# The connectome and neurobiology of a novel model chordate, Ciona intestinalis

> **NIH NIH R01** · UNIVERSITY OF CALIFORNIA SANTA BARBARA · 2020 · $538,317

## Abstract

A comprehensive understanding of nervous system function requires integration of multiple types of data, from
behavioral to anatomical. Ultimately function can be reduced to the patterns of connectivity between cells and
the activation of single neurons. In this application we propose a set of aims that makes use of a unique
organism with optimal qualities for multimodal nervous system investigation: the simple chordate, Ciona
intestinalis. The anatomy of the Ciona larval tadpole CNS shows strong conservation with the CNS of the
vertebrates, including homologs of the forebrain, midbrain/hindbrain, and spinal cord. Despite these conserved
vertebrate-like features the Ciona tadpole is barely 1 mm long and has only ~2500 cells. Moreover the tadpole
CNS has only 177 neurons. While the development of the Ciona CNS has been the subject of investigation for
many years, new research opportunities have opened with the recent completion of the Ciona tadpole CNS
connectome from serial section electron microscopy. The overall goal of this proposal is to build from the
connectome data to identify correlates of behavior at the level of single, identifiable neurons. This project will
be the combined undertaking of three research groups with expertise in Ciona live imaging and transgenesis,
computer vision and image analysis, and electron microscopy and Ciona neuroanatomy. Preliminary data
presented here demonstrate that the transparency and small size of Ciona tadpoles make them ideal for live
imaging of brain activity using genetically encoded Ca2+ or voltage indicators. The aims of this proposal will be,
first, to expand Ciona as a model of nervous system function, including a detailed characterization of behavior,
the generation of a brain atlas at cellular resolution, and the quantification of stereotypy in brain cellular
anatomy and connectivity; and, second, to apply these new tools in the characterization of patterns of neuronal
activity as Ciona larvae respond to sensory cues by taking advantage of state-of-the-art imaging and neural
activity detection methods. The connectome makes specific and novel predictions about patterns of neural
activity, and the relative simplicity of the Ciona CNS will provide an innovative system for validating such
predictions. This project presents challenges in image acquisition, analysis, and multimodal integration that
stretch the limits of current technology, but holds the potential to provide an unparalleled view of chordate CNS
function spanning multiple levels, from behavioral to synaptic.

## Key facts

- **NIH application ID:** 9904776
- **Project number:** 5R01NS103774-04
- **Recipient organization:** UNIVERSITY OF CALIFORNIA SANTA BARBARA
- **Principal Investigator:** BANGALORE S MANJUNATH
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $538,317
- **Award type:** 5
- **Project period:** 2017-07-01 → 2022-03-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9904776

## Citation

> US National Institutes of Health, RePORTER application 9904776, The connectome and neurobiology of a novel model chordate, Ciona intestinalis (5R01NS103774-04). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/9904776. Licensed CC0.

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