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Laurent, G.

Publications and source records attributed to Laurent, G..

9 recordsLinked to original sources

Disentangling Cephalopod Chromatophores Motor Units with Computer Vision

Cephalopod chromatophores are skin pigment organs that enable unmatched camouflage through rapid, flexible and neurally controlled deformation. Although their morphology is well known, the organization of their motor control is not entirely understood. Here, we combine high-resolution videography with a dedicated computer-vision pipeline (CHROMAS) to investigate chromatophore control and their likely innervation in Euprymna berryi and Sepia officinalis. By segmenting chromatophores into radial slices and analyzing anisotropic deformations, we applied dimensionality reduction (PCA) and source separation (ICA) to estimate the number and spatial influence of motor neurons responsible for the control of individual and groups of chromatophores. On average, four independent components were detected (suggesting innervation by four motor neurons), each forming contiguous petal-shaped domains rather than causing uniform expansion. Clustering thousands of components revealed motor units spanning multiple chromatophores, most involving fewer than 14 but occasionally spanning more widely. These motor units displayed a wide variety of geometries, ranging from compact local groups to elongated or fragmented structures; they often overlapped, with repeated co-innervation of chromatophore pairs occurring more often than expected by chance. Expansion was consistently faster and more stereotyped than relaxation, consistent with active contraction (corresponding to chromatophore expansion) and passive recoil (chromatophore contraction). Together, these results show that individual chromatophores are not singular or uniform pixels, but rather contrast elements that can be fractionated into smaller territories, themselves coordinated with those of other chromatophores. This geometry of neural control enables, among others, the generation of "virtual" chromatophores, i.e., functional groupings of adjacent chromatophore territories that act as single units, as well as that of noise in the distribution of pixel shapes.

neuroscience↗

MPI-Guided Photothermal Therapy of Prostate Cancer using Stem Cell Delivery of Magnetotheranostic Nanoflowers

Intratumoral nanoparticle (NP) injection is a commonly used for local hyperthermia. A limitation of this delivery route is the limited NP dispersion and retainment within the tumor, with undesired leakage leading to off-target toxicity. By exploiting their inherent tumor tropism, we have used human mesenchymal stem cells (hMSCs) as delivery vehicles for magnetic theranostic gold-iron oxide nanoflowers (GIONF) to improve their overall intratumoral distribution and retention. GIONF-loaded hMSCs exhibited excellent heating properties for laser photothermal therapy and high tracer performance for visualization and quantification by magnetic particle imaging (MPI). In contrast to naked GIONF, GIONF-hMSCs remained within the prostate tumors one week post-injection, with MPI-guided PTT completely ablating tumors without recurrence.

bioengineering↗

Chromosome-scale genome assembly of the European common cuttlefish Sepia officinalis

Coleoid cephalopods, a subclass of mollusks that includes octopuses, cuttlefish and squid, exhibit sophisticated biological features such as dynamic and neurally driven camouflage behavior, inter-individual communication, single-lens camera-like eyes, the largest brains among invertebrates and a distinctive embryonic development. The common cuttlefish Sepia officinalis has served as a model organism in various research fields, spanning biophysics, neurobiology, behavior, evolution, ecology and biomechanics. More recently, it has become a model to investigate the neural mechanisms underlying cephalopod camouflage, using quantitative behavioral approaches alongside molecular techniques to characterize the identity, evolution and development of neuronal cell types. Despite significant interest in this animal, a high-quality, annotated genome of this species is still lacking. To address this, we sequenced and assembled a chromosome-scale genome for S. officinalis. Our assembly spans 5.68 billion base pairs and comprises 1n=47 repeat-rich chromosome scaffolds. This was unexpected because the haploid karyotypes of other decapods indicate 46 chromosomes. Detailed comparisons of our data to those from published decapod genome assemblies and to another recent genome assembly of S. officinalis (itself suggesting 1n=49 chromosomes) in fact revealed clear homologies between 46 scaffolds across all the datasets. The discrepancies between datasets are explained by highly repetitive regions, impairing proper read alignments. We conclude that the true karyotype of S. officinalis is probably 1n=46 chromosomes, a likely ancestral and if true, conserved decapod karyotype. Our results include a comprehensive gene annotation and full-length transcript prediction, which we used to characterize orthologous gene families across mollusks. We identified several large-scale expansions specific to cephalopods, with many genes specific to neural or non-neural tissues of adult S. officinalis. In summary, this genome should provide a valuable resource for future research on the evolution, brain organization, information processing, development and behavior in this important clade.

