Differential growth and shape formation in plant organs

Three-Dimensional Leaf Edge Reconstruction Combining Two- and Three-Dimensional Approaches

Leaves, crucial for plant physiology, exhibit various morphological traits that meet diverse functional needs. Traditional leaf morphology quantification, largely 2-dimensional (2D), has not fully captured the 3-dimensional (3D) aspects of leaf function. Despite improvements in 3D data acquisition, accurately depicting leaf morphologies, particularly at the edges, is difficult. This study proposes a method for 3D leaf edge reconstruction, combining 2D image segmentation with curve-based 3D reconstruction. Utilizing deep-learning-based instance segmentation for 2D edge detection, structure from motion for estimation of camera positions and orientations, leaf correspondence identification for matching leaves among images, and curve-based 3D reconstruction for estimating 3D curve fragments, the method assembles 3D curve fragments into a leaf edge model through B-spline curve fitting. The method's performances were evaluated on both virtual and actual leaves, and the results indicated that small leaves and high camera noise pose greater challenges to reconstruction. We developed guidelines for setting a reliability threshold for curve fragments, considering factors occlusion, leaf size, the number of images, and camera error; the number of images had a lesser impact on this threshold compared to others. The method was effective for lobed leaves and leaves with fewer than 4 holes. However, challenges still existed when dealing with morphologies exhibiting highly local variations, such as serrations. This nondestructive approach to 3D leaf edge reconstruction marks an advancement in the quantitative analysis of plant morphology. It is a promising way to capture whole-plant architecture by combining 2D and 3D phenotyping approaches adapted to the target anatomical structures.

Assessing the hydromechanical control of plant growth

Multicellular organisms grow and acquire their shapes through the differential expansion and deformation of their cells. Recent research has addressed the role of cell and tissue mechanical properties in these processes. In plants, it is believed that growth rate is a function of the mechanical stress exerted on the cell wall, the thin polymeric layer surrounding cells, involving an effective viscosity. Nevertheless, recent studies have questioned this view, suggesting that cell wall elasticity sets the growth rate or that uptake of water is limiting for plant growth. To assess these issues, we developed a microfluidic device to quantify the growth rates, elastic properties and hydraulic conductivity of individual Marchantia polymorpha plants in a controlled environment with a high throughput. We characterized the effect of osmotic treatment and abscisic acid on growth and hydromechanical properties. Overall, the instantaneous growth rate of individuals is correlated with both bulk elastic modulus and hydraulic conductivity. Our results are consistent with a framework in which the growth rate is determined primarily by the elasticity of the wall and its remodelling, and secondarily by hydraulic conductivity. Accordingly, the coupling between the chemistry of the cell wall and the hydromechanics of the cell appears as key to set growth patterns during morphogenesis.

Chondrocyte hypertrophy in the growth plate promotes stress anisotropy affecting long bone development through chondrocyte column formation

The length of long bones is determined by column formation of proliferative chondrocytes and subsequent chondrocyte hypertrophy in the growth plate during bone development. Despite the importance of mechanical loading in long bone development, the mechanical conditions of the cells within the growth plate, such as the stress field, remain unclear owing to the difficulty in investigating spatiotemporal changes within dynamically growing tissues. In this study, the mechanisms of longitudinal bone growth were investigated from a mechanical perspective through column formation of proliferative chondrocytes within the growth plate before secondary ossification center formation using continuum-based particle models (CbPMs). A one-factor model, which simply describes essential aspects of a biological signaling cascade regulating cell activities within the growth plate, was developed and incorporated into CbPM. Subsequently, the developmental process and maintenance of the growth plate structure and resulting bone morphogenesis were simulated. Thus, stress anisotropy in the proliferative zone that affects bone elongation through chondrocyte column formation was identified and found to be promoted by chondrocyte hypertrophy. These results provide further insights into the mechanical regulation of multicellular dynamics during bone development.

Dehydration-induced corrugated folding in Rhapis excelsa plant leaves

Plant leaves, whose remarkable ability for morphogenesis results in a wide range of petal and leaf shapes in response to environmental cues, have inspired scientific studies as well as the development of engineering structures and devices. Although some typical shape changes in plants and the driving force for such shape evolution have been extensively studied, there remain many poorly understood mechanisms, characteristics, and principles associated with the vast array of shape formation of plant leaves in nature. Here, we present a comprehensive study that combines experiment, theory, and numerical simulations of one such topic-the mechanics and mechanisms of corrugated leaf folding induced by differential shrinking in Rhapis excelsa. Through systematic measurements of the dehydration process in sectioned leaves, we identify a linear correlation between change in the leaf-folding angle and water loss. Building on experimental findings, we develop a generalized model that provides a scaling relationship for water loss in sectioned leaves. Furthermore, our study reveals that corrugated folding induced by dehydration in R. excelsa leaves is achieved by the deformation of a structural architecture-the "hinge" cells. Utilizing such connections among structure, morphology, environmental stimuli, and mechanics, we fabricate several biomimetic machines, including a humidity sensor and morphing devices capable of folding in response to dehydration. The mechanisms of corrugated folding in R. excelsa identified in this work provide a general understanding of the interactions between plant leaves and water. The actuation mechanisms identified in this study also provide insights into the rational design of soft machines.

