Xyloglucan deficiency leads to a reduction in turgor pressure and changes in cell wall properties, affecting early seedling establishment

Xyloglucan is believed to play a significant role in cell wall mechanics of dicot plants. Surprisingly, Arabidopsis plants defective in xyloglucan biosynthesis exhibit nearly normal growth and development. We investigated a mutant line, cslc-Δ5, lacking activity in all five Arabidopsis cellulose synthase like-C (CSLC) genes responsible for xyloglucan backbone biosynthesis. We observed that this xyloglucan-deficient line exhibited reduced cellulose crystallinity and increased pectin levels, suggesting the existence of feedback mechanisms that regulate wall composition to compensate for the absence of xyloglucan. These alterations in cell wall composition in the xyloglucan-absent plants were further linked to a decrease in cell wall elastic modulus and rupture stress, as observed through atomic force microscopy (AFM) and extensometer-based techniques. This raised questions about how plants with such modified cell wall properties can maintain normal growth. Our investigation revealed two key factors contributing to this phenomenon. First, measurements of turgor pressure, a primary driver of plant growth, revealed that cslc-Δ5 plants have reduced turgor, preventing the compromised walls from bursting while still allowing growth to occur. Second, we discovered the conservation of elastic asymmetry (ratio of axial to transverse wall elasticity) in the mutant, suggesting an additional mechanism contributing to the maintenance of normal growth. This novel feedback mechanism between cell wall composition and mechanical properties, coupled with turgor pressure regulation, plays a central role in the control of plant growth and is critical for seedling establishment in a mechanically challenging environment by affecting shoot emergence and root penetration.

Mean-field theory approach to three-dimensional nematic phase transitions in microtubules

Microtubules are dynamic intracellular fibers that have been observed experimentally to undergo spontaneous self-alignment. We formulate a three-dimensional (3D) mean-field theory model to analyze the nematic phase transition of microtubules growing and interacting within a 3D space, then make a comparison with computational simulations. We identify a control parameter G_{eff} and predict a unique critical value G_{eff}=1.56 for which a phase transition can occur. Furthermore, we show both analytically and using simulations that this predicted critical value does not depend on the presence of zippering. The mean-field theory developed here provides an analytical estimate of microtubule patterning characteristics without running time-consuming simulations and is a step towards bridging scales from microtubule behavior to multicellular simulations.

Stiffness transitions in new walls post-cell division differ between Marchantia polymorpha gemmae and Arabidopsis thaliana leaves

Plant morphogenesis is governed by the mechanics of the cell wall-a stiff and thin polymeric box that encloses the cells. The cell wall is a highly dynamic composite material. New cell walls are added during cell division. As the cells continue to grow, the properties of cell walls are modulated to undergo significant changes in shape and size without breakage. Spatial and temporal variations in cell wall mechanical properties have been observed. However, how they relate to cell division remains an outstanding question. Here, we combine time-lapse imaging with local mechanical measurements via atomic force microscopy to systematically map the cell wall's age and growth, with their stiffness. We make use of two systems, Marchantia polymorpha gemmae, and Arabidopsis thaliana leaves. We first characterize the growth and cell division of M. polymorpha gemmae. We then demonstrate that cell division in M. polymorpha gemmae results in the generation of a temporary stiffer and slower-growing new wall. In contrast, this transient phenomenon is absent in A. thaliana leaves. We provide evidence that this different temporal behavior has a direct impact on the local cell geometry via changes in the junction angle. These results are expected to pave the way for developing more realistic plant morphogenetic models and to advance the study into the impact of cell division on tissue growth.

Context-specific functions of transcription factors controlling plant development: From leaves to flowers

Plant development is regulated by transcription factors that often act in more than one process and stage of development. Yet the molecular mechanisms that govern the functional diversity and specificity of these proteins remains far from understood. Flower development provides an ideal context to study these mechanisms since the development of distinct floral organs depends on similar but distinct combinations of transcriptional regulators. Recent work also highlights the importance of leaf polarity regulators as additional key factors in flower initiation, floral organ morphogenesis, and possibly floral organ positioning. A detailed understanding of how these factors work in combination will enable us to address outstanding questions in flower development including how distinct shapes and positions of floral organs are generated. Experimental approaches and computer-based modeling will be required to characterize gene-regulatory networks at the level of single cells.

A 3D gene expression atlas of the floral meristem based on spatial reconstruction of single nucleus RNA sequencing data

Cellular heterogeneity in growth and differentiation results in organ patterning. Single-cell transcriptomics allows characterization of gene expression heterogeneity in developing organs at unprecedented resolution. However, the original physical location of the cell is lost during this methodology. To recover the original location of cells in the developing organ is essential to link gene activity with cellular identity and function in plants. Here, we propose a method to reconstruct genome-wide gene expression patterns of individual cells in a 3D flower meristem by combining single-nuclei RNA-seq with microcopy-based 3D spatial reconstruction. By this, gene expression differences among meristematic domains giving rise to different tissue and organ types can be determined. As a proof of principle, the method is used to trace the initiation of vascular identity within the floral meristem. Our work demonstrates the power of spatially reconstructed single cell transcriptome atlases to understand plant morphogenesis. The floral meristem 3D gene expression atlas can be accessed at http://threed-flower-meristem.herokuapp.com.

Single-cell transcriptomics allows gene expression heterogeneity to be assessed at cellular resolution but the original location of each cell is unknown. Here the authors combine single nuclei RNA-seq with 3D spatial reconstruction of floral meristems to link gene activities with morphology.

