Biology subjects

Lemieux, M.

Publications and source records attributed to Lemieux, M..

8 recordsLinked to original sources

bioRxiv2026

Signatures of brain-wide functional maturation in larval zebrafish

Brain development involves the coordinated organization of cellular activity into distributed functional networks, yet how this organization emerges across an entire vertebrate brain remains poorly understood. Here, we combined brain-wide structural and functional imaging to characterize brain maturation in larval zebrafish from 4 to 8 days post-fertilization. Brain growth was regionally heterogeneous and accompanied by progressive remodeling of mesoscale functional networks, with functional connectivity strengthening or weakening within distinct subnetworks. Spontaneous activity became more correlated in regions exhibiting pronounced neurogenesis, as revealed by HaloTag-based neuronal birthdating. Functional interactions became progressively less constrained by physical distance, while network organization became more modular, suggesting that long-range functional integration develops alongside increasing segregation of large-scale brain systems. At the cellular level, neuronal activity consolidated into larger, more modular functional ensembles whose combinations increasingly differentiated mesoscale modules. Visually responsive neurons redistributed along visual processing pathways, becoming more prevalent in regions further removed from retinal input, while motor-related activity declined broadly across the brain. The forebrain emerged as a major locus of maturation, exhibiting substantial anatomical expansion and a growing population of neurons displaying intrinsic activity fluctuations distinct from sensory and motor processes. Together, these findings reveal coordinated anatomical, cellular, and network-level signatures of early vertebrate brain maturation.

neuroscience↗

bioRxiv2025

A balanced circadian glycolytic rhythm drives cardiomyocyte cell cycle progression during fish heart regeneration.

The ability of heart tissue to repair itself after injury has fascinated scientists for decades1,2. Researchers have long studied the internal body clock, or circadian rhythm, for its role in coordinating daily cycles of metabolism and cell activity3,4, but its relevance to heart repair has remained unknown. This study explores, for the first time, whether natural daily rhythms influence heart regeneration--a process driven by cardiomyocyte proliferation. We discovered that DNA replication, mitosis, oxidative phosphorylation, and glycolysis follow a precise daily order in regenerating zebrafish hearts. Disrupting core clock gene expression abolishes the rhythms of glycolysis and mitosis, preventing cardiomyocyte cell cycle progression and regeneration. Insulin-resistant Astyanax mexicanus cavefish, which have adapted to dark caves, similarly show a loss of mitosis rhythm and cardiomyocyte cell cycle progression, which we find is caused by reduced glycolysis. Despite this reduction, glycolysis rhythm displays a larger amplitude in cavefish--a pattern recapitulated in insulin-resistant zebrafish. Insulin resistance resets metabolic rhythms to the morning, which is equally detrimental to regeneration. Here, we show that successful cardiac regeneration depends on synchronised clock and glucose rhythms, which together orchestrate the cell cycle events essential for cardiomyocyte proliferation and tissue repair.

physiology↗

bioRxiv2024

Structural and genetic determinants of zebrafish functional brain networks

Network science has significantly advanced our understanding of brain networks across species, revealing universal connectivity principles. While human studies based on magnetic resonance imaging (MRI) have established several network principles at macroscopic scales, recent breakthroughs, including high-amplitude regional co-activation patterns and spatially contiguous functional gradients, remain unexplored at cellular resolution in animal models. Here, we employ whole-brain functional imaging at cellular resolution in larval zebrafish, combined with anatomical and spatial genetic expression profile databases, to investigate the structural and genetic basis of functional brain networks. We show that mesoscopic functional connectivity (FC) is a robust measure of brain activity that captures the individuality of larvae. Using a public dataset of thousands of single-neuron reconstructions, we reveal a strong coupling between FC and structural connectivity (SC). Numerous properties of the connectome that account for indirect pathways and diffusion mechanisms individually and collectively predict interregional correlations. The hierarchical modular structure of SC and FC significantly overlaps in space, and modules identified within the connectome constrain the shape of both spontaneous and stimulus-driven activity patterns. Using visual stimuli and tail monitoring, we identify a functional network gradient that maps onto the sensorimotor function of brain regions. Finally, we identify a set of genes whose co-expression in brain regions significantly predicts regional FC. Our findings reproduce several key features of mammalian brain networks in zebrafish, demonstrating the potential for studying large-scale network phenomena in smaller, optically accessible vertebrate brains.

