1. Neuroscience
Download icon

MouseBytes, an open-access high-throughput pipeline and database for rodent touchscreen-based cognitive assessment

Tools and Resources
  • Cited 13
  • Views 2,445
  • Annotations
Cite this article as: eLife 2019;8:e49630 doi: 10.7554/eLife.49630

Abstract

Open Science has changed research by making data accessible and shareable, contributing to replicability to accelerate and disseminate knowledge. However, for rodent cognitive studies the availability of tools to share and disseminate data is scarce. Automated touchscreen-based tests enable systematic cognitive assessment with easily standardized outputs that can facilitate data dissemination. Here we present an integration of touchscreen cognitive testing with an open-access database public repository (mousebytes.ca), as well as a Web platform for knowledge dissemination (https://touchscreencognition.org). We complement these resources with the largest dataset of age-dependent high-level cognitive assessment of mouse models of Alzheimer's disease, expanding knowledge of affected cognitive domains from male and female mice of three mouse strains. We envision that these new platforms will enhance sharing of protocols, data availability and transparency, allowing meta-analysis and reuse of mouse cognitive data to increase the replicability/reproducibility of datasets.

Data availability

Automated quality control (QC) algorithm and the codes are available for free download and modification in GitHub https://github.com/srmemar/Mousebytes-An-open-access-high-throughput-pipeline-and-database-for-rodent-touchscreen-based-dataThe touchscreen processed data were deposited into an open-access application (http://www.mousebytes.ca/).

Article and author information

Author details

  1. Flavio H Beraldo

    Robarts Research Institute, University of Western Ontario, London, Canada
    Competing interests
    No competing interests declared.
  2. Daniel Palmer

    Robarts Research Institute, University of Western Ontario, London, Canada
    Competing interests
    No competing interests declared.
  3. Sara Memar

    Robarts Research Institute, University of Western Ontario, London, Canada
    Competing interests
    No competing interests declared.
  4. David I Wasserman

    Robarts Research Institute, University of Western Ontario, London, Canada
    Competing interests
    No competing interests declared.
  5. Wai-Jane V Lee

    Robarts Research Institute, University of Western Ontario, London, Canada
    Competing interests
    No competing interests declared.
  6. Shuai Liang

    Rotman Research Institute, Baycrest Hospital, Toronto, Canada
    Competing interests
    No competing interests declared.
  7. Samantha D Creighton

    Department of Psychology and Neuroscience Program, University of Guelph, Guelph, Canada
    Competing interests
    No competing interests declared.
  8. Benjamin Kolisnyk

    Robarts Research Institute, University of Western Ontario, London, Canada
    Competing interests
    No competing interests declared.
  9. Matthew F Cowan

    Robarts Research Institute, University of Western Ontario, London, Canada
    Competing interests
    No competing interests declared.
  10. Justin Mels

    Robarts Research Institute, University of Western Ontario, London, Canada
    Competing interests
    No competing interests declared.
  11. Talal S Masood

    Robarts Research Institute, University of Western Ontario, London, Canada
    Competing interests
    No competing interests declared.
  12. Chris Fodor

    Robarts Research Institute, University of Western Ontario, London, Canada
    Competing interests
    No competing interests declared.
  13. Mohammed A Al-Onaizi

    Robarts Research Institute, University of Western Ontario, London, Canada
    Competing interests
    No competing interests declared.
  14. Robert Bartha

    Robarts Research Institute, University of Western Ontario, London, Canada
    Competing interests
    No competing interests declared.
  15. Tom Gee

    Rotman Research Institute, Baycrest Hospital, Toronto, Canada
    Competing interests
    No competing interests declared.
  16. Lisa M Saksida

    Robarts Research Institute, University of Western Ontario, London, Canada
    Competing interests
    Lisa M Saksida, consults for Campden Instruments, Ltd.
  17. Timothy J Bussey

    Robarts Research Institute, University of Western Ontario, London, Canada
    Competing interests
    Timothy J Bussey, consults for Campden Instruments, Ltd.
  18. Stephen S Strother

    Rotman Research Institute, Baycrest Hospital, Toronto, Canada
    Competing interests
    No competing interests declared.
  19. Vania F Prado

    Robarts Research Institute, University of Western Ontario, London, Canada
    Competing interests
    No competing interests declared.
  20. Boyer D Winters

