heinrich-Heine-Str. 12, 08645 Bad Elster, Germany
| | - T. Grummt
- Section Toxicology of Drinking Water and Swimming Pool Water, Federal Environment Agency (UBA), Heinrich-Heine-Str. 12, 08645 Bad Elster, Germany
| | - H. Hollert
- Institute for Environmental Research, Department of Ecosystem Analysis, ABBt–Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
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22
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Berg RW. Neuronal Population Activity in Spinal Motor Circuits: Greater Than the Sum of Its Parts. Front Neural Circuits 2017; 11:103. [PMID: 29311842 PMCID: PMC5742103 DOI: 10.3389/fncir.2017.00103] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Accepted: 11/29/2017] [Indexed: 11/27/2022] Open
Abstract
The core elements of stereotypical movements such as locomotion, scratching and breathing are generated by networks in the lower brainstem and the spinal cord. Ensemble activities in spinal motor networks had until recently been merely a black box, but with the emergence of ultra-thin Silicon multi-electrode technology it was possible to reveal the spiking activity of larger parts of the network. A series of experiments revealed unexpected features of spinal networks, such as multiple spiking regimes and lognormal firing rate distributions. The lognormality renders the widespread idea of a typical firing rate ± standard deviation an ill-suited description, and therefore these findings define a new arithmetic of motor networks. Focusing on the population activity behind motor pattern generation this review summarizes this advance and discusses its implications.
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Affiliation(s)
- Rune W. Berg
- Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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23
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Abstract
Fluorescent protein-based biosensors are indispensable molecular tools for life science research. The invention and development of high-fidelity biosensors for a particular molecule or molecular event often catalyze important scientific breakthroughs. Understanding the structural and functional organization of brain activities remain a subject for which optical sensors are in desperate need and of growing interest. Here, we review genetically encoded fluorescent sensors for imaging neuronal activities with a focus on the design principles and optimizations of various sensors. New bioluminescent sensors useful for deep-tissue imaging are also discussed. By highlighting the protein engineering efforts and experimental applications of these sensors, we can consequently analyze factors influencing their performance. Finally, we remark on how future developments can fill technological gaps and lead to new discoveries.
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Affiliation(s)
- Zhijie Chen
- California Institute for Quantitative Biosciences, QB3, University of California, Berkeley, CA 94720, USA
| | - Tan M. Truong
- Center for Membrane and Cell Physiology, and Biomedical Sciences (BIMS) Graduate Program, University of Virginia, Charlottesville, VA 22908, USA
| | - Hui-wang Ai
- Center for Membrane and Cell Physiology, and Biomedical Sciences (BIMS) Graduate Program, University of Virginia, Charlottesville, VA 22908, USA
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
- Correspondence:
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24
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Affiliation(s)
- Michael B. Orger
- Champalimaud Research, Champalimaud Foundation, 1400-038 Lisbon, Portugal;,
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25
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Abstract
In the last 30 years, the zebrafish has become a widely used model organism for research on vertebrate development and disease. Through a powerful combination of genetics and experimental embryology, significant inroads have been made into the regulation of embryonic axis formation, organogenesis, and the development of neural networks. Research with this model has also expanded into other areas, including the genetic regulation of aging, regeneration, and animal behavior. Zebrafish are a popular model because of the ease with which they can be maintained, their small size and low cost, the ability to obtain hundreds of embryos on a daily basis, and the accessibility, translucency, and rapidity of early developmental stages. This primer describes the swift progress of genetic approaches in zebrafish and highlights recent advances that have led to new insights into vertebrate biology.
