Biology subjects

Naumann, E. A.

Publications and source records attributed to Naumann, E. A..

5 recordsLinked to original sources

bioRxiv2025

Gut stretch evokes rapid neural dynamics in vagal and hindbrain populations of larval zebrafish

Animals sense food quantity and quality to regulate feeding behaviors essential for survival. Enteroendocrine cells (EECs) in the gut epithelium detect luminal distension and nutrients, signaling this information to the brain via vagal sensory neurons. However, how mechanosensory and chemosensory signals are dynamically encoded by gut-brain circuits remains unclear, particularly during early development. Leveraging the transparency and genetic tractability of larval zebrafish, we developed a feeding assay offering liposome-based complex particles designed to release specific nutrients after consumption. By quantifying gut fluorescence after exposure to these particles in 9-day-old zebrafish, we demonstrate that EECs regulate nutrient-specific feeding soon after functional gut formation. To determine how these post-ingestive signals are encoded along the gut-brain circuitry, we developed a microgavage method enabling simultaneous stimulus delivery to the gut and volumetric two-photon calcium imaging. We found that repeated gut distension alone drove widespread activation and suppression in vagal and dorsal hindbrain neurons, emerging as a dominant visceral signal after two days of feeding onset. Although nutrient-evoked responses shared temporal features with distension, allyl isothiocyanate (AITC), an aversive compound found in wasabi, elicited neural dynamics with slower onset kinetics. These findings reveal that fast gut-to-brain communication emerges early in life, with mechanical distension and aversive chemical cues encoded through distinct temporal dynamics in developing interoceptive circuits. HighlightsO_LILarval zebrafish enteroendocrine cells regulate nutrient-specific feeding C_LIO_LILeft and right vagus similarly encode gut distension and nutrients C_LIO_LIGut distension drives rapid, widespread neural responses across the hindbrain C_LIO_LIEnteric stimuli evoke diverse fast neural dynamics in early development C_LI

neuroscience↗

bioRxiv2024

Artificial Embodied Circuits Uncover Neural Architectures of Vertebrate Visuomotor Behaviors

All brains evolve within specific sensory and physical environments1. Traditionally, neuroscience has focused on studying neural circuits in isolation, yet holistic characterization of their function requires integrative brain-body testing2,3. To investigate the neural and biomechanical mechanisms of sensorimotor transformations, we constructed realistic neuromechanical simulations (simZFish) of the larval zebrafish optomotor response, a visual stabilization behavior4,5. By computationally reproducing the body, physical body-water interactions, visual environments, and experimentally derived neural architectures, we closely replicated the behavior of real zebrafish6. Through systematic manipulation of physiological and circuit features, impossible in biological experiments, we demonstrate how embodiment shapes neural circuit architecture and behavior. When challenged with novel visual stimuli, simZFish predicted neuronal response types, which we identified via calcium imaging in the brain of real zebrafish and used to update the simZFish neural network. In virtual rivers, simZFish performed rheotaxis by using current-induced optic flow as navigational cues, compensating for the simulated water flow. Finally, a physical robot (ZBot) validated the role of embodied sensorimotor circuits in maintaining position in a real river with complex fluid dynamics and visual environments. Together, by iterating between simulations, behavioral observations, neural imaging, and robotic testing, we demonstrate the power of an integrative approach to investigating sensorimotor processing. Research HighlightsO_LIDeveloped simZFish, an open-source neuromechanical simulation modeling the zebrafish optomotor response (OMR). C_LIO_LIDemonstrated that simZFish visuomotor neural circuits are sufficient to maintain position in virtual water currents without additional sensory modalities. C_LIO_LIInvestigated how variations in eye geometry influence neural circuit functionality and behavior. C_LIO_LIConducted optic flow analysis of simulated visual input to identify retinal connectivity requirements, uncovering the factors that shape pretectal neurons preference for the lower posterior visual field. C_LIO_LIsimZFish predicted new neural response types confirmed via real zebrafish calcium imaging. C_LIO_LIValidated simZFish circuits with a physical robot, ZBot, performing rheotaxis in a natural river with rich visual and complex flow dynamics compared to idealized lab and simulation experiments. C_LI O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=137 SRC="FIGDIR/small/629427v1_ufig1.gif" ALT="Figure 1"> View larger version (63K): org.highwire.dtl.DTLVardef@11f2acforg.highwire.dtl.DTLVardef@133b1f3org.highwire.dtl.DTLVardef@e808bcorg.highwire.dtl.DTLVardef@1959616_HPS_FORMAT_FIGEXP M_FIG C_FIG Graphical abstractCombining data-driven neuromechanical simulations and robotic testing, we established an integrative framework for investigating embodied neural circuit functions. Leveraging the behavioral, neurobiological, and theoretical foundations of the visually guided optomotor response in larval zebrafish (blue, left), we developed a virtual zebrafish, simZFish (red, middle), to replicate realistic hydrodynamic, anatomical, sensory, neural, and behavioral aspects, permitting the investigation of emergent properties driven by embodiment. Validating these findings using a physical, zebrafish-inspired robot, ZBot (grey, right), in naturalistic environments informs further experiments, hypotheses, and robotic design.

neuroscience↗

bioRxiv2024

Divergent Visuomotor Strategies in Teleosts: Neural Circuit Mechanisms in Zebrafish and Danionella cerebrum

