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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] [What about the content of this article? (0)] [Affiliation(s)] [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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2
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Lalonde RL, Wells HH, Kemmler CL, Nieuwenhuize S, Lerma R, Burger A, Mosimann C. pIGLET: Safe harbor landing sites for reproducible and efficient transgenesis in zebrafish. bioRxiv 2023:2023.12.08.570868. [PMID: 38106217 PMCID: PMC10723424 DOI: 10.1101/2023.12.08.570868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Standard methods for transgenesis in zebrafish depend on random transgene integration into the genome followed by resource-intensive screening and validation. Targeted vector integration into validated genomic loci using phiC31 integrase-based attP/attB recombination has transformed mouse and Drosophila transgenesis. However, while the phiC31 system functions in zebrafish, validated loci carrying attP-based landing or safe harbor sites suitable for universal transgenesis applications in zebrafish have not been established. Here, using CRISPR-Cas9, we converted two well-validated single insertion Tol2-based zebrafish transgenes with long-standing genetic stability into two attP landing sites, called phiC31 Integrase Genomic Loci Engineered for Transgenesis (pIGLET). Generating fluorescent reporters, loxP-based Switch lines, CreERT2 drivers, and gene-regulatory variant reporters in the pIGLET14a and pIGLET24b landing site alleles, we document their suitability for transgenesis applications across cell types and developmental stages. For both landing sites, we routinely achieve 25-50% germline transmission of targeted transgene integrations, drastically reducing the number of required animals and necessary resources to generate individual transgenic lines. We document that phiC31 integrase-based transgenesis into pIGLET14a and pIGLET24b reproducibly results in representative reporter expression patterns in injected F0 zebrafish embryos suitable for enhancer discovery and qualitative and quantitative comparison of gene-regulatory element variants. Taken together, our new phiC31 integrase-based transgene landing sites establish reproducible, targeted zebrafish transgenesis for numerous applications while greatly reducing the workload of generating new transgenic zebrafish lines.
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Affiliation(s)
- Robert L. Lalonde
- University of Colorado, School of Medicine, Anschutz Medical Campus, Department of Pediatrics, Section of Developmental Biology, 12801 E 17th Avenue, Aurora, CO 80045, USA
| | - Harrison H. Wells
- University of Colorado, School of Medicine, Anschutz Medical Campus, Department of Pediatrics, Section of Developmental Biology, 12801 E 17th Avenue, Aurora, CO 80045, USA
| | - Cassie L. Kemmler
- University of Colorado, School of Medicine, Anschutz Medical Campus, Department of Pediatrics, Section of Developmental Biology, 12801 E 17th Avenue, Aurora, CO 80045, USA
| | - Susan Nieuwenhuize
- University of Colorado, School of Medicine, Anschutz Medical Campus, Department of Pediatrics, Section of Developmental Biology, 12801 E 17th Avenue, Aurora, CO 80045, USA
| | - Raymundo Lerma
- University of Colorado, School of Medicine, Anschutz Medical Campus, Department of Pediatrics, Section of Developmental Biology, 12801 E 17th Avenue, Aurora, CO 80045, USA
| | - Alexa Burger
- University of Colorado, School of Medicine, Anschutz Medical Campus, Department of Pediatrics, Section of Developmental Biology, 12801 E 17th Avenue, Aurora, CO 80045, USA
| | - Christian Mosimann
- University of Colorado, School of Medicine, Anschutz Medical Campus, Department of Pediatrics, Section of Developmental Biology, 12801 E 17th Avenue, Aurora, CO 80045, USA