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26
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Mapping brain structure and function: cellular resolution, global perspective. J Comp Physiol A Neuroethol Sens Neural Behav Physiol 2017; 203:245-264. [PMID: 28341866 DOI: 10.1007/s00359-017-1163-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 03/01/2017] [Accepted: 03/02/2017] [Indexed: 12/23/2022]
Abstract
A comprehensive understanding of the brain requires analysis, although from a global perspective, with cellular, and even subcellular, resolution. An important step towards this goal involves the establishment of three-dimensional high-resolution brain maps, incorporating brain-wide information about the cells and their connections, as well as the chemical architecture. The progress made in such anatomical brain mapping in recent years has been paralleled by the development of physiological techniques that enable investigators to generate global neural activity maps, also with cellular resolution, while simultaneously recording the organism's behavioral activity. Combination of the high-resolution anatomical and physiological maps, followed by theoretical systems analysis of the deduced network, will offer unprecedented opportunities for a better understanding of how the brain, as a whole, processes sensory information and generates behavior.
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27
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Duboué ER, Halpern ME. Genetic and Transgenic Approaches to Study Zebrafish Brain Asymmetry and Lateralized Behavior. LATERALIZED BRAIN FUNCTIONS 2017. [DOI: 10.1007/978-1-4939-6725-4_17] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
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28
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Abstract
Sensing and responding to our environment requires functional neurons that act in concert. Neuronal cell loss resulting from degenerative diseases cannot be replaced in humans, causing a functional impairment to integrate and/or respond to sensory cues. In contrast, zebrafish (Danio rerio) possess an endogenous capacity to regenerate lost neurons. Here, we will focus on the processes that lead to neuronal regeneration in the zebrafish retina. Dying retinal neurons release a damage signal, tumor necrosis factor α, which induces the resident radial glia, the Müller glia, to reprogram and re-enter the cell cycle. The Müller glia divide asymmetrically to produce a Müller glia that exits the cell cycle and a neuronal progenitor cell. The arising neuronal progenitor cells undergo several rounds of cell divisions before they migrate to the site of damage to differentiate into the neuronal cell types that were lost. Molecular and immunohistochemical studies have predominantly provided insight into the mechanisms that regulate retinal regeneration. However, many processes during retinal regeneration are dynamic and require live-cell imaging to fully discern the underlying mechanisms. Recently, a multiphoton imaging approach of adult zebrafish retinal cultures was developed. We will discuss the use of live-cell imaging, the currently available tools and those that need to be developed to advance our knowledge on major open questions in the field of retinal regeneration.
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Affiliation(s)
- Manuela Lahne
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - David R Hyde
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
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29
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Orger MB, Portugues R. Correlating Whole Brain Neural Activity with Behavior in Head-Fixed Larval Zebrafish. Methods Mol Biol 2016; 1451:307-320. [PMID: 27464817 DOI: 10.1007/978-1-4939-3771-4_21] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We present a protocol to combine behavioral recording and imaging using 2-photon laser-scanning microscopy in head-fixed larval zebrafish that express a genetically encoded calcium indicator. The steps involve restraining the larva in agarose, setting up optics that allow projection of a visual stimulus and infrared illumination to monitor behavior, and analysis of the neuronal and behavioral data.
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Affiliation(s)
- Michael B Orger
- Champalimaud Neuroscience Programme, Champalimaud Centre for the Unknown, Avenida Brasília, Doca de Pedrouços, Lisbon, 1400-038, Portugal
| | - Ruben Portugues
- Max Planck Institute of Neurobiology, Sensorimotor Control Research Group, Am Klopferspitz 18, Martinsried, 82152, Germany.
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30
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Groneberg AH, Herget U, Ryu S, De Marco RJ. Positive taxis and sustained responsiveness to water motions in larval zebrafish. Front Neural Circuits 2015; 9:9. [PMID: 25798089 PMCID: PMC4351627 DOI: 10.3389/fncir.2015.00009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 02/16/2015] [Indexed: 01/08/2023] Open
Abstract
Larval zebrafish (Danio rerio) have become favored subjects for studying the neural bases of behavior. Here, we report a highly stereotyped response of zebrafish larvae to hydrodynamic stimuli. It involves positive taxis, motion damping and sustained responsiveness to flows derived from local, non-stressful water motions. The response depends on the lateral line and has a high sensitivity to stimulus frequency and strength, sensory background and rearing conditions—also encompassing increased threshold levels of response to parallel input. The results show that zebrafish larvae can use near-field detection to locate sources of minute water motions, and offer a unique handle for analyses of hydrodynamic sensing, sensory responsiveness and arousal with accurate control of stimulus properties.
