Energy costs of salt tolerance in crop plants.

Agriculture is expanding into regions that are affected by salinity. This review considers the energetic costs of salinity tolerance in crop plants and provides a framework for a quantitative assessment of costs. Different sources of energy, and modifications of root system architecture that would maximize water vs ion uptake are addressed. Energy requirements for transport of salt (NaCl) to leaf vacuoles for osmotic adjustment could be small if there are no substantial leaks back across plasma membrane and tonoplast in root and leaf. The coupling ratio of the H+ -ATPase also is a critical component. One proposed leak, that of Na+ influx across the plasma membrane through certain aquaporin channels, might be coupled to water flow, thus conserving energy. For the tonoplast, control of two types of cation channels is required for energy efficiency. Transporters controlling the Na+ and Cl- concentrations in mitochondria and chloroplasts are largely unknown and could be a major energy cost. The complexity of the system will require a sophisticated modelling approach to identify critical transporters, apoplastic barriers and root structures. This modelling approach will inform experimentation and allow a quantitative assessment of the energy costs of NaCl tolerance to guide breeding and engineering of molecular components.

Statistical analysis and modeling of the geometry and topology of plant roots.

The root is an important organ of a plant since it is responsible for water and nutrient uptake. Analyzing and modeling variabilities in the geometry and topology of roots can help in assessing the plant's health, understanding its growth patterns, and modeling relations between plant species and between plants and their environment. In this article, we develop a framework for the statistical analysis and modeling of the geometry and topology of plant roots. We represent root structures as points in a tree-shape space equipped with a metric that quantifies geometric and topological differences between pairs of roots. We then use these building blocks to compute geodesics, i.e., optimal deformations under the metric between root structures, and to perform statistical analysis on root populations. We demonstrate the utility of the proposed framework through an application to a dataset of wheat roots grown in different environmental conditions. We also show that the framework can be used in various applications including classification and regression.

Density functional theory of confined ionic liquids: A survey of the effects of ion type, molecular charge distribution, and surface adsorption.

Ionic liquids confined between two planar charged walls are explored using density functional theory. The effort represents a study of the effects of the molecular structure, molecular charge distribution, and degree of surface adsorption on forces between the surfaces and on the inhomogeneous atom density profiles. Surface adsorption was found to significantly affect both the magnitude and sign of the surface forces, while differences in the distribution of molecular charge did not. On the other hand, different bulk densities were found to produce dramatically different surface forces indicating a difference in the degree of molecular packing at and near surfaces. No long-range forces were found in any of the cases considered. We conclude that in the absence of any specific cation-anion pairing, surface charges are effectively screened, and the surface forces are dominated by short ranged steric and dispersion interactions between adsorbed molecular layers. In many cases, very similar surface forces correspond to very different molecular arrangements, suggesting that unambiguous interpretation of measured surface forces in ionic liquids, in terms of molecular behavior, may be difficult to guarantee.

RootGraph: a graphic optimization tool for automated image analysis of plant roots.

This paper outlines a numerical scheme for accurate, detailed, and high-throughput image analysis of plant roots. In contrast to existing root image analysis tools that focus on root system-average traits, a novel, fully automated and robust approach for the detailed characterization of root traits, based on a graph optimization process is presented. The scheme, firstly, distinguishes primary roots from lateral roots and, secondly, quantifies a broad spectrum of root traits for each identified primary and lateral root. Thirdly, it associates lateral roots and their properties with the specific primary root from which the laterals emerge. The performance of this approach was evaluated through comparisons with other automated and semi-automated software solutions as well as against results based on manual measurements. The comparisons and subsequent application of the algorithm to an array of experimental data demonstrate that this method outperforms existing methods in terms of accuracy, robustness, and the ability to process root images under high-throughput conditions.

Toward a biophysical understanding of the salt stress response of individual plant cells.