Many animals respond to sensory cues with species-specific coordinated movements to successfully navigate their environment. However, the neural mechanisms that support diverse sensorimotor transformations across species with distinct navigational strategies remain largely unexplored. By comparing related teleost species, zebrafish (Danio rerio, ZF) and Danionella cerebrum (DC), we investigated behavioral patterns and neural architectures during the visually guided optomotor response (OMR). Closed-loop behavioral tracking during visual stimulation revealed that larval ZF employ burst-and-glide locomotion, while larval DC display continuous, smooth swimming punctuated with sharp directional turns. Although DC achieve higher average speeds, they lack the direction-dependent velocity modulation observed in ZF. Whole-brain two-photon calcium imaging and tail tracking in head-fixed fish reveals that both species exhibit direction-selective motion encoding in homologous regions, including the retinorecipient pretectum, with DC exhibiting fewer binocular, direction-selective neurons overall. Kinematic analysis of head-fixed behavior reveals that DC sustain significantly longer directed swim events across all stimuli than ZF, highlighting the divergent visuomotor strategies, with ZF reducing tail movement duration in response to oblique, turn-inducing stimuli. Lateralized motor-associated neural activity in the medial and anterior hindbrain of both species suggests a shared circuit motif, with distinct neural circuits that independently control movement vigor and direction. These findings highlight the diversity in visuomotor strategies among teleost species, underscored by shared sensorimotor neural circuit motifs, and establish a robust framework for unraveling the neural mechanisms driving continuous and discrete visually guided locomotion, paving the way for deeper insights into vertebrate sensorimotor functions. Research HighlightsO_LILarval DC exhibit faster swimming than ZF, matching the direction of visual motion. C_LIO_LIDC execute OMR in smooth, curved swimming patterns, interspersed with sharp directional turns. C_LIO_LIZF and DC share similar visuomotor neural architecture, recruiting pretectal and hindbrain regions. C_LIO_LIZF and DC demonstrate lateralized encoding of turns, particularly in medial hindbrain neurons. C_LI In BriefLarval Danionella cerebrum respond to global visual motion cues in smooth, low-angle swimming patterns, interspersed with sharp directional turns, swimming consistently faster than zebrafish. Fouke et al. use behavioral tracking of freely moving and head fixed fish to reveal an evolutionarily conserved visuomotor neural architecture transforming visual motion cues into species-specific locomotor behaviors. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/624938v1_ufig1.gif" ALT="Figure 1"> View larger version (64K): org.highwire.dtl.DTLVardef@13076f4org.highwire.dtl.DTLVardef@d18dc8org.highwire.dtl.DTLVardef@1b35025org.highwire.dtl.DTLVardef@152d2f0_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical AbstractC_FLOATNO C_FIG

neuroscience↗

bioRxiv2021

Gigapixel behavioral and neural activity imaging with a novel multi-camera array microscope

The dynamics of living organisms are organized across many spatial scales. However, current cost-effective imaging systems can measure only a subset of these scales at once. We have created a scalable multi-camera array microscope (MCAM) that enables comprehensive high-resolution recording from multiple spatial scales simultaneously, ranging from cellular structures to large-group behavioral dynamics. By collecting data from up to 96 cameras, we computationally generate gigapixel-scale images and movies with a field of view over hundreds of square centimeters at 5um sensitivity. This allows us to observe the behavior and fine anatomical features of numerous freely moving model organisms on multiple spatial scales, including larval zebrafish, fruit flies, nematodes, carpenter ants, and slime mold. The MCAM architecture allows stereoscopic tracking of the z-position of organisms using the overlapping field of view from adjacent cameras. Further, we demonstrate the ability to acquire dual color fluorescence video of multiple freely moving zebrafish, recording neural activity via ratiometric calcium imaging. Overall, the MCAM provides a powerful platform for investigating cellular and behavioral processes across a wide range of spatial scales by removing the bottlenecks imposed by single-camera image acquisition systems.

bioengineering↗

bioRxiv2021

improv: A flexible software platform for adaptive neuroscience experiments

Current neuroscience research is often limited to testing predetermined hypotheses and post hoc analysis of already collected data. Adaptive experimental designs, in which modeling drives ongoing data collection and selects experimental manipulations, offer a promising alternative. Still, tight integration between models and data collection requires coordinating diverse hardware configurations and complex computations under real-time constraints. Here, we introduce improv, a software platform that allows users to fully integrate custom modeling, analysis, and visualization with data collection and experimental control. We demonstrate both in silico and in vivo how improv enables more efficient experimental designs for discovery and validation across various model organisms and data types. Improv can orchestrate custom real-time behavioral analyses, rapid functional typing of neural responses from large populations via calcium microscopy, and optimal visual stimulus selection. We incorporate real-time machine learning methods for dimension reduction and predictive modeling of latent neural and behavioral features. Finally, we demonstrate how improv can perform model-driven interactive imaging and simultaneous optogenetic photostimulation of visually responsive neurons in the larval zebrafish brain expressing GCaMP6s and the red-shifted opsin rsChRmine. Together, these results demonstrate the power of improv to integrate modeling with data collection and experimental control to achieve next-generation adaptive experiments.

neuroscience↗