Search bioRxiv⌕ Search

Biology subjects

Engert, F.

Publications and source records attributed to Engert, F..

At least 19 recordsLinked to original sources

A mechanical parameter of coasting varies bout to bout and predicts swim timing in larval zebrafish

Most animals move intermittently. Of these, animals that fly and swim move in two stages: during active propulsion, when they beat their wings or swing their tails, and right after, when they glide or coast through the air or water. The kinematics of active movements are typically well studied, but the coasting period afterwards is less understood. We used larval zebrafish as a model of intermittent locomotion. Larval zebrafish swim in discrete bouts lasting ~200 ms, coast for short durations and distances, and then are largely stationary for ~800 ms. We find that larval zebrafish do not coast like a passive object. While they coast for distances that are correlated with the prior swim's strength, as expected from physics, they seem to be able to modulate the mechanics of their coasting: the time constant is not a constant, but varies from coast-to-coast. Furthermore, the time constant is correlated with the duration of the interval between swim bouts. This suggests that larval zebrafish can either shorten or extend their coasting duration, and that coasting inhibits the initiation of the next swim. Finally, the time constant changes quickly, while other swimming kinematics (e.g., distance swum) are autocorrelated over the course of at least several seconds. Altogether, this suggests that fish, and perhaps other animals that move intermittently, actively modulate their post-propulsion movement, possibly to gather sensory feedback in the absence of blurry visual feedback associated with fast locomotion.

neuroscience↗

A neuron-glia circuit anticipates hypoxia to regulate organismal oxygen use

Organisms must regulate metabolic resources such as oxygen (O2) and nutrients despite environmental variability and the energetic costs of their own actions1-3. Such regulation can occur reactively, through homeostatic corrections of recent imbalances, or predictively, through allostatic adjustments that anticipate future demand4,5. Predictive regulation is particularly important because metabolic resources often continue to be consumed for seconds to minutes after motor actions cease as tissues repay incurred costs, making it advantageous to prevent depletion before it occurs6. However, the cellular and circuit mechanisms for allostatic control remain largely unknown5,7,8. Using whole-brain neuronal and astroglial imaging and O2 measurements in behaving zebrafish, we identified a noradrenergic-astroglial circuit that detects, anticipates, and prevents internal O2 depletion. We found that swimming exacerbated internal hypoxia with a multi-second delay, but behavioral adaptations occurred before such self-generated hypoxia manifested, suggesting predictive control, confirmed using computational modeling. Noradrenergic neurons in the nucleus of the solitary tract directly detected brain hypoxia and received efference copies of swimming actions; these inputs summed at the level of membrane voltage to increase spiking and norepinephrine release when actions and resource scarcity co-occurred. Astroglia integrated noradrenergic input into prolonged Ca2+ elevation that tracked the O2 cost of recent actions and thereby predicted O2 debt relative to O2 availability, rising ~8 s before O2 fell. This astroglial prediction reorganized brain-wide activity to suppress locomotion and promote respiration, preempting O2 depletion. Silencing noradrenergic neurons or astroglial signaling abolished these hypoxia coping behaviors, whereas selective activation evoked them. This neuronal-astroglial mechanism constitutes a predictive control system that integrates physiological state with behavioral intent to avert metabolic crisis, revealing a cellular substrate for proactive energy management.

neuroscience↗

Control of wildtype zebrafish optomotor response with a photoswitchable drug

For animals to interact effectively with their environment, the brain must integrate sensory information and generate appropriate motor responses. Multiple neuronal circuits contribute to this process, and identifying their roles remains a central focus in neuroscience. The recently developed photoswitchable compound Carbadiazocine controls neuronal firing across species. It modulates larval zebrafish locomotion and alleviates neuropathic pain in rodents in a reversible, light-induced manner. Given its effects on both motor and somatosensory circuits, we investigated the impact of Carbadiazocine on sensorimotor behaviors. We focused on the optomotor response in zebrafish larvae and assessed its potential as a tool for circuit perturbation and behavioral analysis, for the first time combined with photopharmacology. We performed experiments in head-fixed and free-swimming larvae to assess their capacity to detect and follow the direction of optic flow, as well as to characterize swimming speed patterns and individual tail bout properties following administration of the two Carbadiazocine photoisomers. In both paradigms, treatment with the pre-illuminated compound led to a decrease in accuracy in responding to optic flow (correct turning percentage dropping from [~]95 % to [~]80 % in head-fixed experiments and correctness decreasing from [~]65 % to [~]20 % in free-swimming experiments). Speed analysis revealed an increased number and duration of fast movements with a decrease in number and duration of slow movements, even during periods without visual stimulation. Tail bout analysis further showed an increase in 15-30 Hz bout frequencies, corresponding to incomplete, irregular tail movements. All these effects were absent when the dark-relaxed compound was administered. Together, these findings deepen our understanding of sensorimotor transformations and lay the foundations to probe native neuronal circuits underlying behavior in diverse animal species using a wide dynamic range of photostimulation patterns.