We present and explore a kinetic model of ion transport across and between the membranes of an isolated plant cell with an emphasis on the cell's response to salt (Na(+)) stress. The vacuole, cytoplasm and apoplast are treated as concentric regions separated by tonoplast and plasma membranes. The model includes the transport of Na(+), K(+), Cl(-) and H(+) across both membranes via primary active proton pumps, secondary active antiporters and symporters, as well as passive ion channels. In addition, water transport is included, allowing us to investigate both the osmotic and ionic components of salt stress. The model's predictions of steady state and transient cytosolic pH and Na(+) concentrations were found to be quantitatively comparable to measured experimental values. Through an extensive simulation study we have identified and characterized scenarios in which individual transport processes (H(+) pumps, Na(+)/H(+) antiporters and channels involved in the transport of Na(+)) and their combinations have major effects on the level of Na(+) in each of the cell compartments. This systematic study emulates the effects of overexpressing and inhibiting transporter genes by genetic modification and hence we have compared our simulations with observations from experiments conducted on transgenic plants. The simulations suggest that overexpressing tonoplast Na(+)/H(+) antiporter genes and tonoplast H(+) pump genes lead to an increase in the storage of Na(+) in the vacuole (helping the cell to maintain water uptake under salt stress), with only a transient influence on the cytoplasmic Na(+) concentration. The model predicts effects of varying the expression of transporter genes (individually or in combination) which have yet to be investigated in experiments. For example, our findings indicate that simultaneously overexpressing plasma membrane and tonoplast Na(+)/H(+) antiporter genes would lead to improvements in both ionic and osmotic stress tolerance. The results demonstrate the importance of simultaneously modelling the transport of Na(+) across both the tonoplast and plasma membrane, a task not undertaken previously.

A complete system for 3D reconstruction of roots for phenotypic analysis.

Here we present a complete system for 3D reconstruction of roots grown in a transparent gel medium or washed and suspended in water. The system is capable of being fully automated as it is self calibrating. The system starts with detection of root tips in root images from an image sequence generated by a turntable motion. Root tips are detected using the statistics of Zernike moments on image patches centred on high curvature points on root boundary and Bayes classification rule. The detected root tips are tracked in the image sequence using a multi-target tracking algorithm. Conics are fitted to the root tip trajectories using a novel ellipse fitting algorithm which weighs the data points by its eccentricity. The conics projected from the circular trajectory have a complex conjugate intersection which are image of the circular points. Circular points constraint the image of the absolute conics which are directly related to the internal parameters of the camera. The pose of the camera is computed from the image of the rotation axis and the horizon. The silhouettes of the roots and camera parameters are used to reconstruction the 3D voxel model of the roots. We show the results of real 3D reconstruction of roots which are detailed and realistic for phenotypic analysis.

On the competitive uptake and transport of ions through differentiated root tissues.

We simulate the competitive uptake and transport of a mixed salt system in the differentiated tissues of plant roots. The results are based on a physical model that includes both forced diffusion and convection by the transpiration stream. The influence of the Casparian strip on regulating apoplastic flow, the focus of the paper, is modelled by varying ion diffusive permeabilities, hydraulic reflection coefficients and water permeability for transport across the endodermis-pericycle interface. We find that reducing diffusive permeabilities leads to significantly altered ion concentration profiles in the pericycle and vascular cylinder regions, while increased convective reflectivities affect predominantly ion concentrations in the cortex and endodermis tissues. The self-consistent electric field arising from ion separation is a major influence on predicted ion fluxes and accumulation rates.

Landmark-free statistical analysis of the shape of plant leaves.

