Biology subjects

Barreau, C.

Publications and source records attributed to Barreau, C..

7 recordsLinked to original sources

bioRxiv2025

Dual origins for neural cells during development of the Clytia planula larva

Adult hydrozoan cnidarians undergo extensive tissue turnover, generating neural cell types including nematocytes (stinging cells) and gland cells from interstitial stem cells (i-cells) expressing stemness proteins such as Piwi and Nanos. The contribution of i-cells during embryogenesis, however, has been unclear. Here we address the origin of neural cells during development of the Clytia hemisphaerica planula larva. Marker gene in situ hybridisation revealed that Piwi/Nanos1-expressing cells within the early gastrula presumptive endoderm generate a substantial pool of nematoblasts, a few of which migrate and differentiate in the planula ectoderm. Some neurogenic and neuronal markers, however, showed a markedly distinct expression profile, developing within a basal layer of the aboral/lateral ectoderm during gastrulation. Embryo bisection and lineage tracing experiments confirmed that sensory neurons and secretory cell types derive from gastrula ectoderm, while nematocytes and at least some ganglionic neurons derive from i-cells. Knockdown and inhibitor treatments revealed steps in neuron and nematocyte development regulated by Wnt-{beta}-catenin. We conclude that two distinct neurogenesis pathways operate during Clytia embryogenesis, one involving aboral ectoderm delamination, and one generating mainly nematocytes from i-cell-like precursors. Summary statementDuring embryogenesis in the hydrozoan Clytia neural cell types derive both from Piwi/Nanos expressing "i-cells" and from ectodermal delamination during gastrulation.

developmental biology↗

bioRxiv2025

NUCGEN3D: A synthetic framework for large-scale 3D nuclear segmentation with open-source training data and models

AO_SCPLOWBSTRACTC_SCPLOWRobust nuclear segmentation in 3D microscopy images is a critical yet unresolved challenge in quantitative cell biology, hindered by the scarcity and variability of annotated volumetric datasets. Because such data are difficult to obtain, most state-of-the-art approaches, including Cellpose, segment individual 2D slices and then heuristically reconstruct 3D volumes, thereby losing critical spatial context. Our analysis of expert annotator performance confirms that ignoring 3D context introduces substantial variability in nuclear detection and annotation. While a few 3D models have been trained on small or toy datasets, no large-scale, openly available resource currently exists to enable robust training of high-capacity 3D segmentation networks. To address this, we present NucGen3D, a customizable simulation framework that generates large-scale, annotated 3D microscopy datasets from limited 2D input, specifically the 2018 Data Science Bowl dataset. NucGen3D produces realistic 3D volumes across diverse biological and imaging scenarios, including variations in nuclear morphology, spatial arrangement, acquisition artifacts, and imaging noise. Using this synthetic data, we trained two models from scratch: a 2D convolutional neural network under Cellpose-like conditions, and a fully 3D convolutional model that extends the 2D settings. We evaluated both on a challenging, independent real-world dataset with complex nuclear architectures. Both models, especially the 3D model, consistently outperformed state-of-the-art methods, including those trained on larger annotated datasets or based on more complex architectures. These results demonstrate that synthetic data can effectively substitute for real 3D annotations in training performing models at scale. To promote reproducibility and further research, we release both the NucGen3D framework and the fully trained 3D segmentation model as open source, making this the first end-to-end open resource for large-scale 3D nuclear segmentation.

bioinformatics↗

bioRxiv2025

Mobilizable adipose stromal cells fuel regenerative adipogenesis in injured muscle

Skeletal muscle regeneration is a highly orchestrated process involving the dynamic interplay of multiple cell types. Among these, fibro-adipogenic progenitors (FAPs), a population of resident mesenchymal stromal cells (MSCs), are essential for creating a supportive microenvironment that promotes satellite cell differentiation and modulates immune responses. Our recent work revealed that adipose stromal cells (ASCs) from subcutaneous adipose tissue (ScAT) infiltrate the injured muscle within the first 24h post-injury, contributing significantly to the regenerative process. Consequently, the FAP population in the regenerating muscle comprises both resident FAPs and infiltrated ASCs. In the present study, using single cell RNA-seq in a mouse model with trackable KikGR+ ASCs and bioinformatics analyses, we identify Limch1+/Prg4+ ASCs as the primary Mobilizable ASCs (Mob-ASCs) that migrate to and infiltrate the injury site. Notably, this migration is detectable as early as 14 hours post-injury. We demonstrate that these cells are pre-activated within the ScAT, primed to initiate both migratory and regenerative programs. Intriguingly, bioinformatic inference of key activated transcription factors suggested that adipogenesis is also activated in these cells. Leveraging supervised machine learning, we tracked the fate of Mob-ASCs within the regenerating muscle post-injury, where they continue to execute these programs. Importantly, these cells lineage is cued towards a fate of adipogenesis. In vivo, we observed transient generation of adipocytes with a peak at 7-9 days post-injury to which infiltrated ASCs contributed. In vitro, conditioned media assays further revealed that adipocytes derived from ASCs--but not those from FAPs--enhance myoblasts fusion. Collectively, our findings establish Limch1+/Prg4+ ASCs as the Mobilizable ASC population and suggest that their transient adipogenic differentiation is beneficial for muscle regeneration.

physiology↗

bioRxiv2019

An improved whole life cycle culture protocol for the hydrozoan genetic model Clytia hemisphaerica.