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Collier AD, Abdulai AR, Leibowitz SF. Utility of the Zebrafish Model for Studying Neuronal and Behavioral Disturbances Induced by Embryonic Exposure to Alcohol, Nicotine, and Cannabis. Cells 2023; 12:2505. [PMID: 37887349 PMCID: PMC10605371 DOI: 10.3390/cells12202505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 09/28/2023] [Accepted: 09/28/2023] [Indexed: 10/28/2023] Open
Abstract
It is estimated that 5% of pregnant women consume drugs of abuse during pregnancy. Clinical research suggests that intake of drugs during pregnancy, such as alcohol, nicotine and cannabis, disturbs the development of neuronal systems in the offspring, in association with behavioral disturbances early in life and an increased risk of developing drug use disorders. After briefly summarizing evidence in rodents, this review focuses on the zebrafish model and its inherent advantages for studying the effects of embryonic exposure to drugs of abuse on behavioral and neuronal development, with an emphasis on neuropeptides known to promote drug-related behaviors. In addition to stimulating the expression and density of peptide neurons, as in rodents, zebrafish studies demonstrate that embryonic drug exposure has marked effects on the migration, morphology, projections, anatomical location, and peptide co-expression of these neurons. We also describe studies using advanced methodologies that can be applied in vivo in zebrafish: first, to demonstrate a causal relationship between the drug-induced neuronal and behavioral disturbances and second, to discover underlying molecular mechanisms that mediate these effects. The zebrafish model has great potential for providing important information regarding the development of novel and efficacious therapies for ameliorating the effects of early drug exposure.
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Affiliation(s)
| | | | - Sarah F. Leibowitz
- Laboratory of Behavioral Neurobiology, The Rockefeller University, New York, NY 10065, USA
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Kemmler CL, Smolikova J, Moran HR, Mannion BJ, Knapp D, Lim F, Czarkwiani A, Hermosilla Aguayo V, Rapp V, Fitch OE, Bötschi S, Selleri L, Farley E, Braasch I, Yun M, Visel A, Osterwalder M, Mosimann C, Kozmik Z, Burger A. Conserved enhancers control notochord expression of vertebrate Brachyury. Nat Commun 2023; 14:6594. [PMID: 37852970 PMCID: PMC10584899 DOI: 10.1038/s41467-023-42151-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 09/29/2023] [Indexed: 10/20/2023] Open
Abstract
The cell type-specific expression of key transcription factors is central to development and disease. Brachyury/T/TBXT is a major transcription factor for gastrulation, tailbud patterning, and notochord formation; however, how its expression is controlled in the mammalian notochord has remained elusive. Here, we identify the complement of notochord-specific enhancers in the mammalian Brachyury/T/TBXT gene. Using transgenic assays in zebrafish, axolotl, and mouse, we discover three conserved Brachyury-controlling notochord enhancers, T3, C, and I, in human, mouse, and marsupial genomes. Acting as Brachyury-responsive, auto-regulatory shadow enhancers, in cis deletion of all three enhancers in mouse abolishes Brachyury/T/Tbxt expression selectively in the notochord, causing specific trunk and neural tube defects without gastrulation or tailbud defects. The three Brachyury-driving notochord enhancers are conserved beyond mammals in the brachyury/tbxtb loci of fishes, dating their origin to the last common ancestor of jawed vertebrates. Our data define the vertebrate enhancers for Brachyury/T/TBXTB notochord expression through an auto-regulatory mechanism that conveys robustness and adaptability as ancient basis for axis development.
