Biology subjects

Tomancak, P.

Publications and source records attributed to Tomancak, P..

At least 19 recordsLinked to original sources

bioRxiv2026

Multiple contact sites between cells and the vitelline envelope coordinate tissue flows in Drosophila gastrulation

Gastrulation is thought to be driven primarily by forces generated within individual cells. These cell-intrinsic forces collectively induce tissue-scale flows and transform the monolayered embryo into a multilayered structure. However, as the embryo constitutes a mechanically closed system, these flows must be balanced by regions of resistance or anchoring to enable asymmetric morphogenesis. In the Drosophila embryo, integrin-mediated attachment of the blastoderm to the vitelline envelope has been shown to stabilize germ band extension at the organismal scale. Disrupting such an attachment leads to a characteristic twisting phenotype. Yet, how this attachment shapes concurrent global morphogenetic events remains unclear. We discovered that the integrin -subunit scab, which mediates the attachment, is expressed in three different regions of the cellular blastoderm near prominent invagination events. Through a combination of light-sheet imaging, genetic and mechanical perturbations, we demonstrate that integrin-enhanced friction is essential for unidirectional tissue flows in those regions, with effects including cephalic furrow positioning and epithelial stability. Guided by a minimal physical model, we further show that multiple attachment sites enhance the robustness and reproducibility of global tissue movements. Together, our results indicate that Drosophila gastrulation emerges from a balance between cell-intrinsic force generation and spatially distributed adhesion to the surrounding envelope, which together shape tissue flows at the embryo scale.

developmental biology↗

bioRxiv2026

Embryo-eggshell interaction counteracts chiral bias in early Drosophila morphogenesis

Morphogenetic processes during animal development are remarkably invariant (Duboule, 1994; Hall, 1997; Kalinka et al., 2010; Raff, 1996). This stability is established by the interaction between genetic determination of developmental progression and the constraints imposed by the surrounding embryonic environment (Busby and Steventon, 2021; Gilmour et al., 2017; Gorfinkiel and Martinez Arias, 2021). We discovered that the germ band extension process in Drosophila is rather variable: instead of extending straight towards the head, the germ band tends to twist to the side. Through a combination of experiments and theory, we demonstrated that Scab integrin-mediated attachment to the vitelline envelope stabilizes the germ band and supports its straight extension. Our quantification of germ band extension dynamics also revealed a consistent handedness to the twist of the germ band. We showed that this left-right asymmetry can be altered by manipulating the expression of Myo1D, the molecular determinant of chirality in Drosophila (Lebreton et al., 2018). Our data thus suggest that Myo1D expression causes the early gastrulating blastoderm epithelium to already exhibit inherent chirality and that the resulting destabilization of germ band extension is suppressed by Scab-mediated friction between the blastoderm and the vitelline envelope.

developmental biology↗

bioRxiv2025

Mastodon: the Command Center for Large-Scale Lineage-Tracing Microscopy Datasets

Understanding development in living organisms requires following the divisions, movements, and fates of cells across developing systems. While advances in microscopy have enabled whole-embryo imaging at the cellular level, extracting and analyzing cell lineages from these massive datasets remains a significant computational challenge. We present Mastodon, a scalable, extensible software platform for manual, semi-automated, and automated cell tracking in large images. A purpose-built graph model supports responsive performance for datasets with millions of annotations, making Mastodon a future-proof platform for cell lineage analysis. Built as a Fiji plugin, Mastodon enables interactive visualization, editing, and analysis of complex lineage trees, seamlessly integrated with the raw image data. Comprehension of cell lineages in complex three-dimensional geometries is facilitated by interoperability with the powerful open-source render engine Blender. In three distinct developmental contexts, we demonstrate how Mastodon will accelerate biological insights by providing user-friendly navigation and explorative analysis in complex lineage datasets.

bioinformatics↗

bioRxiv2024

Anisotropic stretch biases the self-organization of actin fibers in multicellular Hydra aggregates

