Plant-environment Interactions Research Articles

A modelling framework to simulate foliar fungal epidemics using functional-structural plant models.

Sustainable agriculture requires the identification of new, environmentally responsible strategies of crop protection. Modelling of pathosystems can allow a better understanding of the major interactions inside these dynamic systems and may lead to innovative protection strategies. In particular, functional-structural plant models (FSPMs) have been identified as a means to optimize the use of architecture-related traits. A current limitation lies in the inherent complexity of this type of modelling, and thus the purpose of this paper is to provide a framework to both extend and simplify the modelling of pathosystems using FSPMs. Different entities and interactions occurring in pathosystems were formalized in a conceptual model. A framework based on these concepts was then implemented within the open-source OpenAlea modelling platform, using the platform's general strategy of modelling plant-environment interactions and extending it to handle plant interactions with pathogens. New developments include a generic data structure for representing lesions and dispersal units, and a series of generic protocols to communicate with objects representing the canopy and its microenvironment in the OpenAlea platform. Another development is the addition of a library of elementary models involved in pathosystem modelling. Several plant and physical models are already available in OpenAlea and can be combined in models of pathosystems using this framework approach. Two contrasting pathosystems are implemented using the framework and illustrate its generic utility. Simulations demonstrate the framework's ability to simulate multiscaled interactions within pathosystems, and also show that models are modular components within the framework and can be extended. This is illustrated by testing the impact of canopy architectural traits on fungal dispersal. This study provides a framework for modelling a large number of pathosystems using FSPMs. This structure can accommodate both previously developed models for individual aspects of pathosystems and new ones. Complex models are deconstructed into separate 'knowledge sources' originating from different specialist areas of expertise and these can be shared and reassembled into multidisciplinary models. The framework thus provides a beneficial tool for a potential diverse and dynamic research community.

Rain Fed Sorghum (Sorghum bicolor L. Moench) Crop Growth Yield Forecasting Model

Agricultural production in Sudan is largely rainfed. For most Sudanese people sorghum is the staple food and its production is critical for national food security. Crop forecasting is the art of predicting crop yields and amounts of production before the harvest actually takes place, typically couple of months in advance. Several techniques can be used for crop forecasting. Crop forecasting relies on computer programs that describe the plant-environment interactions in quantitative terms. Such programs are called models. A twin-track approach was adopted, in which the fieldwork was linked to computer modeling. The outcome of the modeling effort was the development of the crop growth and water productivity prediction model. The model is a deterministic, process-based physical model with daily time-step cropping systems. The model can simulate the soil-plant water budget, crop canopy and root growth, and dry matter production for Sorghum crop. Experiments were done at Sinnar, AbuNa'ama and Gedaref areas during the same season. A simple, two layered soil, water balance model is used, based upon assumptions that the soil has a moderate hydraulic conductivity and no drainage impediment, there is no storage of water in excess of field capacity beyond one day, the water table is deep and there is no significant contribution from groundwater, the water content of the root zone is uniformly distributed at the end of each day, model takes no direct account of soil fertility, technology (mechanization, fertilizer use), varietal differences and farming practices. Inputs are daily date since sowing, mean or average daily temperature in degree Celsius, daily pan evaporation (mm), daily rainfall (mm), which is the only source of infiltration into the soil. Sorghum grain yield is estimated by the model as the main output. The ability of the model to provide reasonable estimate of rain-fed sorghum yield according to Chi square test is reasonable, and therefore, the model can be used for forecasting sorghum yield in the study area.

Infrared spectroscopy of pollen identifies plant species and genus as well as environmental conditions.