The shapes of plant leaves are important features to biologists, as they can help in distinguishing plant species, measuring their health, analyzing their growth patterns, and understanding relations between various species. Most of the methods that have been developed in the past focus on comparing the shape of individual leaves using either descriptors or finite sets of landmarks. However, descriptor-based representations are not invertible and thus it is often hard to map descriptor variability into shape variability. On the other hand, landmark-based techniques require automatic detection and registration of the landmarks, which is very challenging in the case of plant leaves that exhibit high variability within and across species. In this paper, we propose a statistical model based on the Squared Root Velocity Function (SRVF) representation and the Riemannian elastic metric of Srivastava et al. (2011) to model the observed continuous variability in the shape of plant leaves. We treat plant species as random variables on a non-linear shape manifold and thus statistical summaries, such as means and covariances, can be computed. One can then study the principal modes of variations and characterize the observed shapes using probability density models, such as Gaussians or Mixture of Gaussians. We demonstrate the usage of such statistical model for (1) efficient classification of individual leaves, (2) the exploration of the space of plant leaf shapes, which is important in the study of population-specific variations, and (3) comparing entire plant species, which is fundamental to the study of evolutionary relationships in plants. Our approach does not require descriptors or landmarks but automatically solves for the optimal registration that aligns a pair of shapes. We evaluate the performance of the proposed framework on publicly available benchmarks such as the Flavia, the Swedish, and the ImageCLEF2011 plant leaf datasets.

Mathematical modelling of the uptake and transport of salt in plant roots.

In this paper, we present and discuss a mathematical model of ion uptake and transport in roots of plants. The underlying physical model of transport is based on the mechanisms of forced diffusion and convection. The model can take account of local variations in effective ion and water permeabilities across the major tissue regions of plant roots, represented through a discretized coupled system of governing equations including mass balance, forced diffusion, convection and electric potential. We present simulation results of an exploration of the consequent enormous parameter space. Among our findings we identify the electric potential as a major factor affecting ion transport across, and accumulation in, root tissues. We also find that under conditions of a constant but realistic level of bulk soil salt concentration and plant-soil hydraulic pressure, diffusion plays a significant role even when convection by the water transpiration stream is operating.

Modelling of PFAS-surface interactions: Effect of surface charge and solution ions.

PER-: and poly-fluoroalkyl substances (PFAS) are a class of substances of increasing concern as environmental contaminants. The interactions between PFAS and surfaces play an important role in PFAS transport and remediation. Previous studies have found PFAS adsorption to be dependent upon properties including pH, organic matter and particle size, along with PFAS functional group and carbon chain length. It is hypothesised that a theoretical examination of PFAS-surface interactions, via Monte Carlo molecular simulation, would show differences resulting from changes in surface charge, H+, OH-, Ca2+ concentrations and PFAS carbon chain length. Monte Carlo molecular simulations of perfluorooctane and perfluorobutane sulfonic acids interacting with a graphite surface in an aqueous medium were performed. Variations in surface charge, H+, OH- and Ca2+ concentrations were made. The distance-dependent density of molecules from the surface was analysed as a proxy for PFAS adsorption to the surface. Simulation results showed differences in surface behaviour that depended on surface charge, H+, OH- and Ca2+ concentrations, along with carbon chain length, with surface charge playing the most prominent role in controlling PFAS adsorption. For negatively charged surfaces, adsorption due to divalent cation bridging was observed in Ca2+ solutions. Modelling, such as in this study, of the thermodynamic equilibrium behaviour of low concentrations of molecules, in scenarios where both adsorption and mobility of PFAS occur, can aid in the design and testing of sorptive surfaces for amendment-based PFAS remediation.

WheatSpikeNet: an improved wheat spike segmentation model for accurate estimation from field imaging.