genomics↗

FAIRTraits: an environmentally, methodologically and semantically enriched database of plant traits from Mediterranean populations of 240 species

Trait-based approaches have proven, and continue to offer strong potential to tackle key issues in ecology, including: (i) understanding the functioning of organisms and how it relates to the environment, (ii) identifying the rules governing the assembly of communities and the coexistence of species, (iii) understanding how the functioning of organisms scales up to that of ecosystems and controls some of the services they deliver to humans. We present FAIRTraits, a data set of plant traits assembled from a set of studies designed to address these issues in the pedo-climatic context of the Northern Mediterranean Basin, considered both a biodiversity and a climatic hotspot. The FAIR (Findable, Accessible, Interoperable and Reusable) guiding principles were followed to ensure maximum visibility and reusability of these data. FAIRTraits compiles and standardizes trait data collected over the 1997-2023 period on six sites by the same research group, ensuring that a consistent methodology was followed. These data were obtained on individuals from 1,955 populations of 240 species belonging to 155 genera and 48 families (172 herbaceous and 39 woody species). It contains 189,452 records for 183 quantitative traits from the different plant organs (leaves, stems, roots, and reproductive parts), which have been grouped into 10 categories: allocation ratio, architecture, chemistry, dynamics, mechanics, microbial associations, morphology, phenology, physiology and plant size. Trait values are given at the level of individual measurements. Species-level values of height and phenology taken from a Mediterranean flora are also given. Species are characterized by plant family, life cycle, Raunkiaer lifeform, photosynthetic pathway and by an original successional stage indicator value. As trait values strongly depend on environmental conditions, we also provide information on the climatic conditions and soil properties of the sites, as well as on disturbance regimes of the plots in which sampled individuals were collected. The following steps were taken to ensure the FAIRness of the data set. Findable: metadata are described using the Ecological Metadata Language, and are deposited both on the InDoRES (CNRS/MNHN) metadata catalogue and on the GBIF data portal (see below); Accessible: FAIRTraits is available on the InDoRES repository, with a subset available on the GBIF data portal (see below); Interoperable: recognized taxonomical and terminological resources to qualify taxa and attributes have been used whenever possible, and fully described sampling protocols and measurement methods are given both for traits and environmental data. A subset of the data could be mapped onto the Darwin Core biodiversity standard, making it possible to display part of the data set on the GBIF portal, more traditionally used for taxonomic occurrence data. Reusable: (meta)data are thoroughly described using domain-relevant community standards, and the full data set is released under the CC-BY 4.0 license. We believe that these multiple efforts, spanning from the very content of the data set to its careful formatting, will make of FAIRTraits a highly valuable resource for trait-based research, both in terms of data analysis and reusability.

ecology↗

CHROMAS: A Computational Pipeline to Track Chromatophores and Analyze their Dynamics

Cephalopod chromatophores are small dermal neuromuscular organs, each consisting of a pigment-containing cell and 10-20 surrounding radial muscles. Their expansions and contractions, controlled and coordinated by the brain, are used to modify the animals appearance during camouflaging and signaling. Building up on tools developed by this lab, we propose a flexible computational pipeline to track and analyse chromatophore dynamics from high-resolution videos of behaving cephalopods. This suite of functions, which we call CHROMAS, segments and classifies individual chromatophores, compensates for animal movements and skin deformations, thus enabling precise and parallel measurements of chromatophore dynamics and long-term tracking over development. A high-resolution tool for the analysis of chromatophore deformations during behavior reveals details of their motor control and thus, their likely innervation. When applied to many chromatophores simultaneously and combined with statistical and clustering tools, this analysis reveals the complex and distributed nature of the chromatophore motor units. We apply CHROMAS to the skins of the bobtail squid Euprymna berryi and the European cuttlefish Sepia officinalis, illustrating its performance with species with widely different chromatophore densities and patterning behaviors. More generally, CHROMAS offers many flexible and easily reconfigured tools to quantify the dynamics of pixelated biological patterns.

