A structural and functional ground plan for neurons in the hindbrain of zebrafish
Open accessAbstract
The vertebrate hindbrain contains various sensory-motor networks controlling movements of the eyes, jaw, head, and body. Here we show that stripes of neurons with shared neurotransmitter phenotype that extend throughout the hindbrain of young zebrafish reflect a broad underlying structural and functional patterning. The neurotransmitter stripes contain cell types with shared gross morphologies and transcription factor markers. Neurons within a stripe are stacked systematically by extent and location of axonal projections, input resistance, and age, and are recruited along the axis of the stripe during behavior. The implication of this pattern is that the many networks in hindbrain are constructed from a series of neuronal components organized into stripes that are ordered from top to bottom according to a neuron's age, structural and functional properties, and behavioral roles. This simple organization probably forms a foundation for the construction of the networks underlying the many behaviors produced by the hindbrain.
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In R7/R8, the former VPNI cells have somata primarily within a medial glutamatergic parasagittal stripe associated with the Alx transcription factor, and the latter with a more lateral GABAergic parasagittal stripe associated with the Abx1b transcription factor.
“In R7/R8, the former were found to have somata primarily within a medial glutamatergic parasagittal stripe associated with the Alx transcription factor and the latter with a more lateral GABAergic parasagittal stripe associated with the Abx1b transcription factor21,95,96.”
From Predicting modular functions and neural coding of behavior from a synaptic wiring diagram (2024) · cites this paper as [96]
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Transparent Adult Zebrafish as a Tool for In Vivo Transplantation Analysis
White, R. M., Sessa, A., Burke, C., Bowman, T., LeBlanc, J., Ceol, C., Bourque, C., Dovey, M., Goessling, W., Burns, C. E., et al. (2008) · Cell Stem Cell · doi:10.1016/j.stem.2007.11.002 · Cited by 1,408 · see citing works
Circuits controlling vertebrate locomotion: moving in a new direction
Goulding, M. (2009) · Nature Reviews Neuroscience · doi:10.1038/nrn2608 · Cited by 777 · see citing works
Kimura, Y., Okamura, Y., & Higashijima, S.-I. (2006) · The Journal of Neuroscience · doi:10.1523/jneurosci.4993-05.2006 · Cited by 302 · see citing works
Self-citationA confocal study of spinal interneurons in living larval zebrafish
Hale, M. E., Ritter, D. A., & Fetcho, J. R. (2001) · Journal of Comparative Neurology · doi:10.1002/cne.1266 · Cited by 203 · see citing works
Self-citationFunctional dissection of circuitry in a neural integrator
Aksay, E., Olasagasti, I., Mensh, B. D., Baker, R., Goldman, M. S., & Tank, D. W. (2007) · Nature Neuroscience · doi:10.1038/nn1877 · Cited by 134 · see citing works
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Ahrens, M. B., Orger, M. B., Robson, D. N., Li, J. M., & Keller, P. J. (2013) · Nature Methods · doi:10.1038/nmeth.2434 · Cited by 1,392 · see citing works
Brain-wide neuronal dynamics during motor adaptation in zebrafish
Ahrens, M. B., Li, J. M., Orger, M. B., Robson, D. N., Schier, A. F., Engert, F., & Portugues, R. (2012) · Nature · doi:10.1038/nature11057 · Cited by 729 · see citing works
Whole-brain activity maps reveal stereotyped, distributed networks for visuomotor behavior
Portugues, R., Feierstein, C. E., Engert, F., & Orger, M. B. (2014) · Neuron · doi:10.1016/j.neuron.2014.01.019 · Cited by 305 · see citing works
Mapping brain activity at scale with cluster computing
Freeman, J., Vladimirov, N., Kawashima, T., Mu, Y., Sofroniew, N. J., Bennett, D. V., Rosen, J., Yang, C.-T., Looger, L. L., & Ahrens, M. B. (2014) · Nature Methods · doi:10.1038/nmeth.3041 · Cited by 299 · see citing works
From Whole-Brain Data to Functional Circuit Models: The Zebrafish Optomotor Response
Naumann, E. A., Fitzgerald, J. E., Dunn, T. W., Rihel, J., Sompolinsky, H., & Engert, F. (2016) · Cell · doi:10.1016/j.cell.2016.10.019 · Cited by 315 · see citing works
Mapping a sensory-motor network onto a structural and functional ground plan in the hindbrain
Koyama, M., Kinkhabwala, A., Satou, C., Higashijima, S.-I., & Fetcho, J. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1012189108 · Cited by 190 · see citing works
Self-citationHindbrain V2a neurons in the excitation of spinal locomotor circuits during zebrafish swimming