High-Throughput 3D Phenotyping of Plant Shoot Apical Meristems From Tissue-Resolution Data

Confocal imaging is a well-established method for investigating plant phenotypes on the tissue and organ level. However, many differences are difficult to assess by visual inspection and researchers rely extensively on ad hoc manual quantification techniques and qualitative assessment. Here we present a method for quantitatively phenotyping large samples of plant tissue morphologies using triangulated isosurfaces. We successfully demonstrate the applicability of the approach using confocal imaging of aerial organs in Arabidopsis thaliana. Automatic identification of flower primordia using the surface curvature as an indication of outgrowth allows for high-throughput quantification of divergence angles and further analysis of individual flowers. We demonstrate the throughput of our method by quantifying geometric features of 1065 flower primordia from 172 plants, comparing auxin transport mutants to wild type. Additionally, we find that a paraboloid provides a simple geometric parameterisation of the shoot inflorescence domain with few parameters. We utilise parameterisation methods to provide a computational comparison of the shoot apex defined by a fluorescent reporter of the central zone marker gene CLAVATA3 with the apex defined by the paraboloid. Finally, we analyse the impact of mutations which alter mechanical properties on inflorescence dome curvature and compare the results with auxin transport mutants. Our results suggest that region-specific expression domains of genes regulating cell wall biosynthesis and local auxin transport can be important in maintaining the wildtype tissue shape. Altogether, our results indicate a general approach to parameterise and quantify plant development in 3D, which is applicable also in cases where data resolution is limited, and cell segmentation not possible. This enables researchers to address fundamental questions of plant development by quantitative phenotyping with high throughput, consistency and reproducibility.

A multiscale analysis of early flower development in Arabidopsis provides an integrated view of molecular regulation and growth control

We have analyzed the link between the gene regulation and growth during the early stages of flower development in Arabidopsis. Starting from time-lapse images, we generated a 4D atlas of early flower development, including cell lineage, cellular growth rates, and the expression patterns of regulatory genes. This information was introduced in MorphoNet, a web-based platform. Using computational models, we found that the literature-based molecular network only explained a minority of the gene expression patterns. This was substantially improved by adding regulatory hypotheses for individual genes. Correlating growth with the combinatorial expression of multiple regulators led to a set of hypotheses for the action of individual genes in morphogenesis. This identified the central factor LEAFY as a potential regulator of heterogeneous growth, which was supported by quantifying growth patterns in a leafy mutant. By providing an integrated view, this atlas should represent a fundamental step toward mechanistic models of flower development.

KATANIN and CLASP function at different spatial scales to mediate microtubule response to mechanical stress in Arabidopsis cotyledons

Mechanical stress influences cell- and tissue-scale processes across all kingdoms. It remains challenging to delineate how mechanical stress, originating at these different length scales, impacts cell and tissue form. We combine growth tracking of cells, quantitative image analysis, as well as molecular and mechanical perturbations to address this problem in pavement cells of Arabidopsis thaliana cotyledon tissue. We show that microtubule organization based on chemical signals and cell-shape-derived mechanical stress varies during early stages of pavement cell development and is mediated by the evolutionary conserved proteins, KATANIN and CLASP. However, we find that these proteins regulate microtubule organization in response to tissue-scale mechanical stress to different extents in the cotyledon epidermis. Our results further demonstrate that regulation of cotyledon form is uncoupled from the mechanical-stress-dependent control of pavement cell shape that relies on microtubule organization governed by subcellular mechanical stress.

Molecular mechanism of cytokinin-activated cell division in Arabidopsis

Mitogens trigger cell division in animals. In plants, cytokinins, a group of phytohormones derived from adenine, stimulate cell proliferation. Cytokinin signaling is initiated by membrane-associated histidine kinase receptors and transduced through a phosphorelay system. We show that in the Arabidopsis shoot apical meristem (SAM), cytokinin regulates cell division by promoting nuclear shuttling of Myb-domain protein 3R4 (MYB3R4), a transcription factor that activates mitotic gene expression. Newly synthesized MYB3R4 protein resides predominantly in the cytoplasm. At the G2-to-M transition, rapid nuclear accumulation of MYB3R4-consistent with an associated transient peak in cytokinin concentration-feeds a positive feedback loop involving importins and initiates a transcriptional cascade that drives mitosis and cytokinesis. An engineered nuclear-restricted MYB3R4 mimics the cytokinin effects of enhanced cell proliferation and meristem growth.

Cytoskeletal organization in isolated plant cells under geometry control

The cytoskeleton plays a key role in establishing robust cell shape. In animals, it is well established that cell shape can also influence cytoskeletal organization. Cytoskeletal proteins are well conserved between animal and plant kingdoms; nevertheless, because plant cells exhibit major structural differences to animal cells, the question arises whether the plant cytoskeleton also responds to geometrical cues. Recent numerical simulations predicted that a geometry-based rule is sufficient to explain the microtubule (MT) organization observed in cells. Due to their high flexural rigidity and persistence length of the order of a few millimeters, MTs are rigid over cellular dimensions and are thus expected to align along their long axis if constrained in specific geometries. This hypothesis remains to be tested in cellulo Here, we explore the relative contribution of geometry to the final organization of actin and MT cytoskeletons in single plant cells of Arabidopsis thaliana We show that the cytoskeleton aligns with the long axis of the cells. We find that actin organization relies on MTs but not the opposite. We develop a model of self-organizing MTs in three dimensions, which predicts the importance of MT severing, which we confirm experimentally. This work is a first step toward assessing quantitatively how cellular geometry contributes to the control of cytoskeletal organization in living plant cells.

Auxin transport model for leaf venation

The plant hormone auxin controls many aspects of the development of plants. One striking dynamical feature is the self-organization of leaf venation patterns which is driven by high levels of auxin within vein cells. The auxin transport is mediated by specialized membrane-localized proteins. Many venation models have been based on polarly localized efflux-mediator proteins of the PIN family. Here, we investigate a modelling framework for auxin transport with a positive feedback between auxin fluxes and transport capacities that are not necessarily polar, i.e. directional across a cell wall. Our approach is derived from a discrete graph-based model for biological transportation networks, where cells are represented by graph nodes and intercellular membranes by edges. The edges are not a priori oriented and the direction of auxin flow is determined by its concentration gradient along the edge. We prove global existence of solutions to the model and the validity of Murray's Law for its steady states. Moreover, we demonstrate with numerical simulations that the model is able connect an auxin source-sink pair with a mid-vein and that it can also produce branching vein patterns. A significant innovative aspect of our approach is that it allows the passage to a formal macroscopic limit which can be extended to include network growth. We perform mathematical analysis of the macroscopic formulation, showing the global existence of weak solutions for an appropriate parameter range.