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Affiliation(s)
- Antonia H Groneberg
- Developmental Genetics of the Nervous System, Max Planck Institute for Medical Research Heidelberg, Germany
| | - Ulrich Herget
- Developmental Genetics of the Nervous System, Max Planck Institute for Medical Research Heidelberg, Germany
| | - Soojin Ryu
- Developmental Genetics of the Nervous System, Max Planck Institute for Medical Research Heidelberg, Germany
| | - Rodrigo J De Marco
- Developmental Genetics of the Nervous System, Max Planck Institute for Medical Research Heidelberg, Germany
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31
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Grone BP, Baraban SC. Animal models in epilepsy research: legacies and new directions. Nat Neurosci 2015; 18:339-43. [PMID: 25710835 DOI: 10.1038/nn.3934] [Citation(s) in RCA: 168] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 12/21/2014] [Indexed: 12/16/2022]
Abstract
Human epilepsies encompass a wide variety of clinical, behavioral and electrical manifestations. Correspondingly, studies of this disease in nonhuman animals have brought forward an equally wide array of animal models; that is, species and acute or chronic seizure induction protocols. Epilepsy research has a long history of comparative anatomical and physiological studies on a range of mostly mammalian species. Nonetheless, a relatively limited number of rodent models have emerged as the primary choices for most investigations. In many cases, these animal models are selected on the basis of convenience or tradition, although technical or experimental rationale does, and should, factor into these decisions. More complex mammalian brains and genetic model organisms including zebrafish have been studied less, but offer substantial advantages that are becoming widely recognized.
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Affiliation(s)
- Brian P Grone
- Department of Neurological Surgery, University of California, San Francisco, California, USA
| | - Scott C Baraban
- Department of Neurological Surgery, University of California, San Francisco, California, USA
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32
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Bruneel B, Mathä M, Paesen R, Ameloot M, Weninger WJ, Huysseune A. Imaging the zebrafish dentition: from traditional approaches to emerging technologies. Zebrafish 2015; 12:1-10. [PMID: 25560992 PMCID: PMC4298156 DOI: 10.1089/zeb.2014.0980] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The zebrafish, a model organism for which a plethora of molecular and genetic techniques exists, has a lifelong replacing dentition of 22 pharyngeal teeth. This is in contrast to the mouse, which is the key organism in dental research but whose teeth are never replaced. Employing the zebrafish as the main organism to elucidate the mechanisms of continuous tooth replacement, however, poses at least one major problem, related to the fact that all teeth are located deep inside the body. Investigating tooth replacement thus relies on conventional histological methods, which are often laborious, time-consuming and can cause tissue deformations. In this review, we investigate the advantages and limitations of adapting current visualization techniques to dental research in zebrafish. We discuss techniques for fast sectioning, such as vibratome sectioning and high-resolution episcopic microscopy, and methods for in toto visualization, such as Alizarin red staining, micro-computed tomography, and optical projection tomography. Techniques for in vivo imaging, such as two-photon excitation fluorescence and second harmonic generation microscopy, are also covered. Finally, the possibilities of light sheet microscopy are addressed.