During development, groups of cells generate shape by coordinating their mechanical properties through an interplay of self-organization and pre-patterning. Hydra displays a striking planar pattern of actin fibers at the organism scale, and mechanics influence the morphogenesis of biological structures during its pre-patterned regeneration. However, how mechanics participate in the formation of an ordered pattern from a totally disordered state remains unknown. To study this, we used cellular aggregates formed from dissociated Hydra cells, which initially lose all actin polarity yet regenerate a long-range actin pattern. We showed quantitatively that the actin meshwork evolves from a disordered symmetric state to an ordered state in which rotational symmetry is broken, and translation symmetry is partially broken, with the nematic and smectic order parameters increasing over days. During the first hours, the actin meshwork displayed spatial heterogeneity in the nematic order parameter, and ordered domains separated by lines of defects progressively grew and fused. This suggests that local cell-cell interactions drive the transition from disorder to order. To understand the mechanism of ordering, we perturbed the tissues physical constraints. We showed that while topology and geometry do not have a direct effect, anisotropic stretch biases the emerging orientation of the actin meshwork within hours. Surprisingly, although a Wnt protein gradient is expected to play a role in the actin ordering, the stretch-associated alignment happened without a Wnt enrichment. This demonstrates the role of tissue mechanics in the alignment of the actin fibers during the disorder-to-order transition.

developmental biology↗

bioRxiv2024

A genome resource for the marine annelid Platynereis dumerilii

The marine annelid Platynereis dumerilii is a model organism used in many research areas including evolution and development, neurobiology, ecology and regeneration. Here we present the genomes of P. dumerilii (laboratory culture reference and a single individual assembly) and of the closely related P. massiliensis and P. megalops (single individual assembly) to facilitate comparative genomic approaches and help explore Platynereis biology. We used long-read sequencing technology and chromosomal-conformation capture along with extensive transcriptomic resources to obtain and annotate a draft genome assembly of [~]1.47 Gbp for P. dumerilii, of which more than half represent repeat elements. We predict around 29,000 protein-coding genes, with relatively large intron sizes, over 38,000 non-coding genes, and 105 miRNA loci. We further explore the high genetic variation ([~]3% heterozygosity) within the Platynereis species complex. Gene ontology reveals the most variable loci to be associated with pigmentation, development and immunity. The current work sets the stage for further development of Platynereis genomic resources.

genomics↗

bioRxiv2023

Remodelling of cytoskeleton and plasma membrane proteins contributes to drought sensitivity of Arabidopsis rhd2 mutant

NADPH oxidases are enzymes localised in the plasma membrane and emitting superoxide to the extracellular space. By production of superoxide as one type of reactive oxygen species (ROS), they exert pleiotropic functions in plant development and various stress responses. Arabidopsis thaliana RESPIRATORY BURST OXIDASE HOMOLOG PROTEIN C/ROOT HAIR DEFECTIVE 2 (AtRBOHC/RHD2) is an NADPH oxidase with preferential gene expression in roots. Polar localisation and ROS production by this enzyme are essential for root hair elongation. However, the proteome-wide and physiological consequences of RBOHC/RHD2 mutations are unknown. To find out potential new functions of AtRBOHC/RHD2, we employed a differential proteomic analysis of Arabidopsis rhd2-1 mutant, carrying a loss-of-function mutation in RBOHC/RHD2. Proteomic analyses that were validated with independent biochemical, phenotypical and advanced microscopy methods, showed quantitative deregulation of proteins involved in abiotic and biotic stress response, metabolism, vesicular transport and cell wall modification. Considerable differences in the differential proteomes between roots and above-ground parts were found in the mutant. The altered abundance of aquaporins and homeostasis of transmembrane pumps and transporters most likely determine the higher sensitivity of Arabidopsis rhd2-1 mutant to drought. HighlightProteomics and advanced microscopy reveal that the drought sensitivity of Arabidopsis mutant in ROOT HAIR DEFECTIVE 2 is linked to altered homeostasis of plasma membrane proteins and cytoskeleton remodelling.

plant biology↗

bioRxiv2023

Pre-patterned epithelial invagination prevents mechanical instability during fly gastrulation

