Biology subjects

Eckert, J.

Publications and source records attributed to Eckert, J..

13 recordsLinked to original sources

bioRxiv2026

Expecting the unexpected: Great apes anticipate surprise in others

Humans adeptly navigate complex social environments by attempting to anticipate the actions and emotional responses of others. Although our closest ape relatives have sophisticated social cognitive abilities, we do not know whether they have a cognitive understanding of others' emotions. For the epistemic emotion surprise, a cognitive understanding would require sensitivity to an agent's belief, to reality, and to any misalignment between the two, allowing one to model the mental conditions that drive surprise. In a non-invasive eye tracking study with 31 chimpanzees and bonobos, apes showed evidence of a cognitive understanding of surprise: they detected the misalignment between an agent's belief and reality, exhibiting greater pupil dilation right before an agent encountered an unexpected outcome relative to an expected one. This suggests that apes and humans share a more complex understanding of others' mental lives than previously thought, capacities that likely evolved millions of years ago in a common ancestor.

animal behavior and cognition↗

bioRxiv2026

Vimentin bridges scales to convert polarized cell locomotion into coordinated collective migration

Collective cell migration is central in development and disease. Vimentin is an intermediate filament protein expressed by epithelial cells at the edge of wounds where collective cell migration is most efficient. Yet, its functional role in this context remains underexplored. Here, we show that vimentin, over-expressed in cells undergoing partial epithelial to mesenchymal transition at the edge of epithelial monolayers, has a multiscale impact on the whole monolayer mechano-dynamics. Vimentin knock-down delays wound closure, reduces cell coordination, while increasing traction forces exerted by cells on the substratum. It also disrupts the directionality of leader cells migration, as well as the cohesion and coordinated motion of cells deep in the monolayer. We further show that vimentin promotes the conversion of polarized cell locomotion into coordinate collective migration by polarizing actin, focal adhesions and traction forces, sustaining leader cells lamellipodium protrusive activity and directionality, while allowing mechanical coupling of leader with follower cells. Altogether, we show that vimentin is essential for bridging polarized single cell locomotion and coordinated collective migration to allow efficient collective migration. Significant statementEpithelial cells migrate coordinately to repair tissue. Vimentin, transiently enriched at the wound edge plays a key role in guiding this process by converting polarized cell locomotion into coordinate collective migration, enabling leader cells to polarize, form stable protrusions, and maintain directed migration, while allowing mechanical coupling of front cells with followers, necessary for efficient coordinated collective migration. These findings reveal vimentin, a known EMT marker, as a novel positive regulator of efficient wound healing.

cell biology↗

bioRxiv2025

Skin microbiome composition and function in the development of atopic diseases during infancy

BackgroundAtopic dermatitis (AD), food sensitization (FS), and food allergy (FA) frequently co-occur in infancy, but the factors driving distinct atopic phenotypes remain unclear. While FLG null mutations are major genetic risk factors for AD, they explain only a fraction of disease heritability, suggesting a potential role for the skin microbiome. ObjectiveTo determine how early-life skin microbiome composition and its interaction with host genetics contribute to distinct atopic phenotypes in infancy. MethodsWe analyzed >1,000 skin swabs from 429 infants in the VITALITY cohort using deep shotgun metagenomic sequencing at 2-3 months (pre-diagnosis) and 12 months (post-diagnosis). Differential abundance, strain-level, and microbial genome-wide association analyses were performed to identify taxonomic and functional features associated with AD, FS, FA, and their co-occurrence, as well as with FLG mutation status. ResultsWithin AD, microbial signatures differed by co-occurring FA or FS. At 12 months, Staphylococcus epidermidis was enriched in infants with AD alone, whereas infants with AD and FA exhibited decreased Staphylococcus hominis and Lactococcus species, along with increased Dermacoccus nishinomiyaensis and Malassezia slooffiae. At 2-3 months, early skin dysbiosis characterized by enrichment of Staphylococcus species was associated with subsequent development of AD with FS or FA, but not AD alone. Among infants with AD, FLG mutation carriers exhibited additional microbial shifts, including reduced Streptococcus species and increased Malassezia slooffiae. Strain-level analyses revealed mother-infant sharing of skin microbial taxa associated with AD, and microbial genome-wide association analyses identified species-specific genes linked to AD severity. ConclusionsInfant atopic phenotypes are associated with distinct, phenotype-specific features of the skin microbiome that emerge both before and after clinical disease onset. By resolving microbial differences within AD according to allergic co-occurrence, host genetics, and early-life timing, this study highlights the infant skin microbiome as a potential target for early risk stratification.

