Biology subjects

Meroz, Y.

Publications and source records attributed to Meroz, Y..

14 recordsLinked to original sources

bioRxiv2026

Robust Organ Shape During Growth Requires Local Morphogen Signaling and Global Curvature Feedback

Precise organ shape during development requires feedback between organ-scale geometry and cell-level growth dynamics. Here, we use the apical hook of dicotyledonous plants as a model to study this multiscale control. This protective structure forms a [~]180{degrees} bend that is stably maintained despite rapid elongation. Combining quantitative growth mapping, multiscale modeling, and hormone analysis, we identify the cellular dynamics underlying hook maintenance. Contrary to the prevailing model, hook stability does not arise from sustained inner-outer growth asymmetry. Instead, stable curvature emerges from a biphasic, self-similar growth pattern that remains spatially fixed despite continuous cell flux. Auxin-driven growth asymmetry induces bending but is spatially restricted and insufficient to maintain shape. By contrast, a graded, auxin-independent autotropic response provides curvature-dependent growth regulation that counteracts bending and stabilizes shape against perturbations. Together, these findings establish a general principle in which local morphogen-driven bending and global geometry-dependent feedback jointly maintain robust organ shape during growth. HighlightsO_LISelf-similar growth maintains apical hook curvature despite continuous cell flux C_LIO_LICurvature stability emerges from coordinated axial and differential growth C_LIO_LIAuxin asymmetry is spatially restricted and insufficient for shape maintenance C_LIO_LICurvature-dependent feedback ensures robust and optimized hook shape C_LI

plant biology↗

bioRxiv2026

Nonlinear distributed sensing of light patterns leads to perceptual distortions in plants

Many organisms lack centralized sensory-processing systems, navigating complex environments through local integration of spatially distributed stimuli (e.g., chemotaxis of cells, bacteria, or growing neurons). Here we propose the first general physical and geometric framework to describe how such distributed sensing translates into integrated directional responses. We study plants, multicellular decentralized systems that grow towards light (phototropism), which can come from multiple directions and at different intensities. We develop a model in which light is sensed locally on the shoot circumference, transduced nonlinearly, and integrated vectorially; the model is informed and validated by unilateral and bilateral lighting, and out-of-plane illumination experiments on sunflower seedlings. We show that seedlings respond to the vectorial sum of transduced signals rather than to the physical sum of incident light, which can create systematic deviations between maximal physical illumination and growth direction, akin to optical illusions. This framework further predicts that symmetrical, opposing cues cancel each other out, which we validate experimentally using a weaker symmetry-breaking light source.

plant biology↗

bioRxiv2026

Circumnutations drive embodied mechanical sensing and support selection in twining plants

Climbing plants use self-generated oscillatory movements called circumnutations to search their environment for supports to attach to. Yet little is known about what information these movements provide. Here we show that circumnutations enable climbing plants to actively assess the mechanical stability of a newly encountered support and determine whether to initiate twining. Analogous to whisking in mammals, circumnutating shoots generate predictable mechanical loading that probes support resistance. Force measurements of freely circumnutating bean shoots reveal that contact forces follow a characteristic sinusoidal pattern. We develop a minimal physical model of this system, and experimentally informed simulations recover the measured force trajectories. We find that the stem-support interaction is captured by a simple torque balance between external loading and the intrinsic bending moment of the stem, equivalent to a cantilever beam with a rotating load. Analysis of force trajectories, supported by experimentally informed simulations, shows that force amplitude is set by stem stiffness and geometry, whereas the characteristic timescale is governed by the circumnutation rate. Twining occurs only after the stem reaches a critical torque threshold, corresponding to a threshold deformation of the stem that likely serves as the mechanical trigger for twining initiation, reflecting both sufficient support stability and a minimal geometric overshoot required for grasp. Motorized-stage experiments further demonstrate that increasing the effective circumnutation rate accelerates twining initiation to minutes, whereas reducing it can suppress twining despite prolonged contact. Together, these results establish embodied mechanical sensing in plants and show how morphology and self-generated motion enable support selection without centralized control.

biophysics↗

bioRxiv2026

Segment Any Plant (SAP): Foundation-Model Segmentation for Plant Time-Series Phenotyping