BackgroundIt is imperative to have reliable and timely methodologies for analysis and monitoring of seed plants in order to determine climate-related plant processes. Moreover, impact of environment on plant fitness is predominantly based on studies of female functions, while the contribution of male gametophytes is mostly ignored due to missing data on pollen quality. We explored the use of infrared spectroscopy of pollen for an inexpensive and rapid characterization of plants.MethodologyThe study was based on measurement of pollen samples by two Fourier transform infrared techniques: single reflectance attenuated total reflectance and transmission measurement of sample pellets. The experimental set, with a total of 813 samples, included five pollination seasons and 300 different plant species belonging to all principal spermatophyte clades (conifers, monocotyledons, eudicots, and magnoliids).ResultsThe spectroscopic-based methodology enables detection of phylogenetic variations, including the separation of confamiliar and congeneric species. Furthermore, the methodology enables measurement of phenotypic plasticity by the detection of inter-annual variations within the populations. The spectral differences related to environment and taxonomy are interpreted biochemically, specifically variations of pollen lipids, proteins, carbohydrates, and sporopollenins. The study shows large variations of absolute content of nutrients for congenital species pollinating in the same environmental conditions. Moreover, clear correlation between carbohydrate-to-protein ratio and pollination strategy has been detected. Infrared spectral database with respect to biochemical variation among the range of species, climate and biogeography will significantly improve comprehension of plant-environment interactions, including impact of global climate change on plant communities.

Improved sanguinarine production via biotic and abiotic elicitations and precursor feeding in cell suspensions of latex-less variety of Papaver somniferum with their gene expression studies and upscaling in bioreactor

Elicitors play an important role in challenging the plant defense system through plant-environment interaction and thus altering the secondary metabolite production. Culture filtrates of four endophytic fungi, namely, Chaetomium globosum, Aspergillus niveoglaucus, Paecilomyces lilacinus, and Trichoderma harzianum were tested on embryogenic cell suspensions of latex-less Papaver somniferum in dose-dependent kinetics. Besides this, abiotic elicitors salicylic acid, hydrogen peroxide, and carbon dioxide were also applied for improved sanguinarine production. Maximum biomass accumulation (growth index (GI) = 293.50 ± 14.82) and sanguinarine production (0.090 ± 0.008 % dry wt.) were registered by addition of 3.3 % v/v T. harzanium culture filtrate. Interestingly, it was further enhanced (GI = 323.40 ± 25.30; 0.105 ± 0.008 % dry wt.) when T. harzanium culture filtrate was employed along with 50 μM shikimate. This was also supported by real-time (RT) (qPCR), where 8-9-fold increase in cheilanthifoline synthase (CFS), stylopine synthase (STS), tetrahydroprotoberberine cis-N-methyltransferase (TNMT), and protopine 6-hydroxylase (P6H) transcripts was observed. Among abiotic elicitors, while hydrogen peroxide and carbon dioxide registered low level of sanguinarine accumulation, maximum sanguinarine content was detected by 250 μM salicylic acid (0.058 ± 0.003 % dry wt.; GI = 172.75 ± 13.40). RT (qPCR) also confirms the downregulation of sanguinarine pathway on CO2 supplementation. Various parameters ranging from agitation speed (70 rpm), impeller type (marine), media volume (2 l), inoculum weight (100 g), and culture duration (9 days) were optimized during upscaling in 5-l stirred tank bioreactor to obtain maximum sanguinarine production (GI = 434.00; 0.119 ± 0.070 % dry wt.). Addition of 3.3 % v/v T. harzanium culture filtrate and 50-μM shikimate was done on the 6th day of bioreactor run.

Fusarium inhibition by wild populations of the medicinal plant Salvia africana-lutea L. linked to metabolomic profiling