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Affiliation(s)
- Bart Bruneel
- Evolutionary Developmental Biology, Ghent University, Ghent, Belgium
| | - Markus Mathä
- IMG Centre for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Rik Paesen
- BIOMED, University Hasselt and Transnational University Limburg, Diepenbeek, Belgium
| | - Marcel Ameloot
- BIOMED, University Hasselt and Transnational University Limburg, Diepenbeek, Belgium
| | - Wolfgang J. Weninger
- IMG Centre for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Ann Huysseune
- Evolutionary Developmental Biology, Ghent University, Ghent, Belgium
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Feierstein CE, Portugues R, Orger MB. Seeing the whole picture: A comprehensive imaging approach to functional mapping of circuits in behaving zebrafish. Neuroscience 2014; 296:26-38. [PMID: 25433239 DOI: 10.1016/j.neuroscience.2014.11.046] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 11/07/2014] [Accepted: 11/19/2014] [Indexed: 11/17/2022]
Abstract
In recent years, the zebrafish has emerged as an appealing model system to tackle questions relating to the neural circuit basis of behavior. This can be attributed not just to the growing use of genetically tractable model organisms, but also in large part to the rapid advances in optical techniques for neuroscience, which are ideally suited for application to the small, transparent brain of the larval fish. Many characteristic features of vertebrate brains, from gross anatomy down to particular circuit motifs and cell-types, as well as conserved behaviors, can be found in zebrafish even just a few days post fertilization, and, at this early stage, the physical size of the brain makes it possible to analyze neural activity in a comprehensive fashion. In a recent study, we used a systematic and unbiased imaging method to record the pattern of activity dynamics throughout the whole brain of larval zebrafish during a simple visual behavior, the optokinetic response (OKR). This approach revealed the broadly distributed network of neurons that were active during the behavior and provided insights into the fine-scale functional architecture in the brain, inter-individual variability, and the spatial distribution of behaviorally relevant signals. Combined with mapping anatomical and functional connectivity, targeted electrophysiological recordings, and genetic labeling of specific populations, this comprehensive approach in zebrafish provides an unparalleled opportunity to study complete circuits in a behaving vertebrate animal.
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Affiliation(s)
- C E Feierstein
- Champalimaud Neuroscience Programme, Champalimaud Centre for the Unknown, Avenida Brasília, Doca de Pedrouços, Lisbon 1400-038, Portugal
| | - R Portugues
- Max Planck Institute of Neurobiology, Am Klopferspitz 18, 82152, Germany
| | - M B Orger
- Champalimaud Neuroscience Programme, Champalimaud Centre for the Unknown, Avenida Brasília, Doca de Pedrouços, Lisbon 1400-038, Portugal.
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Prevedel R, Yoon YG, Hoffmann M, Pak N, Wetzstein G, Kato S, Schrödel T, Raskar R, Zimmer M, Boyden ES, Vaziri A. Simultaneous whole-animal 3D imaging of neuronal activity using light-field microscopy. Nat Methods 2014; 11:727-730. [PMID: 24836920 PMCID: PMC4100252 DOI: 10.1038/nmeth.2964] [Citation(s) in RCA: 388] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Accepted: 04/22/2014] [Indexed: 12/20/2022]
Abstract
High-speed, large-scale three-dimensional (3D) imaging of neuronal activity poses a major challenge in neuroscience. Here we demonstrate simultaneous functional imaging of neuronal activity at single-neuron resolution in an entire Caenorhabditis elegans and in larval zebrafish brain. Our technique captures the dynamics of spiking neurons in volumes of ∼700 μm × 700 μm × 200 μm at 20 Hz. Its simplicity makes it an attractive tool for high-speed volumetric calcium imaging.
