Biology subjects

Portugues, R.

Publications and source records attributed to Portugues, R..

At least 19 recordsLinked to original sources

bioRxiv2026

Innate sensorimotor policies constrain cerebellar adaptive correction

Innate sensorimotor policies enable rapid and reliable behavior but can become ineffective when environments change. How these policies interact with feedback-driven processes to support behavioral flexibility remains unclear. Using closed-loop virtual reality in larval zebrafish, we reversed the visual consequences of self-generated turns. Larvae initially followed their innate mapping and then rapidly switched to corrective turns in the opposite direction. Purkinje cell ablation abolished this correction while preserving innate optomotor responses. Imaging revealed outcome-invariant sensorimotor representations in granule cells and an outcome-dependent modulation of inferior olive neurons and Purkinje cells. Correction weakened as the optic-flow angle increased, despite persistent error-related representations. The innate behavioral repertoire also shifted as the optic-flow angle increased, making corrective turns less likely. An actor-critic model initialized with the measured behavioral repertoire reproduced the limits of correction. Together, these results show that adaptive behavior emerges from the interaction between an innate feed-forward policy and an olivo-cerebellar instructive signal, revealing innate behavioral structure as a fundamental constraint on cerebellar adaptation.

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bioRxiv2026

Behavioral alignment as an organizing principle in sensory coding

The ultimate goal of sensory coding is to extract and represent the cues required for adaptive motor output. This suggests that sensory codes and behavioral outcomes may align, and a variety of studies have argued that both biological and engineered sensory systems represent stimuli similarly when they play similar roles in behavior. However, the extent to which behavioral demands determine sensory coding throughout the brain is largely unknown. Here we propose that behavioral alignment is a general principle that organizes sensory representations, and we show that carefully measured behavior can predictively account for visual encoding across the entire zebrafish brain. We discover population codes that represent visual motion stimuli according to the optomotor responses elicited by them, indicating that information required for behavioral selection is explicitly encoded in sensory populations. Brain-like neuronal responses result when sensory codes are optimized for efficiency and aligned to behavior. These results provide a paradigm for understanding sensory representations through the behaviors they drive.

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bioRxiv2025

A multi-ring shifter network computes head direction in zebrafish

From insects to fish to mammals, many species have an internal compass: a set of recurrently connected neurons that combine motor feedback, vestibular signals, and external cues to compute the animals heading direction. Whether the underlying mechanism is universal across different species is unresolved. In Drosophila, for instance, the central complex contains three connected, yet anatomically separate, functional neuron rings. Two rings receive countervailing velocity signals that shift neuronal activity bumps around all three rings. An alternative, classical continuous-attractor model invokes only one ring but requires velocity-modulated synaptic connections. A single-ring compass has been discovered in the anterior hindbrain of zebrafish. Using theory and experiments, we find, however, that three rings, including two shifter rings, are intermingled on the same anatomical scaffold. Zebrafish and Drosophila, therefore, use the same basic compass mechanism, suggestive of convergent evolution.

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bioRxiv2025

Algorithmic dissection of optic flow memory in larval zebrafish

The visual stabilization behavior in the larval zebrafish reflects the history of optic flow experienced in the recent past. This integrative process has gained traction in recent years as a simplified, tractable model of working memory and decision-making. Yet, its algorithmic bases are poorly understood. In the present study, we first demonstrate that fish integrate externally generated optic flow over time, disregarding self-generated optic flow. This observation suggests that the fish integrates optic flow to better estimate the state of the environment, rather than to keep track of their position. Second, through reverse correlation and delay-based paradigms, we reveal multiple timescales involved in the optic flow integration. With the help of quantitative modeling, we show that the fish becomes more forgetful about the past optic flow in a more dynamic visual environment. Next, with whole-brain, light-sheet calcium imaging, we find that optic flow selective neurons throughout the brain exhibit neural signatures of motor efference copies, mirroring the behavioral findings. Lastly, with two photon calcium imaging, we show that inferior olive neurons integrate forward and backward flow separately, giving clues to how the multiple timescales of the optic flow integration is implemented. Overall, the results here refine our algorithmic and functional understanding of the history dependence of the visual stabilization behaviors in the larval zebrafish, paving the way for deciphering its circuit implementations.

