Biology subjects

Gros, J.

Publications and source records attributed to Gros, J..

16 recordsLinked to original sources

bioRxiv2026

Dehydration-Responsive Left-Handed G-Quadruplexes Expandthe Sequence Repertoire

G-quadruplexes (G4s) are widely studied noncanonical nucleic-acid structures that carry important biological functions. Typically, G4s form from G-rich sequences containing at least four tracts of more than two consecutive guanines, yet a plethora of unconventional G4-forming sequences have been identified, including sequences that fold into G4s only under specific conditions. These G4 states remain poorly resolved. Here we identify dehydration-responsive left-handed G4s (drLHG4s), a class of left-handed G4 (LHG4) structures accessible under dehydrating conditions. Using d(GT)n repeats, we show that left-handed folding depends on repeat length, salt condition and solvent conditions. Systematic mutational analysis reveals a broader but register-constrained sequence space, while high-resolution crystal structures of d-GTGGTGTGTGGTG, a sequence that folded robustly under dehydrating conditions, establish a bulged LHG4 architecture and reveal a distinctive hydration sphere. We further show that selected peptides and a cationic zinc phthalocyanine derivative, ZnTEGQPyrPc, containing four triethylene glycol methyl ether tails can induce LHG4 states. Together, our findings reveal a dehydration-responsive G4 landscape and expand the experimentally accessible sequence space of LHG4 folding.

biophysics↗

bioRxiv2026

EpiCure (Epithelial Curation): a versatile and handy tool for curation of epithelial segmentation

Investigating single-cell dynamics and morphology in tissues and embryos requires highly accurate quantitative analysis of microscopy images. Despite significant advances in the field of bioimage analysis, even the most sophisticated segmentation and tracking algorithms inevitably produce errors (e.g. : over segmentation, missing objects, miss-connected objects). Although error rate may be small, their propagation throughout a time-lapse sequence has catastrophic effects on the accuracy of tracking and extraction of single cell parameters. Extracting single cell temporal information in the context of tissue/embryo requires thus expert curation to identify and correct segmentation errors. In the movies commonly used in developmental biology and stem cell research, both the number of imaged cells and the duration of recording are large, making this manual correction task extremely time-consuming. This has now become a major bottleneck in the fields of development, stem cell biology and bioimage analysis. We present here EpiCure (Epithelial Curation), a versatile tool designed to streamline and accelerate manual curation of segmentation and tracking in 2D movies of large epithelial tissues. EpiCure uses temporal information and morphometric parameters to automatically identify segmentation and tracking errors and provides user-friendly tools to correct them. It focuses on ergonomics and offers several visualization options to help navigating in movies of tissue covering a large number of cells, speeding up the detection of errors and their curation. EpiCure is highly interoperable and supports input from a wide range of segmentation tools. It also includes multiple export filters, enabling seamless integration with downstream analysis pipelines. In this paper, using movies from several animal models, we highlight the importance of curating cell segmentation and tracking for accurate downstream analysis, and demonstrate how EpiCure helps the curation process for extracting accurate single cell dynamics and cellular events detection, making it faster and amenable on large dataset.

developmental biology↗

bioRxiv2026

Variable effects of biocontrol bacteria on potato resistance against black leg caused by soft rot Pectobacteriaceae in the field

Blackleg disease in potato, caused by soft rot Pectobacteriaceae, is a substantial cause of loss in seed potato production. Recent research has attempted to identify bacteria with antagonistic activity against several diseases, among which blackleg. However, most biocontrol agents have been tested only in-vitro or in the greenhouse. In this study, we tested the effect of bacterial biocontrol agents in a four-year field experiment against blackleg caused by Pectobacterium brasiliense and Dickeya solani. Effects of the treatments on disease incidence was highly variable between years and also differed between cultivars, soil type and even replicates. Disease incidence was on average higher in sandy soil compared to clay soil and higher in the cultivar Kondor than Mozart. For a subset of the bacterial isolates genome mining could detect the presence of genes involved in the production of antibiotics and siderophores, but this was not correlated with disease incidence in the field. Moreover, most isolates were able to survive in storage on tubers from inoculation until planting. Thus, we conclude that while the used isolates showed the potential for antagonistic activity and were present on tubers when planting, no antagonist treatment could consistently decrease disease incidence. Inoculation of the isolates on the tuber surface might have been insufficient for plant colonization.