animal behavior and cognition↗

Ultra-high density electrodes improve detection, yield, and cell type specificity of brain recordings

To understand the neural basis of behavior, it is essential to sensitively and accurately measure neural activity at single neuron and single spike resolution. Extracellular electrophysiology delivers this, but it has biases in the neurons it detects and it imperfectly resolves their action potentials. To minimize these limitations, we developed a silicon probe with much smaller and denser recording sites than previous designs, called Neuropixels Ultra (NP Ultra). This device samples neuronal activity at ultra-high spatial density ([~]10 times higher than previous probes) with low noise levels, while trading off recording span. NP Ultra is effectively an implantable voltage-sensing camera that captures a planar image of a neurons electrical field. We use a spike sorting algorithm optimized for these probes to demonstrate that the yield of visually-responsive neurons in recordings from mouse visual cortex improves up to [~]3-fold. We show that NP Ultra can record from small neuronal structures including axons and dendrites. Recordings across multiple brain regions and four species revealed a subset of extracellular action potentials with unexpectedly small spatial spread and axon-like features. We share a large-scale dataset of these brain-wide recordings in mice as a resource for studies of neuronal biophysics. Finally, using ground-truth identification of three major inhibitory cortical cell types, we found that these cell types were discriminable with approximately 75% success, a significant improvement over lower-resolution recordings. NP Ultra improves spike sorting performance, detection of subcellular compartments, and cell type classification to enable more powerful dissection of neural circuit activity during behavior.

neuroscience↗

Sequential propagation and routing of activity in a cortical network

Single spikes can trigger repeatable firing sequences in cortical networks. The mechanisms that support reliable propagation of activity from such small events and their functional consequences remain unclear. By constraining a recurrent network model with experimental statistics from turtle cortex, we generate reliable and temporally precise sequences from single spike triggers. We find that rare strong connections support sequence propagation, while dense weak connections modulate propagation reliability. We identify sections of sequences corresponding to divergent branches of strongly connected neurons which can be selectively gated. Applying eternal inputs to specific neurons in the sparse backbone of strong connections can effectively control propagation and route activity within the network. Finally, we demonstrate that concurrent sequences interact reliably, generating a highly combinatorial space of sequence activations. Our results reveal the impact of individual spikes in cortical circuits, detailing how repeatable sequences of activity can be triggered, sustained, and controlled during cortical computations.

neuroscience↗

Spatial tissue profiling by imaging-free molecular tomography

Genomics techniques are currently being adapted to provide spatially resolved omics profiling. However, the adaptation of each new method typically requires the setup of specific detection strategies or specialized instrumentation. A generic approach to spatially resolve different types of high throughput data is missing. Here, we describe an imaging-free framework to localize high throughput readouts within a tissue by combining compressive sampling and image reconstruction. We implemented this framework to transform a low-input RNA sequencing protocol into an imaging-free spatial transcriptomics technique (STRP-seq) and validated this method with a transcriptome profiling of the murine brain. To verify the broad applicability of STRP-seq, we applied the technique on the brain of the Australian bearded dragon Pogona vitticeps. Our results reveal the molecular anatomy of the telencephalon of this lizard, providing evidence for a marked regionalization of the reptilian pallium and subpallium. Overall, the proposed framework constitutes a new approach that allows upgrading in a generic fashion conventional genomic assays to spatially resolved techniques.

genomics↗

Survival of self-replicating molecules under transient compartmentalization with natural selection

The problem of the emergence and survival of self-replicating molecules in origin-of-life scenarios is plagued by the error catastrophe, which is usually escaped by considering effects of compartmentalization, as in the stochastic corrector model. By addressing the problem in a simple system composed of a self-replicating molecule (a replicase) and a parasite molecule that needs the replicase for copying itself, we show that transient (rather than permanent) compartmentalization is sufficient to the task. We also exhibit a regime in which the concentrations of the two kinds of molecules undergo sustained oscillations. Our model should be relevant not only for origin-of-life scenarios but also for describing directed evolution experiments, which increasingly rely on transient compartmentalization with pooling and natural selection.

biophysics↗