Quantitative studies of plant growth and environmental responses increasingly rely on time-series imaging, yet automated segmentation remains challenging due to continuous growth, large non-rigid morphological change, and frequent self-occlusion. Traditional image-processing pipelines and task-specific deep learning models often require extensive annotated datasets and retraining, limiting portability across species, developmental stages, and imaging conditions. Here we present SAP (Segment Any Plant), a plant-focused framework that leverages the pretrained Segment Anything Model 2 (SAM2) to enable few-shot, training-free segmentation of plant time-series imagery. SAP integrates interactive prompting, automated temporal mask propagation, and centerline extraction within a web-based interface, allowing users to move from raw images to quantitative descriptors of organ shape and dynamics without programming expertise. Across multiple systems, including Arabidopsis thaliana rosette development, root growth, sunflower gravitropism, and confocal root microscopy, SAP achieves high segmentation accuracy (mean IoU 0.89-0.93) and sub-pixel centerline precision from single-frame prompting. By reducing the need for task-specific retraining, SAP provides a transferable framework for reproducible time-series phenotyping across diverse experimental contexts.

biophysics↗

bioRxiv2025

Understanding Shape and Residual Stress Dynamics in Rod-Like Plant Organs

Residual stresses are common in rod-like plant organs such as roots and shoots, arising from mechanical incompatibilities between tissues with differing intrinsic lengths. Although mechanical regulation of cell wall growth is well established, the role of internally generated stresses in organ-scale morphogenesis remains poorly understood. Here, we introduce a tractable theoretical framework that couples structural residual stresses to growth-driven shape dynamics. We represent rod-like organs as bundles of morphoelastic rods connected in parallel, each corresponding to a distinct concentric tissue layer. Assuming elastic strain-driven growth and rod-like symmetry, the resulting mechanical constraints yield transparent analytical relationships linking tissue heterogeneity to macroscopic observables such as axial strain rates, bending dynamics, and residual stress distributions. Using a minimal two-layer model representing the epidermis and inner tissues, we show how tissue incompatibilities can generate phenomena including effective autotropism, mechanical memory, and discontinuous growth dynamics following cell division. Overall, our framework demonstrates how residual stresses may contribute to plant morphogenesis and provides a foundation for future investigations of mechano-chemical growth control in plants.

biophysics↗

bioRxiv2025

Dual-Axial Force Measurements of Non-Tethered Plants

Growing plants are remarkable at negotiating obstacles in their unstructured and changing environments. Measuring the mechanical interactions of growing plants with surrounding objects is a critical step towards deciphering thigmotropic responses underpinning complex growth strategies. Yet, available force-measurement systems have limited capacity to capture weak (sub-mN) forces in freely moving plant organs - such as the forces applied by a growing shoot pushing at an obstacle. We developed a measurement system based on the deflection of a pendulum by a freely moving shoot. Crucially, unlike many force-measurement systems, the organ is not tethered to the device. Moreover, force is measured along two axes, as opposed to one axis in commonly used methods such as cantilevers. Orthogonal cameras track the 3D position of the rod and shoot, yielding the rod deflection angle and, using a mechanical torque equilibrium equation, allowing to extract the force applied by the plant over time. This system is relevant for measuring weak forces in macro-sized systems (such as growth or turgor pressures), and the force detection range can be tuned by altering rod mass and length. We demonstrate the system with bean (Phaseolus vulgaris) shoots, measuring the forces they apply on a candidate support during inherent circumnutation movements, prior to twining. Such measurements lay the foundations for deciphering how climbing plants assess whether to twine or not - an open question since Darwins first observations.

biophysics↗

bioRxiv2024

The growth-driven penetration strategy of plant roots is mechanically more efficient than pushing

Plant roots are considered highly efficient soil explorers. As opposed to the push-driven penetration strategy commonly used by many digging organisms, roots penetrate by growing, adding new cells at the tip, and elongating over a well-defined growth zone. However, a comprehensive understanding of the mechanical aspects associated with root penetration is currently lacking. We perform penetration experiments following Arabidopsis thaliana roots growing into an agar gel environment, and a needle of similar dimensions pushed into the same agar. We measure and compare the environmental deformations in both cases by following the displacement of fluorescent beads embedded within the gel, combining confocal microscopy and Digital Volume Correlation (DVC) analysis. We find that deformations are generally smaller for the growing roots. To better understand the mechanical differences between the two penetration strategies we develop a computational model informed by experiments. Simulations show that, compared to push-driven penetration, grow-driven penetration reduces frictional forces and mechanical work, with lower propagation of displacements in the surrounding medium. These findings shed light on the complex interaction of plant roots with their environment, providing a quantitative understanding based on a comparative approach.

biophysics↗

bioRxiv2023

On the mechanical origins of waving, coiling and skewing in Arabidopsis thaliana roots