microbiology↗

bioRxiv2025

Actin and myosin dynamics during epithelial remodeling in avian gastrulation

Epithelial remodeling is powered by contractile forces exerted by the actomyosin cytoskeleton. In invertebrates, pulsatile contractile flows of the medio-apical actomyosin cortex have been shown to be critical in promoting junction contraction that ultimately drive cell rearrangements, apical constriction, and cell extrusion. However, how actomyosin dynamics drives epithelial remodeling in amniotes remains poorly understood. In this study, we generated transgenic quail lines reporting actin and myosin and investigate their dynamics in gastrulating embryos. We show that during this process, epithelial remodeling events are closely associated with the contraction of junctional myosin. Although we observe medio-apical contractile flows, those appear to contribute to junction contraction by promoting junctional myosin recruitment. Notably, by characterizing live and apoptotic cell extrusions and their associated actomyosin dynamics, we provide new insights into the cellular processes underlying primitive streak formation and the emergence of germ layers.

developmental biology↗

bioRxiv2025

An active torque dipole across tissue layers drives avian left-right symmetry breaking

Unlike in mice, frogs, and fish, left-right (L/R) body axis formation in avian embryos does not arise from the chiral beat of cilia. Instead, a counter-clockwise tissue rotation around Hensens node, the organizer of amniote development, repositions cells expressing L/R sidedness genes. Yet, the physical origin of this rotation remains elusive. Here, we provide evidence that in quail embryos, the node tissue generates an active chiral torque of [~]6{micro}N{micro}m to drive the chiral tissue flow. Microsurgery experiments reveal that this torque depends on actomyosin molecular activity, is generated within the dorsal node tissue, and requires the underlying ventral meso-/endoderm to act as a mechanical substrate sustaining the counter-torque. We conclude that a dorsoventrally oriented tissue-scale active torque dipole at the node translates cell-scale chirality to organismal L/R asymmetry, adding a mechanical dimension to the canonical function of embryonic organizers as signaling hubs.

biophysics↗

bioRxiv2025

Live imaging and functional characterization of the avian hypoblast redefine the mechanisms of primitive streak induction

In birds and mammals, the formation of the primitive streak, the hallmark of the primary axis and site of gastrulation, is thought to occur when an anterior displacement of the hypoblast (visceral endoderm in mice) lifts its inhibition on the posterior epiblast, enabling the activation of NODAL signaling. Although the anterior movement of the murine visceral endoderm is well documented, the dynamics of the avian hypoblast remain poorly understood. Here, using live imaging and quantitative image analysis, we find that the hypoblast is mechanically coupled to the epiblast and does not migrate away from its posterior end. Instead, the hypoblast moves and deforms passively, in response to the forces transmitted from the epiblast that shape the primitive streak, after its induction. Furthermore, we show that the posterior hypoblast does not exert an inhibitory effect on the epiblast but instead expresses NODAL, which activates primitive streak formation. NODAL concomitantly regulates gene expression in the hypoblast, patterning it along the anteroposterior axis. Our results thus redefine how the primary axis is established in avians, demonstrating that the displacement of the hypoblast and its concomitant anteroposterior patterning are consequences -- rather than drivers -- of primitive streak induction, downstream of NODAL signaling. Essential summaryNODAL asymmetric expression in the hypoblast activates primitive streak formation in the avian embryo.

developmental biology↗

bioRxiv2025

Direct measurements of active forces and material properties unveil the active mechanics of early embryogenesis