BackgroundSalvia africana-lutea L., an important medicinal sage used in the Western Cape (South Africa), can be termed a ‘broad-spectrum remedy’ suggesting the presence of a multiplicity of bioactive metabolites. This study aimed at assessing wild S. africana-lutea populations for chemotypic variation and anti-Fusarium properties.MethodsSamples were collected from four wild growing population sites (Yzerfontein, Silwerstroomstrand, Koeberg and Brackenfell) and one garden growing location in Stellenbosch. Their antifungal activities against Fusarium verticillioides (strains: MRC 826 and MRC 8267) and F. proliferatum (strains: MRC 6908 and MRC 7140) that are aggressive mycotoxigenic phytopathogens were compared using an in vitro microdilution assay. To correlate antifungal activity to chemical profiles, three techniques viz. Gas chromatography-mass spectrometry (GC-MS); Liquid chromatography-mass spectrometry (LC-MS) and 1H Nuclear Magnetic Resonance (NMR) were employed. Principal Component Analysis (PCA) was applied to the NMR data. The partial least squares-discriminant analysis (PLS-DA) was used to integrate LC-MS and NMR data sets. All statistics were performed with the SIMCA-P + 12.0 software.ResultsThe dichloromethane:methanol (1:1; v/v) extracts of the plant species collected from Stellenbosch demonstrated the strongest inhibition of F. verticillioides and F. proliferatum with minimum inhibitory concentration (MIC) values of 0.031 mg ml-1 and 0.063 mg ml-1 respectively. GC-MS showed four compounds which were unique to the Stellenbosch extracts. By integrating LC-MS and 1H NMR analyses, large chemotype differences leading to samples grouping by site when a multivariate analysis was performed, suggested strong plant-environment interactions as factors influencing metabolite composition. Signals distinguishing the Stellenbosch profile were in the aromatic part of the 1H NMR spectra.ConclusionsThis study shows the potential of chemotypes of Salvia africana-lutea in controlling fungal growth and consequently mycotoxin production. Products for use in the agricultural sector may be developed from such chemotypes.

Fine mapping and metabolic and physiological characterization of the glume glaucousness inhibitor locus Iw3 derived from wild wheat

This research provided the first view of metabolic and physiological effect of a tissue-specific glaucousness inhibitor in wheat and laid foundation for map-based cloning of the Iw3 locus. Cuticular wax constitutes the outermost layer of plant skin, and its composition greatly impacts plant appearance and plant-environment interaction. Epicuticular wax in the upper part of adult wheat plants can form the glaucousness, which is associated with drought tolerance. In this research, we characterized a glume-specific glaucousness inhibitor, Iw3, by fine mapping, physiological, and molecular approaches. Iw3 inhibits glaucousness formation by altering wax composition. Compared to the wild type, Iw3 eliminated β-diketone, reduced 47 % primary alcohols, but increased aldehyde 400-fold and alkanes fivefold, which led to 30 % reduction of total glume wax load. Loss of the glaucousness increased cuticle permeability, suggesting an important role in drought sensitivity. Genetically, the glaucousness-inhibiting effect by Iw3 is partially dominant in a dosage-dependent manner. We localized the Iw3 locus within a 0.13-cM interval delimited by marker loci Xpsp3000 and XWL3096. Of the 53 wax genes assayed, we detected transcription changes in nine genes by Iw3, downregulation of Cer4-1 and upregulation of other five Cer4 and three KCS homologs. All these results provided initial insights into Iw3-mediated regulation of wax metabolism and paved way for in-depth characterization of the Iw3 locus and the glaucousness-related β-diketone pathway.

Analysis of diterpenes and triterpenes from plant foliage and roots.

Terpene specialized metabolites exhibit multiple functions in plant-environment interactions and plant development. Molecular biologists investigating the biochemistry and molecular function of terpenes need to apply robust but yet sensitive analytical methods optimized and adapted to the structural diversity and often varying concentrations of terpene compounds in plant tissues. Here we present hands-on protocols for sample preparation and GC-MS or LC-MS/MS analysis of selected diterpene and triterpene hydrocarbons or oxygenated derivatives from roots and shoots of Arabidopsis and rice.