Growth directions and stiffness across cell layers determine whether tissues stay smooth or buckle

From smooth to buckled, nature exhibits organs of various shapes and forms. How cellular growth patterns produce smooth organ shapes such as leaves and sepals remains unclear. Here we show that unidirectional growth and comparable stiffness across both epidermal layers of Arabidopsis sepals are essential for smoothness. We identified a mutant with ectopic ASYMMETRIC LEAVES 2 (AS2) expression on the outer epidermis. Our analysis reveals that ectopic AS2 expression causes outer epidermal buckling at early stages of sepal development, due to conflicting growth directions and unequal epidermal stiffnesses. Aligning growth direction and increasing stiffness of the outer epidermis restores smoothness. Furthermore, buckling influences auxin efflux transporter protein PIN-FORMED 1 polarity to generate outgrowth in the later stages, suggesting that buckling is sufficient to initiate outgrowths. Our findings suggest that in addition to molecular cues influencing tissue mechanics, tissue mechanics can also modulate molecular signals, giving rise to well-defined shapes.

Inter-plane feedback coordinates cell morphogenesis and maintains 3D tissue organization in the Drosophila pupal retina

How complex organs coordinate cellular morphogenetic events to achieve three-dimensional (3D) form is a central question in development. The question is uniquely tractable in the late Drosophila pupal retina, where cells maintain stereotyped contacts as they elaborate the specialized cytoskeletal structures that pattern the apical, basal and longitudinal planes of the epithelium. In this study, we combined cell type-specific genetic manipulation of the cytoskeletal regulator Abelson (Abl) with 3D imaging to explore how the distinct cellular morphogenetic programs of photoreceptors and interommatidial pigment cells (IOPCs) organize tissue pattern to support retinal integrity. Our experiments show that photoreceptor and IOPC terminal differentiation is unexpectedly interdependent, connected by an intercellular feedback mechanism that coordinates and promotes morphogenetic change across orthogonal tissue planes to ensure correct 3D retinal pattern. We propose that genetic regulation of specialized cellular differentiation programs combined with inter-plane mechanical feedback confers spatial coordination to achieve robust 3D tissue morphogenesis.

A 3-component module maintains sepal flatness in Arabidopsis

As in origami, morphogenesis in living systems heavily relies on tissue curving and folding, through the interplay between biochemical and biomechanical cues. In contrast, certain organs maintain their flat posture over several days. Here we identified a pathway, which is required for the maintenance of organ flatness, taking the sepal, the outermost floral organ, in Arabidopsis as a model system. Through genetic, cellular and mechanical approaches, our results demonstrate that global gene expression regulator VERNALIZATION INDEPENDENCE 4 (VIP4) fine-tunes the mechanical properties of sepal cell walls and maintains balanced growth on both sides of the sepals, mainly by orchestrating the distribution pattern of AUXIN RESPONSE FACTOR 3 (ARF3). vip4 mutation results in softer cell walls and faster cell growth on the adaxial sepal side, which eventually cause sepals to bend outward. Downstream of VIP4, ARF3 works through modulating auxin signaling to down-regulate pectin methylesterase VANGUARD1, resulting in decreased cell wall stiffness. Our work unravels a 3-component module, which relates hormonal patterns to organ curvature, and actively maintains sepal flatness during its growth.

Surface stress and shape relaxation of gelling droplets

Solidification is a heterogeneous transformation from liquid to solid, which usually combines transport, phase transition and mechanical strain. Predicting the shapes resulting from such a complex process is fascinating and has a wide range of implications from morphogenesis in biological tissues to industrial processes. For soft solids initially at equilibrium, elastic stresses, whether tensile or compressive, can be induced by heterogeneous volumetric deformations of the material. These stresses trigger surface instabilities leading to variations of curvature and shape of the solids. In this article, we study the shape evolution of elongated droplets of polymer and particle suspensions undergoing a solidification process caused by the inward diffusion of a gelling agent from the surface. We show experimentally and numerically that there appears a layer of gelled material growing at the surface. Due to volume contraction, this layer induces tensile stresses and drives a flow in the ungelled liquid core, resulting in the relaxation of the droplets toward spherical shapes. Over time, the thickness of this elastic membrane grows, hence the bending stiffness required to change its shape eventually balances the surface stresses, which arrests the relaxation process. These results provide general rules to understand the shape of solidifying materials combining both tension and bending driven deformations.

Orthogonal coupling of a 3D cytoskeletal scaffold coordinates cell morphogenesis and maintains tissue organization in the Drosophila pupal retina

How complex three-dimensional (3D) organs coordinate cellular morphogenetic events to achieve the correct final form is a central question in development. The question is uniquely tractable in the late Drosophila pupal retina where cells maintain stereotyped contacts as they elaborate the specialized cytoskeletal structures that pattern the apical, basal and longitudinal planes of the epithelium. In this study, we combined cell type-specific genetic manipulation of the cytoskeletal regulator Abelson (Abl) with 3D imaging to explore how the distinct cellular morphogenetic programs of photoreceptors and interommatidial pigment cells coordinately organize tissue pattern to support retinal integrity. Our experiments revealed an unanticipated intercellular feedback mechanism whereby correct cellular differentiation of either cell type can non-autonomously induce cytoskeletal remodeling in the other Abl mutant cell type, restoring retinal pattern and integrity. We propose that genetic regulation of specialized cellular differentiation programs combined with inter-plane mechanical feedback confers spatial coordination to achieve robust 3D tissue morphogenesis.