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bioRxiv2025

A zebrafish circuit for behavioral credit assignment

Improving behavioral performance relies on the ability to associate decisions with their positive and negative outcomes. Although neurons that associate actions with their consequences have been identified across multiple brain regions, the circuit-level mechanisms underlying this integration remain poorly understood. Here, using an operant thermoregulatory assay, we show that larval zebrafish maintain a short-term memory of action-outcome associations and that the dorsal habenula-interpeduncular nucleus (dHb-IPN) pathway is necessary for this process. Consistently, a population of intermediate IPN neurons encodes actions only when they lead to a thermal reward, suggesting a major role in establishing short-term associations and influencing subsequent decisions. We then combine circuit mapping and axon imaging to show that actions and reward signals are conveyed by GABAergic prepontine and glutamatergic dHb neurons, respectively. Finally, the integration between motor and sensory streams relies on presynaptic GABAB receptor-mediated modulation of dHb axon terminals by prepontine neurons. These results link a crucial computation for adaptive behavior to a specific circuit mechanism.

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bioRxiv2025

Multimodal synapse analysis reveals restricted integration of transplanted neurons remodeled by TREM2

Neuron transplantation offers a promising approach for circuit restoration after injury, but depends crucially on adequate synaptic integration. Yet, our knowledge of the effects of the host injury environment on transplanted neuron (tN) network integration remains limited. Here, we used a stab wound injury model to examine how tN synapses mature and integrate using multimodal read-outs. Morphological, ultrastructural and functional electrophysiological analysis of tN synapses indicated that tN integration and functional maturation are partially stunted. Spatial transcriptomics revealed persistent inflammatory signatures at the transplant site including Trem2 upregulation. Strikingly, in an environment devoid of TREM2, synaptic integration as well as functional maturation of tNs, including action potential maturation and spontaneous firing, were almost fully rescued. Spatial transcriptomics further showed reduced inflammatory pathways and improved maturation of tNs in Trem2-/- brains. This study highlights the importance of tackling chronic inflammation for adequate tN integration.

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bioRxiv2024

Mechanisms for plastic landmark anchoring in zebrafish compass neurons

Vision is a sensory modality particularly important for navigation, as it can inform animals of their current heading (i.e. visual landmarks) as well as its changes (i.e. optic flow). It has been shown that head direction (HD) neurons in various species incorporate the visual cues into their heading estimates. However, circuit mechanisms underlying this process remain still elusive in vertebrates. Here, we asked if and how the recently identified HD cells in the larval zebrafish - one of the smallest vertebrate models - incorporate visual information. By combining two-photon microscopy with a panoramic virtual reality setup, we demonstrate that the zebrafish HD cells can reliably track the orientation of multiple visual scenes, exploiting both landmark and optic flow cues. The mapping between landmark cues and the heading estimates is idiosyncratic across fish, and experience-dependent. Furthermore, we show that the landmark tracking requires the lateralized projection from the habenula to the interpeduncular nucleus (IPN), where the HD neuron processes innervate. The physiological and morphological parallels suggest that a Hebbian mechanism similar to the fly ring neuron is at work in the habenula axons. Overall, the observations that the hindbrain HD cells of the larval zebrafish lacking an elaborate visual telencephalon shed new light on the evolution of the navigation circuitry in vertebrates.

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bioRxiv2024

Anatomical and functional organization of the interpeduncular nucleus in larval zebrafish

The habenulo-interpeduncular pathway is a highly conserved neural circuit across vertebrates, but the anatomical and functional architecture of the interpeduncular nucleus (IPN) remains poorly understood. Here, we use a combination of immunohistochemistry, volumetric electron microscopy (EM), and two-photon imaging to provide the first detailed characterization of the internal organization of the IPN in larval zebrafish. We show that the IPN receives extensive projections from the tegmentum, and reveal a strict segregation between the dorsal (dIPN) and ventral (vIPN) subcircuits, with minimal cross-communication. In the dIPN, we characterise in detail the inputs and outputs of r1{pi} neurons, which have been recently identified as representing the animals heading direction. In the vIPN, we identify six distinct glomerular structures, each exhibiting specific patterns of reciprocal connections and projection pathways. Finally, we demonstrate that the connectivity and spontaneous activity patterns of habenular axons are shaped by the local anatomical features of the IPN, suggesting a role for the local interneurons in modulating presynaptic dynamics. Together, these results enhance our understanding of the internal organization of the IPN, and provide a framework for future investigations into both its physiology and its involvement in behavior.