animal behavior and cognition↗

Engineering human protein switches for functional control of CARs and transcription factors via oral drug administration

While CAR T cells have revolutionized the treatment of certain hematologic malignancies, they can cause severe toxicities, which are expected to be exacerbated with next-generation CAR Ts engineered for improved proliferation, persistence, and efficacy. Therefore, regulatory systems are urgently needed to be able to control these living drugs directly in patients. Here, we engineered a molecular switch, in which the interaction of two human proteins is efficiently induced with the orally available and non-toxic drug A1120. We demonstrate the versatility of this switch by regulating CAR signaling and transcriptional activity in human T cells in vitro and in vivo. Both systems were tightly controlled in the absence of the drug but strongly activated upon administration of the small molecule. Since this switch enables the regulation of diverse systems including CARs and transcription factors, we anticipate that it represents an important step towards next-generation cellular therapies with improved safety and efficacy.

synthetic biology↗

Emergence of Functional Heart-Brain Circuits in a Vertebrate

The early formation of sensorimotor circuits is essential for survival. While the development and function of exteroceptive circuits and their associated motor pathways are well characterized, far less is known about the circuits that convey viscerosensory inputs to the brain and transmit visceromotor commands from the central nervous system to internal organs. Technical limitations, such as the in utero development of viscerosensory and visceromotor circuits and the invasiveness of procedures required to access them, have hindered studies of their functional development in mammals. Using larval zebrafish, which are genetically accessible and optically transparent, we tracked, in vivo, how cardiosensory and cardiomotor neural circuits assemble and begin to function. We uncovered a staged program. First, a minimal efferent circuit suffices for heart-rate control: direct brain-to-heart vagal motor innervation is required, intracardiac neurons are not, and heart rate is governed exclusively by the motor vagus nerve. Within the hindbrain, we functionally localize a cholinergic vagal premotor locus that engages this early efferent control. Second, sympathetic innervation arrives and enhances the dynamics and amplitude of cardiac responses, as neurons in the most anterior sympathetic ganglia acquire the ability to drive cardiac acceleration. These neurons exhibit proportional, integral, and derivative-like relationships to heart rate, consistent with controller motifs that shape gain and dynamics. Third, vagal sensory neurons innervate the heart. Distinct subsets increase activity when heart rate falls or rises, and across spontaneous fluctuations, responses to aversive stimuli, and optogenetically evoked cardiac perturbations, their dynamics are captured by a single canonical temporal kernel with neuron-specific phase offsets, supporting a population code for heart rate. This temporally segregated maturation isolates three experimentally tractable regimes: unidirectional brain-to-heart communication, dual efferent control, and closed-loop control after sensory feedback engages, providing a framework for mechanistic dissection of organism-wide heart-brain circuits.

neuroscience↗

Divergent spatiotemporal integration of whole-field visual motion in medaka and zebrafish.