microbiology↗

bioRxiv2025

Resilience in zebrafish embryoids

It is unresolved how morphogenetic cell movements and Nodal signalling are involved in the formation of the embryonic body during gastrulation. We address this question by using the zebrafish embryoid model system, which consists of cultured blastula cells lacking yolk and signalling derived from the yolk syncytial layer (YSL). Zebrafish embryoids form a cylindrical-like structure under serum-free growth culture conditions. We find that embryoids elongate without directed convergence and maintain their proliferation rate and cell mixing behaviour. Surprisingly, they undergo budding activity that has not been reported in zebrafish embryos yet. Here, the constitutively active Nodal receptor type I promotes internalisation-like gastrulation movements and induces the expression of shield genetic markers in embryoids. This work demonstrates that the absence of the yolk and signalling derived from the YSL does not affect the cell behaviour, while the constitutively active Nodal receptor type I impacts budding, internalisation movement and the emergence of the second shield. Summary statementWe demonstrate that the cell behaviour during gastrulation is robust to the deficiency of yolk topology and signalling originating from the yolk syncytial layer.

developmental biology↗

bioRxiv2025

Capturing Nematic Order on Tissue Surfaces of Arbitrary Geometry

A leading paradigm for understanding the large-scale behavior of tissues is via generalizations of liquid crystal physics; much like liquid crystals, tissues combine fluid-like, viscoelastic behaviors with local orientational order, such as nematic symmetry. Whilst aspects of quantitative agreement have been achieved for flat monolayers, the most striking features of tissue morphogenesis -- such as symmetry breaking, folding and invagination -- concern surfaces with complex curved geometries. As yet, however, characterizing such complex behaviors in three dimensions has been frustrated due to the absence of proper image analysis methods; current state-of-the-art methods almost exclusively rely on two-dimensional (2D) intensity projections of multiple image planes, which superimpose data and lose geometric information that can be crucial. Here, we describe an analysis pipeline that properly captures the nematic order of tissue surfaces of arbitrary geometry, which we demonstrate in the context of in vitro multicellular aggregates, and in vivo zebrafish hearts. For the former, we correlate the number of topological defects with the aggregates surface area and verify theoretical predictions, whilst for the latter, we link biological properties to physical concepts (Laplace pressure) through spatio-temporal correlations of the heart geometry with fluorescence signals of intracellular proteins. Our analysis enables access to the hidden third dimension of conventional image acquisition via stacked 2D planes and highlights how such characterizations can deliver meaningful physical insight.

biophysics↗

bioRxiv2023

A genome catalog of the early-life human skin microbiome

Metagenome-assembled genomes have greatly expanded the reference genomes for skin microbiome. However, the current reference genomes are largely based on samples from adults in North America and lack representation from infants and individuals from other continents. Here we used ultra-deep shotgun metagenomic sequencing to profile the skin microbiota of 215 infants at age 2-3 months and 12 months who were part of the VITALITY trial in Australia as well as 67 maternally-matched samples. Based on the infant samples, we present the Early-Life Skin Genomes (ELSG) catalog, comprising 9,194 bacterial genomes from 1,029 species, 206 fungal genomes from 13 species, and 39 eukaryotic viral sequences. This genome catalog substantially expands the diversity of species previously known to comprise human skin microbiome and improves the classification rate of sequenced data by 25%. The protein catalog derived from these genomes provides insights into the functional elements such as defense mechanisms that distinguish early-life skin microbiome. We also found evidence for vertical transmission at the microbial community, individual skin bacterial species and strain levels between mothers and infants. Overall, the ELSG catalog uncovers the skin microbiome of a previously underrepresented age group and population and provides a comprehensive view of human skin microbiome diversity, function, and transmission in early life.

genomics↗

bioRxiv2023

Cell-Cell Separation Device: measurement of intercellular detachment forces.