Despite progress in probing tissue mechanics, direct long-term measurements in live embryonic epithelia are lacking. This limits our understanding of amniote embryonic morphogenesis, which takes place over hours or days. Here, we introduce a combined technological and analytical framework to directly measure active forces and material properties in developing quail embryos, in a minimally invasive way. We find that the embryonic epithelium behaves elastically on short timescales with a modulus [~] 2 nN {middle dot} m-1 but flows over longer timescales with a viscosity [~] 4 N {middle dot} s {middle dot} m-1, and that both properties are under active regulation. Notably, we demonstrate that cell division is an active epithelial fluidizer, with division rates correlating with tissue fluidity. This fluidization is crucial for the emergence of the primary embryonic axis, which we show is shaped by a force [~] 2 N. Altogether, our approach delivers a complete and quantitative view of early embryonic mechanics, and opens new avenues for biomechanical studies in live embryos and tissues.

developmental biology↗

bioRxiv2024

CRISPR/Cas9-based somatic knock-in of reporters in the avian embryo in ovo

Gene editing and protein tagging are at the heart of modern developmental and cell biology. The advent of CRISPR/Cas9 based methods offers the possibility to develop customized approaches for genomic manipulations in non-classical experimental models. Here, we show that highly efficient somatic knock-ins of long DNA fragments can be achieved in the developing chick neural tube in ovo. We compare different types of repair matrices and different methods for the delivery of the CRISPR/Cas9 machinery, and find that an all plasmid-based approach and short arms of homology provide an easy and efficient method to achieve high frequencies of knock-in insertions with virtually no background signal. We use this method to target fluorescent reporters and dynamically monitor the subcellular distribution of endogenously expressed tagged proteins, as well as to insert the Gal4-VP16 transcription factor or the Cre recombinase at specific loci to label neural sub-populations in the chick embryonic spinal cord. Finally, we show that the method can also be applied to target the epiblast and somitic mesoderm.

developmental biology↗

bioRxiv2024

A tension-induced morphological transition shapes the avian extra-embryonic territory

The segregation of the extra-embryonic lineage is one of the earliest events and a key step in amniote development. Whereas the regulation of extra-embryonic cell fate specification has been extensively studied, little is known about the morphogenetic events underlying the formation of this lineage. Here, taking advantage of the amenability of avian embryos to live and quantitative imaging, we investigate the cell- and tissue-scale dynamics of epiboly, the process during which the epiblast expands to engulf the entire yolk. We show that tension arising from the outward migration of the epiblast border on the vitelline membrane stretches extra-embryonic cells, which reversibly transition from a columnar to squamous morphology. The propagation of this tension is strongly attenuated in the embryonic territory, which concomitantly undergoes fluid-like motion, culminating in the formation of the primitive streak. We formulate a simple viscoelastic model in which the tissue responds elastically to isotropic stress but flows in response to shear stress, and show that it recapitulates the flows and deformation of both embryonic and extra-embryonic tissues. Together, our results clarify the mechanical basis of early avian embryogenesis and provide a framework unifying the divergent mechanical behaviors observed in the contiguous embryonic and extra-embryonic territories that make up the epiblast. HighlightsO_LIThe extra-embryonic region expands radially during epiboly C_LIO_LICell area increase accounts for the rapid extra-embryonic expansion C_LIO_LIEpiboly-induced tension reversibly stretches extra-embryonic cells C_LIO_LIA simple viscoelastic model recovers the morphogenesis of the entire epiblast C_LI

developmental biology↗

bioRxiv2023

Using a micro-device with a deformable ceiling to probe stiffness heterogeneities within 3D cell aggregates

Recent advances in the field of mechanobiology have led to the development of methods to characterize single-cell or monolayer mechanical properties and link them to their functional behaviour. However, there remains a strong need to establish this link for three-dimensional multicellular aggregates, which better mimic tissue function. Here we present a platform to actuate and observe many such aggregates within one deformable micro-device. The platform consists of a single PDMS piece cast on a 3D-printed mold and bonded to a glass slide or coverslip. It consists of a chamber containing cell spheroids, which is adjacent to air cavities that are fluidically independent. Controlling the air pressure in these air cavities leads to a vertical displacement of the chambers ceiling. The device can be used in static or dynamic modes over time-scales of seconds to hours, with displacement amplitudes from a few m to several tens of microns. Further, we show how the compression protocols can be used to obtain measurements of stiffness heterogeneities within individual co-culture spheroids, by comparing image correlations of spheroids at different levels of compression with finite element simulations. The labeling of the cells and their cytoskeleton is combined with image correlation methods to relate the structure of the co-culture spheroid with its mechanical properties at different locations. The device is compatible with various microscopy techniques, including confocal microscopy, which can be used to observe the displacements and rearrangements of single cells and neighborhoods within the aggregate. The complete experimental and imaging platform can now be used to provide multi-scale measurements that link single-cell behavior with the global mechanical response of the aggregates.