Cross-species comparisons offer leverage for identifying conserved and divergent neural computations underlying innate behavior. Visual motion integration is a fundamental operation that stabilizes position relative to the moving environment and supports object tracking, yet how its underlying algorithms vary across closely related vertebrate brains remains poorly understood. We investigated how zebrafish (Danio rerio) and medaka (Oryzias latipes) larvae implement visual motion integration using distinct spatiotemporal filters that trade speed for persistence through separable control modules. Using controlled whole-field motion stimuli, we found that medaka pool motion signals over visual fields nearly twice as large as those of zebrafish and exhibit enhanced weighting of peripheral inputs, whereas zebrafish rely more strongly on motion signals directly beneath the body. Temporally, zebrafish respond robustly to motion signals with lifetimes as short as 100 ms, whereas medaka require stimulus durations exceeding one second and maintain motion-driven activity for several seconds after stimulus offset. Decomposition of turning behavior revealed separable control modules for large and small corrective maneuvers, with species differences arising primarily from prolonged temporal integration in medaka small-turn control. Together, these differences reveal species-specific tuning of spatial kernels and temporal filters underlying visuomotor control. Our results demonstrate how alterations in basic computational motifs, spatiotemporal pooling, gain, and persistence, can generate divergent visuomotor strategies across closely related vertebrate brains. Significance StatementAnimals rely on visual motion to stabilize positions and interact with dynamic environments, yet how these computations vary across related species remains unclear. By comparing larval zebrafish and medaka, we show that visually similar vertebrates implement motion integration using distinct spatiotemporal strategies. Medaka integrate motion over larger visual fields and retain motion signals for seconds, whereas zebrafish favor rapid, spatially restricted integration. These differences arise from separable control modules governing fine and large motor adjustments. Our results reveal how small changes in core computational motifs--pooling, gain, and persistence--can generate divergent sensorimotor strategies across evolution.

neuroscience↗

Imaging cellular activity simultaneously across all organs of a vertebrate reveals body-wide circuits

All cells in an animal collectively ensure, moment-to-moment, the survival of the whole organism in the face of environmental stressors1,2. Physiology seeks to elucidate the intricate network of interactions that sustain life, which often span multiple organs, cell types, and timescales, but a major challenge lies in the inability to simultaneously record time-varying cellular activity throughout the entire body. We developed WHOLISTIC (WHole Organism Live Imaging System for recording Tissue and IntraCellular activity), a method to image second-timescale, time-varying intracellular dynamics across cell-types of the vertebrate body. By advancing and integrating volumetric fluorescence microscopy, machine learning, and pancellular transgenic expression of calcium sensors in transparent young Danio rerio (zebrafish) and with proof of concept in adult Danionella, the method enables real-time recording of cellular dynamics across the organism. Calcium is a universal intracellular messenger, with a large array of cellular processes depending on changes in calcium concentration across varying time-scales, making it an ideal proxy of cellular activity3. Using this platform to screen the dynamics of most cells in the body, we discovered unexpected responses of specific cell types to stimuli, such as chondrocyte reactions to cold, meningeal responses to ketamine, and state-dependent activity, such as oscillatory ependymal-cell activity during periods of extended motor quiescence. At the organ scale, the method uncovered pulsating traveling waves along the kidney nephron. At the multi-organ scale, we uncovered muscle synergies and independencies, as well as muscle-organ interactions. Integration with optogenetics allowed us to all-optically determine the causal direction of brain-body interactions. At the whole-organism scale, the method captured the rapid brainstem-controlled redistribution of blood flow across the body. Finally, we advanced Whole-Body Expansion Microscopy4 to provide ground-truth molecular and ultrastructural anatomical context, explaining the spatiotemporal structure of activity captured by WHOLISTIC. Together, these innovations establish a new paradigm for systems biology, bridging cellular and organismal physiology, with broad implications for both fundamental research and drug discovery.

neuroscience↗

Collective Behavior in Medaka Fish Depends on Discrete Kinematic States of Swimming Behavior

Complex collective behaviors such as schooling are believed to emerge from simple, individual-level computations that translate incoming information from conspecifics into actions. Recently, it has been proposed that discrete behavioral modes, or internal states, may modulate these computations, affecting the resulting collective behaviors. Direct evidence for such hierarchical control remains limited due to challenges in inferring hidden perception-action computations and uncovering discrete behavioral modes from continuous behaviors. To address this, we analyzed swimming behaviors of Medaka fish (Oryzias latipes) throughout development. At the group level, Medaka exhibit synchronized swimming formations that develop early, emerging around two weeks of age and stabilizing within one month. Unlike many teleost species that use burst-and-coast swim patterns, Medaka exhibit continuous tail and body undulations. We show that this continuous behavior can be segmented into three distinct kinematic states: acceleration, deceleration, and prolonged constant speed swimming. Using state-dependent computational models, we tested how Medaka translate social information from neighbors into actions across these kinematic states. The models revealed distinct computations governing social information processing and decision making in each state. Moreover, social responsiveness varied significantly between states--it was strongest during constant-speed epochs, intermediate during accelerations, and lowest during decelerations. Compared to similarly-sized zebrafish that employ burst-and-coast kinematics, Medaka exhibited greater diversity in state-dependent social interaction computations, ultimately resulting in stronger coordinated swimming. These findings highlight discrete behavioral modes as key modulators of social interaction computations underlying collective behavior.