Mechanical forces are crucial for driving and shaping tissue morphogenesis during embryonic development, but their relevance for the evolution of development remains poorly understood. Here, we show that a morphogenetic innovation present in fly embryos--a deep epithelial fold known as the cephalic furrow--plays a mechanical role during Drosophila gastrulation. By integrating in vivo experiments and in silico simulations, we find that the formation of the cephalic furrow prevents mechanical instabilities at the head-trunk epithelium by absorbing the compressive stresses generated by concurrent morphogenetic movements of gastrulation, the expansion of mitotic domains and the germ band extension. Furthermore, by comparing the expression of known and novel genes involved in cephalic furrow formation between fly species, we find that the presence of the cephalic furrow is linked to changes in the expression of buttonhead transcription factor at the head-trunk boundary. These data suggest that the genetic control of cephalic furrow formation was established through the integration of a new player into the ancestral head-trunk patterning system, and that mechanical instability may have been the selective pressure associated with the evolution of the cephalic furrow. Our findings uncover empirical evidence for how mechanical forces can influence the evolution of morphogenetic innovations in early development.

developmental biology↗

bioRxiv2020

Interactive design of GPU-accelerated Image Data Flow Graphs and cross-platform deployment using multi-lingual code generation

Modern life science relies heavily on fluorescent microscopy and subsequent quantitative bio-image analysis. The current rise of graphics processing units (GPUs) in the context of image processing enables batch processing large amounts of image data at unprecedented speed. In order to facilitate adoption of this technology in daily practice, we present an expert system based on the GPU-accelerated image processing library CLIJ: The CLIJ-assistant keeps track of which operations formed an image and suggests subsequent operations. It enables new ways of interaction with image data and image processing operations because its underlying GPU-accelerated image data flow graphs (IDFGs) allow changes to parameters of early processing steps and instantaneous visualization of their final results. Operations, their parameters and connections in the IDFG are stored at any point in time enabling the CLIJ-assistant to offer an undo-function for virtually unlimited rewinding parameter changes. Furthermore, to improve reproducibility of image data analysis workflows and interoperability with established image analysis platforms, the CLIJ-assistant can generate code from IDFGs in programming languages such as ImageJ Macro, Java, Jython, JavaScipt, Groovy, Python and C++ for later use in ImageJ, Fiji, Icy, Matlab, QuPath, Jupyter Notebooks and Napari. We demonstrate the CLIJ-assistant for processing image data in multiple scenarios to highlight its general applicability. The CLIJ-assistant is open source and available online: https://clij.github.io/assistant/

bioinformatics↗

bioRxiv2019

Imaging plant germline differentiation within Arabidopsis flower by light sheet microscopy

In higher plants, germline differentiation occurs during a relatively short period within developing flowers. Understanding of the mechanisms that govern germline differentiation lags behind other plant developmental processes. This is largely because the germline is restricted to relatively few cells buried deep within floral tissues, which makes them difficult to study. To overcome this limitation, we have developed a methodology for live imaging of the germ cell lineage within floral organs of Arabidopsis using light sheet fluorescence microscopy. We have established reporter lines, cultivation conditions, and imaging protocols for high-resolution microscopy of developing flowers continuously for up to several days. We used multiview imagining to reconstruct a three-dimensional model of a flower at subcellular resolution. We demonstrate the power of this approach by capturing male and female meiosis, asymmetric pollen division, movement of meiotic chromosomes, and unusual restitution mitosis in tapetum cells. This method will enable new avenues of research into plant sexual reproduction.

plant biology↗

bioRxiv2019

Regionalized tissue fluidization by an actomyosin cable is required for epithelial gap closure during insect gastrulation

Many animal embryos pull and close an epithelial sheet around the spherical or ellipsoidal egg surface during a gastrulation process known as epiboly. The ovoidal geometry dictates that the epithelial sheet first expands and subsequently compacts. Moreover, the epithelial sheet spreading over the sphere is mechanically stressed and this stress needs to be released. Here we show that during extraembryonic tissue (serosa) epiboly in the red flour beetle Tribolium castaneum, the non-proliferative serosa becomes regionalized into two distinct territories: a dorsal region under higher tension away from the leading edge with larger non-rearranging cells, and a more fluid ventral region under lower tension surrounding the leading edge with smaller cells undergoing cell intercalation. Our results suggest that fluidization of the leading edge is caused by a heterogeneous actomyosin cable that drives sequential eviction and intercalation of individual cells away from the serosa margin. Since this developmental solution utilized during epiboly resembles the mechanism of wound healing in other systems, we propose actomyosin cable-driven local tissue fluidization as a conserved morphogenetic module for closure of epithelial gaps.