The rapid-tome, a 3D-printed microtome, and an updated hand-sectioning method for high-quality plant sectioning

BACKGROUND

Microscopic analysis of plant anatomy is a common procedure in biology to study structure and function that requires high-quality sections for accurate measurements. Hand sectioning of specimens is typically limited to moderately soft tissue while harder samples prohibit sectioning by hand and/or result in inconsistent thicknesses.

RESULTS

Here we present both a clearly described hand-sectioning method and a novel microtome design that together provide the means to section a variety of plant sample types. The described hand-sectioning method for herbaceous stems works well for softer subjects but is less suitable for samples with secondary growth (e.g., wood production). Instead, the "Rapid-Tome" is a novel tool for sectioning both soft and tougher high-aspect-ratio samples, such as stems and roots, with excellent sample control. The Rapid-Tome can be 3D-printed in approximately 18 h on a mid-quality printer common at university maker spaces. After printing and trimming, Rapid-Tome assembly takes a few minutes with five metal parts common at hardware stores. Users sectioned a variety of plant samples including the hollow internodes of switchgrass (Panicum virgatum), fibrous switchgrass roots containing aerenchyma, and woody branches of eastern red cedar (Juniperus virginiana) and American sycamore (Platanus occidentalis). A comparative analyses with Rapid-Tome-produced sections readily revealed a significant difference in seasonal growth of sycamore xylem vessel area in spring (49%) vs. summer (23%). Additionally, high school students with no prior experience produced sections with the Rapid-Tome adequate for comparative analyses of various plant samples in less than an hour.

CONCLUSIONS

The described hand-sectioning method is suitable for softer tissues, including hollow-stemmed grasses and similar samples. In addition, the Rapid-Tome provides capacity to safely produce high-quality sections of tougher plant materials at a fraction of the cost of traditional microtomes combined with excellent sample control. The Rapid-Tome features rapid sectioning, sample advancement, blade changes, and sample changes; it is highly portable and can be used easily with minimal training making production of thin sections accessible for classroom and outreach use, in addition to research.

Curvature-Regulated Multiphase Patterns in Tori

Biological functions in living systems are closely related to their geometries and morphologies. Toroidal structures, which widely exist in nature, present interesting features containing positive, zero, and negative Gaussian curvatures within one system. Such varying curvatures would significantly affect the growing or dehydrating morphogenesis, as observed in various intricate patterns in abundant biological structures. To understand the underlying morphoelastic mechanism and to determine the crucial factors that govern the patterning in toroidal structures, we develop a core-shell model and derive a scaling law to characterize growth- or dehydration-induced instability patterns. We find that the eventual patterns are mainly determined by two dimensionless parameters that are composed of stiffness and curvature of the system. Moreover, we construct a phase diagram showing the multiphase wrinkling pattern selection in various toroidal structures in terms of these two parameters, which is confirmed by our experimental observations. Physical insights into the multiphase transitions and existence of bistable modes are further provided by identifying hysteresis loops and the Maxwell equal-energy conditions. The universal law for morphology selection on core shell structures with varying curvatures can fundamentally explain and precisely predict wrinkling patterns of diverse toroidal structures, which may also provide a platform to design morphology-related functional surfaces.

Swelling-Dependent Shape-Based Transformation of a Human Mesenchymal Stromal Cells-Laden 4D Bioprinted Construct for Cartilage Tissue Engineering

3D bioprinting is usually implemented on flat surfaces, posing serious limitations in the fabrication of multilayered curved constructs. 4D bioprinting, combining 3D bioprinting with time-dependent stimuli-induced transformation, enables the fabrication of shape-changing constructs. Here, a 4D biofabrication method is reported for cartilage engineering based on the differential swelling of a smart multi-material system made from two hydrogel-based materials: hyaluronan and alginate. Two ink formulations are used: tyramine-functionalized hyaluronan (HAT, high-swelling) and alginate with HAT (AHAT, low-swelling). Both inks have similar elastic, shear-thinning, and printability behavior. The inks are 3D printed into a bilayered scaffold before triggering the shape-change by using liquid immersion as stimulus. In time (4D), the differential swelling between the two zones leads to the scaffold's self-bending. Different designs are made to tune the radius of curvature and shape. A bioprinted formulation of AHAT and human bone marrow cells demonstrates high cell viability. After 28 days in chondrogenic medium, the curvature is clearly present while cartilage-like matrix production is visible on histology. A proof-of-concept of the recently emerged technology of 4D bioprinting with a specific application for the design of curved structures potentially mimicking the curvature and multilayer cellular nature of native cartilage is demonstrated.