塔里木盆地南缘旱生芦苇生态特征与水盐因子关系

In recent years,ecologists have experienced an increased awareness of the importance of plant-environment interactions. Studies have demonstrated that spatial ecosystem heterogeneity and availability of resources influence plant growth. Understanding the ecological response characteristics of plants and environmental laws influencing arid land vegetation in different water-salt environments should be quite valuable to scientists. To better understand the ecological characteristics of plants and factors that potentially control them such as water availability and salinity in arid regions,we conducted a study in Phragmites australis in dry habitats of the Yutian Oasis along the Keriya River,in the southern marginal zones of the Tarim Basin,Xinjiang,China. Using previously collected observational data related to water-salt distribution laws and the natural water-salt gradient caused by distance from the river,four sample regions were established parallel to the river from east to west,extending from the river to the desert. We analyzed the patterns and correlations of ecological characteristics of Phragmites australis and water-salt indicators in the field,using traditional statistics and redundancy analysis( RDA) in combination with CANOCO software( version 4.5). The statistical analysis revealed that plant ground cover was as low as less than 10%; the belowground biomass was greater than aboveground because of the way desert vegetation adapted to the arid environment. The sampled region was severely dry and salinated; soil moisture contentwas low,with a mean value of 7.22%. The average depth to ground water was 4.23m and soil salt content reached as high as18.24g /kg. Phragmites australis has a high tolerance to aridity and salt stress; the average plant height,coverage and aboveground biomass decreased gradually while the belowground biomass increased as distance from the river to the desert increased; there were also concurrent and expected gradient changes in water-salt indicators. Redundancy analysis showed that water was the key environmental factor influencing the growth of Phragmites australis. A significant correlation was found between ground water depth /soil moisture and the ecological characteristics of Phragmites australis including plant height,coverage,biomass; the sodium adsorption ratio( SAR) /total salt correlation with ecological characteristics was less significant while other indicators had no significant correlation with the plant's ecological characteristics. The importance of water-salt indicators to ecological characteristics of Phragmites australis could be arranged as ground water depth soil moisture SAR total salt HCO-3 pH Cl-/SO2-4. The results suggest that water has greater impact on Phragmites australis than salt,because water limits the plant's survival,growth and reproduction. When a plant is affected by an arid continental climate for long periods,the plant is usually influenced by both water and salt. Any study of Phragmites australis analyzing the effects of different water or soil salinity conditions independently would be fatally flawed; but must be considered together. Our study shows that redundancy analysis of ordination methods can be beneficially used in research into the relationship between plants and environmental factors; when combined with traditional statistics,the two methods can provide comprehensive information. The redundancy analysis can effectively reveal relationships between ecological characteristics of plants and water-salt indicators. The characteristics of Phragmites australis deserve more research,especially research related to the microscopic physiological effects of water-salt interaction.

GmFNSII-Controlled Soybean Flavone Metabolism Responds to Abiotic Stresses and Regulates Plant Salt Tolerance

Flavones, a major group of flavonoids in most plant tissues, play multiple roles in plant-environment interactions. In our study, the expression of the two soybean flavone synthase genes, GmFNSII-1 and GmFNSII-2, was significantly increased by methyl jasmonate (MeJA), glucose, mannitol and NaCl treatment, which were also found to increase flavone aglycone accumulation in Glycine max (L.) Merrill. In the GmFNSII-1 promoter, a specific CGTCA motif in the region (-979 bp to -806 bp) involved in the MeJA response was identified. Promoter deletion analysis of GmFNSII-2 revealed the presence of osmotic-responsive (-1,143 bp to -767 bp) and glucose-repressive sequence elements (-767 bp to -475 bp), which strongly supported the hypothesis that glucose induces soybean flavone production by acting as both an osmotic factor and a sugar signaling molecule simultaneously. Silencing of the GmFNSII gene clearly reduced the production of flavone aglycones (apigenin, luteolin and 7,4'-dihydroxyflavone) in hairy roots. The GmFNSII-RNAi (RNA interference) roots that had a reduced level of flavones accompanied by more malondialdehyde and H2O2 accumulation were more sensitive to salt stress compared with those of the control, and we concluded that flavones, as antioxidants, are associated with salt tolerance.

Applications of Delayed Fluorescence from Photosystem II

While photosystem II (PSII) of plants utilizes light for photosynthesis, part of the absorbed energy may be reverted back and dissipated as long-term fluorescence (delayed fluorescence or DF). Because the generation of DF is coupled with the processes of forward photosynthetic activities, DF contains the information about plant physiological states and plant-environment interactions. This makes DF a potentially powerful biosensing mechanism to measure plant photosynthetic activities and environmental conditions. While DF has attracted the interest of many researchers, some aspects of it are still unknown because of the complexity of photosynthetic system. In order to provide a holistic picture about the usefulness of DF, it is meaningful to summarize the research on DF applications. In this short review, available literature on applications of DF from PSII is summarized.

