Biology subjects

Panier, T.

Publications and source records attributed to Panier, T..

12 recordsLinked to original sources

bioRxiv2026

Fiber-Coupled Rotating Two-Photon Light-Sheet Microscopy for Physiological Vestibular Imaging in Larval Zebrafish

Physiological vestibular stimulation requires macroscopic rotation of the animal, making simultaneous high-resolution neural imaging technically demanding. Here we present a fiber-coupled rotating two-photon light-sheet microscope for physiological pitch-axis vestibular imaging in larval zebrafish. Two-photon excitation is attractive in this context because near-infrared excitation avoids visible-light contamination of the visual environment. Femtosecond pulses were delivered to the rotating microscope through a broadband hollow-core negative-curvature fiber previously characterized in static light-sheet configurations. The rotating instrument maintained the axial mechanical stability required for cellular-resolution imaging, with submicron mean axial displacement over the characterized angular range. Fiber performance under rotation was also stable: bend-induced transmission changes were small in the relevant curvature regime, and circular input polarization suppressed rotation-dependent polarization artefacts to below 1\% in the sample plane. The dominant rotation-sensitive optical limitation was not the fiber but perturbation of the thermal lens in the sample chamber. Reducing fluid motion along the excitation path suppressed this artefact and restored stable imaging during dynamic rotation. With this system, we recorded brain-wide vestibular responses during sinusoidal pitch stimulation and resolved anatomically organized cellular response patterns across the brain. These results establish rotating two-photon light-sheet microscopy as a practical solution for vestibular imaging in experiments that require physiological stimulation together with darkness or controlled visual conditions.

neuroscience↗

bioRxiv2025

A sensorimotor instability drives a locomotor transition during fish development

Animals rely on movement to survive -- to explore their environment, find food and mates and avoid danger. During development, changes in body shape, muscle strength and physiological needs drive the continuous adjustment of locomotor patterns. How these changes are orchestrated in a flexible and adaptive manner remains unknown. We explore this question in Danionella cerebrum, a miniature freshwater fish that is emerging as an important vertebrate model in systems neuroscience. We identify a clear transition in locomotion, from continuous to burst-and-coast swimming occurring around 3 weeks of age. We demonstrate that this transition is an energy saving strategy, and that it reflects an insta-bility in the sensorimotor process governing speed regulation. Rather than a preprogrammed developmental switch, it is therefore directly tied to the animal swimming strength. We confirmed this finding by manipulating sensory feedback in order to induce a similar transition at fixed developmental stages. Together, our results illustrate a dynamic interplay between body, brain, and environment during development, offering new insights into the principles governing adaptive locomotion.

biophysics↗

bioRxiv2025

Logarithmic coding leads to adaptive stabilization in the presence of sensorimotor delays

Animals respond to sensory stimuli with motor actions, which in turn generate new sensory inputs. This sensorimotor loop is constrained by time delays that impose a trade-off between responsiveness and stability. Additionally, as the relationship between a motor command and the corresponding sensory feedback is context-dependent, the response must be adapted in real time. It is generally believed that this adaptation process relies on an internal model that is continuously updated through prediction error minimization. Here, we experimentally reveal an alternative strategy based on a simpler feedback mechanism that does not require any internal model. We developed a virtual reality system for the miniature transparent fish Danionella cerebrum that enables in vivo brain-wide imaging during fictive navigation. By systematically manipulating the feedback parameters, we dissected the motor control process that allows the animal to stabilize its position using optic flow. The sensorimotor loop can be fully described by a single delay differential equation, whose solutions quantitatively capture the observed behavior across all experimental conditions. Both behavioral and neural data indicate that the observed adaptive response arises from the logarithmic nonlinearities at the sensory (Weber-Fechner law) and motor (Hennemans size principle) ends. These fundamental properties of the nervous system, conserved across species and sensory modalities, have traditionally been interpreted in terms of efficient coding. Our findings unveil a distinct functional role for such nonlinear transformations: ensuring stability in sensorimotor control despite inherent delays and sensory uncertainty.

neuroscience↗

bioRxiv2025

Experimental and theoretical approaches reveal that antimicrobial blue light killing efficiency decreases with biofilm growth in a Pseudomonas aeruginosa model.