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bioRxiv2024

The representation of visual motion and landmark position aligns with heading direction in the zebrafish interpeduncular nucleus

Sensory information is fundamental for navigation. Visual motion is used by animals to estimate their traveling distance and direction, and visual landmarks allow animals to tether their location and orientation to their environment. How such signals are integrated in the vertebrate brain is poorly understood. Here we investigate the representation of directional whole field visual motion and landmark position in a circuit in the larval zebrafish consisting of the habenula, interpeduncular nucleus (IPN) and anterior hindbrain (aHB). This circuit has been recently implicated in the representation of heading direction. Using calcium imaging we show that these stimuli are represented in the habenula, IPN and aHB. We further show that their representation in the IPN of both these stimuli is topographically arranged in a way that aligns itself with the representation of the heading signal in this region. We use neuronal ablations to show that the landmark responses, but not the whole field motion responses, require intact habenula input to the IPN. Overall our findings suggest the IPN as a site for integration of the heading signal from the aHB with visual information, shedding light on how different types of navigational signals are processed in the vertebrate brain.

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bioRxiv2023

The Preoptic Area and Dorsal Habenula Jointly Support Homeostatic Navigation in Larval Zebrafish

Animals must maintain physiological processes within an optimal temperature range despite changes in their environment. While the preoptic area of the hypothalamus (PoA) acts as a thermostat in mammals through autonomic and behavioral adaptations, its role in temperature regulation of animals lacking internal homeostatic mechanisms is not known. Through novel behavioral assays, wholebrain functional imaging and neural ablations, we show that larval zebrafish achieve thermoregulation through movement and a neural network connecting the PoA to brain areas enabling spatial navigation. PoA drives reorientation when thermal conditions are worsening and conveys this information for instructing future motor actions to the navigation-controlling habenula (Hb) - interpeduncular nucleus (IPN) circuit. These results suggest a conserved function of the PoA in thermoregulation acting through species- specific neural networks. We propose that homeostatic navigation arose from an ancient chemotaxis navigation circuit that was subsequently extended to serve in other sensory modalities.

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bioRxiv2023

Dimensionality reduction reveals separate translation and rotation populations in the zebrafish hindbrain

In many brain areas, neuronal activity is associated with a variety of behavioral and environmental variables. In particular, neuronal responses in the zebrafish hindbrain relate to oculomotor and swimming variables, as well as sensory information. However, the precise functional organization of the neurons has been difficult to unravel since neuronal responses are heterogeneous. Here we used dimensionality reduction methods on neuronal population data to reveal the role of the hindbrain in visually-driven oculomotor behavior and swimming. We imaged neuronal activity in zebrafish expressing GCaMP6s in the nucleus of almost all neurons, while monitoring the behavioral response to gratings that rotated with different speeds. We then used reduced-rank regression, a method that condenses the sensory and motor variables into a smaller number of features, to predict the fluorescence traces of all ROIs (regions of interest). Despite the potential complexity of the visuo-motor transformation, our analysis revealed that the bulk of population activity can be explained by only two features. Based on the contribution of these features to each ROIs activity, ROIs formed three clusters. One cluster was related to vergent movements and swimming, whereas the other two clusters related to leftward and rightward rotation. Voxels corresponding to these clusters were segregated anatomically, with leftward and rightward rotation clusters located selectively to the left and right hemispheres, respectively. Just as described in many cortical areas, our analysis revealed that single neuron complexity co-exists with a simpler population-level description, thereby providing insights into the organization of visuo-motor transformations in the hindbrain.