Study on the Mechanism of Elastic Instability Caused by Natural Growth in Orthotropic Material

Compared to synthetic materials, naturally grown biological materials have more specific behavioral patterns and life connotations in their morphological evolution over millions of years of environmental evolution on Earth. In this paper, we investigate the physical mechanisms and manifestations of out-of-plane deformation instability. Firstly, the origin of the instability phenomenon caused by the growth of the leaf is introduced. Leaf instability problems are modeled using rectangular thin plates. Secondly, the variation in the critical intrinsic strain with the principal shear modulus is obtained by numerical solution. The post-buckling behavior of the growth instability is further analyzed by general static analysis, and we obtain the phase diagram of morphogenesis of thin plant organs as functions of the principal shear modulus and off-axis angle. The research results enhance the understanding of the mechanism of elastic instability caused by natural growth in orthotropic materials.

Characterization of the MADS-Box Gene Family in Akebia trifoliata and Their Evolutionary Events in Angiosperms

As the largest clade of modern plants, flower plants have evolved a wide variety of flowers and fruits. MADS-box genes play key roles in regulating plant morphogenesis, while basal eudicots have an evolutionarily important position of acting as an evolutionary bridge between basal angiosperms and core eudicots. Akebia trifoliata is an important member of the basal eudicot group. To study the early evolution of angiosperms, we identified and characterized the MADS-Box gene family on the whole-genome level of A. trifoliata. There were 47 MADS-box genes (13 type I and 34 type II genes) in the A. trifoliata genome; type I genes had a greater gene length and coefficient of variation and a smaller exon number than type II genes. A total of 27 (57.4%) experienced whole or segmental genome duplication and purifying selection. A transcriptome analysis suggested that three and eight genes were involved in whole fruit and seed development, respectively. The diversification and phylogenetic analysis of 1479 type II MADS-box genes of 22 angiosperm species provided some clues indicating that a γ whole genome triplication event of eudicots possibility experienced a two-step process. These results are valuable for improving A. trifoliata fruit traits and theoretically elucidating evolutionary processes of angiosperms, especially eudicots.

Chiral topographic instability in shrinking spheres

Many biological structures exhibit intriguing morphological patterns adapted to environmental cues, which contribute to their important biological functions and also inspire material designs. Here, we report a chiral wrinkling topography in shrinking core-shell spheres, as observed in excessively dehydrated passion fruit and experimentally demonstrated in silicon core-shells under air extraction. Upon shrinkage deformation, the surface initially buckles into a buckyball pattern (periodic hexagons and pentagons) and then transforms into a chiral mode. The neighbouring chiral cellular patterns can further interact with each other, resulting in secondary symmetry breaking and the formation of two types of topological network. We develop a core-shell model and derive a universal scaling law to understand the underlying morphoelastic mechanism and to effectively describe and predict such chiral symmetry breaking far beyond the critical instability threshold. Moreover, we show experimentally that the chiral characteristic adapted to local perturbation can be harnessed to effectively and stably grasp small-sized objects of various shapes and made of different stiff and soft materials. Our results not only reveal chiral instability topographies, providing fundamental insights into the surface morphogenesis of the deformed core-shell spheres that are ubiquitous in the real world, but also demonstrate potential applications of adaptive grasping based on delicate chiral localization.

3D printing of nanowrinkled architectures via laser direct assembly

Structural wrinkles in nature have been widely imitated to enhance the surface functionalities of objects, especially three-dimensional (3D) architectured wrinkles, holding promise for emerging applications in mechanical, electrical, and biological processes. However, the fabrication of user-defined 3D nanowrinkled architectures is a long-pending challenge. Here, we propose a bottom-up laser direct assembly strategy to fabricate multidimensional nanowrinkled architectures in a single-material one-step process. Through the introduction of laser-induced thermal transition into a 3D nanoprinting process for leading the point-by-point nanoscale wrinkling and the self-organization of wrinkle structures, we have demonstrated the program-controlled and on-demand fabrication of multidimensional nanowrinkled structures. Moreover, the precise control of wrinkle morphology with an optimal wavelength of 40 nanometers and the regulation of the dynamic transformation of wrinkled cellular microstructures via interfacial stress mismatch engineering have been achieved. This study provides a universal protocol for constructing nearly arbitrary nanowrinkled architectures and facilitates a new paradigm in nanostructure manufacturing.

Leaf morphogenesis: The multifaceted roles of mechanics

Plants produce a rich diversity of biological forms, and the diversity of leaves is especially notable. Mechanisms of leaf morphogenesis have been studied in the past two decades, with a growing focus on the interactive roles of mechanics in recent years. Growth of plant organs involves feedback by mechanical stress: growth induces stress, and stress affects growth and morphogenesis. Although much attention has been given to potential stress-sensing mechanisms and cellular responses, the mechanical principles guiding morphogenesis have not been well understood. Here we synthesize the overarching roles of mechanics and mechanical stress in multilevel and multiple stages of leaf morphogenesis, encompassing leaf primordium initiation, phyllotaxis and venation patterning, and the establishment of complex mature leaf shapes. Moreover, the roles of mechanics at multiscale levels, from subcellular cytoskeletal molecules to single cells to tissues at the organ scale, are articulated. By highlighting the role of mechanical buckling in the formation of three-dimensional leaf shapes, this review integrates the perspectives of mechanics and biology to provide broader insights into the mechanobiology of leaf morphogenesis.