animal behavior and cognition↗

Fishexplorer: A multimodal cellular atlas platform for neuronal circuit dissection in larval zebrafish

Understanding how neural circuits give rise to behavior requires comprehensive knowledge of neuronal morphology, connectivity, and function. Atlas platforms play a critical role in enabling the visualization, exploration, and dissemination of such information. Here, we present FishExplorer, an interactive and expandable community platform designed to integrate and analyze multimodal brain data from larval zebrafish. FishExplorer supports datasets acquired through light microscopy (LM), electron microscopy (EM), and X-ray imaging, all co-registered within a unified spatial coordinate system which enables seamless comparison of neuronal morphologies and synaptic connections. To further assist circuit analysis, FishExplorer includes a suite of tools for querying and visualizing connectivity at the whole-brain scale. By integrating data from recent large-scale EM reconstructions (presented in companion studies), FishExplorer enables researchers to validate circuit models, explore wiring principles, and generate new hypotheses. As a continuously evolving resource, FishExplorer is designed to facilitate collaborative discovery and serve the growing needs of the teleost neuroscience community.

neuroscience↗

Caffeine-regulated molecular switches for functional control of CAR T cells in vivo

The limited controllability of CAR T cells in patients represents a key challenge of this highly potent immunotherapy. A molecular ON-switch, which can be regulated with a non-toxic and readily available small molecule drug, would represent a major advance towards controllable CAR T therapeutics. For that purpose, we engineered caffeine-responsive heterodimeric ON-switches (CaffSwitches) and demonstrate their high caffeine-dependency and virtually absent leakiness. When incorporating these CaffSwitches into CARs, the resulting CaffCARs were efficiently activated by caffeine concentrations achieved in human plasma after drinking one cup of coffee. Moreover, CaffCAR T cells also showed efficient tumor clearance in an in vivo mouse model, which was completely abolished in the absence of caffeine. This tight control was even observed with c-Jun overexpressing CaffCAR T cells, despite their massive expansion. Together, we anticipate that these novel CaffSwitches will be valuable tools for the development of safe and efficient next generation CAR T cells.

synthetic biology↗

Lrrns define a visual circuit underlying brightness and contrast perception

Brightness and contrast are fundamental features of vision, crucial for object detection, environmental navigation, and feeding. Here, we identify a brightness-and contrast-processing circuit in the zebrafish visual system and uncover the role of Leucine-rich repeat neuronal (Lrrn) cell adhesion molecules (CAMs) in regulating its assembly. Deep-projecting retinal ganglion cells (RGCs) serve as the first synaptic relay to the brain requiring Lrrn2 and Lrrn3a for precise axonal targeting and connectivity within the optic tectum. Genetic targeting of these CAMs leads to circuit disorganization and impairments in contrast sensitivity, leading to deficits in visually guided behaviors. Additionally, ultrastructural circuit reconstruction and functional imaging analysis revealed their critical role in luminance processing. These studies define a fundamental visual processing pathway and establish Lrrn CAMs as essential molecular drivers of its assembly.