neuroscience↗

bioRxiv2024

Effects of intergenerational transmission of small intestinal bacteria cultured from stunted Bangladeshi children with enteropathy

Environmental enteric dysfunction (EED), a small intestinal disorder found at a high prevalence in stunted children, is associated with gut mucosal barrier disruption and decreased absorptive capacity1-4. To test the hypothesis that intergenerational transmission of a perturbed small intestinal microbiota contributes to undernutrition by inducing EED5, we characterized two consortia of bacterial strains cultured from duodenal aspirates from stunted Bangladeshi children with EED - one of which induced local and systemic inflammation in female gnotobiotic mice. Offspring of dams colonized with the inflammatory consortium exhibited impaired prenatal and postnatal growth, as well as immunologic changes phenocopying features of EED in children. Dam-to-pup transmission of the inflammatory consortium produced, in recently weaned offspring, alterations in inter-cellular signaling pathways related to intestinal epithelial cell renewal, barrier integrity and immune function. Cohousing of mice harboring the inflammatory or non-inflammatory consortia and subsequent screening of candidate disease-promoting bacterial isolates identified Campylobacter concisus, an organism typically found in the oral microbiota, as a contributor to enteropathy. The C. concisus strain induced, in a host nitric oxide synthase (NOS)-dependent manner, pro-inflammatory cytokine signaling. Moreover, host-derived nutrients generated by NOS augmented C. concisus growth. This preclinical model should facilitate identification of small intestinal microbiota-targeted therapeutics for (intergenerational) undernutrition.

systems biology↗

bioRxiv2024

Development of sensorimotor responses in larval zebrafish: a comparison between wild-type and GCaMP6s transgenic line

During early development, zebrafish larvae exhibit stereotypical behaviors, which rapidly become more complex. Thus, the generation of mutant transgenic lines that maintain transparency throughout their larval stage and that can be used to record brain activity has offered strategic opportunities to investigate the underlying neural correlates of behavior establishment. However, few studies have documented the behavioral profile of these lines during larval development. Here, we set up a behavioral characterization using diverse stimuli (light and vibration) throughout larval development to compare the responses of a transgenic strain expressing a pan-neuronal calcium indicator (GCaMP6s) with that of a wild-type strain. Interestingly, we report a drastic switch in behavioral responses to light transitions at 11 days post-fertilization (dpf) and to vibration stimuli at 14 dpf in both lines. These data highlight a specific time window of behavioral complexification. Meanwhile, we found no major difference in the maturation of sensorimotor responses between GCaMP6s and wild-type strains. Thus, these results support using GCaMP6s strain in investigating the neural mechanisms underlying the developmental maturation of sensorimotor responses. We observed nevertheless some minor differences that suggest careful attention should be taken when using mutant/transgenic lines for behavioral studies. Highlights- Longitudinal investigation of sensorimotor responses by zebrafish during their larval development - During the second week of development, larval zebrafish switch their motor response to light transition - Pan-neuronal nuclear expression of GCaMP6s has little impact on larval fish response to various stimuli

neuroscience↗

bioRxiv2024

Quantitative Analysis of Miniature Synaptic Calcium Transients Using Positive Unlabeled Deep Learning