Groovy and Gnarly: Surface Wrinkles as a Multifunctional Motif for Terrestrial and Marine Environments

From large ventral pleats of humpback whales to nanoscale ridges on flower petals, wrinkled structures are omnipresent, multifunctional, and found at hugely diverse scales. Depending on the particulars of the biological system-its environment, morphology, and mechanical properties-wrinkles may control adhesion, friction, wetting, or drag; promote interfacial exchange; act as flow channels; or contribute to stretching, mechanical integrity, or structural color. Undulations on natural surfaces primarily arise from stress-induced instabilities of surface layers (e.g., buckling) during growth or aging. Variation in the material properties of surface layers and in the magnitude and orientation of intrinsic stresses during growth lead to a variety of wrinkling morphologies and patterns which, in turn, reflect the wide range of biophysical challenges wrinkled surfaces can solve. Therefore, investigating how surface wrinkles vary and are implemented across biological systems is key to understanding their structure-function relationships. In this work, we synthesize the literature in a metadata analysis of surface wrinkling in various terrestrial and marine organisms to review important morphological parameters and classify functional aspects of surface wrinkles in relation to the size and ecology of organisms. Building on our previous and current experimental studies, we explore case studies on nano/micro-scale wrinkles in biofilms, plant surfaces, and basking shark filter structures to compare developmental and structure-vs-function aspects of wrinkles with vastly different size scales and environmental demands. In doing this and by contrasting wrinkle development in soft and hard biological systems, we provide a template of structure-function relationships of biological surface wrinkles and an outlook for functionalized wrinkled biomimetic surfaces.

Ripples at Edges of Blooming Lilies and Torn Plastic Sheets

Ripples arise at edges of petals of blooming Lilium casablanca flowers and at edges of torn plastic sheets. In both systems, ripples are a consequence of excess length along the edge of a sheet. Through the use of time-lapse videos of blooming lilies and published images of torn plastic sheets, we find that ripples in both systems are well-described by the scaling relationship a∝w(L-w), where a is amplitude, w is wavelength, and L is arc length. A phenomenological relationship previously reported for self-similar ripple patterns, namely 〈a〉∝〈w〉, can be recovered by assuming that buckling stress is constant. Excess length along petal edges can also influence their overall Gaussian curvature, such that petals invert from a cup shape to a saddle shape upon blooming. Previous simulations of these shape changes have assumed that petal thickness decreases at least quadratically. Here, we evaluate tomograms of several varieties of lily buds and find that this assumption is valid along the short axis of the buds, but not the long axis. A challenge of employing traditional tomography methods to measure petal thickness is that the sample is destroyed; a single bud cannot be followed through the entire blooming process. To address this challenge, we provide proof of principle that the non-destructive, label-free method of X-ray tomography produces high-contrast 3-dimensional scans on time scales short enough to follow lily blooming.

Photomorphogenesis of Diverse Autonomous Traveling Waves in a Monolithic Soft Artificial Muscle

Biological organisms (e.g., batoid fish, etc.) possess the remarkable ability to morph their soft, sheet-like tissues into wavy morphologies and self-oscillate to make traveling waves, enabling myriad functionalities in propulsion, locomotion, and transportation. In contrast, current manmade soft robotic systems cannot adaptively make wavy morphologies and concurrently achieve wave propagation because the controllable actuation of desired 3D morphologies in entirely soft materials is a formidable challenge due to their continuously deformable bodies that own a large number of actuable degrees of freedom. Here, we report a bioinspired robotic system that not only allows photomorphogenesis of on-demand 3D wavy morphologies but also enables autonomous wave propagation in a monolithic soft artificial muscle (MSAM). This system employs a conceptually different design strategy based on a combination of two principles derived from plant morphogenesis and the undulatory motion of ray fish. The former offers a shaping principle based on differential growth that enables morphing MSAM into target wavy configurations, while the latter inspires a driving principle that induces autonomous propagation of shaped waves by rhythmic motor patterns. This waving system can be used as adaptive "soft engines/motors" that enable directional locomotion, intelligent transportation of cargo, and autonomous propulsion. It even produces programmable, complex artificial peristaltic waves. Our design allows controllable formation of 3D wavy morphologies and autonomous wave behaviors in the soft robotic system that would be useful for broad applications in adaptive, self-regulated mechanical systems for advanced robotics, soft machines, and energy harvest.

Methods for numerical simulation of knit based morphable structures: knitmorphs

Shape morphing behavior has applications in many fields such as soft robotics, actuators and sensors, solar cells, tight packaging, flexible electronics, and biomedicine. The most common approach to achieve shape morphing structures is through shape memory alloys or hydrogels. These two materials undergo differential strains which generate a variety of shapes. In this work, we demonstrate the novel concept that 2D knits comprising of yarns from different materials can be morphed into different three-dimensional shapes thereby forming a bridge between traditional knitting and shape changing structures. This concept is referred to as Knitmorphs. Our computational analysis acts as the proof of concept revealing that knitted patterns of varying materials morph into complex shapes, such as saddle, axisymmetric cup, and a plate with waves when subjected to thermal loads. Two-dimensional circular models of plain and rib developed on CAD packages are imported to the finite element analysis software Abaqus, followed by post-processing into wires and assigning fiber material properties of different thermal coefficients of expansion and stiffness. We also propose potential applications for the concept of programmable knits for developing robots based upon jellyfish like locomotion, and complex structures similar to wind turbine blades. This novel concept is meant to introduce a new field for design when considering morphable structures.