neuroscience↗

A Spinal Circuit for Hypoxia-Evoked Motor Output in Zebrafish Larvae

Oxygen availability is a critical environmental variable that shapes animal physiology and behavior. In larval zebrafish, acute hypoxia elicits a distinct increase in rhythmic pectoral fin movements, a behavior thought to facilitate oxygen uptake. While peripheral oxygen sensors such as neuroepithelial cells (NECs) and Merkel-like cells (MLCs) have been well characterized, the motor circuits responsible for executing this behavior remain unknown. Four distinct lower motor nerve branches in the spinal cord have been shown to innervate the pectoral fin muscles and are candidate effectors of hypoxia-induced behaviors. Here, we identify the neural pathways that transform hypoxia detection into a dedicated motor output. Using high-speed behavioral tracking, we confirm that hypoxia reliably increases pectoral fin beat frequency without affecting locomotor tail activity or visually guided swimming. Two-photon calcium imaging in Tg(ChaTa:Gal4;UAS:GCaMP6s) larvae reveals that a subset of cholinergic spinal motor neurons is selectively active during hypoxia-induced fin movements. Targeted laser ablation of pectoral fin motor nerves abolishes the response, demonstrating the necessity of descending input for this behavior. Our findings define a distributed, partially redundant motor circuit that implements a homeostatic fin response to hypoxia. By establishing a mechanistic framework for this behavior in a genetically accessible vertebrate model, this work enables future studies of oxygen sensing, sensorimotor integration, and the neural basis of homeostatic motor control.

neuroscience↗

Cardiac interoception impacts behavior and brain-wide neuronal dynamics

We sought to explore the question as to whether an animals behavior can be modified by internal physiological changes. We focused on the optomotor response, in which an animal moves in response to visual gratings, because it is quantitative, robust, and evolutionarily conserved. Using larval zebrafish, we demonstrate that engagement in the optomotor response is inversely related to heart rate. We modulate heart rate by external threat, activation or blockade of the sympathetic nervous system, pharmacological blockade of the cardiac pacemaker channel, and direct optogenetic pacing of the heart, and find that the correlation persists through all perturbations. We find neurons in the primary sensory ganglia and several regions of the brain whose activity reflects changes in heart rate, some more active during bradycardia and some during tachycardia. Specifically, we show that the area postrema, known to be a center of cardiovascular integration, shows particularly strong encoding of heart rate, both following threat and during optogenetic cardiac pacing. We suggest that there may be neural mechanisms to assess heart rate changes over time, and that this interoceptive measurement is used to regulate other neural circuits and behavioral output.

neuroscience↗

Whole-brain, all-optical interrogation of neuronal dynamics underlying gut interoception in zebrafish

Internal signals from the body and external signals from the environment are processed by brain-wide circuits to guide behavior. However, the complete brain-wide circuit activity underlying interoception--the perception of bodily signals--and its interactions with sensorimotor circuits remain unclear due to technical barriers to accessing whole-brain activity at the cellular level during organ physiology perturbations. We developed an all-optical system for whole-brain neuronal imaging in behaving larval zebrafish during optical uncaging of gut-targeted nutrients and visuo-motor stimulation. Widespread neural activity throughout the brain encoded nutrient delivery, unfolding on multiple timescales across many specific peripheral and central regions. Evoked activity depended on delivery location and occurred with amino acids and D-glucose, but not L-glucose. Many gut-sensitive neurons also responded to swimming and visual stimuli, with brainstem areas primarily integrating gut and motor signals and midbrain regions integrating gut and visual signals. This platform links body-brain communication studies to brain-wide neural computation in awake, behaving vertebrates.

neuroscience↗

Correlative light and electron microscopy reveals the fine circuit structure underlying evidence accumulation in larval zebrafish

AbstractEvidence accumulation is a fundamental neural computation essential for adaptive behavior, yet its synaptic implementation remains unclear. Addressing this challenge critically depends on linking neural dynamics to circuit structure within the same brain. Here, we combine functional calcium imaging with large-scale ultrastructural electron microscopy (EM) to uncover the wiring logic of visual evidence accumulation in larval zebrafish. In a functionally imaged EM dataset of the anterior hindbrain, we identify conserved morphological cell types whose activity patterns define distinct computational roles. Bilateral inhibition, disinhibition, and recurrent connectivity emerge as key circuit motifs shaping these dynamics. To generalize our findings across animals, we develop a photoconversion-based pipeline to label and reconstruct functionally characterized neurons, enabling us to train a classifier that predicts functional identity from morphology alone. Applying this classifier to a second, whole-brain EM dataset lacking functional data reveals matching connectivity patterns, significantly augmenting its applicability for detailed circuit dissections. Based on these results, we develop and constrain a biophysically realistic neural network model that captures observed dynamics and yields predictions we tested and confirmed experimentally. Our work illustrates how hypothesis-driven connectomics can uncover the synaptic basis of sensory-motor computations and establishes a novel framework for cross-animal circuit dissection in the vertebrate brain.