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Affiliation(s)
- Robert Prevedel
- Research Institute of Molecular Pathology, Vienna, Austria
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
- Research Platform Quantum Phenomena & Nanoscale Biological Systems (QuNaBioS), University of Vienna, Austria
| | - Young-Gyu Yoon
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- MIT Media Lab, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - Maximilian Hoffmann
- Research Institute of Molecular Pathology, Vienna, Austria
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
- Research Platform Quantum Phenomena & Nanoscale Biological Systems (QuNaBioS), University of Vienna, Austria
| | - Nikita Pak
- MIT Media Lab, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- Department of Mechanical Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - Gordon Wetzstein
- MIT Media Lab, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - Saul Kato
- Research Institute of Molecular Pathology, Vienna, Austria
| | - Tina Schrödel
- Research Institute of Molecular Pathology, Vienna, Austria
| | - Ramesh Raskar
- MIT Media Lab, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - Manuel Zimmer
- Research Institute of Molecular Pathology, Vienna, Austria
| | - Edward S Boyden
- MIT Media Lab, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology(MIT), Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- McGovern Institute, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - Alipasha Vaziri
- Research Institute of Molecular Pathology, Vienna, Austria
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
- Research Platform Quantum Phenomena & Nanoscale Biological Systems (QuNaBioS), University of Vienna, Austria
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Portugues R, Feierstein CE, Engert F, Orger MB. Whole-brain activity maps reveal stereotyped, distributed networks for visuomotor behavior. Neuron 2014; 81:1328-1343. [PMID: 24656252 DOI: 10.1016/j.neuron.2014.01.019] [Citation(s) in RCA: 177] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/24/2013] [Indexed: 02/04/2023]
Abstract
Most behaviors, even simple innate reflexes, are mediated by circuits of neurons spanning areas throughout the brain. However, in most cases, the distribution and dynamics of firing patterns of these neurons during behavior are not known. We imaged activity, with cellular resolution, throughout the whole brains of zebrafish performing the optokinetic response. We found a sparse, broadly distributed network that has an elaborate but ordered pattern, with a bilaterally symmetrical organization. Activity patterns fell into distinct clusters reflecting sensory and motor processing. By correlating neuronal responses with an array of sensory and motor variables, we find that the network can be clearly divided into distinct functional modules. Comparing aligned data from multiple fish, we find that the spatiotemporal activity dynamics and functional organization are highly stereotyped across individuals. These experiments systematically reveal the functional architecture of neural circuits underlying a sensorimotor behavior in a vertebrate brain.
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Affiliation(s)
- Ruben Portugues
- Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
| | - Claudia E Feierstein
- Champalimaud Neuroscience Programme, Avenida Brasília, Doca de Pedrouços, Lisbon 1400-038, Portugal
| | - Florian Engert
- Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
| | - Michael B Orger
- Champalimaud Neuroscience Programme, Avenida Brasília, Doca de Pedrouços, Lisbon 1400-038, Portugal.
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Functional Architecture of an Optic Flow-Responsive Area that Drives Horizontal Eye Movements in Zebrafish. Neuron 2014; 81:1344-1359. [DOI: 10.1016/j.neuron.2014.02.043] [Citation(s) in RCA: 122] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/18/2014] [Indexed: 02/03/2023]
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Hiroi M, Ohkura M, Nakai J, Masuda N, Hashimoto K, Inoue K, Fiala A, Tabata T. Principal component analysis of odor coding at the level of third-order olfactory neurons in Drosophila. Genes Cells 2013; 18:1070-81. [PMID: 24118654 DOI: 10.1111/gtc.12094] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Accepted: 08/23/2013] [Indexed: 01/26/2023]
Abstract
Olfactory information in Drosophila is conveyed by projection neurons from olfactory sensory neurons to Kenyon cells (KCs) in the mushroom body (MB). A subset of KCs responds to a given odor molecule, and the combination of these KCs represents a part of the neuronal olfactory code. KCs are also thought to function as coincidence detectors for memory formation, associating odor information with a coincident punishment or reward stimulus. Associative conditioning has been shown to modify KC output. This plasticity occurs in the vertical lobes of MBs containing α/α' branches of KCs, which is shown by measuring the average Ca(2+) levels in the branch of each lobe. We devised a method to quantitatively describe the population activity patterns recorded from axons of >1000 KCs at the α/α' branches using two-photon Ca(2+) imaging. Principal component analysis of the population activity patterns clearly differentiated the responses to distinct odors.
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Affiliation(s)
- Makoto Hiroi
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-0032, Japan
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