Recently, the use of antimicrobial blue light (aBL) has gained interest across various applications. However, a comprehensive framework that addresses the key factors driving bacterial photoinhibition remains lacking--particularly concerning biofilms, the predominant bacterial lifestyle. The goal of this work was to evaluate the potential of photokilling in this wide-spread microbial adherent community type, and to decipher the specific mechanisms at stake. To investigate aBL killing efficiency, we conducted experiments in a Pseudomonas aeruginosa biofilm model using a well-defined millifluidic device that allows real-time microscopy and quantitative analysis of a living biofilm under local irradiation at a defined light dose. In addition, we developed a theoretical model for light-biofilm interaction that accounts for the threedimensional structure of the bacterial biofilm. To inform our model, we examined the light doseresponse in isolated cells and found a profile indicative of a multi-target mechanism of lethality. By comparing the experimental and theoretical results, we identified a loss in killing efficiency as the biofilm grows, due in part to the increase in thickness of the living material inherent to this mode of development. Our findings also highlight a reduction in the intrinsic bacterial sensitivity to blue light as biofilm development progresses, which we attribute to the low oxygen levels typical of densely populated bacterial environments. These findings reveal new features of the photokilling mechanism and redefine the approach to designing effective antimicrobial photoinactivation strategies by integrating the key physical characteristics of bacterial biofilms. Significance StatementAwareness of the bacterial worlds global importance is steadily growing in both science and society. Among the critical challenges, the continuing increase in multidrug resistance to antibiotics represents a major public health concern reinforcing the urgency of alternative antimicrobial therapies with photoinactivation as a promising approach. However, its full potential can only be achieved through a better understanding of the involved mechanisms in relevant environments. In this study, we combined experimental and theoretical approaches to investigate the photoinactivation of bacteria within a developing biofilm, the dominant bacterial lifestyle. Our comprehensive analysis sheds light on the mechanisms and limitations of photoinactivation in the fight against microbes, which is essential for designing novel antibacterial phototherapies.

biophysics↗

bioRxiv2025

Non-invasive characterization of oocyte deformability in micro-constrictions

Oocytes naturally present mechanical defects that hinder their development after fertilization. Thus, in the context of assisted reproduction, oocyte selection based on their mechanical properties has great potential to improve the quality of the resulting embryos and the success rate of these procedures. However, the use of mechanical properties as a quantifiable selective criterion requires robust and non-destructive measurement tools. This study developed a constriction-based microfluidic device that monitors the deformation of mouse oocytes under controlled pressure. The device can distinguish mechanically aberrant oocyte groups from healthy control ones. Based on a mathematical model, we propose that deformability measurements infer both oocyte tension and elasticity, elasticity being the most discriminating factor in our geometry. Despite force transmission during oocyte deformation, no long-term damage was observed. This non-invasive characterization of mouse oocyte deformability in micro-constrictions allows for a significant advance in assessing the mechanical properties of mammalian oocytes and has potential application as a quantifiable selective criterion in medically assisted reproduction. TeaserA measurement method for translating advances in oocyte mechanics into selection criteria for improving medically assisted reproduction.

developmental biology↗

bioRxiv2023

A Versatile and Open Source One- and Two-Photon Light-Sheet Microscope Design

Two-photon light sheet microscopy offers great potential for a range of biological applications. Still, its practical implementation is impeded by the high cost of laser sources, the complexity of construction, and the challenges associated with adapting to existing microscope setups. Here, we release an open-source design that addresses these limitations by providing detailed building instructions for transforming a brightfield microscope into a versatile one- and two-photon light sheet system. Our design incorporates a specially designed broadband hollow core fiber, enabling the simultaneous utilization of visible laser alongside an expansive pulsed laser source from another setup. This integration allows for uncompromised image resolution and speed. Furthermore, the design reduces the complexity of construction, alignment, and overall cost, thereby significantly enhancing the accessibility of this technology (https://github.com/LJPZebra/OLU).

neuroscience↗

bioRxiv2023

Magnetic actuation of otoliths allows behavioral and brain-wide neuronal exploration of vestibulo-motor processing in larval zebrafish.

The vestibular system in the inner ear plays a central role in sensorimotor control by informing the brain about the orientation and acceleration of the head. However, most experiments in neurophysiology are performed using head-fixed configurations, depriving animals of vestibular inputs. To overcome this limitation, we decorated the utricular otolith of the vestibular system in larval zebrafish with paramagnetic nanoparticles. This procedure effectively endowed the animal with magneto-sensitive capacities: applied magnetic field gradients induced forces on the otoliths resulting in robust behavioral responses comparable to that evoked by rotating the animal by up to 25{degrees}. We recorded the whole-brain neuronal response to this fictive motion stimulation using light-sheet functional imaging. Experiments performed in unilaterally injected fish revealed the activation of a commissural inhibition between the brain hemispheres. This magnetic-based stimulation technique for larval zebrafish opens new perspectives to functionally dissect the neural circuits underlying vestibular processing and to develop multisensory virtual environments, including vestibular feedback. HighlightsO_LIAfter injecting a ferrofluid into the inner ear of a larval zebrafish, the ear-stones can be actuated via magnetic forces. C_LIO_LIThis method allows one to elicit vestibular-like behavioral responses without impairing physiological inner ear functions. C_LIO_LIIt is compatible with brain-scale functional imaging and thus offers a promising avenue to investigate the neural underpinnings of vestibular-driven behaviors. C_LI eTOCFerrofluid injection into zebrafish inner ear allows magnetic manipulation of ear-stones to evoke vestibular responses in static animals. This in vivo method is compatible with brain-scale imaging, offering a promising approach to investigate neural mechanisms underlying vestibular-driven behaviors.