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bioRxiv2022

Comparing the representation of a simple visual stimulus across the cerebellar network

The cerebellum is a highly conserved structure of the vertebrate central nervous system that plays a role in the timing and calibration of motor sequences. Its function is supported by the convergence of fibers from granule cells (GCs) and inferior olive neurons (IONs) onto Purkinje cells (PCs). Theories of cerebellar function postulate that IONs convey error signals to PCs that, paired with the contextual information provided by GCs, can be used as a teaching signal to guide motor learning. Here, we use the larval zebrafish to investigate (i) how sensory representations of the same stimulus vary across GCs and IONs and (ii) how PC activity reflects these two different input streams. We use population calcium imaging to measure the cell responses to flashes of diverse luminance and duration to show that IONs and GCs encode different stimulus properties. First, most GCs show tonic and graded responses, as opposed to IONs, whose activity peaks only at on and off luminance transitions, in agreement with the notion that GCs and IONs encode context and error information, respectively. Secondly, we show that GC activity is patterned over time: some neurons had sustained responses for the entire duration of the stimulus, while in others activity was ramping up with slow time constants. This suggests that, by performing temporal integration, GCs could provide a basis that PCs may use to decode time. Finally, we show how PC activity can be largely reconstructed by a linear combination of granule cells and inferior olive neurons. Together, our observations give support to the notion of an error signal coming from IONs, and provide the first experimental evidence for a temporal patterning of GC activity over many seconds.

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bioRxiv2022

Neural dynamics and architecture of the heading direction circuit in a vertebrate brain

Animals can use different strategies to navigate. They may guide their movements by relying on external cues in their environment or, alternatively, by using an internal cognitive map of the space around them and their position within it. An essential part of this representation are heading cells, neurons whose activity depends on the heading direction of the animal. Although those cells have been found in vertebrates, the full network has never been observed and there is very little mechanistic understanding of how these cells acquire their response properties. In this study, we use volumetric functional imaging in larval zebrafish to observe, for the first time in a vertebrate, a full network that encodes allocentric heading direction. This network of approximately one hundred inhibitory neurons is arranged in an anatomical circle in the anterior hindbrain. Its activity is driven purely by the integration of internally generated signals, indicating that a simple vertebrate brain can encode maps of how an animal moves within its surroundings. Single cell reconstructions of electron micrographs allow us to uncover how the connectivity pattern of neurons within the network supports the implementation of a ring attractor network. The neurons we identify share features with neurons in the dorsal tegmentum nucleus of rodents and the fly central complex, showing that similar connectivity and mechanistic principles underlie the generation of cognitive maps of heading direction across the animal kingdom.

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bioRxiv2021

Structural and functional organization of visual responses in the inferior olive of larval zebrafish

The olivo-cerebellar system plays an important role in vertebrate sensorimotor control. According to a classical theory of cerebellar cortex, the inferior olive (IO) provides Purkinje cells with error information which drives motor learning in the cerebellum. Here we investigate the sensory representations in the IO of larval zebrafish and their spatial organization. Using single-cell labeling of genetically identified IO neurons we find that they can be divided into at least two distinct groups based on their spatial location, dendritic morphology, and axonal projection patterns. In the same genetically targeted population, we recorded calcium activity in response to a set of visual stimuli using 2-photon imaging. We found that most IO neurons showed direction selective and binocular responses to visual stimuli and that functional properties were spatially organized within the IO. Light-sheet functional imaging that allowed for simultaneous activity recordings at the soma and axonal level revealed tight coupling between soma location, axonal projections and functional properties of IO neurons. Taken together, our results suggest that anatomically-defined classes of inferior olive neurons correspond to distinct functional types, and that topographic connections between IO and cerebellum contribute to organization of the cerebellum into distinct functional zones.