developmental biology↗

bioRxiv2019

CLIJ: Enabling GPU-accelerated image processing in Fiji

Graphics processing units (GPU) allow image processing at unprecedented speed. We present CLIJ, a Fiji plugin enabling end-users with entry level experience in programming to benefit from GPU-accelerated image processing. Freely programmable workflows can speed up image processing in Fiji by factor 10 and more using high-end GPU hardware and on affordable mobile computers with built-in GPUs.

bioinformatics↗

bioRxiv2019

Ordered patterning of the sensory system is susceptible to stochastic features of gene expression

Sensory neuron numbers and positions are precisely organized to accurately map environmental signals in the brain. However, this precision must emerge from biochemical processes within and between cells that are stochastic. We measured intrinsic noise in senseless protein output, a key determinant of sensory fate, during Drosophila development. Perturbing microRNA regulation or genomic locus of senseless transcription produced distinct noise signatures. Genomic location altered protein stochasticity in an allelic-pairing dependent manner (transvection). This generated sensory pattern disorder without perturbing protein abundance. In contrast, loss of microRNA repression of senseless increased protein abundance but not sensory pattern disorder. This suggests that gene expression stochasticity is a critical feature that must be constrained during development to allow rapid yet accurate cell fate resolution. One Sentence SummaryLife on the Margin: balancing speed and accuracy during animal development.

developmental biology↗

bioRxiv2019

Yorkie controls tube length and apical barrier integrity in the developing Drosophila airways

Epithelial organ size and shape depend on cell shape changes, cell-matrix communication and apical membrane growth. The Drosophila embryonic tracheal network is an excellent model to study these processes. Here, we show that the transcriptional co-activator of the Hippo pathway, Yorkie (YAP in vertebrates), plays distinct roles in the developing Drosophila airways. Yorkie exerts a cytoplasmic function by binding Drosophila Twinstar, the orthologue of the vertebrate actin-severing protein Cofilin, to regulate F-actin levels and apical cell membrane size, which are required for proper tracheal tube elongation. Second, Yorkie controls water-tightness of tracheal tubes by transcriptional regulation of the enzyme{delta} -aminolevulinate synthase (Alas). We conclude that Yorkie has a dual role in tracheal development to ensure proper tracheal growth and functionality. Short SummaryThis work identified an alternative role of the transcriptional co-activator Yorkie (Yki) in controlling water impermeability and tube size of the developing Drosophila airways. Tracheal impermeability is triggered by Yki-mediated transcriptional regulation of{delta} -aminolevulinate synthase, Alas, whereas tube elongation is controlled by binding of Yki to the actin severing factor Twinstar.

developmental biology↗

bioRxiv2018

Surface tension determines tissue shape and growth kinetics

The growth of tissue is an essential process controlling morphogenesis and regeneration of organs [1]. In general tissue forming cells are interactive and motile [2], which can give rise to emergent physical properties such as viscous fluid behaviour as has been shown for epithelial monolayers during embryogenesis [3, 4], and for cell-agglomerates [5] with a measurable surface tension [6]. However, the mechanical integrity of tissues is provided by extracellular matrices (ECM) that turn tissues into solids with well-defined elastic properties [7]. Paradoxically, it has been shown by in-vitro experiments that even osteoid-like tissue with large amounts of ECM grows according to rules reminiscent of fluid behavior [8, 9]. Motivated by this conundrum, we show here quantitatively, by constraining growing tissues to surfaces of con ...

biophysics↗

bioRxiv2018

Integrin-mediated attachment of the blastoderm to the vitelline envelope impacts gastrulation of insects