neuroscience↗

bioRxiv2021

Evolutionary divergence of locomotion in two related vertebrate species

Locomotion exists in diverse forms in nature and is adapted to the environmental constraints of each species1. However, little is known about how closely related species with similar neuronal circuitry can evolve different navigational strategies to explore their environments. We established a powerful approach in comparative neuroethology to investigate evolution of neuronal circuits in vertebrates by comparing divergent swimming pattern of two closely related larval fish species, Danionella translucida (DT) and Danio rerio or zebrafish (ZF)2,3. During swimming, we demonstrate that DT utilizes lower half tail-beat frequency and amplitude to generate a slower and continuous swimming pattern when compared to the burst-and-glide swimming pattern in ZF. We found a high degree of conservation in the brain anatomy between the two species. However, we revealed that the activity of a higher motor region, referred here as the Mesencephalic Locomotion Maintenance Neurons (MLMN) correlates with the duration of swim events and differs strikingly between DT and ZF. Using holographic stimulation, we show that the activation of the MLMN is sufficient to increase the frequency and duration of swim events in ZF. Moreover, we propose two characteristics, availability of dissolved oxygen and timing of swim bladder inflation, which drive the observed differences in the swim pattern. Our findings uncover the neuronal circuit substrate underlying the evolutionary divergence of navigational strategies and how they are adapted to their respective environmental constraints.

neuroscience↗

bioRxiv2020

Larval zebrafish use olfactory detection of sodium and chloride to avoid salt-water

Salinity levels constrain the habitable environment of all aquatic organisms. Zebrafish are freshwater fish that cannot tolerate high salt environments and would, therefore, benefit from neural mechanisms that enable the navigation of salt gradients to avoid high salinity. Yet, zebrafish lack epithelial sodium channels, the primary conduit land animals use to taste sodium. This suggests fish may possess novel, undescribed mechanisms for salt detection. In the present study, we show that zebrafish, indeed, respond to small temporal increases in salt by reorienting more frequently. Further, we use calcium imaging techniques to identify the olfactory system as the primary sense used for salt detection, and we find that a specific subset of olfactory receptor neurons encodes absolute salinity concentrations by detecting monovalent anions and cations. In summary, our study establishes that zebrafish larvae have the ability to navigate, and thus detect salinity gradients, and that this is achieved through previously undescribed sensory mechanisms for salt detection.

neuroscience↗

bioRxiv2019

From behavior to circuit modeling of light-seeking navigation in zebrafish larvae

Bridging brain-scale circuit dynamics and organism-scale behavior is a central challenge in neuroscience. It requires the concurrent development of minimal behavioral and neural circuit models that can quantitatively capture basic sensorimotor operations. Here we focus on light-seeking navigation in zebrafish larvae. Using a virtual reality assay, we first characterize how motor and visual stimulation sequences govern the selection of discrete swim-bout events that subserve the fish navigation in the presence of a distant light source. These mechanisms are combined into a comprehensive Markov-chain model of navigation that quantitatively predict the stationary distribution of the fishs body orientation under any given illumination profile. We then map this behavioral description onto a neuronal model of the ARTR, a small neural circuit involved in the orientation-selection of swim bouts. We demonstrate that this visually-biased decision-making circuit can similarly capture the statistics of both spontaneous and contrast-driven navigation.

animal behavior and cognition↗

bioRxiv2019

Probabilistic Models of Larval Zebrafish Behavior: Structure on Many Scales

Nervous systems have evolved to combine environmental information with internal state to select and generate adaptive behavioral sequences. To better understand these computations and their implementation in neural circuits, natural behavior must be carefully measured and quantified. Here, we collect high spatial resolution video of single zebrafish larvae swimming in a naturalistic environment and develop models of their action selection across exploration and hunting. Zebrafish larvae swim in punctuated bouts separated by longer periods of rest called interbout intervals. We take advantage of this structure by categorizing bouts into discrete types and representing their behavior as labeled sequences of bout-types emitted over time. We then construct probabilistic models - specifically, marked renewal processes - to evaluate how bout-types and interbout intervals are selected by the fish as a function of its internal hunger state, behavioral history, and the locations and properties of nearby prey. Finally, we evaluate the models by their predictive likelihood and their ability to generate realistic trajectories of virtual fish swimming through simulated environments. Our simulations capture multiple timescales of structure in larval zebrafish behavior and expose many ways in which hunger state influences their action selection to promote food seeking during hunger and safety during satiety.

animal behavior and cognition↗

bioRxiv2018

Whole-brain calcium imaging during physiological vestibular stimulation in larval zebrafish

During in vivo functional imaging, animals are head-fixed and thus deprived from vestibular inputs, which severely hampers the design of naturalistic virtual environments. To overcome this limitation, we developed a miniaturized ultra-stable light-sheet microscope that can be dynamically rotated during imaging along with a head-restrained zebrafish larva. We demonstrate that this system enables whole-brain functional imaging at single-cell resolution under controlled vestibular stimulation. We recorded for the first time the dynamic whole-brain response of a vertebrate to physiological vestibular stimulation. This development largely expands the potential of virtual-reality systems to explore complex multisensory-motor integration in 3D.

neuroscience↗