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Affiliation(s)
- Cassie L Kemmler
- Section of Developmental Biology, Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Jana Smolikova
- Institute of Molecular Genetics of the ASCR, v. v. i., Prague, Czech Republic
| | - Hannah R Moran
- Section of Developmental Biology, Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Brandon J Mannion
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Comparative Biochemistry Program, University of California, Berkeley, CA, 94720, USA
| | - Dunja Knapp
- Technische Universität Dresden, CRTD Center for Regenerative Therapies Dresden, Dresden, Germany
| | - Fabian Lim
- Department of Medicine, Health Sciences, University of California San Diego, La Jolla, CA, USA
- Department of Molecular Biology, Biological Sciences, University of California San Diego, La Jolla, CA, USA
- Biological Sciences Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Anna Czarkwiani
- Technische Universität Dresden, CRTD Center for Regenerative Therapies Dresden, Dresden, Germany
| | - Viviana Hermosilla Aguayo
- Program in Craniofacial Biology, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Department of Orofacial Sciences, University of California San Francisco, San Francisco, CA, USA
- Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
| | - Vincent Rapp
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Olivia E Fitch
- Department of Integrative Biology and Ecology, Evolution and Behavior Program, Michigan State University, East Lansing, MI, USA
| | - Seraina Bötschi
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Licia Selleri
- Program in Craniofacial Biology, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Department of Orofacial Sciences, University of California San Francisco, San Francisco, CA, USA
- Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
| | - Emma Farley
- Department of Medicine, Health Sciences, University of California San Diego, La Jolla, CA, USA
- Department of Molecular Biology, Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Ingo Braasch
- Department of Integrative Biology and Ecology, Evolution and Behavior Program, Michigan State University, East Lansing, MI, USA
| | - Maximina Yun
- Technische Universität Dresden, CRTD Center for Regenerative Therapies Dresden, Dresden, Germany
- Max Planck Institute for Molecular Cell Biology and Genetics, Dresden, Germany
- Cluster of Excellence Physics of Life, Technische Universität Dresden, Dresden, Germany
| | - Axel Visel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- School of Natural Sciences, University of California Merced, Merced, CA, USA
| | - Marco Osterwalder
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
- Department of Cardiology, Bern University Hospital, Bern, Switzerland
| | - Christian Mosimann
- Section of Developmental Biology, Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Zbynek Kozmik
- Institute of Molecular Genetics of the ASCR, v. v. i., Prague, Czech Republic.
| | - Alexa Burger
- Section of Developmental Biology, Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
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Yakovlev MA, Liang K, Zaino CR, Vanselow DJ, Sugarman AL, Lin AY, La Riviere PJ, Zheng Y, Silverman JD, Leichty JC, Huang SX, Cheng KC. Quantitative Geometric Modeling of Blood Cells from X-ray Histotomograms of Whole Zebrafish Larvae. bioRxiv 2023:2023.05.23.541939. [PMID: 37292910 PMCID: PMC10245913 DOI: 10.1101/2023.05.23.541939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Tissue phenotyping is foundational to understanding and assessing the cellular aspects of disease in organismal context and an important adjunct to molecular studies in the dissection of gene function, chemical effects, and disease. As a first step toward computational tissue phenotyping, we explore the potential of cellular phenotyping from 3-Dimensional (3D), 0.74 µm isotropic voxel resolution, whole zebrafish larval images derived from X-ray histotomography, a form of micro-CT customized for histopathology. As proof of principle towards computational tissue phenotyping of cells, we created a semi-automated mechanism for the segmentation of blood cells in the vascular spaces of zebrafish larvae, followed by modeling and extraction of quantitative geometric parameters. Manually segmented cells were used to train a random forest classifier for blood cells, enabling the use of a generalized cellular segmentation algorithm for the accurate segmentation of blood cells. These models were used to create an automated data segmentation and analysis pipeline to guide the steps in a 3D workflow including blood cell region prediction, cell boundary extraction, and statistical characterization of 3D geometric and cytological features. We were able to distinguish blood cells at two stages in development (4- and 5-days-post-fertilization) and wild-type vs. polA2 huli hutu ( hht ) mutants. The application of geometric modeling across cell types to and across organisms and sample types may comprise a valuable foundation for computational phenotyping that is more open, informative, rapid, objective, and reproducible.