Kimura, Y., Satou, C., Fujioka, S., Shoji, W., Umeda, K., Ishizuka, T., Yawo, H., & Higashijima, S.-I. (2013) · Current Biology · doi:10.1016/j.cub.2013.03.066 · Cited by 186 · see citing works
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Visually guided gradation of prey capture movements in larval zebrafish
Patterson, B. W., Abraham, A. O., MacIver, M. A., & McLean, D. L. (2013) · Journal of Experimental Biology · doi:10.1242/jeb.087742 · Cited by 122 · see citing works
Lhx3-Chx10 Reticulospinal Neurons in Locomotor Circuits
Bretzner, F., & Brownstone, R. M. (2013) · The Journal of Neuroscience · doi:10.1523/jneurosci.5231-12.2013 · Cited by 99 · see citing works
Pujala, A., & Koyama, M. (2019) · eLife · doi:10.7554/elife.42135 · Cited by 80 · see citing works
Self-citationWhitening of odor representations by the wiring diagram of the olfactory bulb
Wanner, A. A., & Friedrich, R. W. (2020) · Nature Neuroscience · doi:10.1038/s41593-019-0576-z · Cited by 79 · see citing works
Electron Microscopic Reconstruction of Functionally Identified Cells in a Neural Integrator
Vishwanathan, A., Daie, K., Ramirez, A. D., Lichtman, J. W., Aksay, E. R. F., & Seung, H. S. (2017) · Current Biology · doi:10.1016/j.cub.2017.06.028 · Cited by 74 · see citing works
Carbo-Tano, M., Lapoix, M., Jia, X., Thouvenin, O., Pascucci, M., Auclair, F., Quan, F. B., Albadri, S., Aguda, V., Farouj, Y., et al. (2023) · Nature Neuroscience · doi:10.1038/s41593-023-01418-0 · Cited by 58 · see citing works
Spatial Patterns of Persistent Neural Activity Vary with the Behavioral Context of Short-Term Memory
Daie, K., Goldman, M. S., & Aksay, E. R. F. (2015) · Neuron · doi:10.1016/j.neuron.2015.01.006 · Cited by 42 · see citing works
Ryczko, D., Auclair, F., Cabelguen, J., & Dubuc, R. (2016) · Journal of Comparative Neurology · doi:10.1002/cne.23911 · Cited by 46 · see citing works
A Structural and Genotypic Scaffold Underlying Temporal Integration
Lee, M. M., Arrenberg, A. B., & Aksay, E. R. F. (2015) · The Journal of Neuroscience · doi:10.1523/jneurosci.3045-14.2015 · Cited by 27 · see citing works
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Vishwanathan, A., Sood, A., Wu, J., Ramirez, A. D., Yang, R., Kemnitz, N., Ih, D., Turner, N., Lee, K., Tartavull, I., et al. (2024) · Nature Neuroscience · doi:10.1038/s41593-024-01784-3 · Cited by 25 · see citing works
“…were found to have somata primarily within a medial glutamatergic parasagittal https://doi.org/10.1038/s41593-024-01784-3 stripe associated with the Alx transcription factor and the latter with a more lateral GABAergic parasagittal stripe associated with the Abx1b transcription factor 21,95,96 .”
InfluentialComputational modeling of speed microcircuits in larval zebrafish spinal cord with <i>Sili</i> Fish
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- Authors
- Kinkhabwala, A., Riley, M., Koyama, M., Monen, J., Satou, C., Kimura, Y., Higashijima, S.-I., & Fetcho, J.
- Affiliations
- Princeton University (US)
- Cornell University (US)
- National Institutes of Natural Sciences (JP)
- ORCID
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2011-01-03
- Volume
- 108
- Issue
- 3
- Pages
- 1164-1169
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC3024665
- OpenAlex
- W2055388433
- Cited by
- 203
- References
- 5
- Citations by year
- 2026: 7 · 2025: 9 · 2024: 12 · 2023: 8 · 2022: 12 · 2021: 11 · 2020: 19 · 2019: 10 · 2018: 20 · 2017: 14 · 2016: 11 · 2015: 15 · 2014: 17 · 2013: 20 · 2012: 14
- FWCI
- 8.44
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Science Foundation (0333366)
- National Institutes of Health
- Japan Society for the Promotion of Science
- National Institute of General Medical Sciences (T32GM007469)
- National Institute of Neurological Disorders and Stroke (NS26539, R37NS026539, R01NS026539)
- Division of Graduate Education
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Zebrafish Biomedical Research Applications
- Life Sciences › Neuroscience › Cellular and Molecular Neuroscience › Neuroscience and Neuropharmacology Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
- Keywords
- hindbrain, zebrafish, neurotransmitter phenotype, axonal projections, input resistance, sensorimotor network
- MeSH terms
- Age Factors, Animals, Calcium, Electrophysiology, Interneurons, Models, Neurological, Nerve Net, Rhombencephalon, Zebrafish, Neurotransmitter Agents, Microscopy, Confocal, Body Patterning, Animals, Genetically Modified
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