Biology subjects

Stokkermans, A.

Publications and source records attributed to Stokkermans, A..

7 recordsLinked to original sources

bioRxiv2026

A mobile optical coherence microscope for studying aquatic organisms in- and outside the laboratory

High-resolution, three-dimensional imaging of live organisms has largely depended on laboratory-bound microscopes, limiting quantitative analysis of morphology and dynamics to species that survive transport and thrive under lab-controlled conditions. Here we present a mobile optical coherence microscopy (OCM) platform that overcomes this constraint, delivering [~]2.5 {micro}m axial resolution, label-free, volumetric imaging of live aquatic organisms in both laboratory and remote field environments. We demonstrate the platform across a broad range of aquatic organisms from the lab and field, spanning multiple phyla - including cnidarians, poriferans, annelids, arthropods and echinoderms - resolving internal anatomy, tissue boundaries and organismal morphology at micrometer scale without fixation, fluorescent labeling, or specialized sample preparation. High-speed acquisition, with up to 250 kHz A-line rate and 7.7 Hz volume rate, further enabled morphodynamic imaging of live biological processes, including cellular aggregate motility, embryonic cell division, and organ-level peristaltic dynamics in intact, living animals. To demonstrate field deployability, the platform was operated during the EMBL TREC pan-European expedition, enabling on-site, label-free imaging of marine organisms and plankton immediately upon collection. By decoupling high-resolution volumetric imaging from fixed laboratory settings, mobile OCM opens a path toward field-ready quantitative morphological and dynamic phenotyping of aquatic life.

bioengineering↗

bioRxiv2026

The limits of scaling in aggregation-driven patterning of cell collectives

Robust development requires maintaining correct proportions as overall size varies. What controls and limits this scaling remains poorly understood due to the complex interplay of mechanical and biochemical embryonic factors. Combining confinement of dissociated embryonic presomitic mesoderm cells with imaging and chemical perturbations, we identified cell aggregation as the initial event in de novo posterior pole formation. Using a continuum model based solely on cell-cell attraction, we quantitatively map how the time available for aggregation-driven patterning limits the maximum scalable system size. Small systems allow rapid, robust pattern scaling, whereas coarsening dynamics substantially delay scaled patterns in large systems. Our experiments quantitatively confirm these predicted scaling regimes. Together, our results reveal a developmental time-size tradeoff governing the scaling of aggregation-driven patterns.

biophysics↗

bioRxiv2025

Boundary-guided cell alignment drives mouse epiblast maturation

Symmetry breaking and pattern formation are critical events that occur throughout embryonic development. In early mouse development, a mass of non-polarized epiblast (EPI) cells in the blastocyst forms the egg-cylinder, while cells become apico-basally polarized and build a radial configuration. Yet, what drives the formation of this tissue architecture remains unclear. Here, we demonstrate that orientational patterning of EPI cells is dictated by heterogeneous tissue boundaries, which then defines central lumen positioning. We show that EPI cells progressively orient perpendicular to the visceral endoderm (VE) boundary enriched with laminin and active integrin {beta}1, but parallel to the extraembryonic ectoderm interface. These orientation dynamics are consistent with general boundary-induced alignment effects in polar materials, with a topological defect predicting the position where the pro-amniotic cavity nucleates. Knockout of laminin {gamma}1 and integrin {beta}1 confirms the essential role of adhesion at the EPI-VE-boundary. The established EPI pattern, in turn, facilitates ERK activation to ensure proper EPI maturation. Together, these findings present the mechanistic basis and functional significance of EPI tissue patterning.

developmental biology↗

bioRxiv2023

Molecular profiling of sponge deflation reveals an ancient relaxant-inflammatory response