bioengineering↗

bioRxiv2021

Self-organized tissue mechanics underlie embryonic regulation

Early amniote development is a highly regulative and self-organized process, capable to adapt to interference through cell-cell interactions, which are widely believed to be mediated by molecules. Analyzing intact and mechanically perturbed avian embryos, we show that the mechanical forces that drive embryogenesis self-organize in an analog of Turings molecular reaction-diffusion model, with contractility locally self-activating and the ensuing tension acting as a long-range inhibitor. This mechanical feedback governs the persistent pattern of tissue flows that shape the embryo and steers the concomitant emergence of embryonic territories by modulating gene expression, ensuring the formation of a single embryo under normal conditions, yet allowing the emergence of multiple, well-proportioned embryos upon perturbations. Thus, mechanical forces are a central signal in embryonic self-organization, feeding back onto gene expression to canalize both patterning and morphogenesis.

developmental biology↗

bioRxiv2021

DProj: A toolbox for local 2D projection and accurate morphometrics of large 3D microscopy images.

BO_SCPLOWACKGROUNDC_SCPLOWQuantitative imaging of epithelial tissues prompts for bioimage analysis tools that are widely applicable and accurate. In the case of imaging 3D tissues, a common pre-processing step consists in projecting the acquired 3D volume on a 2D plane mapping the tissue surface. Indeed, while segmenting the tissue cells is amenable on 2D projections, it is still very difficult and cumbersome in 3D. However, for many specimen and models used in Developmental and Cell Biology, the complex content of the image volume surrounding the epithelium in a tissue often reduces the visibility of the biological object in the projection, compromising its subsequent analysis. In addition, the projection may distort the geometry of the tissue and can lead to strong artifacts in the morphology measurement. RO_SCPLOWESULTSC_SCPLOWHere we introduce a user-friendly toolbox built to robustly project epithelia on their 2D surface from 3D volumes, and to produce accurate morphology measurement corrected for the projection distortion, even for very curved tissues. Our toolbox is built upon two components. LocalZProjector is a user-friendly and configurable Fiji plugin that generates 2D projections and height-maps from potentially large 3D stacks (larger than 40 GB per time-point) by only incorporating signal of the planes with local highest variance/mean intensity, despite a possibly complex image content. DeProj is a MATLAB tool that generates correct morphology measurements by combining the height-map output (such as the one offered by LocalZProjector) and the results of a cell segmentation on the 2D projection, hence effectively deprojecting the 2D segmentation in 3D. In this paper we demonstrate their effectiveness over a wide range of different biological samples. We then compare its performance and accuracy against similar existing tools. CO_SCPLOWONCLUSIONSC_SCPLOWWe find that LocalZProjector performs well even in situations where the volume to project also contains un-wanted signal in other layers. We show that it can process large images without a pre-processing step. We study the impact of geometrical distortions on morphological measurements induced by the projection. We measured very large distortions which are then corrected by DeProj, providing accurate outputs.

bioinformatics↗

bioRxiv2019

The quail as an avian model system: its genome provides insights into social behaviour, seasonal biology and infectious disease response