Quantitative analysis of auxin sensing in leaf primordia argues against proposed role in regulating leaf dorsoventrality

Dorsoventrality in leaves has been shown to depend on the pre-patterned expression of KANADI and HD-ZIPIII genes within the plant shoot apical meristem (SAM). However, it has also been proposed that asymmetric auxin levels within initiating leaves help establish leaf polarity, based in part on observations of the DII auxin sensor. By analyzing and quantifying the expression of the R2D2 auxin sensor, we find that there is no obvious asymmetry in auxin levels during Arabidopsis leaf development. We further show that the mDII control sensor also exhibits an asymmetry in expression in developing leaf primordia early on, while it becomes more symmetric at a later developmental stage as reported previously. Together with other recent findings, our results argue against the importance of auxin asymmetry in establishing leaf polarity.

Anisotropic growth is achieved through the additive mechanical effect of material anisotropy and elastic asymmetry

Fast directional growth is a necessity for the young seedling; after germination, it needs to quickly penetrate the soil to begin its autotrophic life. In most dicot plants, this rapid escape is due to the anisotropic elongation of the hypocotyl, the columnar organ between the root and the shoot meristems. Anisotropic growth is common in plant organs and is canonically attributed to cell wall anisotropy produced by oriented cellulose fibers. Recently, a mechanism based on asymmetric pectin-based cell wall elasticity has been proposed. Here we present a harmonizing model for anisotropic growth control in the dark-grown Arabidopsis thaliana hypocotyl: basic anisotropic information is provided by cellulose orientation) and additive anisotropic information is provided by pectin-based elastic asymmetry in the epidermis. We quantitatively show that hypocotyl elongation is anisotropic starting at germination. We present experimental evidence for pectin biochemical differences and wall mechanics providing important growth regulation in the hypocotyl. Lastly, our in silico modelling experiments indicate an additive collaboration between pectin biochemistry and cellulose orientation in promoting anisotropic growth.

The interaction of transcription factors controls the spatial layout of plant aerial stem cell niches

The plant shoot apical meristem holds a stem cell niche from which all aerial organs originate. Using a computational approach we show that a mixture of monomers and heterodimers of the transcription factors WUSCHEL and HAIRY MERISTEM is sufficient to pattern the stem cell niche, and predict that immobile heterodimers form a regulatory "pocket" surrounding the stem cells. The model achieves to reproduce an array of perturbations, including mutants and tissue size modifications. We also show its ability to reproduce the recently observed dynamical shift of the stem cell niche during the development of an axillary meristem. The work integrates recent experimental results to answer the longstanding question of how the asymmetry of expression between the stem cell marker CLAVATA3 and its activator WUSCHEL is achieved, and recent findings of plasticity in the system.

Cell type boundaries organize plant development

In plants the dorsoventral boundary of leaves defines an axis of symmetry through the centre of the organ separating the top (dorsal) and bottom (ventral) tissues. Although the positioning of this boundary is critical for leaf morphogenesis, how the boundary is established and how it influences development remains unclear. Using live-imaging and perturbation experiments we show that leaf orientation, morphology and position are pre-patterned by HD-ZIPIII and KAN gene expression in the shoot, leading to a model in which dorsoventral genes coordinate to regulate plant development by localizing auxin response between their expression domains. However we also find that auxin levels feedback on dorsoventral patterning by spatially organizing HD-ZIPIII and KAN expression in the shoot periphery. By demonstrating that the regulation of these genes by auxin also governs their response to wounds, our results also provide a parsimonious explanation for the influence of wounds on leaf dorsoventrality.

Different reprogramming propensities in plants and mammals: Are small variations in the core network wirings responsible?

Although the plant and animal kingdoms were separated more than 1,6 billion years ago, multicellular development is for both guided by similar transcriptional, epigenetic and posttranscriptional machinery. One may ask to what extent there are similarities and differences in the gene regulation circuits and their dynamics when it comes to important processes like stem cell regulation. The key players in mouse embryonic stem cells governing pluripotency versus differentiation are Oct4, Sox2 and Nanog. Correspondingly, the WUSCHEL and CLAVATA3 genes represent a core in the Shoot Apical Meristem regulation for plants. In addition, both systems have designated genes that turn on differentiation. There is very little molecular homology between mammals and plants for these core regulators. Here, we focus on functional homologies by performing a comparison between the circuitry connecting these players in plants and animals and find striking similarities, suggesting that comparable regulatory logics have been evolved for stem cell regulation in both kingdoms. From in silico simulations we find similar differentiation dynamics. Further when in the differentiated state, the cells are capable of regaining the stem cell state. We find that the propensity for this is higher for plants as compared to mammalians. Our investigation suggests that, despite similarity in core regulatory networks, the dynamics of these can contribute to plant cells being more plastic than mammalian cells, i.e. capable to reorganize from single differentiated cells to whole plants—reprogramming. The presence of an incoherent feed-forward loop in the mammalian core circuitry could be the origin of the different reprogramming behaviour.

Sewage sludge as fertiliser - environmental assessment of storage and land application options

Sewage sludge (SS) contains beneficial plant nutrients and organic matter, and therefore application of SS on agricultural land helps close nutrient loops. However, spreading operations are restricted to certain seasons and hence the SS needs to be stored. Storage and land application of SS are both potential sources of greenhouse gases and ammonia, leading to global warming, acidification and eutrophication. Covering the stored SS, treating it with urea and choosing the correct time for land application all have the potential to reduce emissions from the system. Using life cycle assessment (LCA), this study compares storage and land application options of SS in terms of global warming potential (GWP), acidification potential, eutrophication potential and primary energy use. The system with covered storage has the lowest impact of all categories. Systems with autumn application are preferable to spring application for all impact categories but, when nitrate leaching is considered, spring application is preferable in terms of eutrophication and primary energy use and, for some SS treatments, GWP. Ammonia addition reduces nitrous oxide and ammonia emissions during storage, but increases these emissions after land application. Storage duration has a large impact on GWP, while amount of chemical nitrogen fertiliser substituted has a large impact on primary energy use.