A hallmark of animals is the coordination of whole-body movement. Neurons and muscles are central to this, yet coordinated movements also exist in sponges that lack these cell types. Sponges are sessile animals with a complex canal system for filter-feeding. They undergo whole-body movements resembling "contractions" that lead to canal closure and water expulsion. Here, we combine 3D optical coherence microscopy, pharmacology, and functional proteomics to elucidate anatomy, molecular physiology, and control of these movements. We find them driven by the relaxation of actomyosin stress fibers in epithelial canal cells, which leads to whole-body deflation via collapse of the incurrent and expansion of the excurrent system, controlled by an Akt/NO/PKG/A pathway. A concomitant increase in reactive oxygen species and secretion of proteinases and cytokines indicate an inflammation-like state reminiscent of vascular endothelial cells experiencing oscillatory shear stress. This suggests an ancient relaxant-inflammatory response of perturbed fluid-carrying systems in animals. HighlightsO_LISponge deflation is driven by tension release in actomyosin stress fibers of epithelial pinacocytes C_LIO_LIAkt kinase/Nitric oxide/Protein kinase G/A regulate actomyosin relaxation C_LIO_LIAgitation-induced deflation coincides with an inflammatory state C_LIO_LIThe sponge relaxant-inflammatory response is evolutionary related to similar responses in the vertebrate vascular system C_LI

molecular biology↗

bioRxiv2023

Temporal variability and cell mechanics control robustness in mammalian embryogenesis

How living systems achieve precision in form and function despite their intrinsic stochasticity is a fundamental yet open question in biology. Here, we establish a quantitative morphomap of pre-implantation embryogenesis in mouse, rabbit and monkey embryos, which reveals that although blastomere divisions desynchronise passively without compensation, 8-cell embryos still display robust 3D structure. Using topological analysis and genetic perturbations in mouse, we show that embryos progressively change their cellular connectivity to a preferred topology, which can be predicted by a simple physical model where noise and actomyosin-driven compaction facilitate topological transitions lowering surface energy. This favours the most compact embryo packing at the 8- and 16-cell stage, thus promoting higher number of inner cells. Impairing mitotic desynchronisation reduces embryo packing compactness and generates significantly more cell mis-allocation and a lower proportion of inner-cell-mass-fated cells, suggesting that stochasticity in division timing contributes to achieving robust patterning and morphogenesis.

developmental biology↗

bioRxiv2021

Ethology of morphogenesis reveals the design principles of cnidarian size and shape development

During development, organisms interact with their natural habitats while undergoing morphological changes, yet it remains unclear whether the interplay between developing systems and their environments impacts animal morphogenesis. Here, we use the cnidarian Nematostella vectensis as a developmental model to uncover a mechanistic link between organism size, shape and behavior. Using quantitative live imaging, including extensive behavioral profiling, combined with molecular and biophysical experiments, we demonstrate that the muscular hydraulic machinery that controls body movement directly drives larva-polyp morphogenesis. Unexpectedly, size and shape development are differentially controlled by antagonistic muscles. A simple theoretical model shows how a combination of slow-priming and fast-pumping pressures generated by muscular hydraulics acts as a global mechanical regulator that coordinates tissue remodeling. Altogether, our findings illuminate how dynamic behavioral modes in the environment can be harnessed to drive morphogenetic trajectories, establishing ethology as a critical component of organismal morphogenesis - termed ethology of morphogenesis.

developmental biology↗

bioRxiv2020

Feeding-dependent tentacle development in the sea anemone Nematostella vectensis

In cnidarians, axial patterning is not restricted to embryonic development but continues throughout a prolonged life history filled with unpredictable environmental changes. How this developmental capacity copes with fluctuations of food availability and whether it recapitulates embryonic mechanisms remain poorly understood. To address these questions, we utilize the tentacles of the sea anemone Nematostella vectensis as a novel paradigm for developmental patterning across distinct life history stages. As a result of embryonic development, Nematostella polyps feature four primary tentacles, while adults have 16 or more. By analyzing over 1000 growing polyps, we find that tentacle progression is remarkably stereotyped and occurs in a feeding-dependent manner. Mechanistically, we show that discrete Fibroblast growth factor receptor b (Fgfrb)-positive ring muscles prefigure the sites of new tentacles in unfed polyps. In response to feeding, a Target of Rapamycin (TOR)-dependent mechanism controls the expansion of Fgfrb expression in oral tissues which defines tentacle primordia. Using a combination of genetic, cellular and molecular approaches, we demonstrate that FGFRb regionally enhances TOR signaling activity and promotes polarized growth, a spatial pattern that is restricted to polyp but not to embryonic tentacle primordia. These findings reveal an unexpected plasticity of tentacle development, and show that the crosstalk between TOR-mediated nutrient signaling and FGFRb pathway couples post-embryonic body patterning with food availability.

developmental biology↗