The jellyfish species Clytia hemisphaerica (Cnidaria, Hydrozoa) has emerged as a new experimental model animal in the last decade. Favorable characters include a fully transparent body suitable for microscopy, daily gamete production and a relatively short life cycle. Furthermore, whole genome sequence assembly and efficient gene editing techniques using CRISPR/Cas9 have opened new possibilities for genetic studies. The quasi-immortal vegetatively-growing polyp colony stage provides a practical means to maintain mutant strains. In the context of developing Clytia as a genetic model, we report here an improved whole life cycle culture method including an aquarium tank system designed for culture of the tiny jellyfish form. We have compared different feeding regimes using Artemia larvae as the food and demonstrate that the stage-dependent feeding control is the key for rapid and reliable medusa and polyp rearing. Metamorphosis of the planula larvae into a polyp colony can be efficiently induced using a new synthetic peptide. The optimized procedures detailed here make it practical to generate new genetically modified Clytia strains and to safely maintain their whole life cycle in the laboratory.

developmental biology↗

bioRxiv2018

The genome of the jellyfish Clytia hemisphaerica and the evolution of the cnidarian life-cycle

Jellyfish (medusae) are a distinctive life-cycle stage of medusozoan cnidarians. They are major marine predators, with integrated neurosensory, muscular and organ systems. The genetic foundations of this complex form are largely unknown. We report the draft genome of the hydrozoan jellyfish Clytia hemisphaerica and use multiple transcriptomes to determine gene use across life-cycle stages. Medusa, planula larva and polyp are each characterised by distinct transcriptome signatures reflecting abrupt life cycle transitions, and all deploy a mixture of phylogenetically old and new genes. Medusa specific transcription factors, including many with bilaterian orthologs, associate with diverse neurosensory structures. Compared to Clytia, the polyp-only hydrozoan Hydra has lost many of the medusa-expressed transcription factors, despite similar overall rates of gene content and sequence evolution. Absence of expression and gene loss among Clytia orthologs of genes patterning the anthozoan aboral pole, secondary axis and endomesoderm support simplification of planulae and polyps in Hydrozoa, including loss of bilateral symmetry. Consequently, although the polyp and planula are generally considered the ancestral cnidarian forms, in Clytia the medusa maximally deploys ancestral cnidarian-bilaterian transcription factor gene complexity.

evolutionary biology↗

bioRxiv2017

Inhibition of granulocyte ROS production by opioids prevents regeneration

Inhibition of regeneration and induction of healing are classic outcomes of tissue repair in adult mammals. Here, by using gain and loss of function experiments, we demonstrate that both endogenous and exogenous opioids prevent tissue regeneration in adults, by inhibiting the early reactive oxygen species (ROS) production occurring after lesion and required for regeneration. These effects can be overcome and regeneration induced by the use of an opioid antagonist. These results, obtained in both gold-standard adult zebrafish and a newly-developed model of regeneration in adult mammals, demonstrate that this mechanism can be considered as a general paradigm in vertebrates. In addition, we show that opioids act via signaling through peripheral mu-receptors expressed on granulocytes. This work clearly demonstrates the deleterious role of opioids on tissue regeneration through the control of ROS production in vertebrates and thus questions about opioid-based analgesia in perioperative care.

physiology↗

bioRxiv2017

Jellyfish Oocyte Maturation Inducing Hormone And Neuroendocrine Regulation Of Reproduction

Oocyte meiotic maturation is a critical process for sexually reproducing animals, and its core cytoplasmic regulators are highly conserved between species. In contrast, the few known Maturation Inducing Hormones (MIHs) that act on oocytes to initiate this process have highly variable molecular natures. Using the hydrozoan jellyfish species Clytia and Cladonema, which undergo oocyte maturation in response to dark-light and light-dark transitions respectively, we deduced from gonad transcriptome data amidated tetrapeptide sequences and found that synthetic peptides could induce maturation of isolated oocytes at nanomolar concentrations. Antibody preabsorption experiments conclusively demonstrated that these W/RPRPamide-related neuropeptides account for endogenous MIH activity produced by isolated gonads. We further showed that the MIH peptides are synthesised by neural-type cells in the gonad, are released following dark-light / light-dark transitions, and probably act on the oocyte surface. They are produced by male as well as female jellyfish and can trigger both sperm and egg release, suggesting a role in spawning coordination. We propose an evolutionary link between hydrozoan MIH and the neuropeptide hormones that regulate reproduction upstream of MIH in bilaterian species.

developmental biology↗