Phenotyping is used in plant breeding to identify genotypes with desirable characteristics, such as drought tolerance, disease resistance, and high-yield potentials. It may also be used to evaluate the effect of environmental circumstances, such as drought, heat, and salt, on plant growth and development. Wheat spike density measure is one of the most important agronomic factors relating to wheat phenotyping. Nonetheless, due to the diversity of wheat field environments, fast and accurate identification for counting wheat spikes remains one of the challenges. This study proposes a meticulously curated and annotated dataset, named as SPIKE-segm, taken from the publicly accessible SPIKE dataset, and an optimal instance segmentation approach named as WheatSpikeNet for segmenting and counting wheat spikes from field imagery. The proposed method is based on the well-known Cascade Mask RCNN architecture with model enhancements and hyperparameter tuning to provide state-of-the-art detection and segmentation performance. A comprehensive ablation analysis incorporating many architectural components of the model was performed to determine the most efficient version. In addition, the model's hyperparameters were fine-tuned by conducting several empirical tests. ResNet50 with Deformable Convolution Network (DCN) as the backbone architecture for feature extraction, Generic RoI Extractor (GRoIE) for RoI pooling, and Side Aware Boundary Localization (SABL) for wheat spike localization comprises the final instance segmentation model. With bbox and mask mean average precision (mAP) scores of 0.9303 and 0.9416, respectively, on the test set, the proposed model achieved superior performance on the challenging SPIKE datasets. Furthermore, in comparison with other existing state-of-the-art methods, the proposed model achieved up to a 0.41% improvement of mAP in spike detection and a significant improvement of 3.46% of mAP in the segmentation tasks that will lead us to an appropriate yield estimation from wheat plants.

A Whole Leaf Comparative Study of Stomatal Conductance Models.

We employed a detailed whole leaf hydraulic model to study the local operation of three stomatal conductance models distributed on the scale of a whole leaf. We quantified the behavior of these models by examining the leaf-area distributions of photosynthesis, transpiration, stomatal conductance, and guard cell turgor pressure. We gauged the models' local responses to changes in environmental conditions of carbon dioxide concentration, relative humidity, and light irradiance. We found that a stomatal conductance model that includes mechanical processes dependent on local variables predicts a spatial variation of physiological activity across the leaf: the leaf functions of photosynthesis and transpiration are not uniformly operative even when external conditions are uniform. The gradient pattern of hydraulic pressure which is needed to produce transpiration from the whole leaf is derived from the gradient patterns of turgor pressures of guard cells and epidermal cells and consequently leads to nonuniform spatial distribution patterns of transpiration and photosynthesis via the mechanical stomatal model. Our simulation experiments, comparing the predictions of two versions of a mechanical stomatal conductance model, suggest that leaves exhibit a more complex spatial distribution pattern of both photosynthesis and transpiration rate and more complex dependencies on environmental conditions when a non-linear relationship between the stomatal aperture and guard cell and epidermal cell turgor pressures is implemented. Our model studies offer a deeper understanding of the mechanism of stomatal conductance and point to possible future experimental measurements seeking to quantify the spatial distributions of several physiological activities taking place over a whole leaf.

Interrogating the relationship between the microstructure of amphiphilic poly(ethylene glycol-b-caprolactone) copolymers and their colloidal assemblies using non-interfering techniques.

Understanding the microstructural parameters of amphiphilic copolymers that control the formation and structure of aggregated colloids (e.g., micelles) is essential for the rational design of hierarchically structured systems for applications in nanomedicine, personal care and food formulations. Although many analytical techniques have been employed to study such systems, in this investigation we adopted an integrated approach using non-interfering techniques - diffusion nuclear magnetic resonance (NMR) spectroscopy, dynamic light scattering (DLS) and synchrotron small-angle X-ray scattering (SAXS) - to probe the relationship between the microstructure of poly(ethylene glycol-b-caprolactone) (PEG-b-PCL) copolymers [e.g., block molecular weight (MW) and the mass fraction of PCL (fPCL)] and the structure of their aggregates. Systematic trends in the self-assembly behaviour were determined using a large family of well-defined block copolymers with variable PEG and PCL block lengths (number-average molecular weights (Mn) between 2 and 10 and 0.5-15 kDa, respectively) and narrow dispersity (Ð < 1.12). For all of the copolymers, a clear transition in the aggregate structure was observed when the hydrophobic fPCL was increased at a constant PEG block Mn, although the nature of this transition is also dependent on the PEG block Mn. Copolymers with low Mn PEG blocks (2 kDa) were observed to transition from unimers and loosely associated unimers to metastable aggregates and finally, to cylindrical micelles as the fPCL was increased. In comparison, copolymers with PEG block Mn of between 5 and 10 kDa transitioned from heterogenous metastable aggregates to cylindrical micelles and finally, well-defined ellipsoidal micelles (of decreasing aspect ratios) as the fPCL was increased. In all cases, the diffusion NMR spectroscopy, DLS and synchrotron SAXS results provided complementary information and the grounds for a phase diagram relating copolymer microstructure to aggregation behaviour and structure. Importantly, the absence of commonly depicted spherical micelles has implications for applications where properties may be governed by shape, such as, cellular uptake of nanomedicine formulations.