By masterfully balancing directed growth and passive mechanics, plant roots are remarkably capable of navigating complex heterogeneous environments to find resources. Here we present a theoretical and numerical framework which allows us to interrogate and simulate the mechanical impact of solid interfaces on the growth pattern of plant organs. We focus on the well-known waving, coiling and skewing patterns exhibited by roots of Arabidopsis thaliana when grown on inclined surfaces, serving as a minimal model of the intricate interplay with solid substrates. By modelling growing slender organs as Cosserat rods that mechanically interact with the environment, our simulations verify hypotheses of waving and coiling arising from the combination of active gravitropism and passive root-plane responses. Skewing is instead related to intrinsic twist due to cell file rotation. Numerical investigations are outfitted with an analytical framework that consistently relates transitions between straight, waving, coiling and skewing patterns with substrate tilt angle. Simulations are found to corroborate theory and recapitulate a host of reported experimental observations, thus providing a systematic approach for studying in silico plant organs behavior in relation to their environment. SignificancePlant roots exhibit an exceptional ability to navigate in heterogeneous soil environments while overcoming obstacles. Our study combines theory and experimental observations to interrogate and simulate the mechanical impact of obstacles on organ growth. As a test case we focus on well-known observations of waving, coiling and skewing growth patterns of Arabidopsis thaliana roots grown on inclined substrates. Overall, our study explains a broad set of experimental observations through the minimal ingredients of gravitropism and passive mechanics. Our numerical framework provides an in silico laboratory, yielding quantitative insight into the dynamics of growing organs at the intersection of active processes and passive mechanics, applicable beyond plants to any slender growing system, from neurons or fungal hyphae to novel soft robots.

plant biology↗

bioRxiv2023

A quantitative model for spatio-temporal dynamics of root gravitropism

Plant organs adapt their morphology according to environmental signals through growth-driven processes called tropisms. While much effort has been directed in the development of mathematical models describing the tropic dynamics of aerial organs, these cannot provide a good description of roots due to intrinsic physiological differences. Here we present a mathematical model informed by gravitropic experiments on Arabidopsis thaliana roots, assuming a sub-apical growth profile and apical sensing. The model quantitatively recovers the full spatio-temporal dynamics observed in experiments. An analytical solution of the model enables us to evaluate the gravitropic and proprioceptive sensitivities of roots, while also allowing us to corroborate the requirement of proprioception in describing root dynamics. Lastly, we find that the dynamics are analogous to a damped harmonic oscillator, providing intuition regarding the source of the observed oscillatory behavior. In all, the model not only provides a quantitative description of root tropic dynamics, but also provides a mathematical framework for the future investigation of roots in complex media.

plant biology↗

bioRxiv2023

Revealing how memory shapes time-dependent computational processes in plant tropisms

Mounting evidence suggests that plants engage complex computational processes to quantify and integrate sensory information over time, enabling remarkable adaptive growth strategies. However, quantitative understanding of these computational processes is limited. We report experiments probing the dependence of gravitropic responses of wheat coleoptiles on previous stimuli. First, building on a mathematical model that identifies this dependence as a form of memory, or a filter, we use experimental observations to reveal the mathematical principles of how coleoptiles integrate multiple stimuli over time. Next, we perform two-stimulus experiments, informed by model predictions, to reveal fundamental computational processes. We quantitatively show that coleoptiles respond not only to sums but also to differences between stimuli over different timescales, constituting first evidence that plants can compare stimuli - crucial for search and regulation processes. These timescales also coincide with oscillations observed in gravitropic responses of wheat coleoptiles, suggesting shoots may combine memory and movement in order to enhance posture control and sensing capabilities.

plant biology↗

bioRxiv2022

Noise-mediated self-organization in mutually shading sunflowers

Circumnutations are widespread in plants and typically associated with exploratory movements, however a quantitative understanding of their role remains elusive. In this study we report, for the first time, the role of noisy circumnutations in facilitating an optimal growth pattern within a crowded group of mutually shading plants. We revisit the problem of self-organization observed for sunflowers, mediated by shade response interactions. Our analysis reveals that circumnutation movements conform to a bounded random walk characterized by a remarkably broad distribution of velocities, covering three orders of magnitude. In motile animal systems such wide distributions of movement velocities are frequently identified with enhancement of behavioral processes, suggesting that circumnutations may serve as a source of functional noise. To test our hypothesis, we developed a Langevin-type parsimonious model of interacting growing disks, informed by experiments, successfully capturing the characteristic dynamics of individual and multiple interacting plants. Employing our simulation framework we examine the role of circumnutations in the system, and find that the observed breadth of the velocity distribution represents a sharp transition in the force-noise ratio, conferring advantageous effects by facilitating exploration of potential configurations, leading to an optimized arrangement with minimal shading. These findings represent the first report of functional noise in plant movements, and establishes a theoretical foundation for investigating how plants navigate their environment by employing computational processes such as task-oriented processes, optimization, and active sensing. Since plants move by growing, space and time are coupled, and dynamics of self-organization lead to emergent 3D patterns. As such this system provides conceptual insight for other interacting growth-driven systems such fungal hyphae, neurons and self-growing robots, as well as active matter systems where agents interact with past trajectories of their counterparts, such as stigmergy in social insects. This foundational insight has implications in statistical physics, ecological dynamics, agriculture, and even swarm robotics. One sentence summary of paperThe study highlights noisy circumnutations as a strategy plants use for optimizing growth in crowded conditions.