Whether at the intramolecular or cellular scale in organisms, cell-cell adhesion adapt to external mechanical cues arising from the static environment of cells and from dynamic interactions between neighboring cells. Cell-cell adhesions need to resist detachment forces to secure the integrity and internal organization of organisms. In the past, various techniques have been developed to characterize adhesion properties of molecules and cells in vitro, and to understand how cells sense and probe their environment. Atomic force microscopy and dual-pipette aspiration, where cells are mainly present in suspension, are common methods for studying detachment forces of cell-cell adhesions. How cell-cell adhesion forces are developed for adherent and environment-adapted cells, however, is less clear. Here, we designed the Cell-Cell Separation Device (CC-SD), a microstructured substrate that measures both intercellular forces and external stresses of cells towards the matrix. The design is based on micropillar arrays originally designed for cell traction-force measurements. We designed PDMS micropillar-blocks, to which cells could adhere and be able to connect to each other across the gap. Controlled stretching of the whole substrate changed the distance between blocks and increased gap size. That allowed us to apply strains to cell-cell contacts, eventually leading to cell-cell adhesion detachment, which was measured by pillar deflections. The CC-SD provided an increase of the gap between the blocks of up to 2.4-fold, which was sufficient to separate substrate-attached cells with fully developed F-actin network. Simultaneously measured pillar deflections allowed us to address cellular response to the intercellular strain applied. The CC-SD thus opens up possibilities for the analysis of intercellular force detachments and sheds light on the robustness of cell-cell adhesions in dynamic processes in tissue development.

biophysics↗

bioRxiv2022

Hexanematic crossover in epithelial monolayers depends on cell adhesion and cell density

Changes in tissue geometry during developmental processes are associated with collective migration of cells. Recent experimental and numerical results suggest that these changes could leverage on the coexistence of nematic and hexatic orientational order at different length scales. How this multiscale organization is affected by the material properties of the cells and their substrate is presently unknown. In this study, we address these questions in monolayers of Madin-Darby canine kidney cells having various cell densities and molecular repertoires. At small length scales, confluent monolayers are characterized by a prominent hexatic order, independent of the presence of E-cadherin, monolayer density, and underlying substrate stiffness. However, all three properties affect the meso-scale tissue organization. The length scale at which hexatic order transits to nematic order, the "hexanematic" crossover scale, strongly depends on cell-cell adhesions and correlates with monolayer density. Our study demonstrates how epithelial organization is affected by mechanical properties, and provides a robust description of tissue organization during developmental processes.

biophysics↗

bioRxiv2022

Epithelia are multiscale active liquid crystals

Biological processes such as embryogenesis, wound healing and cancer progression, crucially rely on the ability of epithelial cells to coordinate their mechanical activity over length scales order of magnitudes larger than the typical cellular size. While regulated by signalling pathways, such as YAP (yes-associated protein), MAPK (mitogen-activated protein kinase) and Wnt, this behavior is believed to additionally hinge on a minimal toolkit of physical mechanisms, of which liquid crystal order is the most promising candidat. Yet, experimental and theoretical studies have given so far inconsistent results in this respect: whereas nematic order is often invoked in the interpretation of experimental data, computational models have instead suggested that hexatic order could in fact emerge in the biologically relevant region of parameter space. In this article we resolve this dilemma. Using a combination of in vitro experiments on Madin-Darby canine kidney cells (MDCK), numerical simulations and analytical work, we demonstrate that both nematic and hexatic order is in fact present in epithelial layers, with the former being dominant at large length scales and the latter at small length scales. In MDCK GII cells on uncoated glass, these different types of liquid crystal order crossover at 34 {micro}m, corresponding approximatively to clusters of 21 cells. Our work sheds light on the emergent organization of living matter, provides a new set of tools for analyzing the structure of epithelia and paves the way toward a comprehensive and predictive mesoscopic theory of tissues.

biophysics↗

bioRxiv2021

Single cell micro-pillar-based characterization of endothelial and fibroblast cell mechanics

Mechanotransduction, the ability of cells to sense and respond to the mechanical cues from their microenvironment, plays an important role in numerous cellular processes, ranging from cell migration to differentiation. Several techniques have been developed to investigate the underlying mechanisms of mechanotransduction, in particular, force measurement-based techniques. However, we still lack basic single cell quantitative comparison on the mechanical properties of commonly used cell types, such as endothelial and fibroblast cells. Such information is critical to provide a precedent for studying complex tissues and organs that consist of various cell types. In this short communication, we report on the mechanical characterization of the commonly used endothelial and fibroblast cells at the single cell level. Using a micropillar-based assay, we measured the traction force profiles of these cells. Our study showcases differences between the two cell types in their traction force distribution and morphology. The results reported can be used as a reference and to lay the groundwork for future analysis of numerous disease models involving these cells.

biophysics↗

bioRxiv2021

Characterization of Cell-Induced Astigmatism in High-Resolution Imaging.