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bioRxiv2021

Functional and ultrastructural analysis of reafferent mechanosensation in larval zebrafish

All animals need to differentiate between exafferent stimuli, which are caused by the environment, and reafferent stimuli, which are caused by their own movement. In the case of mechanosensation in aquatic animals, the exafferent inputs are water vibrations in the animals proximity, which need to be distinguished from the reafferent inputs arising from fluid drag due to locomotion. Both of these inputs are detected by the lateral line, a collection of mechanosensory organs distributed along the surface of the body. In this study, we characterize in detail how the hair cells, which are the receptor cells of the lateral line, discriminate between such reafferent and exafferent signals in zebrafish larvae. Using dye labeling of the lateral line nerve, we visualize two parallel descending inputs that can influence lateral line sensitivity. We combine functional imaging with ultra-structural EM circuit reconstruction to show that cholinergic signals originating from the hindbrain transmit efference copies that cancel out self-generated reafferent stimulation during locomotion, and that dopaminergic signals from the hypothalamus may have a role in threshold modulation both in response to locomotion and salient stimuli. We further gain direct mechanistic insight into the core components of this circuit by loss-of-function perturbations using targeted ablations and gene knockouts. We propose that this simple circuit is the core implementation of mechanosensory reafferent suppression in these young animals and that it might form the first instantiation of state-dependent modulation found at later stages in development.

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bioRxiv2021

Oligodendrocyte Precursor Cells Sculpt the Visual System by Regulating Axonal Remodeling

Many oligodendrocyte precursor cells (OPCs) do not differentiate to form myelin, suggesting additional roles of this cell population. The zebrafish optic tectum contains OPCs in regions devoid of myelin. Elimination of these OPCs impaired precise control of retinal ganglion cell axon arbor size during formation and maturation of retinotectal connectivity, and in consequence impaired visual acuity. Therefore, OPCs fine-tune neural circuit structure and function independently of their canonical role to make myelin.

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bioRxiv2020

The cerebellum recalibrates a feedback controller involved in motor control

Animals must adapt their behavior to survive in a changing environment. Behavioral adaptations can be evoked by two mechanisms: feedback control and internal-model-based control. Feedback controllers can maintain the sensory state of the animal at a desired level under different environmental conditions. In turn, internal models learn the relationship between behavior and resulting sensory consequences in order to modify the behavior when this relationship changes. Here, we present multiple perturbations in visual feedback to larval zebrafish performing the optomotor response and show that they react to these perturbations through a feedback control mechanism. In contrast, if a perturbation is long-lasting, fish adapt their behavior by updating a cerebellum-dependent internal model. We use modelling and functional imaging to show that neuronal requirements for these mechanisms are met in the larval zebrafish brain. Our results illustrate the role of the cerebellum in encoding internal models and how these can calibrate neuronal circuits involved in reactive behaviors depending on the interactions between animal and environment. HighlightsO_LIBehavioral reactions to unexpected changes in visual feedback are implemented by a feedback control mechanism C_LIO_LIA long-lasting change in visual feedback updates the state of the neuronal controller C_LIO_LIThe cerebellar internal model mediates this recalibration C_LI

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bioRxiv2019

Valence and state-dependent population coding in dopaminergic neurons in the fly mushroom body

Neuromodulation permits flexibility of synapses, neural circuits and ultimately behavior. One neuromodulator, dopamine, has been studied extensively in its role as reward signal during learning and memory across animal species. Newer evidence suggests that dopaminergic neurons (DANs) can modulate sensory perception acutely, thereby allowing an animal to adapt its behavior and decision-making to its internal and behavioral state. In addition, some data indicate that DANs are heterogeneous and convey different types of information as a population. We have investigated DAN population activity and how it could encode relevant information about sensory stimuli and state by taking advantage of the confined anatomy of DANs innervating the mushroom body (MB) of the fly Drosophila melanogaster. Using in vivo calcium imaging and a custom 3D image registration method, we find that the activity of the population of MB DANs is predictive of the innate valence of an odor as well as the metabolic and mating state of the animal. Furthermore, DAN population activity is strongly correlated with walking or running, consistent with a role of dopamine in conveying behavioral state to the MB. Together our data and analysis suggest that distinct DAN population activities encode innate odor valence, movement and physiological state in a MB-compartment specific manner. We propose that dopamine shapes innate odor perception through combinatorial population coding of sensory valence, physiological and behavioral context.

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