1. Neuroscience
Download icon

Brain-wide cellular resolution imaging of Cre transgenic zebrafish lines for functional circuit-mapping

  1. Kathryn M Tabor
  2. Gregory D Marquart
  3. Christopher Hurt
  4. Trevor S Smith
  5. Alexandra K Geoca
  6. Ashwin A Bhandiwad
  7. Abhignya Subedi
  8. Jennifer L Sinclair
  9. Hannah M Rose
  10. Nicholas F Polys
  11. Harold A Burgess  Is a corresponding author
  1. National Institute of Child Health and Human Development, United States
  2. Virginia Polytechnic Institute and State University, United States
Tools and Resources
  • Cited 13
  • Views 3,279
  • Annotations
Cite this article as: eLife 2019;8:e42687 doi: 10.7554/eLife.42687

Abstract

Decoding the functional connectivity of the nervous system is facilitated by transgenic methods that express a genetically encoded reporter or effector in specific neurons; however, most transgenic lines show broad spatiotemporal and cell-type expression. Increased specificity can be achieved using intersectional genetic methods which restrict reporter expression to cells that co-express multiple drivers, such as Gal4 and Cre. To facilitate intersectional targeting in zebrafish, we have generated more than 50 new Cre lines, and co-registered brain expression images with the Zebrafish Brain Browser, a cellular resolution atlas of 264 transgenic lines. Lines labeling neurons of interest can be identified using a web-browser to perform a 3D spatial search (zbbrowser.com). This resource facilitates the design of intersectional genetic experiments and will advance a wide range of precision circuit-mapping studies.

Data availability

Registered individual confocal brain scans have been deposited in Dryad https://doi.org/10.5061/dryad.tk467n8

The following data sets were generated

Article and author information

Author details

  1. Kathryn M Tabor

    Division of Developmental Biology, National Institute of Child Health and Human Development, Bethesda, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. Gregory D Marquart

    Division of Developmental Biology, National Institute of Child Health and Human Development, Bethesda, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-9811-5372
  3. Christopher Hurt

    Division of Developmental Biology, National Institute of Child Health and Human Development, Bethesda, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Trevor S Smith

    Division of Developmental Biology, National Institute of Child Health and Human Development, Bethesda, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Alexandra K Geoca

    Division of Developmental Biology, National Institute of Child Health and Human Development, Bethesda, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Ashwin A Bhandiwad

    Division of Developmental Biology, National Institute of Child Health and Human Development, Bethesda, United States
    Competing interests
    The authors declare that no competing interests exist.
  7. Abhignya Subedi

    Division of Developmental Biology, National Institute of Child Health and Human Development, Bethesda, United States
    Competing interests
    The authors declare that no competing interests exist.
  8. Jennifer L Sinclair

    Division of Developmental Biology, National Institute of Child Health and Human Development, Bethesda, United States
    Competing interests
    The authors declare that no competing interests exist.
  9. Hannah M Rose

    Division of Developmental Biology, National Institute of Child Health and Human Development, Bethesda, United States
    Competing interests
    The authors declare that no competing interests exist.
  10. Nicholas F Polys

    Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, United States
    Competing interests
    The authors declare that no competing interests exist.
  11. Harold A Burgess

    Division of Developmental Biology, National Institute of Child Health and Human Development, Bethesda, United States
    For correspondence
    burgessha@mail.nih.gov
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1966-7801

Funding

Eunice Kennedy Shriver National Institute of Child Health and Human Development (1ZIAHD008884-04)

  • Harold A Burgess

Virginia Tech Advanced Research Computing (NA)

  • Nicholas F Polys

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Ethics

Animal experimentation: This study was performed in strict accordance with the recommendations in the Guide for the Care and Use of Laboratory Animals of the National Institutes of Health. All of the animals were handled according to approved institutional animal care and use committee (IACUC) protocols (#15-039) of the Eunice Kennedy Shriver National Institute of Child Health and Human Development.

Reviewing Editor

  1. Indira M Raman, Northwestern University, United States

Publication history

  1. Received: October 8, 2018
  2. Accepted: February 7, 2019
  3. Accepted Manuscript published: February 8, 2019 (version 1)
  4. Version of Record published: February 27, 2019 (version 2)

Copyright

This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.

Metrics

  • 3,279
    Page views
  • 478
    Downloads
  • 13
    Citations

Article citation count generated by polling the highest count across the following sources: Crossref, Scopus, PubMed Central.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Download citations (links to download the citations from this article in formats compatible with various reference manager tools)

Open citations (links to open the citations from this article in various online reference manager services)

Further reading

    1. Neuroscience
    Benoit P Delhaye et al.
    Research Article

    Human tactile afferents provide essential feedback for grasp stability during dexterous object manipulation. Interacting forces between an object and the fingers induce slip events that are thought to provide information about grasp stability. To gain insight into this phenomenon, we made a transparent surface slip against a fixed fingerpad while monitoring skin deformation at the contact. Using microneurography, we simultaneously recorded the activity of single tactile afferents innervating the fingertips. This unique combination allowed us to describe how afferents respond to slip events and to relate their responses to surface deformations taking place inside their receptive fields. We found that all afferents were sensitive to slip events, but FA-I afferents in particular faithfully encoded compressive strain rates resulting from those slips. Given the high density of FA-I afferents in fingerpads, they are well suited to detect incipient slips and to provide essential information for the control of grip force during manipulation.

    1. Neuroscience
    Caroline S Lee et al.
    Research Article

    Learning about temporal structure is adaptive because it enables the generation of expectations. We examined how the brain uses experience in structured environments to anticipate upcoming events. During fMRI, individuals watched a 90-second movie clip six times. Using a Hidden Markov Model applied to searchlights across the whole brain, we identified temporal shifts between activity patterns evoked by the first vs. repeated viewings of the movie clip. In many regions throughout the cortex, neural activity patterns for repeated viewings shifted to precede those of initial viewing by up to 15 seconds. This anticipation varied hierarchically in a posterior (less anticipation) to anterior (more anticipation) fashion. We also identified specific regions in which the timing of the brain's event boundaries were related to those of human-labeled event boundaries, with the timing of this relationship shifting on repeated viewings. With repeated viewing, the brain's event boundaries came to precede human-annotated boundaries by 1-4 seconds on average. Together, these results demonstrate a hierarchy of anticipatory signals in the human brain and link them to subjective experiences of events.