Fluctuations of the transcription factor ATML1 generate the pattern of giant cells in the Arabidopsis sepal

Multicellular development produces patterns of specialized cell types. Yet, it is often unclear how individual cells within a field of identical cells initiate the patterning process. Using live imaging, quantitative image analyses and modeling, we show that during Arabidopsis thaliana sepal development, fluctuations in the concentration of the transcription factor ATML1 pattern a field of identical epidermal cells to differentiate into giant cells interspersed between smaller cells. We find that ATML1 is expressed in all epidermal cells. However, its level fluctuates in each of these cells. If ATML1 levels surpass a threshold during the G2 phase of the cell cycle, the cell will likely enter a state of endoreduplication and become giant. Otherwise, the cell divides. Our results demonstrate a fluctuation-driven patterning mechanism for how cell fate decisions can be initiated through a random yet tightly regulated process.

A continuous growth model for plant tissue

Morphogenesis in plants and animals involves large irreversible deformations. In plants, the response of the cell wall material to internal and external forces is determined by its mechanical properties. An appropriate model for plant tissue growth must include key features such as anisotropic and heterogeneous elasticity and cell dependent evaluation of mechanical variables such as turgor pressure, stress and strain. In addition, a growth model needs to cope with cell divisions as a necessary part of the growth process. Here we develop such a growth model, which is capable of employing not only mechanical signals but also morphogen signals for regulating growth. The model is based on a continuous equation for updating the resting configuration of the tissue. Simultaneously, material properties can be updated at a different time scale. We test the stability of our model by measuring convergence of growth results for a tissue under the same mechanical and material conditions but with different spatial discretization. The model is able to maintain a strain field in the tissue during re-meshing, which is of particular importance for modeling cell division. We confirm the accuracy of our estimations in two and three-dimensional simulations, and show that residual stresses are less prominent if strain or stress is included as input signal to growth. The approach results in a model implementation that can be used to compare different growth hypotheses, while keeping residual stresses and other mechanical variables updated and available for feeding back to the growth and material properties.

Auxin Acts through MONOPTEROS to Regulate Plant Cell Polarity and Pattern Phyllotaxis

The periodic formation of plant organs such as leaves and flowers gives rise to intricate patterns that have fascinated biologists and mathematicians alike for hundreds of years [1]. The plant hormone auxin plays a central role in establishing these patterns by promoting organ formation at sites where it accumulates due to its polar, cell-to-cell transport [2, 3, 4, 5, 6]. Although experimental evidence as well as modeling suggest that feedback from auxin to its transport direction may help specify phyllotactic patterns [7, 8, 9, 10, 11, 12], the nature of this feedback remains unclear [13]. Here we reveal that polarization of the auxin efflux carrier PIN-FORMED 1 (PIN1) is regulated by the auxin response transcription factor MONOPTEROS (MP) [14]. We find that in the shoot, cell polarity patterns follow MP expression, which in turn follows auxin distribution patterns. By perturbing MP activity both globally and locally, we show that localized MP activity is necessary for the generation of polarity convergence patterns and that localized MP expression is sufficient to instruct PIN1 polarity directions non-cell autonomously, toward MP-expressing cells. By expressing MP in the epidermis of mp mutants, we further show that although MP activity in a single-cell layer is sufficient to promote polarity convergence patterns, MP in sub-epidermal tissues helps anchor these polarity patterns to the underlying cells. Overall, our findings reveal a patterning module in plants that determines organ position by orienting transport of the hormone auxin toward cells with high levels of MP-mediated auxin signaling. We propose that this feedback process acts broadly to generate periodic plant architectures.

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Auxin-regulated MP expression and activity predict PIN1 polarity changes at the SAM

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Localized MP activity is necessary to mediate periodic organ formation

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MP orients PIN1 polarity non-cell autonomously to promote local auxin accumulation

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Sub-epidermal MP activity is required to stabilize auxin distribution patterns

Shifting foundations: the mechanical cell wall and development

The cell wall has long been acknowledged as an important physical mediator of growth in plants. Recent experimental and modelling work has brought the importance of cell wall mechanics into the forefront again. These data have challenged existing dogmas that relate cell wall structure to cell/organ growth, that uncouple elasticity from extensibility, and those which treat the cell wall as a passive and non-stressed material. Within this review we describe experiments and models which have changed the ways in which we view the mechanical cell wall, leading to new hypotheses and research avenues. It has become increasingly apparent that while we often wish to simplify our systems, we now require more complex multi-scale experiments and models in order to gain further insight into growth mechanics. We are currently experiencing an exciting and challenging shift in the foundations of our understanding of cell wall mechanics in growth and development.

An epidermis-driven mechanism positions and scales stem cell niches in plants

How molecular patterning scales to organ size is highly debated in developmental biology. We explore this question for the characteristic gene expression domains of the plant stem cell niche residing in the shoot apical meristem. We show that a combination of signals originating from the epidermal cell layer can correctly pattern the key gene expression domains and notably leads to adaptive scaling of these domains to the size of the tissue. Using live imaging, we experimentally confirm this prediction. The identified mechanism is also sufficient to explain de novo stem cell niches in emerging flowers. Our findings suggest that the deformation of the tissue transposes meristem geometry into an instructive scaling and positional input for the apical plant stem cell niche.

A Model Analysis of Mechanisms for Radial Microtubular Patterns at Root Hair Initiation Sites

Plant cells have two main modes of growth generating anisotropic structures. Diffuse growth where whole cell walls extend in specific directions, guided by anisotropically positioned cellulose fibers, and tip growth, with inhomogeneous addition of new cell wall material at the tip of the structure. Cells are known to regulate these processes via molecular signals and the cytoskeleton. Mechanical stress has been proposed to provide an input to the positioning of the cellulose fibers via cortical microtubules in diffuse growth. In particular, a stress feedback model predicts a circumferential pattern of fibers surrounding apical tissues and growing primordia, guided by the anisotropic curvature in such tissues. In contrast, during the initiation of tip growing root hairs, a star-like radial pattern has recently been observed. Here, we use detailed finite element models to analyze how a change in mechanical properties at the root hair initiation site can lead to star-like stress patterns in order to understand whether a stress-based feedback model can also explain the microtubule patterns seen during root hair initiation. We show that two independent mechanisms, individually or combined, can be sufficient to generate radial patterns. In the first, new material is added locally at the position of the root hair. In the second, increased tension in the initiation area provides a mechanism. Finally, we describe how a molecular model of Rho-of-plant (ROP) GTPases activation driven by auxin can position a patch of activated ROP protein basally along a 2D root epidermal cell plasma membrane, paving the way for models where mechanical and molecular mechanisms cooperate in the initial placement and outgrowth of root hairs.