Organizing your space: The potential for integrating spatial transcriptomics and 3D imaging data in plants

Plant cells communicate information for the regulation of development and responses to external stresses. A key form of this communication is transcriptional regulation, accomplished via complex gene networks operating both locally and systemically. To fully understand how genes are regulated across plant tissues and organs, high resolution, multi-dimensional spatial transcriptional data must be acquired and placed within a cellular and organismal context. Spatial transcriptomics (ST) typically provides a two-dimensional spatial analysis of gene expression of tissue sections that can be stacked to render three-dimensional data. For example, X-ray and light-sheet microscopy provide sub-micron scale volumetric imaging of cellular morphology of tissues, organs, or potentially entire organisms. Linking these technologies could substantially advance transcriptomics in plant biology and other fields. Here, we review advances in ST and 3D microscopy approaches and describe how these technologies could be combined to provide high resolution, spatially organized plant tissue transcript mapping.

Hierarchical self-assembly into chiral nanostructures

One basic principle regulating self-assembly is associated with the asymmetry of constituent building blocks or packing models. Using asymmetry to manipulate molecular-level devices and hierarchical functional materials is a promising topic in materials sciences and supramolecular chemistry. Here, exemplified by recent major achievements in chiral hierarchical self-assembly, we show how chirality may be utilized in the design, construction and evolution of highly ordered and complex chiral nanostructures. We focus on how unique functions can be developed by the exploitation of chiral nanostructures instead of single basic units. Our perspective on the future prospects of chiral nanostructures via the hierarchical self-assembly strategy is also discussed.

Recent Progress in Active Mechanical Metamaterials and Construction Principles

Active mechanical metamaterials (AMMs) (or smart mechanical metamaterials) that combine the configurations of mechanical metamaterials and the active control of stimuli-responsive materials have been widely investigated in recent decades. The elaborate artificial microstructures of mechanical metamaterials and the stimulus response characteristics of smart materials both contribute to AMMs, making them achieve excellent properties beyond the conventional metamaterials. The micro and macro structures of the AMMs are designed based on structural construction principles such as, phase transition, strain mismatch, and mechanical instability. Considering the controllability and efficiency of the stimuli-responsive materials, physical fields such as, the temperature, chemicals, light, electric current, magnetic field, and pressure have been adopted as the external stimuli in practice. In this paper, the frontier works and the latest progress in AMMs from the aspects of the mechanics and materials are reviewed. The functions and engineering applications of the AMMs are also discussed. Finally, existing issues and future perspectives in this field are briefly described. This review is expected to provide the basis and inspiration for the follow-up research on AMMs.

External Mechanical Cues Reveal a Katanin-Independent Mechanism behind Auxin-Mediated Tissue Bending in Plants

Tissue folding is a central building block of plant and animal morphogenesis. In dicotyledonous plants, hypocotyl folds to form hooks after seedling germination that protects their aerial stem cell niche during emergence from soil. Auxin response factors and auxin transport are reported to play a key role in this process. Here, we show that the microtubule-severing enzyme katanin contributes to hook formation. However, by exposing hypocotyls to external mechanical cues mimicking the natural soil environment, we reveal that auxin response factors ARF7/ARF19, auxin influx carriers, and katanin are dispensable for apical hook formation, indicating that these factors primarily play the role of catalyzers of tissue bending in the absence of external mechanical cues. Instead, our results reveal the key roles of the non-canonical TMK-mediated auxin pathway, PIN efflux carriers, and cellulose microfibrils as components of the core pathway behind hook formation in the presence or absence of external mechanical cues.

Reduction in organ-organ friction is critical for corolla elongation in morning glory

In complex structures such as flowers, organ-organ interactions are critical for morphogenesis. The corolla plays a central role in attracting pollinators: thus, its proper development is important in nature, agriculture, and horticulture. Although the intraorgan mechanism of corolla development has been studied, the importance of organ-organ interactions during development remains unknown. Here, using corolla mutants of morning glory described approximately 200 years ago, we show that glandular secretory trichomes (GSTs) regulate floral organ interactions needed for corolla morphogenesis. Defects in GST development in perianth organs result in folding of the corolla tube, and release of mechanical stress by sepal removal restores corolla elongation. Computational modeling shows that the folding occurs because of buckling caused by mechanical stress from friction at the distal side of the corolla. Our results suggest a novel function of GSTs in regulating the physical interaction of floral organs for macroscopic morphogenesis of the corolla.

How Mechanical Forces Shape Plant Organs

Plants produce organs of various shapes and sizes. While much has been learned about genetic regulation of organogenesis, the integration of mechanics in the process is also gaining attention. Here, we consider the role of forces as instructive signals in organ morphogenesis. Turgor pressure is the primary cause of mechanical signals in developing organs. Because plant cells are glued to each other, mechanical signals act, in essence, at multiple scales, through cell wall contiguity and water flux. In turn, cells use such signals to resist mechanical stress, for instance, by reinforcing their cell walls. We show that the three elemental shapes behind plant organs - spheres, cylinders and lamina - can be actively maintained by such a mechanical feedback. Combinations of this 3-letter alphabet can generate more complex shapes. Furthermore, mechanical conflicts emerge at the boundary between domains exhibiting different growth rates or directions. These secondary mechanical signals contribute to three other organ shape features - folds, shape reproducibility and growth arrest. The further integration of mechanical signals with the molecular network offers many fruitful prospects for the scientific community, including the role of proprioception in organ shape robustness or the definition of cell and organ identities as a result of an interplay between biochemical and mechanical signals.

