# Molecular profiling of the zebra finch brain

> **NIH NIH R03** · OREGON HEALTH & SCIENCE UNIVERSITY · 2020 · $154,000

## Abstract

Project Summary
Avian model organisms, including songbirds (zebra finches, canaries, starlings), parrots, chicken, quail, and
pigeons have contributed much to our understanding of brain function and disorders that affect neural
development, function, and cognition. Furthermore, many bird groups are being increasingly recognized as
having enlarged brains that are capable of advanced cognitive and learning skills that rival and even surpass
those in mammals. Despite these contributions, we still lack a clear understanding of how the molecular brain
organization in birds compares to that in mammals, including humans. To address this gap, we utilized
resource building funds from the NINDS and NIGMS to develop the Zebra finch Expression Brain Atlas
(ZEBrA), currently the largest in situ hybridization database of brain gene expression for any avian species.
ZEBrA is a publicly accessible website with a database containing >3,500 high resolution digital images of
brain sections from adult male zebra finches that are aligned to a reference histological atlas, and hybridized to
reveal the brain-wide expression of >720 genes of relevance for brain development, physiology, plasticity, and
vocal learning. Notably, nearly 200 of these genes have been linked to speech and/or neural disorders in
humans, and/or constitute shared molecular specializations of analogous brain regions for vocal production
and learning in birds and humans. Many expression patterns in ZEBrA have also revealed previously
unsuspected subdomains that are not visible with conventional histological techniques, as well as enrichments
in discrete nuclei within circuits that underlie specific behaviors (e.g., vocal production and learning). Despite
these findings, a quantitative analysis of the ZEBrA database has not yet been performed, which has hindered
our ability to perform accurate comparative analyses with similar resources from mammals (e.g. Allen
Institute's Mouse Brain Atlas - MBA). We propose here to use image analysis methods to extract equivalent
regional gene expression data from both databases. The outcomes in finch will define regional molecular
profiles of major brain areas and specialized nuclei of the vocal control and learning circuitry, the latter a
cognitive trait of high relevance to human speech and language. The ZEBrA and MBA data will also be
compared to derive insights into how avian and mammalian brains relate or diverge molecularly. Such insights
will help to further validate the use of avian species as informative model organisms for understanding the
molecular basis of brain function and cognitive skills, as well as the genetic basis of brain disorders of high
relevance to humans.

## Key facts

- **NIH application ID:** 10062755
- **Project number:** 1R03NS115145-01A1
- **Recipient organization:** OREGON HEALTH & SCIENCE UNIVERSITY
- **Principal Investigator:** Claudio V Mello
- **Activity code:** R03 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $154,000
- **Award type:** 1
- **Project period:** 2020-08-01 → 2023-07-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10062755

## Citation

> US National Institutes of Health, RePORTER application 10062755, Molecular profiling of the zebra finch brain (1R03NS115145-01A1). Retrieved via AI Analytics 2026-05-27 from https://api.ai-analytics.org/grant/nih/10062755. Licensed CC0.

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