Multiple functions of polyphenols in plants inhabiting unfavorable Mediterranean areas

The significance of polyphenols, with emphasis to flavonoids, in the responses of Mediterranean plants to unfavorable environments, is discussed based on their ability to serve multiple functions in plant–environment interactions. Plants challenged against multiple stressors, as usually occurs in the Mediterranean basin, make a great investment in the biosynthesis of carbon-based-secondary-compounds, i.e., defense compounds sensu lato. Polyphenols are probably the most versatile secondary metabolites, thus allowing plants to respond promptly to unpredictable stress agents of different origin. Each individual species indeed displays a rich arsenal of polyphenol structures, which have different inter- and intra-cellular distribution. This review article is centered on the functions of polyphenols, particularly flavonoids as UV-screening, antioxidant and developmental regulators, and the relative significance of these roles in the acclimation/adaptation of plants to severe constrains of the Mediterranean climate. Here we suggest that flavonoids serve major roles as antioxidants rather than UV-screening pigments in Mediterranean plants challenged against an excess of sunlight irradiance. Furthermore, we discuss about the potential of flavonoids, particularly antioxidant flavones and flavonols, to regulate the development of organs and the whole plant. This ability may have great value for the ecology of plants inhabiting unfavorable Mediterranean environments, but this matter needs further investigation.

A Medicago truncatula ABCG transporter modulates the level of isoflavonoids

Full size ABCG transporters have been proposed to be implicated in the active transmembrane traffic of various secondary metabolites. Despite the importance of ABCG-based transport for plant-environment interactions, these proteins are still poorly characterised in legumes. The functional characterisation of, recently identified, Medicago ABCG10 was conducted by gene expression analyses, protein localization, as well as metabolites quantification. Biological assays were performed with control and MtABCG10-silenced material. The MtABCG10 mRNA accumulated upon the application of fungal oligosaccharides on plant roots. Spatial expression pattern analysis with a reporter gene revealed that the MtABCG10 promoter is active mostly within the vascular tissues in various organs. The corresponding protein is located in the plasma membrane. Silencing of MtABCG10 in hairy roots resulted in lower accumulation of the phenylpropanoid pathway-derived phytoalexin and its precursors. In addition, we observed that MtABCG10-silenced composite plants are more susceptible to infection with Fusarium oxysporum. Based upon the presented data, we propose that the MtABCG10 is a modulator of isoflavonoid levels during the defence response associated with de novo synthesis of Medicago phytoalexin.

Global transcriptome profiles of Camellia sinensis during cold acclimation

BackgroundTea is the most popular non-alcoholic health beverage in the world. The tea plant (Camellia sinensis (L.) O. Kuntze) needs to undergo a cold acclimation process to enhance its freezing tolerance in winter. Changes that occur at the molecular level in response to low temperatures are poorly understood in tea plants. To elucidate the molecular mechanisms of cold acclimation, we employed RNA-Seq and digital gene expression (DGE) technologies to the study of genome-wide expression profiles during cold acclimation in tea plants.ResultsUsing the Illumina sequencing platform, we obtained approximately 57.35 million RNA-Seq reads. These reads were assembled into 216,831 transcripts, with an average length of 356 bp and an N50 of 529 bp. In total, 1,770 differentially expressed transcripts were identified, of which 1,168 were up-regulated and 602 down-regulated. These include a group of cold sensor or signal transduction genes, cold-responsive transcription factor genes, plasma membrane stabilization related genes, osmosensing-responsive genes, and detoxification enzyme genes. DGE and quantitative RT-PCR analysis further confirmed the results from RNA-Seq analysis. Pathway analysis indicated that the “carbohydrate metabolism pathway” and the “calcium signaling pathway” might play a vital role in tea plants’ responses to cold stress.ConclusionsOur study presents a global survey of transcriptome profiles of tea plants in response to low, non-freezing temperatures and yields insights into the molecular mechanisms of tea plants during the cold acclimation process. It could also serve as a valuable resource for relevant research on cold-tolerance and help to explore the cold-related genes in improving the understanding of low-temperature tolerance and plant-environment interactions.