Ca2+ imaging methods are widely used for studying cellular activity in the brain, allowing detailed analysis of dynamic processes across various scales. Enhanced by high-contrast optical microscopy and fluorescent Ca2+ sensors, this technique can be used to reveal localized Ca2+ fluctuations within neurons, including in sub-cellular compartments, such as the dendritic shaft or spines. Despite advances in Ca2+ sensors, the analysis of miniature Synaptic Calcium Transients (mSCTs), characterized by variability in morphology and low signal-to-noise ratios, remains challenging. Traditional threshold-based methods struggle with the detection and segmentation of these small, dynamic events. Deep learning (DL) approaches offer promising solutions but are limited by the need for large annotated datasets. Positive Unlabeled (PU) learning addresses this limitation by leveraging unlabeled instances to increase dataset size and enhance performance. This approach is particularly useful in the case of mSCTs that are scarce and small, associated with a very small proportion of the foreground pixels. PU learning significantly increases the effective size of the training dataset, improving model performance. Here, we present a PU learning-based strategy for detecting and segmenting mSCTs. We evaluate the performance of two 3D deep learning models, StarDist-3D and 3D U-Net, which are well established for the segmentation of small volumetric structures in microscopy datasets. By integrating PU learning, we enhance the 3D U-Nets performance, demonstrating significant gains over traditional methods. This work pioneers the application of PU learning in Ca2+ imaging analysis, offering a robust framework for mSCT detection and segmentation. We also demonstrate how this quantitative analysis pipeline can be used for subsequent mSCTs feature analysis. We characterize morphological and kinetic changes of mSCTs associated with the application of chemical long-term potentiation (cLTP) stimulation in cultured rat hippocampal neurons. Our data-driven approach shows that a cLTP-inducing stimulus leads to the emergence of new active dendritic regions and differently affects mSCTs subtypes.

bioinformatics↗

bioRxiv2022

Functional Contribution of Mesencephalic Locomotor Region Nuclei to Locomotor Recovery After Spinal Cord Injury

Spinal cord injury (SCI) results in a disruption of information between the brain and the spinal locomotor circuit. Although the spinal cord contains all the neural circuits to generate locomotion, people with SCI are unable to walk due to the absence of descending commands from the brain. Electrical stimulation of supraspinal locomotor centers, such as the Mesencephalic Locomotor Region (MLR), can promote locomotor recovery in acute and chronic SCI rodent models. Although clinical trials are currently underway in SCI patients, there is still debate about the organization of this supraspinal locomotor center and which anatomical correlate of the MLR should be targeted to promote functional recovery. Combining kinematics, electromyographic recordings, anatomical analysis, and mouse genetics, our study reveals that glutamatergic neurons of the cuneiform nucleus contribute to locomotor recovery by enhancing motor efficacy in flexor and extensor hindlimb muscles, and by increasing locomotor rhythm and speed on a treadmill, over ground, and during swimming in mice with chronic SCI. In contrast, glutamatergic neurons of the pedunculopontine nucleus slow down locomotion. Therefore, our study identifies the cuneiform nucleus and its glutamatergic neurons as a therapeutical target to improve locomotor recovery in patients living with SCI. One Sentence SummaryGlutamatergic neurons of the mesencephalic locomotor region contribute to spontaneous locomotor recovery following spinal cord injury and selective activation of a discrete glutamatergic subpopulation in this region can further improve functional outcome in chronic spinal cord injury.

neuroscience↗

bioRxiv2020

Neuronal activity remodels the F-actin based submembrane lattice in dendrites but not axons of hippocampal neurons

The nanoscale organization of the F-actin cytoskeleton in neurons comprises membrane-associated periodical rings, bundles, and longitudinal fibers. The F-actin rings have been observed predominantly in axons but only sporadically in dendrites, where fluorescence nanoscopy reveals various patterns of F-actin arranged in mixed patches. These complex dendritic F-actin patterns pose a challenge for investigating quantitatively their regulatory mechanisms. We developed here a weakly supervised deep learning segmentation approach of fluorescence nanoscopy images of F-actin in cultured hippocampal neurons. This approach enabled the quantitative assessment of F-actin remodeling, revealing the disappearance of the rings during neuronal activity in dendrites, but not in axons. The dendritic F-actin cytoskeleton of activated neurons remodeled into longitudinal fibers. We show that this activity-dependent remodeling involves Ca2+ and NMDA-dependent mechanisms. This highly dynamic restructuring of dendritic F-actin based submembrane lattice into longitudinal fibers may serve to support activity-dependent membrane remodeling, protein trafficking and neuronal plasticity.

neuroscience↗