Simulation and verification of hydraulic properties and organic matter degradation in sand filters for greywater treatment

To evaluate the treatment performance of vertical flow sand filters, the HYDRUS wetland module was used to simulate treatment in an experimental set-up. The laboratory filters were intermittently dosed with artificial greywater at a hydraulic loading rate of 0.032 m³ m⁻² day⁻¹ and an organic loading rate of 0.014 kg BOD5 m⁻² day⁻¹. The hydraulic properties of the filter were characterised, as were inflow and outflow concentrations of chemical oxygen demand (COD), biochemical oxygen demand (BOD), ammonia, nitrate and total nitrogen. The inverse simulation function of the HYDRUS software was used to calibrate the water flow model. The observed effect of water flowing faster along the column wall was included in the inverse simulations. The biokinetic model was calibrated by fitting heterotrophic biomass growth to measurements of potential respiration rate. Emphasis was put on simulating outflow concentrations of organic pollutants. The simulations were conducted using three models of varying degree of calibration effort and output accuracy. The effluent concentration was 245 mg COD L⁻¹ for the laboratory filters, 134 mg COD mg L⁻¹ for the model excluding wall flow effects and 338 mg COD mg L⁻¹ for the model including wall flow effects.

Environmental impact of recycling nutrients in human excreta to agriculture compared with enhanced wastewater treatment

Human excreta are potential sources of plant nutrients, but are today usually considered a waste to be disposed of. The requirements on wastewater treatment plants (WWTPs) to remove nitrogen and phosphorus are increasing and to meet these requirements, more energy and chemicals are needed by WWTPs. Separating the nutrient-rich wastewater fractions at source and recycling them to agriculture as fertiliser is an alternative to removing them at the WWTP. This study used life cycle assessment methodology to compare the environmental impact of different scenarios for recycling the nutrients in the human excreta as fertiliser to arable land or removing them in an advanced WWTP. Three scenarios were assessed. In blackwater scenario, blackwater was source-separated and used as fertiliser. In urine scenario, the urine fraction was source-separated and used as fertiliser and the faecal water treated in an advanced WWTP. In NP scenario, chemical fertiliser was used as fertiliser and the toilet water treated in an advanced WWTP. The emissions from the WWTP were the same for all scenarios. This was fulfilled by the enhanced reduction in the WWTP fully removing the nutrients from the excreta that were not source-separated in the NP and urine scenarios. Recycling source-separated wastewater fractions as fertilisers in agriculture proved efficient for conserving energy and decreasing global warming potential (GWP). However, the blackwater and urine scenarios had a higher impact on potential eutrophication and potential acidification than the WWTP-chemical fertiliser scenario, due to large impacts by the ammonia emitted from storage and after spreading of the fertilisers. The cadmium input to the arable soil was very small with urine fertiliser. Source separation and recycling of excreta fractions as fertiliser thus has potential for saving energy and decreasing GWP emissions associated with wastewater management. However, for improved sustainability, the emissions from storage and after spreading of these fertilisers must decrease.

Subcellular and supracellular mechanical stress prescribes cytoskeleton behavior in Arabidopsis cotyledon pavement cells

Although it is a central question in biology, how cell shape controls intracellular dynamics largely remains an open question. Here, we show that the shape of Arabidopsis pavement cells creates a stress pattern that controls microtubule orientation, which then guides cell wall reinforcement. Live-imaging, combined with modeling of cell mechanics, shows that microtubules align along the maximal tensile stress direction within the cells, and atomic force microscopy demonstrates that this leads to reinforcement of the cell wall parallel to the microtubules. This feedback loop is regulated: cell-shape derived stresses could be overridden by imposed tissue level stresses, showing how competition between subcellular and supracellular cues control microtubule behavior. Furthermore, at the microtubule level, we identified an amplification mechanism in which mechanical stress promotes the microtubule response to stress by increasing severing activity. These multiscale feedbacks likely contribute to the robustness of microtubule behavior in plant epidermis.

DOI:http://dx.doi.org/10.7554/eLife.01967.001

The surfaces of plants are covered in epithelial cells that come in many different shapes, suggesting that individual cells must have some control over their own shape. An unusually shaped epithelial cell is the pavement cell, which looks like a jigsaw puzzle piece and is found in the leaves of many flowering plants. Relatively little was known about the exact contribution of mechanical properties of the wall to this shape. Furthermore, although it was known that parts of pavement cells are rich in microtubules—tubes of protein that act as a scaffold inside the cell— the possibility that shape impacts the behavior of microtubules was not fully addressed.

Now, using a combination of computer modelling and experiments, Sampathkumar et al. reveal that the shape of the pavement cells relies in part on the response of the microtubules to stress. In an individual cell, microtubules align along the direction of the largest stress, with a protein severing those microtubules that are not aligned in this direction. As the stress inside a cell is determined in part by the cell’s shape, this sets up a feedback loop: the stress resulting from the cell shape aligns the microtubules that reinforce the cell wall, thus maintaining the shape of the cell.

An external stress applied to the epithelium can override this internal stress. Because all of the plant cells are under turgor pressure from the inside, pressure from the outside, like squeezing a balloon, changes the stress pattern, causing the realignment of the microtubules so as to resist the new stress. This shows that the microtubules respond to local stresses within a cell, and are continually responsive to stress changes.