A Life Cycle for Modeling Biology at Different Scales

Modeling has become a popular tool for inquiry and discovery across biological disciplines. Models allow biologists to probe complex questions and to guide experimentation. Modeling literacy among biologists, however, has not always kept pace with the rise in popularity of these techniques and the relevant advances in modeling theory. The result is a lack of understanding that inhibits communication and ultimately, progress in data gathering and analysis. In an effort to help bridge this gap, we present a blueprint that will empower biologists to interrogate and apply models in their field. We demonstrate the applicability of this blueprint in two case studies from distinct subdisciplines of biology; developmental-biomechanics and evolutionary biology. The models used in these fields vary from summarizing dynamical mechanisms to making statistical inferences, demonstrating the breadth of the utility of models to explore biological phenomena.

Programmable Deformations of Biomimetic Composite Hydrogels Embedded with Printed Fibers

Shape deformations are prevalent in nature, which are closely related to the heterogeneous structures with a feature of fibrous elements embedded in a matrix. The microfibers with specific orientations act as either passive geometrical constraints in an active matrix or active elements in a passive matrix, which generate programmed internal stresses and drive shape morphing under external stimuli. Morphing materials can be designed in a biomimetic way, yet it is challenging to fabricate composite hydrogels with well-distributed fibers by a facile strategy. Here, we demonstrate the fabrication of microfiber-embedded hydrogels facilitated by the extrusion-based printing technology. Programmed deformations are achieved in these hydrogels with microfibers distributed in the upper and/or bottom layers of the gel matrix. Under external stimuli, the microfibers and the gel matrix have different responses that produce internal stresses and result in programmable deformations of the composite gel. Multiple shape transformations are realized in the hydrogel by embedding multiple types of responsive microfibers in the passive or active matrix, which is fabricated with the assistance of multinozzle printing. A soft hook is designed to show the capacity of the composite hydrogel to hold and move an object in a saline solution. This facile and versatile strategy provides an alternative way to prepare biomimetic hydrogels with potential applications in biomedical devices, flexible electronics, and soft robots.

Half a century of amyloids: past, present and future

Amyloid diseases are global epidemics with profound health, social and economic implications and yet remain without a cure. This dire situation calls for research into the origin and pathological manifestations of amyloidosis to stimulate continued development of new therapeutics. In basic science and engineering, the cross-β architecture has been a constant thread underlying the structural characteristics of pathological and functional amyloids, and realizing that amyloid structures can be both pathological and functional in nature has fuelled innovations in artificial amyloids, whose use today ranges from water purification to 3D printing. At the conclusion of a half century since Eanes and Glenner's seminal study of amyloids in humans, this review commemorates the occasion by documenting the major milestones in amyloid research to date, from the perspectives of structural biology, biophysics, medicine, microbiology, engineering and nanotechnology. We also discuss new challenges and opportunities to drive this interdisciplinary field moving forward.

Plant 3D (P3D): a plant phenotyping toolkit for 3D point clouds

MOTIVATION

Developing methods to efficiently analyze 3D point cloud data of plant architectures remain challenging for many phenotyping applications. Here, we describe a tool that tackles four core phenotyping tasks: classification of cloud points into stem and lamina points, graph skeletonization of the stem points, segmentation of individual lamina and whole leaf labeling. These four tasks are critical for numerous downstream phenotyping goals, such as quantifying plant biomass, performing morphological analyses of plant shapes and uncovering genotype to phenotype relationships. The Plant 3D tool provides an intuitive graphical user interface, a fast 3D rendering engine for visualizing plants with millions of cloud points, and several graph-theoretic and machine-learning algorithms for 3D architecture analyses.

AVAILABILITY AND IMPLEMENTATION

P3D is open-source and implemented in C++. Source code and Windows installer are freely available at https://github.com/iziamtso/P3D/.

CONTACT

iziamtso@ucsd.edu or navlakha@cshl.edu.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Rapid Volatilization Induced Mechanically Robust Shape-Morphing Structures toward 4D Printing

Inspired by diverse shape-shifting phenomena in nature, various man-made shape programmable materials have been developed for applications in actuators, deployable devices, and soft robots. However, fabricating mechanically robust shape-morphing structures with on-demand, rapid shape-transformation capability, and high load-bearing capacity is still a great challenge. Herein, we report a mechanically robust and rapid shape-shifting material system enabled by the volatilization of a non-fully-reacted, volatile component in a partially cured cross-linking network obtained from photopolymerization. Volume shrinkage induced by the loss of the volatile component is exploited to drive complex shape transformations. After shape transformation, the residual monomers, cross-linkers, and photoinitiators that cannot volatilize still exist in the network, which is ready for a further photopolymerization to significantly stiffen the initial material. Guided by analytic models and finite element analysis, we experimentally demonstrate that a variety of shape transformations can be achieved, including both 2D-to-3D and 3D-to-3D' transformations, such as a buckyball self-folding from a 2D hexagonal lattice sheet and multiple pop-up structures transforming from their initial compact configurations. Moreover, we show that an ultra-low-weight 3D Miura-ori structure transformed from a 2D sheet can hold more than 1600 times its weight after stiffness improvement via postcuring. This work provides a versatile and low-cost method to fabricate rapid and robust shape-morphing structures for potential applications in soft robots, deployable antennas, and optical devices.