On the Efficacy of Water Transport in Leaves. A Coupled Xylem-Phloem Model of Water and Solute Transport.

In this paper, we present and use a coupled xylem/phloem mathematical model of passive water and solute transport through a reticulated vascular system of an angiosperm leaf. We evaluate the effect of leaf width-to-length proportion and orientation of second-order veins on the indexes of water transport into the leaves and sucrose transport from the leaves. We found that the most important factor affecting the steady-state pattern of hydraulic pressure distribution in the xylem and solute concentration in the phloem was leaf shape: narrower/longer leaves are less efficient in convecting xylem water and phloem solutes than wider/shorter leaves under all conditions studied. The degree of efficiency of transport is greatly influenced by the orientation of second-order veins relative to the main vein for all leaf proportions considered; the dependence is non-monotonic with efficiency maximized when the angle is approximately 45° to the main vein, although the angle of peak efficiency depends on other conditions. The sensitivity of transport efficiency to vein orientation increases with increasing vein conductivity. The vein angle at which efficiency is maximum tended to be smaller (relative to the main vein direction) in narrower leaves. The results may help to explain, or at least contribute to our understanding of, the evolution of parallel vein systems in monocot leaves.

Density functional theory of confined ionic liquids: the influence of power-law attractions on molecule distributions and surface forces.

Interaction energies and density profiles for two model ionic liquids, [C4mim+][BF4 -] and [C4mim+][TFSI-], confined between charged planar walls are studied within a density functional theory framework. The results of these simulations are also compared with results assuming a simpler linear hexamer-monomer, cation-anion system. We focus attention on the effect on the atom site distributions and the surface forces of an additional, specific attractive potential between oppositely charged molecules. We consider both short- and long-ranged attractive potentials in order to span the degree to which the ionic counterions associate. Independent of its strength, we interpret the results found with the short-ranged potential to be a manifestation of limited molecular association. In contrast, depending on its strength, the results found with the long-ranged potential suggest a much stronger and possibly longer ranged associations of ionic groups. Both potentials are found to influence the behavior of the surface force at small separations, while the long-ranged attractive potential has the greater influence of the two on the long-ranged behavior of the surface force.

A Comprehensive Biophysical Model of Ion and Water Transport in Plant Roots. III. Quantifying the Energy Costs of Ion Transport in Salt-Stressed Roots of Arabidopsis.

Salt stress defense mechanisms in plant roots, such as active Na+ efflux and storage, require energy in the form of ATP. Understanding the energy required for these transport mechanisms is an important step toward achieving an understanding of salt tolerance. However, accurate measurements of the fluxes required to estimate these energy costs are difficult to achieve by experimental means. As a result, the magnitude of the energy costs of ion transport in salt-stressed roots relative to the available energy is unclear, as are the relative contributions of different defense mechanisms to the total cost. We used mathematical modeling to address three key questions about the energy costs of ion transport in salt-stressed Arabidopsis roots: are the energy requirements calculated on the basis of flux data feasible; which transport steps are the main contributors to the total energy costs; and which transport processes could be altered to minimize the total energy costs? Using our biophysical model of ion and water transport we calculated the energy expended in the trans-plasma membrane and trans-tonoplast transport of Na+, K+, Cl-, and H+ in different regions of a salt-stressed model Arabidopsis root. Our calculated energy costs exceeded experimental estimates of the energy supplied by root respiration for high external NaCl concentrations. We found that Na+ exclusion from, and Cl- uptake into, the outer root were the major contributors to the total energy expended. Reducing the leakage of Na+ and the active uptake of Cl- across outer root plasma membranes would lower energy costs while enhancing exclusion of these ions. The high energy cost of ion transport in roots demonstrates that the energetic consequences of altering ion transport processes should be considered when attempting to improve salt tolerance.