DOI:http://dx.doi.org/10.7554/eLife.01967.002

Stress and strain provide positional and directional cues in development

The morphogenesis of organs necessarily involves mechanical interactions and changes in mechanical properties of a tissue. A long standing question is how such changes are directed on a cellular scale while being coordinated at a tissular scale. Growing evidence suggests that mechanical cues are participating in the control of growth and morphogenesis during development. We introduce a mechanical model that represents the deposition of cellulose fibers in primary plant walls. In the model both the degree of material anisotropy and the anisotropy direction are regulated by stress anisotropy. We show that the finite element shell model and the simpler triangular biquadratic springs approach provide equally adequate descriptions of cell mechanics in tissue pressure simulations of the epidermis. In a growing organ, where circumferentially organized fibers act as a main controller of longitudinal growth, we show that the fiber direction can be correlated with both the maximal stress direction and the direction orthogonal to the maximal strain direction. However, when dynamic updates of the fiber direction are introduced, the mechanical stress provides a robust directional cue for the circumferential organization of the fibers, whereas the orthogonal to maximal strain model leads to an unstable situation where the fibers reorient longitudinally. Our investigation of the more complex shape and growth patterns in the shoot apical meristem where new organs are initiated shows that a stress based feedback on fiber directions is capable of reproducing the main features of in vivo cellulose fiber directions, deformations and material properties in different regions of the shoot. In particular, we show that this purely mechanical model can create radially distinct regions such that cells expand slowly and isotropically in the central zone while cells at the periphery expand more quickly and in the radial direction, which is a well established growth pattern in the meristem.

The MOSS Physcomitrella patens reproductive organ development is highly organized, affected by the two SHI/STY genes and by the level of active auxin in the SHI/STY expression domain

In order to establish a reference for analysis of the function of auxin and the auxin biosynthesis regulators SHORT INTERNODE/STYLISH (SHI/STY) during Physcomitrella patens reproductive development, we have described male (antheridial) and female(archegonial) development in detail, including temporal and positional information of organ initiation. This has allowed us to define discrete stages of organ morphogenesis and to show that reproductive organ development in P. patens is highly organized and that organ phyllotaxis differs between vegetative and reproductive development. Using the PpSHI1 and PpSHI2 reporter and knockout lines, the auxin reporters GmGH3(pro):GUS and PpPINA(pro):GFP-GUS, and the auxin-conjugating transgene PpSHI2(pro):IAAL, we could show that the PpSHI genes, and by inference also auxin, play important roles for reproductive organ development in moss. The PpSHI genes are required for the apical opening of the reproductive organs, the final differentiation of the egg cell, and the progression of canal cells into a cell death program. The apical cells of the archegonium, the canal cells, and the egg cell are also sites of auxin responsiveness and are affected by reduced levels of active auxin, suggesting that auxin mediates PpSHI function in the reproductive organs.

On evaluating models in Computational Morphodynamics

Recent advances in experimental plant biology have led to an increased potential to investigate plant development at a systems level. The emerging research field of Computational Morphodynamics has the aim to lead this development by combining dynamic spatial experimental data with computational models of molecular networks, growth, and mechanics in a multicellular context. The increased number of published models may lead to a diversification of our understanding of the systems, and methods for evaluating, comparing, and sharing models are main challenges for the future. We will discuss this problem using ideas originating from physics and use recent computational models of plant development as examples.

WUSCHEL protein movement mediates stem cell homeostasis in the Arabidopsis shoot apex

WUSCHEL (WUS) is a homeodomain transcription factor produced in cells of the niche/organizing center (OC) of shoot apical meristems. WUS specifies stem cell fate and also restricts its own levels by activating a negative regulator, CLAVATA3 (CLV3), in adjacent cells of the central zone (CZ). Here we show that the WUS protein, after being synthesized in cells of the OC, migrates into the CZ, where it activates CLV3 transcription by binding to its promoter elements. Using a computational model, we show that maintenance of the WUS gradient is essential to regulate stem cell number. Migration of a stem cell-inducing transcription factor into adjacent cells to activate a negative regulator, thereby restricting its own accumulation, is a theme that is unique to plant stem cell niches.

Models of sequestration and receptor cross-talk for explaining multiple mutants in plant stem cell regulation

BACKGROUND

Stem cells reside in a plant's shoot meristem throughout its life and are main regulators of above-ground plant development. The stem cell maintenance depends on a feedback network between the CLAVATA and WUSCHEL genes. The CLAVATA3 peptide binds to the CLAVATA1 receptor leading to WUSCHEL inhibition. WUSCHEL, on the other hand, activates CLAVATA3 expression. Recent experiments suggest a second pathway where CLAVATA3 inhibits WUSCHEL via the CORYNE receptor pathway. An interesting question, central for understanding the receptor signaling, is why the clavata1-11 null mutant has a weaker phenotype compared with the clavata1-1 non-null mutant. It has been suggested that this relies on interference from the mutated CLAVATA1 acting on the CORYNE pathway.

RESULTS

We present two models for the CLAVATA-WUSCHEL feedback network including two receptor pathways for WUSCHEL repression and differing only by the hypothesized mechanisms for the clavata1-1 non-null mutant. The first model is an implementation of the previously suggested interference mechanism. The other model assumes an unaltered binding between CLAVATA3 and the mutated CLAVATA1 but with a loss of propagated signal into the cell. We optimize the models using data from wild type and four single receptor mutant experiments and use data from two receptor double mutant experiments in a validation step. Both models are able to explain all seven phenotypes and in addition qualitatively predict CLAVATA3 perturbations. The two models for the clavata1-1 mutant differ in the direct mechanism of the mutant, but they also predict other differences in the dynamics of the stem cell regulating network. We show that the interference hypothesis leads to an abundance of receptors, while the loss-of-signal hypothesis leads to sequestration of CLAVATA3 and relies on degradation or internalization of the bound CLAVATA1 receptor.

CONCLUSIONS

Using computational modeling, we show that an interference hypothesis and a more parsimonious loss-of-signal hypothesis for a clavata1 non-null mutant both lead to behaviors predicting wild type and six receptor mutant experiments. Although the two models have identical implementations of the unperturbed feedback network for stem cell regulation, we can point out model-predicted differences that may be resolved in future experiments.

Alignment between PIN1 polarity and microtubule orientation in the shoot apical meristem reveals a tight coupling between morphogenesis and auxin transport

Imaging and computational modeling of the Arabidopsis shoot meristem epidermis suggests that biomechanical signals coordinately regulate auxin efflux carrier distribution and microtubule patterning to orchestrate the extent and directionality of growth.