Interplay between Cell Wall and Auxin Mediates the Control of Differential Cell Elongation during Apical Hook Development

Differential growth plays a crucial role during morphogenesis [1-3]. In plants, development occurs within mechanically connected tissues, and local differences in cell expansion lead to deformations at the organ level, such as buckling or bending [4, 5]. During early seedling development, bending of hypocotyl by differential cell elongation results in apical hook structure that protects the shoot apical meristem from being damaged during emergence from the soil [6, 7]. Plant hormones participate in apical hook development, but not how they mechanistically drive differential growth [8]. Here, we present evidence of interplay between hormonal signals and cell wall in auxin-mediated differential cell elongation using apical hook development as an experimental model. Using genetic and cell biological approaches, we show that xyloglucan (a major primary cell wall component) mediates asymmetric mechanical properties of epidermal cells required for hook development. The xxt1 xxt2 mutant, deficient in xyloglucan [9], displays severe defects in differential cell elongation and hook development. Analysis of xxt1 xxt2 mutant reveals a link between cell wall and transcriptional control of auxin transporters PINFORMEDs (PINs) and AUX1 crucial for establishing the auxin response maxima required for preferential repression of elongation of the cells on the inner side of the hook. Genetic evidence identifies auxin response factor ARF2 as a negative regulator acting downstream of xyloglucan-dependent control of hook development and transcriptional control of polar auxin transport. Our results reveal a crucial feedback process between the cell wall and transcriptional control of polar auxin transport, underlying auxin-dependent control of differential cell elongation in plants.

Moulding three-dimensional curved structures by selective heating

It is of interest to fabricate curved surfaces in three dimensions from homogeneous material in the form of flat sheets. The aim is not just to obtain a surface which has a desired intrinsic Riemannian metric, but to get the desired embedding inR 3 up to translations and rotations. In this paper, we demonstrate three generic methods of moulding a flat sheet of thermo-responsive plastic by selective contraction induced by targeted heating. These methods do not involve any cutting and gluing, which is a property they share with origami. The first method is inspired by tailoring, which is the usual method for making garments out of plain pieces of cloth. Unlike usual tailoring, this method produces the desired embedding inR 3 . The second method just aims to bring about the desired new Riemannian metric via an appropriate pattern of local contractions, without directly controlling the embedding. The third method is based on triangulation, and seeks to induce the desired local distances. This results in getting the desired embedding inR 3 . The second and the third methods, and also the first method for the special case of surfaces of revolution, are algorithmic in nature. We explain these methods and show examples.

Water Affects Morphogenesis of Growing Aquatic Plant Leaves

Lotus leaves floating on water usually experience short-wavelength edge wrinkling that decays toward the center, while the leaves growing above water normally morph into a global bending cone shape with long rippled waves near the edge. Observations suggest that the underlying water (liquid substrate) significantly affects the morphogenesis of leaves. To understand the biophysical mechanism under such phenomena, we develop mathematical models that can effectively account for inhomogeneous differential growth of floating and freestanding leaves to quantitatively predict formation and evolution of their morphology. We find, both theoretically and experimentally, that the short-wavelength buckled configuration is energetically favorable for growing membranes lying on liquid, while the global buckling shape is more preferable for suspended ones. Other influencing factors such as the stem or vein, heterogeneity, and dimension are also investigated. Our results provide a fundamental insight into a variety of plant morphogenesis affected by water foundation and suggest that such surface instabilities can be harnessed for morphology control of biomimetic deployable structures using substrate or edge actuation.

Machine Learning Approaches to Improve Three Basic Plant Phenotyping Tasks Using Three-Dimensional Point Clouds

Developing automated methods to efficiently process large volumes of point cloud data remains a challenge for three-dimensional (3D) plant phenotyping applications. Here, we describe the development of machine learning methods to tackle three primary challenges in plant phenotyping: lamina/stem classification, lamina counting, and stem skeletonization. For classification, we assessed and validated the accuracy of our methods on a dataset of 54 3D shoot architectures, representing multiple growth conditions and developmental time points for two Solanaceous species, tomato (Solanum lycopersicum cv 75 m82D) and Nicotiana benthamiana Using deep learning, we classified lamina versus stems with 97.8% accuracy. Critically, we also demonstrated the robustness of our method to growth conditions and species that have not been trained on, which is important in practical applications but is often untested. For lamina counting, we developed an enhanced region-growing algorithm to reduce oversegmentation; this method achieved 86.6% accuracy, outperforming prior methods developed for this problem. Finally, for stem skeletonization, we developed an enhanced tip detection technique, which ran an order of magnitude faster and generated more precise skeleton architectures than prior methods. Overall, our improvements enable higher throughput and accurate extraction of phenotypic properties from 3D point cloud data.