    Department of Psychology and Neuroscience Program, University of Guelph, Guelph, Canada
    For correspondence
    bwinters@uoguelph.ca
    Competing interests
    No competing interests declared.
  21. Marco A M Prado

    Robarts Research Institute, University of Western Ontario, London, Canada
    For correspondence
    mprado@robarts.ca
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-3028-5778

Funding

Weston Brain Institute

  • Robert Bartha
  • Stephen S Strother
  • Boyer D Winters
  • Marco A M Prado

Canada Open Neuroscience Platform

  • Sara Memar
  • Timothy J Bussey
  • Marco A M Prado

Mitacs

  • Daniel Palmer
  • Lisa M Saksida
  • Timothy J Bussey

CIFAR

  • Lisa M Saksida

Canadian Institutes of Health Research (MOP136930)

  • Marco A M Prado

Alzheimer's Society

  • Vania F Prado
  • Marco A M Prado

Canada First Research Excellence Fund (BrainsCAN)

  • Robert Bartha
  • Lisa M Saksida
  • Timothy J Bussey
  • Vania F Prado
  • Marco A M Prado

Brain Canada

  • Vania F Prado
  • Marco A M Prado

Canadian Institutes of Health Research (MOP126000)

  • Vania F Prado
  • Marco A M Prado

Canadian Institutes of Health Research (MOP89919)

  • Vania F Prado
  • Marco A M Prado

Natural Sciences and Engineering Research Council of Canada

  • Lisa M Saksida
  • Timothy J Bussey
  • Vania F Prado

Canada Research Chairs

  • Lisa M Saksida
  • Marco A M Prado

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

Ethics

Animal experimentation: Procedures were conducted in accordance with approved animal protocols at the University of Western Ontario (2016/104) and the University of Guelph (3481) following the Canadian Council of Animal Care and National Institutes of Health guidelines.

Reviewing Editor

  1. Andrew Holmes, NIH, United States

Publication history

  1. Received: June 24, 2019
  2. Accepted: December 11, 2019
  3. Accepted Manuscript published: December 11, 2019 (version 1)
  4. Version of Record published: December 27, 2019 (version 2)

Copyright

© 2019, Beraldo et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

Metrics

  • 2,445
    Page views
  • 227
    Downloads
  • 13
    Citations

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

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. Developmental Biology
    2. Neuroscience
    Tania Moreno-Mármol et al.
    Research Article

    The vertebrate eye-primordium consists of a pseudostratified neuroepithelium, the optic vesicle (OV), in which cells acquire neural retina or retinal pigment epithelium (RPE) fates. As these fates arise, the OV assumes a cup-shape, influenced by mechanical forces generated within the neural retina. Whether the RPE passively adapts to retinal changes or actively contributes to OV morphogenesis remains unexplored. We generated a zebrafish Tg(E1-bhlhe40:GFP) line to track RPE morphogenesis and interrogate its participation in OV folding. We show that, in virtual absence of proliferation, RPE cells stretch and flatten, thereby matching the retinal curvature and promoting OV folding. Localized interference with the RPE cytoskeleton disrupts tissue stretching and OV folding. Thus, extreme RPE flattening and accelerated differentiation are efficient solutions adopted by fast-developing species to enable timely optic cup formation. This mechanism differs in amniotes, in which proliferation drives RPE expansion with a much-reduced need of cell flattening.

    1. Neuroscience
    Pierre-Luc Rochon et al.
    Research Article

    Nearly 50 different mouse retinal ganglion cell (RGC) types sample the visual scene for distinct features. RGC feature selectivity arises from their synapses with a specific subset of amacrine (AC) and bipolar cell (BC) types, but how RGC dendrites arborize and collect input from these specific subsets remains poorly understood. Here we examine the hypothesis that RGCs employ molecular recognition systems to meet this challenge. By combining calcium imaging and type-specific histological stains we define a family of circuits that express the recognition molecule Sidekick 1 (Sdk1) which include a novel RGC type (S1-RGC) that responds to local edges. Genetic and physiological studies revealed that Sdk1 loss selectively disrupts S1-RGC visual responses which result from a loss of excitatory and inhibitory inputs and selective dendritic deficits on this neuron. We conclude that Sdk1 shapes dendrite growth and wiring to help S1-RGCs become feature selective.