Morphogenesis during multicellular development is regulated by intercellular signaling molecules as well as by the mechanical properties of individual cells. In particular, normal patterns of organogenesis in plants require coordination between growth direction and growth magnitude. How this is achieved remains unclear. Here we show that in Arabidopsis thaliana, auxin patterning and cellular growth are linked through a correlated pattern of auxin efflux carrier localization and cortical microtubule orientation. Our experiments reveal that both PIN1 localization and microtubule array orientation are likely to respond to a shared upstream regulator that appears to be biomechanical in nature. Lastly, through mathematical modeling we show that such a biophysical coupling could mediate the feedback loop between auxin and its transport that underlies plant phyllotaxis.

The proper development of plant organs such as leaves or flowers depends both on localized growth, which can be controlled by the plant hormone auxin, and directional growth, which is dependent on each cell's microtubule cytoskeleton. In this paper we show that at the shoot apex where organs initiate the orientation of the microtubule cytoskeleton is correlated with the orientation of the auxin transporter PIN1, suggesting coordination between growth patterning at the tissue level and directional growth at the cellular level. Recent work has indicated that mechanical signals play a role in orienting the plant microtubule network, and here we show that such signals can also orient PIN1. In addition, we demonstrate through mathematical modeling that an auxin transport system that is coordinated by mechanical signals akin to those we observed in vivo is sufficient to give rise to the patterns of organ outgrowth found in the plant Arabidopsis thaliana.

Modeling auxin-regulated development

The phytohormone auxin plays an essential role in many aspects of plant growth and development. Its patterning, intercellular transport, and means of signaling have been extensively studied both in experiments and computational models. Here, we present a review of models of auxin-regulated development in different plant tissues. This includes models of organ initiation in the shoot apical meristem, development of vascular strands in leafs and stems, and auxin-related functioning in roots. The examples show how mathematical modeling can help to examine expected and unexpected behavior of the system, challenge our knowledge and hypotheses, obtain quantitative results, or suggest new experiments and ways to approach a problem.

A cell-based model for quorum sensing in heterogeneous bacterial colonies

Although bacteria are unicellular organisms, they have the ability to act in concert by synthesizing and detecting small diffusing autoinducer molecules. The phenomenon, known as quorum sensing, has mainly been proposed to serve as a means for cell-density measurement. Here, we use a cell-based model of growing bacterial microcolonies to investigate a quorum-sensing mechanism at a single cell level. We show that the model indeed predicts a density-dependent behavior, highly dependent on local cell-clustering and the geometry of the space where the colony is evolving. We analyze the molecular network with two positive feedback loops to find the multistability regions and show how the quorum-sensing mechanism depends on different model parameters. Specifically, we show that the switching capability of the network leads to more constraints on parameters in a natural environment where the bacteria themselves produce autoinducer than compared to situations where autoinducer is introduced externally. The cell-based model also allows us to investigate mixed populations, where non-producing cheater cells are shown to have a fitness advantage, but still cannot completely outcompete producer cells. Simulations, therefore, are able to predict the relative fitness of cheater cells from experiments and can also display and account for the paradoxical phenomenon seen in experiments; even though the cheater cells have a fitness advantage in each of the investigated groups, the overall effect is an increase in the fraction of producer cells. The cell-based type of model presented here together with high-resolution experiments will play an integral role in a more explicit and precise comparison of models and experiments, addressing quorum sensing at a cellular resolution.

Unicellular organisms have the ability to communicate with each other via signaling molecules, leading to correlated behaviors resembling that of higher organisms. This process, called quorum sensing, allows the cells to monitor the population size or density in a decentralized fashion and perform a common task when these parameters exceed predefined threshold values. The quorum sensing mechanism has been implicated in diverse functions such as producing bioluminescence, virulence factors, and initiating biofilm formation. Complex emergent behaviors, such as quorum sensing, can be hard to analyze and understand without the assistance of mathematical and computational models. Here, we present a cell-based model of proliferating bacterial microcolonies and investigate how population-level responses can emerge from the signaling and mechanical properties of individual cells. We study both signaling variations within homogeneous (homotypic) bacterial populations as well as signaling and competition in mixed heterotypic populations. We investigate in particular how population size, local cell density, and spatial confinement affect colony growth and predict strategies for facilitating quorum sensing. We also show that the interplay between “honest” quorum sensing signal producing bacteria and non-producing “cheaters” can lead to emergent feedback regulation via differentiated growth that provides only a transient benefit for cheating cells.

Modeling plant growth and pattern formation

Plants continue to grow and generate new organs in symmetric patterns throughout their lives. This development requires an interconnected regulation of genes, hormones, and anisotropic growth, which in part is guided by environmental cues. Recently, several studies have used a combination of experiments and mathematical modeling to elucidate the mechanisms behind different growth and molecular patterns in plants. The computational models were used to investigate the often non-intuitive consequences of different hypotheses, and the in silico simulations of the models inspired further experimentation.

Natural course of knee osteoarthritis in middle-aged subjects with knee pain: 12-year follow-up using clinical and radiographic criteria

OBJECTIVE

To explore the natural course of knee osteoarthritis (OA) in a middle-aged population with chronic knee pain.

METHODS

A population-based sample of 143 subjects (mean age 45 (range 35-54), 44% women) with knee pain (>3 months) at inclusion was studied. Weight-bearing posteroanterior tibiofemoral (TF) radiographs were obtained at baseline and 12 years later, and classified according to Kellgren/Lawrence (K/L). Patellofemoral (PF) OA was determined at 5- and 12-years' follow-up using a skyline view and a cut-off point of <5 mm joint space width. The ACR clinical criteria were used at baseline.

RESULTS

Seventy-six (53%) had no TF OA (K/L 0) at baseline, but 49 had clinical OA. Overall, 65/76 (86%) developed incident TF OA over 12 years (K/L >or=1): 44/49 (90%) of the subjects with clinical OA and 21/27 (78%) without clinical OA. Progression was found in 65/67 (97%) with TF OA at baseline. Of the 84 with no PF OA at the 5-year examination, 26 (31%) developed PF OA over 7 years.