The Japanese quail (Coturnix japonica) is a popular domestic poultry species and an increasingly significant model species in avian developmental, behavioural and disease research. We have produced a high-quality quail genome sequence, spanning 0.93 Gb assigned to 33 chromosomes. In terms of contiguity, assembly statistics, gene content and chromosomal organization, the quail genome shows high similarity to the chicken genome. We demonstrate the utility of this genome through three diverse applications. First, we identify selection signatures and candidate genes associated with social behaviour in the quail genome, an important agricultural and domestication trait. Second, we investigate the effects and interaction of photoperiod and temperature on the transcriptome of the quail medial basal hypothalamus, revealing key mechanisms of photoperiodism. Finally, we investigate the response of quail to H5N1 influenza infection. In quail lung, many critical immune genes and pathways were downregulated, and this may be key to the susceptibility of quail to H5N1. This genome will facilitate further research into diverse research questions using the quail as a model avian species.

genomics↗

bioRxiv2018

A tensile ring drives tissue flows to shape the gastrulating amniote embryo

Tissue morphogenesis is driven by local cellular deformations, themselves powered by contractile actomyosin networks. While it is well demonstrated that cell-generated forces at the microscopic scale underlie a variety of local morphogenetic processes (e.g. lengthening/ narrowing1-4, bending5-8, or folding9,10), how such local forces are transmitted across tissues to shape them at a mesoscopic scale remains largely unknown. Here, by performing a quantitative analysis of gastrulation in entire avian embryos, we show that the formation of the primitive streak and the associated large-scale rotational tissue flows (i.e. polonaise movements11,12) are integral parts of a global process that is captured by the laws of fluid mechanics. We identify a large-scale supracellular actomyosin ring (2 mm in diameter and 250 m thick) that shapes the embryo by exerting a graded tension along the margin between the embryonic and extra-embryonic territories. Tissue-wide flows arise from the transmission of these localized forces across the embryonic disk and are quantitatively recapitulated by a fluid-mechanical model based on the Stokes equations for viscous flow. We further show that cell division, the main driver of cell rearrangements at this stage13, is required for fluid-like behavior and for the progress of gastrulation movements. Our results demonstrate the power of a hydrodynamic approach to tissue-wide morphogenetic processes14-16 and provide a simple, unified mechanical picture of amniote gastrulation. A tensile embryo margin, in addition to directing tissue motion, could act as an interface between mechanical and molecular cues, and play a central role in embryonic self-organization.

developmental biology↗

bioRxiv2018

Pervasive Transcription Fine-tunes Replication Origin Activity

RNA polymerase (RNAPII) transcription occurs pervasively, which raises the important question of its functional impact on other DNA-associated processes, including replication. In budding yeast, replication originates from Autonomously Replicating Sequences (ARSs), generally located in intergenic regions. The influence of transcription on ARSs function has been studied for decades, but these earlier studies have necessarily neglected the role of non-annotated transcription. We studied the relationships between pervasive transcription and replication origin activity using high-resolution transcription maps. We show that ARSs alter the pervasive transcription landscape by pausing and terminating neighboring RNAPII transcription, thus limiting the occurrence of pervasive transcription within origins. We provide evidence that quasi-symmetrical binding of the ORC complex to ARS borders is responsible for pausing/termination. We also show that low, physiological levels of pervasive transcription impact the function of replication origins. Overall, our results have important implications for understanding the impact of genomic location on origin function.

genetics↗

bioRxiv2018

Timed collinear activation of Hox genes during gastrulation controls the avian forelimb position

Limb position along the body is highly consistent within one species but very variable among vertebrates. Despite major advances in our understanding of limb patterning in three dimensions, how limbs reproducibly form along the anteroposterior axis remains largely unknown. Hox genes have long been suspected to control limb position, however supporting evidences are mostly correlative and their role in this process remains unclear. Here we show that Hox genes determine the avian forelimb position in a two-step process: first, their sequential collinear activation during gastrulation controls the relative position of their own successive expression domains along the body axis. Then, within these collinear domains, Hox genes differentially activate or repress the genetic cascade responsible for forelimb initiation. Furthermore, we provide evidences that changes in the timing of collinear Hox gene activation might underlie natural variation in forelimb position between different birds. Altogether our results which characterize the cellular and molecular mechanisms underlying the regulation and natural variation of forelimb position in avians, show a direct and early role for Hox genes in this process.

developmental biology↗