plant biology↗

bioRxiv2020

A general 3D model for growth dynamics of sensory-growth systems: from plants to robotics

In recent years there has been a rise in interest in the development of self-growing robotics inspired by the moving-by-growing paradigm of plants. In particular, climbing plants capitalize on their slender structures to successfully negotiate unstructured environments, while employing a combination of two classes of growth-driven movements: tropic responses, which direct growth in the direction of an external stimulus, and inherent nastic movements, such as periodic circumnutations, which promote exploration. In order to emulate these complex growth dynamics in a 3D environment, a general and rigorous mathematical framework is required. Here we develop a general 3D model for rod-like organs adopting the Frenet-Serret frame, providing a useful framework from the standpoint of robotics control. Differential growth drives the dynamics of the organ, governed by both internal and external cues. We describe the numerical method required to implement this model, and perform numerical simulations of a number of key scenarios, showcasing the applicability of our model. In the case of responses to external stimuli, we consider a distant stimulus (such as sunlight and gravity), a point stimulus (a point light source), and a line stimulus which emulates twining of a climbing plant around a support. We also simulate circumnutations, the response to an internal oscillatory cue, associated with search processes. Lastly we also demonstrate the superposition of both the response to an external stimulus together with circumnutations. Lastly we consider a simple example illustrating the possible use of an optimal control approach in order to recover tropic dynamics, in a way which may be relevant for robotics use. In all, the model presented here is general and robust, paving the way for a deeper understanding of plant response dynamics, as well as novel control systems for newly developed self-growing robots.

biophysics↗

bioRxiv2019

A Framework for Collective Behavior in Plant Inspired Growth-Driven Systems, Based on Kinematics of Allotropism

A variety of biological systems are not motile, but sessile in nature, relying on growth as the main driver of their movement. Groups of such growing organisms can form complex structures, such as the functional architecture of growing axons, or the adaptive structure of plant root systems. These processes are not yet understood, however the decentralized growth dynamics bear similarities to the collective behavior observed in groups of motile organisms, such as flocks of birds or schools of fish. Equivalent growth mechanisms make these systems amenable to a theoretical framework inspired by tropic responses of plants, where growth is considered implicitly as the driver of the observed bending towards a stimulus. We introduce two new concepts related to plant tropisms: point tropism, the response of a plant to a nearby point signal source, and allotropism, the growth-driven response of plant organs to neighboring plants. We first analytically and numerically investigate the 2D dynamics of single organs responding to point signals fixed in space. Building on this we study pairs of organs interacting via allotropism, i.e.each organ senses signals emitted at the tip of their neighbor and responds accordingly. In the case of local sensing we find a rich phase space. We describe the different phases, as well as the sharp transitions between them. We also find that the form of the phase space depends on initial conditions. This work sets the stage towards a theoretical framework for the investigation and understanding of systems of interacting growth-driven individuals.

biophysics↗

bioRxiv2018

Spatiotemporal Integration in Plant Tropisms

Tropisms, growth-driven responses to environmental stimuli, cause plant organs to respond in space and time and reorient themselves. Classical experiments from nearly a century ago reveal that plant shoots respond to the integrated history of light and gravity stimuli rather than just responding instantaneously. We introduce a temporally non-local response function for the dynamics of shoot growth formulated as an integro-differential equation whose solution allows us to qualitatively reproduce experimental observations associated with intermittent and unsteady stimuli. Furthermore, an analytic solution for the case of a pulse light stimulus expresses the response function as function of experimentally tractable variables for the phototropic response of Arabidopsis hypocotyls. All together, our model enables us to predict tropic responses to time-varying stimuli, manifested in temporal integration phenomena, and sets the stage for the incorporation of additional effects such as multiple stimuli, gravitational sagging etc.

plant biology↗