An Automatic Field Plot Extraction Method From Aerial Orthomosaic Images.

Unmanned aerial vehicles have an immense capacity for remote imaging of plants in agronomic field research trials. Traits extracted from the plots can explain development of the plants coverage, growth, flowering status, and related phenomenon. An important prerequisite step to obtain such information is to find the exact position of plots to extract them from an orthomosaic image. Extraction of plots using tools which assume a uniform spacing is often erroneous because the plots may neither be perfectly aligned nor equally distributed in a field. A novel approach is proposed which uses image-based optimization algorithm to find the alignment of plots. The method begins with a uniformly spaced grid of plots which is iteratively aligned with regions of high vegetation index, i.e., the underlying plots. The approach is validated and tested on two different orthomosaic images of fields containing wheat plots with simulated and real alignment problems, respectively. The result of alignment is compared to manually located ground truth position of plots and the errors are quantitatively analyzed. The effectiveness of the proposed method is confirmed in accurately estimating the phenotypic trait of canopy coverage compared to the common methods of extraction from uniform grids or trimmed grids. The software developed in this study is available from SourceForge, https://sourceforge.net/projects/phenalysis/.

A Comprehensive Biophysical Model of Ion and Water Transport in Plant Roots. II. Clarifying the Roles of SOS1 in the Salt-Stress Response in Arabidopsis.

SOS1 transporters play an essential role in plant salt tolerance. Although SOS1 is known to encode a plasma membrane Na+/H+ antiporter, the transport mechanisms by which these transporters contribute to salt tolerance at the level of the whole root are unclear. Gene expression and flux measurements have provided conflicting evidence for the location of SOS1 transporter activity, making it difficult to determine their function. Whether SOS1 transporters load or unload Na+ from the root xylem transpiration stream is also disputed. To address these areas of contention, we applied a mathematical model to answer the question: what is the function of SOS1 transporters in salt-stressed Arabidopsis roots? We used our biophysical model of ion and water transport in a salt-stressed root to simulate a wide range of SOS1 transporter locations in a model Arabidopsis root, providing a level of detail that cannot currently be achieved by experimentation. We compared our simulations with available experimental data to find reasonable parameters for the model and to determine likely locations of SOS1 transporter activity. We found that SOS1 transporters are likely to be operating in at least one tissue of the outer mature root, in the mature stele, and in the epidermis of the root apex. SOS1 transporter activity in the mature outer root cells is essential to maintain low cytosolic Na+ levels in the root and also restricts the uptake of Na+ to the shoot. SOS1 transporters in the stele actively load Na+ into the xylem transpiration stream, enhancing the transport of Na+ and water to the shoot. SOS1 transporters acting in the apex restrict cytosolic Na+ concentrations in the apex but are unable to maintain low cytosolic Na+ levels in the mature root. Our findings suggest that targeted, tissue-specific overexpression or knockout of SOS1 may lead to greater salt tolerance than has been achieved with constitutive gene changes. Tissue-specific changes to the expression of SOS1 could be used to identify the appropriate balance between limiting Na+ uptake to the shoot while maintaining water uptake, potentially leading to enhancements in salt tolerance.

Correction to: Detection and analysis of wheat spikes using Convolutional Neural Networks.

[This corrects the article DOI: 10.1186/s13007-018-0366-8.].