During gastrulation, physical forces reshape the simple embryonic tissue to form a complex body plan of multicellular organisms1. These forces often cause large-scale asymmetric movements of the embryonic tissue2,3. In many embryos, the tissue undergoing gastrulation movements is surrounded by a rigid protective shell4,5. While it is well recognized that gastrulation movements depend on forces generated by tissue-intrinsic contractility6,7, it is not known if interactions between the tissue and the protective shell provide additional forces that impact gastrulation. Here we show that a particular part of the blastoderm tissue of the red flour beetle Tribolium castaneum tightly adheres in a temporally coordinated manner to the vitelline envelope surrounding the embryo. This attachment generates an additional force that counteracts the tissue-intrinsic contractile forces to create asymmetric tissue movements. Furthermore, this localized attachment is mediated by a specific integrin, and its knock-down leads to a gastrulation phenotype consistent with complete loss of attachment. Moreover, analysis of another integrin in the fruit fly Drosophila melanogaster suggests that gastrulation in this organism also relies on adhesion between the blastoderm and the vitelline. Together, our findings reveal a conserved mechanism whereby the spatiotemporal pattern of tissue adhesion to the vitelline envelope provides controllable counter-forces that shape gastrulation movements in insects.

developmental biology↗

bioRxiv2017

Content-Aware Image Restoration: Pushing the Limits of Fluorescence Microscopy

Fluorescence microscopy is a key driver of discoveries in the life-sciences, with observable phenomena being limited by the optics of the microscope, the chemistry of the fluorophores, and the maximum photon exposure tolerated by the sample. These limits necessitate trade-offs between imaging speed, spatial resolution, light exposure, and imaging depth. In this work we show how image restoration based on deep learning extends the range of biological phenomena observable by microscopy. On seven concrete examples we demonstrate how microscopy images can be restored even if 60-fold fewer photons are used during acquisition, how near isotropic resolution can be achieved with up to 10-fold under-sampling along the axial direction, and how tubular and granular structures smaller than the diffraction limit can be resolved at 20-times higher frame-rates compared to state-of-the-art methods. All developed image restoration methods are freely available as open source software in Python, FO_SCPLOWIJIC_SCPLOW, and KO_SCPLOWNIMEC_SCPLOW.

bioinformatics↗

bioRxiv2017

Cadherin Fat2 directs cellular mechanics to promote epithelial rotation

Left and right symmetry breaking is involved in many developmental processes that are important to form bodies and organs. One of them is the epithelial rotation of developing organs. However, how epithelial cells move, how they break symmetry to define common direction of their collective movement and what function rotational epithelial motions have in morphogenesis remain elusive. Here, we identified a dynamic actomyosin network with preferred retrograde contractility at the basal side of the rotating follicle epithelium in Drosophila oogenesis. We provide evidence that unidirectional epithelial rotation is a result of actomyosin asymmetry cue transmission onto a tissue plane synchronized by the atypical cadherin Fat2, a key planar cell polarity regulator in Drosophila oogenesis. We found that Fat2 directs actomyosin contractility to move the epithelial tissue in order to provide directed elongation of follicle cells. In contrast, loss of Fat2 results in anisotropic non-muscle Myosin II pulses that are disorganized in plane and deform cell shape, tissue and Drosophila eggs. Our data indicate that directed elongation of follicle cells is critical for proper Drosophila egg morphogenesis. Together, we demonstrate the importance of atypical cadherins in the control of cell mechanics, left/right symmetry breaking and its propagation onto the tissue scale to facilitate proper organ morphogenesis. This process may be evolutionarily conserved in rotating animal organs.

developmental biology↗

bioRxiv2017

Control of Hox transcription factor concentration and cell-to-cell variability by an auto-regulatory switch

The variability in transcription factor concentration among cells is an important developmental determinant, yet how variability is controlled remains poorly understood. Studies of variability have focused predominantly on monitoring mRNA production noise. Little information exists about transcription factor protein variability, since this requires the use of quantitative methods with single-molecule sensitivity. Using Fluorescence Correlation Spectroscopy (FCS), we characterized the concentration and variability of 14 endogenously tagged TFs in live Drosophila imaginal discs. For the Hox TF Antennapedia we investigated whether protein variability results from random stochastic events or is developmentally regulated. We found that Antennapedia transitioned from low concentration/high variability early, to high concentration/low variability later, in development. FCS and temporally resolved genetic studies uncovered that Antennapedia itself is necessary and sufficient to drive a developmental regulatory switch from auto-activation to auto-repression, thereby reducing variability. This switch is controlled by progressive changes in relative concentrations of preferentially activating and repressing Antennapedia isoforms, which bind chromatin with different affinities. Mathematical modelling demonstrated that the experimentally supported auto-regulatory circuit can explain the increase of Antennapedia concentration and suppression of variability over time.

genetics↗