# Reverse Engineering the Brain Stem Circuits that Govern Exploratory Behavior

> **NIH NIH U19** · UNIVERSITY OF CALIFORNIA, SAN DIEGO · 2020 · $2,983,524

## Abstract

Overview - Abstract
 Brainstem function is necessary for life-sustaining functions such as breathing and for survival functions,
such as foraging for food. Individual motor actions are activated by specific brainstem cranial motor nuclei. The
specificity of individual motor actions reflects the participation of motor nuclei in circuits within closed loops
between sensors and muscle actuators. However, these loops are also nested and connect to feedback and
feedforward pathways, which underlie coordination between orofacial motor actions. A key question for this
proposal is how different actions are coordinated to form a rich repertoire of behaviors, such as rhythmic
motions linked to breathing, and the orchestrated displacements of the head, nose, tongue, and vibrissae
during exploration. We postulate that the best candidate interface for orofacial motor coordination are premotor
and pre2motor neuron populations in the brainstem reticular formation: these neurons project to cranial motor
nuclei, receive descending inputs from outside of the brainstem, and interconnected to each other.
 Our approach exploits and expands upon a broad spectrum of innovative experimental tools. These include
state-of-the-art behavioral methods to study motor actions and their coordination into behaviors. From an
experimental perspective, the underlying neuronal circuitry for each orofacial motor action may be accessed
via transsynaptic transport starting at the muscle activators or associated sensors in the periphery. These
studies will make use of molecular, genetic, and functional labeling methods to enable cell phenotyping and
circuit tracing. These data will establish the "Components", i.e., brainstem nuclei connectivity for all Research
Projects. These studies are complemented by in vivo electrophysiology and optogenetics in order measure and
perturb the signal flow during exploration and decision-making: these studies will establish orofacial “Wiring
Diagrams”. The sum of these techniques will permit us to elucidate the functions of intrinsic brainstem circuits
and their modulation by descending pathways.
 Our data will be integrated in two ways. First we will begin development of computational models of the
dynamics of active sensing by the orofacial motor plant and brainstem circuits. These will initially focus on the
vibrissa system, starting with characterizations of mechanics and mechano-neuronal transformations of
vibrissa movement and extending to exploration of brainstem circuits that drive vibrissa set-point and rhythmic
whisking. Finally, vibrissa feedforward pathways will be computationally modeled to explore how sensory input
affects vibrissa dynamics. Second, to record connectivity data that arises from our experimental tracing studies,
we will construct an Trainable Texture-based Digital Atlas that utilizes machine learning to automate
anatomical annotation of brainstem nuclei. The Atlas is designed to allow accurate 3D alignment of labeled
neuron...

## Key facts

- **NIH application ID:** 9930683
- **Project number:** 5U19NS107466-03
- **Recipient organization:** UNIVERSITY OF CALIFORNIA, SAN DIEGO
- **Principal Investigator:** Martin Deschenes
- **Activity code:** U19 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $2,983,524
- **Award type:** 5
- **Project period:** 2018-09-15 → 2023-05-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9930683

## Citation

> US National Institutes of Health, RePORTER application 9930683, Reverse Engineering the Brain Stem Circuits that Govern Exploratory Behavior (5U19NS107466-03). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/9930683. Licensed CC0.

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