High-resolution and super-resolution techniques become more frequently used in thick, inhomogeneous samples. In particular for imaging life cells and tissue in which one wishes to observe a biological process at minimal interference and in the natural environment, sample inhomogeneities are unavoidable. Yet sample-inhomogeneities are paralleled by refractive index variations, for example between the cell organelles and the surrounding medium, that will result in the refraction of light, and therefore lead to sample-induced astigmatism. Astigmatism in turn will result in positional inaccuracies of observations that are at the heart of all super-resolution techniques. Here we introduce a simple model and define a figure-of-merit that allows one to quickly assess the importance of astigmatism for a given experimental setting. We found that astigmatism caused by the cells nucleus can easily lead to aberrations up to hundreds of nanometers, well beyond the accuracy of all super-resolution techniques. The astigmatism generated by small objects, like bacteria or vesicles, appear to be small enough to be of any significance in typical super-resolution experimentation.

biophysics↗

bioRxiv2020

Hypergravity affects Cell Traction Forces of Fibroblasts.

Cells sense and react on changes of the mechanical properties of their environment, and likewise respond to external mechanical stress applied to them. Whether the gravitational field, as overall body force, modulates cellular behavior is however unclear. Different studies demonstrated that micro- and hypergravity influences the shape and elasticity of cells, initiate cytoskeleton reorganization, and influence cell motility. All these cellular properties are interconnected, and contribute to forces that cells apply on their surrounding microenvironment. Yet, studies that investigated changes of cell traction forces under hypergravity conditions are scarce. Here we performed hypergravity experiments on 3T3 fibroblast cells using the Large Diameter Centrifuge at the European Space and Technology Centre (ESA-ESTEC). cells were exposed to hypergravity of up to 19.5g for 16 h in both the upright and the inverted orientation with respect to the g-force vector. We observed a decrease in cellular traction forces when the gravitational field was increased up to 5.4g, followed by an increase of traction forces for higher gravity fields up to 19.5g independent of the orientation of the gravity vector. We attribute the switch in cellular response to shear-thinning at low g-forces, followed by significant rearrangement and enforcement of the cytoskeleton at high g-forces. SIGNIFICANCEThe behavior of cells critically depend on the mechanical properties of their environment. For example external stresses and strains lead to decisions in cell differentiation as well as to collective-migration in metastasis. Gravity, as a permanently acting body force, is one of those externs stresses. We demonstrate the impact of gravitational challenges on forces that cells apply to their environment. We observed a switch in cellular response with a decrease in cell traction forces for low bypgrarayiv. conditions, followed by a significant increase in cell traction forces at higher g-level. This particular cellular response reflects a switch in croskeletal organization, similar to that observed for cells in fluids where shear forces act.

biophysics↗

bioRxiv2018

Do long-tailed macaques engage in intuitive statistics?

Human infants, apes and capuchins have been found to engage in intuitive statistics, generating predictions from populations to samples based on proportional information. This suggests that statistical reasoning might depend on some core knowledge that is shared with other species. Here, we investigated whether such intuitive statistical reasoning is also present in a species of Old World monkeys, to aid in the reconstruction of the evolution of this capacity. In a series of 7 test conditions, 11 long-tailed macaques were offered different pairs of populations containing varying proportions of preferred vs. neutral food items. One population always contained a higher proportion of preferred items than the other. An experimenter simultaneously drew one item out of each population, hid them in her fists and presented them to the monkey to choose. Results revealed that at least one individual seemed to make systematic population-to-sample inferences and consistently chose the sample from the population with the more favorable distribution of preferred vs. neutral food items. While it is not clear whether she used relative or absolute quantities of food, she seemed to understand the difference between a correct choice and a favorable draw and thus some basic principles of intuitive statistics.

animal behavior and cognition↗