CONCLUSION

A majority of the subjects with chronic knee pain developed knee OA over 12 years. It is concluded that knee pain is often the first sign of knee OA.

Increased serum levels of the brain damage marker S100B after apnea in trained breath-hold divers: a study including respiratory and cardiovascular observations

The concentration of the protein S100B in serum is used as a brain damage marker in various conditions. We wanted to investigate whether a voluntary, prolonged apnea in trained breath-hold divers resulted in an increase of S100B in serum. Nine trained breath-hold divers performed a protocol mimicking the procedures they use during breath-hold training and competition, including extensive preapneic hyperventilation and glossopharyngeal insufflation, in order to perform a maximum-duration apnea, i.e., “static apnea” (average: 335 s, range: 281–403 s). Arterial blood samples were collected and cardiovascular variables recorded. Arterial partial pressures of O2 and CO2 (PaO2 and PaCO2) were 128 Torr and 20 Torr, respectively, at the start of apnea. The degree of asphyxia at the end of apnea was considerable, with PaO2 and PaCO2 reaching 28 Torr and 45 Torr, respectively. The concentration of S100B in serum transiently increased from 0.066 μg/l at the start of apnea to 0.083 μg/l after the apnea ( P < 0.05). The increase in S100B is attributed to the asphyxia or to other physiological responses to apnea, for example, increased blood pressure, and probably indicates a temporary opening of the blood-brain barrier. It is not possible to conclude that the observed increase in S100B levels in serum after a maximal-duration apnea reflects a serious injury to the brain, although the results raise concerns considering negative long-term effects. At the least, the results indicate that prolonged, voluntary apnea affects the integrity of the central nervous system and do not preclude cumulative effects.

Comparing microbial die-off in separately collected faeces with ash and sawdust additives

In a urine diversion dry toilet (UDDT), the urine and faeces are collected separately in order to recycle their nutrient content unmixed. In a UDDT, an additive e.g. lime, wood ash, dry soil or sawdust, depending on which one is easily accessed by the users, is usually sprinkled to the faeces after each defecation. The purpose of the additive is primarily to keep away the flies and odours and to contribute to primary treatment of the faeces. In this paper, ash and sawdust were applied separately to source-separated faeces during the collection phase, and then the die-off of indicators and pathogens in the mixtures was studied. The die-off of E. coli in the faeces/ash mixture was faster initially (first 7 days) compared to that achieved in the faeces/sawdust mixture even though the die-off achieved after 30-50 days was nearly similar for both mixtures. E. coli was not detected in faeces/ash after about 2 months, but was detected after 2 months in the faeces/sawdust mixture. Enterococcus spp. did not decrease below detection in faeces/ash or faeces/sawdust mixture but higher numbers (difference of about 2 logs) were detected at all times in faeces/sawdust than in faeces/ash mixture. The difference in the die-off in the mixtures of faeces/ash and faeces/sawdust was attributed to the differences in the characteristics of the additives, namely, high alkaline mineral content (giving high pH) and lower moisture content of ash compared to sawdust. It is recommended to increase use of ash as additive over sawdust in urine diversion dry toilets.

Substrate composition and moisture in composting source-separated human faeces and food waste

The composting of a faeces/ash mixture and food waste in relative proportions of 1:0, 1:1 and 1:3 was studied in three successive experiments conducted in Kampala, Uganda in 216 L reactors insulated with 75 mm styrofoam or not insulated. The faeces/ash mixture alone exceeded 50 degrees C for < or = 12 days in insulated reactors, but did not reach or maintain 50 degrees C in non-insulated reactors. Inclusion of food waste kept temperatures above 50 degrees C for over two weeks in insulated reactors except when the substrate was too wet. Escherichia coli and total coliform concentrations decreased below detection in material that exceeded 50 degrees C for at least six days. Enterococcus spp. decreased below detection in material that exceeded 50 degrees C for at least two weeks, but remained detectable after 1.5 months in material that exceeded 50 degrees C for less than two weeks, suggesting that a period of at least two weeks above 50 degrees C, combined with mixing, is needed to achieve sanitation. Initially substrates that were too wet proved a challenge to composting and ways of decreasing substrate moisture should be investigated. The results obtained are applicable to the management of small- to medium-scale composting of faeces/ash and food waste at household and institution levels, e.g. schools and restaurants.

Bench-scale composting of source-separated human faeces for sanitation

In urine-diverting toilets, urine and faeces are collected separately so that nutrient content can be recycled unmixed. Faeces should be sanitized before use in agriculture fields due to the presence of possible enteric pathogens. Composting of human faeces with food waste was evaluated as a possible method for this treatment. Temperatures were monitored in three 78-L wooden compost reactors fed with faeces-to-food waste substrates (F:FW) in wet weight ratios of 1:0, 3:1 and 1:1, which were observed for approximately 20 days. To achieve temperatures higher than 15 degrees C above ambient, insulation was required for the reactors. Use of 25-mm thick styrofoam insulation around the entire exterior of the compost reactors and turning of the compost twice a week resulted in sanitizing temperatures (>or=50 degrees C) to be maintained for 8 days in the F:FW=1:1 compost and for 4 days in the F:FW=3:1 compost. In these composts, a reduction of >3 log(10) for E. coli and >4 log(10) for Enterococcus spp. was achieved. The F:FW=1:0 compost, which did not maintain >or=50 degrees C for a sufficiently long period, was not sanitized, as the counts of E. coli and Enterococcus spp. increased between days 11 and 15. This research provides useful information on the design and operation of family-size compost units for the treatment of source-separated faeces and starchy food residues, most likely available amongst the less affluent rural/urban society in Uganda.

Developmental patterning by mechanical signals in Arabidopsis

A central question in developmental biology is whether and how mechanical forces serve as cues for cellular behavior and thereby regulate morphogenesis. We found that morphogenesis at the Arabidopsis shoot apex depends on the microtubule cytoskeleton, which in turn is regulated by mechanical stress. A combination of experiments and modeling shows that a feedback loop encompassing tissue morphology, stress patterns, and microtubule-mediated cellular properties is sufficient to account for the coordinated patterns of microtubule arrays observed in epidermal cells, as well as for patterns of apical morphogenesis.