neuroscience↗

Swimming motions evoke Ca2+ events in vascular endothelial cells of larval zebrafish via mechanical activation of Piezo1

Calcium signaling in blood vessels regulates their growth1,2, immune response3, and vascular tone4. Vascular endothelial cells are known to be mechanosensitive5-7, and it has been assumed that this mechanosensation mediates calcium responses to pulsatile blood flow8-10. Here we show that in larval zebrafish, the dominant trigger for vascular endothelial Ca2+ events comes from body motion, not heartbeat-driven blood flow. Through a series of pharmacological and mechanical perturbations, we showed that body motion is necessary and sufficient to induce endothelial Ca2+ events, while neither neural activity nor blood circulation is either necessary or sufficient. Knockout and temporally restricted knockdown of piezo1 eliminated the motion-induced Ca2+ events. Our results demonstrate that swimming-induced tissue motion is an important driver of endothelial Ca2+ dynamics in larval zebrafish. HighlightsO_LISwimming motions in larval zebrafish evoke large, rapid, and pervasive Ca2+ transients in vascular endothelial cells. C_LIO_LIThese Ca2+ transients do not require neural firing, muscular electrical activity, endocrine factors, or heart-driven blood flow. C_LIO_LIMechanical forces are necessary and sufficient for endothelial Ca2+ transients. C_LIO_LIEndothelial Ca2+ transients require the mechanosensitive ion channel Piezo1. C_LI

physiology↗

Paired and solitary ionocytes in the zebrafish olfactory epithelium

The sense of smell is generated by electrical currents that are influenced by the concentration of ions in olfactory sensory neurons and mucus. In contrast to the extensive morphological and molecular characterization of sensory neurons, there has been little description of the cells that control ion concentrations in the zebrafish olfactory system. Here, we report the molecular and ultrastructural characterization of zebrafish olfactory ionocytes. Transcriptome analysis suggests that the zebrafish olfactory epithelium contains at least three different ionocyte types, which resemble Na+/K+-ATPase-rich (NaR), H+-ATPase-rich (HR), and Na+/Cl- cotransporter (NCC) cells, responsible for calcium, pH, and chloride regulation, respectively, in the zebrafish skin. In the olfactory epithelium, NaR-like and HR-like ionocytes are usually adjacent to one another, whereas NCC-like cells are usually solitary. The distinct subtypes are differentially distributed: NaR-like/HR-like cell pairs are found broadly within the olfactory epithelium, whereas NCC-like cells reside within the peripheral non-sensory multiciliated cell zone. Comparison of gene expression and serial-section electron microscopy analysis indicates that the NaR-like cells wrap around the HR-like cells and are connected to them by shallow tight junctions. The development of olfactory ionocyte subtypes is also differentially regulated, as pharmacological Notch inhibition leads to a loss of NaR-like and HR-like cells, but does not affect NCC-like ionocyte number. These results provide a molecular and anatomical characterization of olfactory ionocytes in a stenohaline freshwater teleost. The paired ionocytes suggest that both transcellular and paracellular transport regulate ion concentrations in the olfactory epithelium, while the solitary ionocytes may enable independent regulation of ciliary beating.

neuroscience↗

Sleep Disruption Improves Performance in Simple Olfactory and Visual Decision-Making Tasks

Sleep disruption drastically impacts cognitive functions including decision-making and attention across many different species. In this study, we leveraged the small size and conserved vertebrate brain structure of larval zebrafish to investigate how sleep disruption modulates visual-and olfactory-decision-making. Strikingly, sleep disruption improved performance in both paradigms. Specifically, sleep disruption lengthens reaction times and increases correct decisions in a visual motion discrimination task, an effect that we attribute to longer integration periods in disrupted animals. Using a drift diffusion model, we predict specific circuit changes underlying these effects. Additionally, we demonstrate that sleep disruption heightens odor sensitivity in an olfactory decision-making task, likely mediated by cortisol. Our findings lay essential groundwork for investigating the brain circuit changes that arise from sleep disruption across species.

neuroscience↗