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Kemmler CL, Smolikova J, Moran HR, Mannion BJ, Knapp D, Lim F, Czarkwiani A, Hermosilla Aguayo V, Rapp V, Fitch OE, Bötschi S, Selleri L, Farley E, Braasch I, Yun M, Visel A, Osterwalder M, Mosimann C, Kozmik Z, Burger A. Conserved enhancer logic controls the notochord expression of vertebrate Brachyury. bioRxiv 2023:2023.04.20.536761. [PMID: 37131681 PMCID: PMC10153258 DOI: 10.1101/2023.04.20.536761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The cell type-specific expression of key transcription factors is central to development. Brachyury/T/TBXT is a major transcription factor for gastrulation, tailbud patterning, and notochord formation; however, how its expression is controlled in the mammalian notochord has remained elusive. Here, we identify the complement of notochord-specific enhancers in the mammalian Brachyury/T/TBXT gene. Using transgenic assays in zebrafish, axolotl, and mouse, we discover three Brachyury-controlling notochord enhancers T3, C, and I in human, mouse, and marsupial genomes. Acting as Brachyury-responsive, auto-regulatory shadow enhancers, deletion of all three enhancers in mouse abolishes Brachyury/T expression selectively in the notochord, causing specific trunk and neural tube defects without gastrulation or tailbud defects. Sequence and functional conservation of Brachyury-driving notochord enhancers with the brachyury/tbxtb loci from diverse lineages of fishes dates their origin to the last common ancestor of jawed vertebrates. Our data define the enhancers for Brachyury/T/TBXTB notochord expression as ancient mechanism in axis development.
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Affiliation(s)
- Cassie L. Kemmler
- Section of Developmental Biology, Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Jana Smolikova
- Institute of Molecular Genetics of the ASCR, v. v. i., Prague, Czech Republic
| | - Hannah R. Moran
- Section of Developmental Biology, Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Brandon J. Mannion
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Comparative Biochemistry Program, University of California, Berkeley, CA 94720, USA
| | - Dunja Knapp
- Technische Universität Dresden, CRTD/Center for Regenerative Therapies Dresden, Dresden, Germany
| | - Fabian Lim
- Department of Medicine, Health Sciences, University of California San Diego, La Jolla, CA, USA
- Department of Molecular Biology, Biological Sciences, University of California San Diego, La Jolla, CA USA
- Biological Sciences Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Anna Czarkwiani
- Technische Universität Dresden, CRTD/Center for Regenerative Therapies Dresden, Dresden, Germany
| | - Viviana Hermosilla Aguayo
- Program in Craniofacial Biology, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Department of Orofacial Sciences, University of California San Francisco, San Francisco, CA, USA
- Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
| | - Vincent Rapp
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Olivia E. Fitch
- Department of Integrative Biology and Ecology, Evolution and Behavior Program, Michigan State University, East Lansing, MI, USA
| | - Seraina Bötschi
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Licia Selleri
- Program in Craniofacial Biology, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Department of Orofacial Sciences, University of California San Francisco, San Francisco, CA, USA
- Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
| | - Emma Farley
- Department of Medicine, Health Sciences, University of California San Diego, La Jolla, CA, USA
- Department of Molecular Biology, Biological Sciences, University of California San Diego, La Jolla, CA USA
| | - Ingo Braasch
- Department of Integrative Biology and Ecology, Evolution and Behavior Program, Michigan State University, East Lansing, MI, USA
| | - Maximina Yun
- Technische Universität Dresden, CRTD/Center for Regenerative Therapies Dresden, Dresden, Germany
- Max Planck Institute for Molecular Cell Biology and Genetics, Dresden, Germany
- Cluster of Excellence Physics of Life, Technische Universität Dresden, Dresden, Germany
| | - Axel Visel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- School of Natural Sciences, University of California Merced, Merced, CA, USA
| | - Marco Osterwalder
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
- Department of Cardiology, Berne University Hospital, Berne, Switzerland
| | - Christian Mosimann
- Section of Developmental Biology, Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Zbynek Kozmik
- Institute of Molecular Genetics of the ASCR, v. v. i., Prague, Czech Republic
| | - Alexa Burger
- Section of Developmental Biology, Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
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