Thermography to explore plant–environment interactions

Stomatal regulation is a key determinant of plant photosynthesis and water relations, influencing plant survival, adaptation, and growth. Stomata sense the surrounding environment and respond rapidly to abiotic and biotic stresses. Stomatal conductance to water vapour (g s) and/or transpiration (E) are therefore valuable physiological parameters to be monitored in plant and agricultural sciences. However, leaf gas exchange measurements involve contact with leaves and often interfere with leaf functioning. Besides, they are time consuming and are limited by the sampling characteristics (e.g. sample size and/or the high number of samples required). Remote and rapid means to assess g s or E are thus particularly valuable for physiologists, agronomists, and ecologists. Transpiration influences the leaf energy balance and, consequently, leaf temperature (T leaf). As a result, thermal imaging makes it possible to estimate or quantify g s and E. Thermal imaging has been successfully used in a wide range of conditions and with diverse plant species. The technique can be applied at different scales (e.g. from single seedlings/leaves through whole trees or field crops to regions), providing great potential to study plant-environment interactions and specific phenomena such as abnormal stomatal closure, genotypic variation in stress tolerance, and the impact of different management strategies on crop water status. Nevertheless, environmental variability (e.g. in light intensity, temperature, relative humidity, wind speed) affects the accuracy of thermal imaging measurements. This review presents and discusses the advantages of thermal imaging applications to plant science, agriculture, and ecology, as well as its limitations and possible approaches to minimize them, by highlighting examples from previous and ongoing research.

Physiology and toxicology of hormone-disrupting chemicals in higher plants

Higher plants are exposed to natural environmental organic chemicals, associated with plant-environment interactions, and xenobiotic environmental organic chemicals, associated with anthropogenic activities. The effects of these chemicals result not only from interaction with metabolic targets, but also from interaction with the complex regulatory networks of hormone signaling. Purpose-designed plant hormone analogues thus show extensive signaling effects on gene regulation and are as such important for understanding plant hormone mechanisms and for manipulating plant growth and development. Some natural environmental chemicals also act on plants through interference with the perception and transduction of endogenous hormone signals. In a number of cases, bioactive xenobiotics, including herbicides that have been designed to affect specific metabolic targets, show extensive gene regulation effects, which are more in accordance with signaling effects than with consequences of metabolic effects. Some of these effects could be due to structural analogies with plant hormones or to interference with hormone metabolism, thus resulting in situations of hormone disruption similar to animal cell endocrine disruption by xenobiotics. These hormone-disrupting effects can be superimposed on parallel metabolic effects, thus indicating that toxicological characterisation of xenobiotics must take into consideration the whole range of signaling and metabolic effects. Hormone-disruptive signaling effects probably predominate when xenobiotic concentrations are low, as occurs in situations of residual low-level pollutions. These hormone-disruptive effects in plants may thus be of importance for understanding cryptic effects of low-dosage xenobiotics, as well as the interactive effects of mixtures of xenobiotic pollutants.

Plasticity in above- and belowground resource acquisition traits in response to single and multiple environmental factors in three tree species.

Functional trait plasticity is a major component of plant adjustment to environmental stresses. Here, we explore how multiple local environmental gradients in resources required by plants (light, water, and nutrients) and soil disturbance together influence the direction and amplitude of intraspecific changes in leaf and fine root traits that facilitate capture of these resources. We measured population-level analogous above- and belowground traits related to resource acquisition, i.e. “specific leaf area”–“specific root length” (SLA–SRL), and leaf and root N, P, and dry matter content (DMC), on three dominant understory tree species with contrasting carbon and nutrient economics across 15 plots in a temperate forest influenced by burrowing seabirds. We observed similar responses of the three species to the same single environmental influences, but partially species-specific responses to combinations of influences. The strength of intraspecific above- and belowground trait responses appeared unrelated to species resource acquisition strategy. Finally, most analogous leaf and root traits (SLA vs. SRL, and leaf versus root P and DMC) were controlled by contrasting environmental influences. The decoupled responses of above- and belowground traits to these multiple environmental factors together with partially species-specific adjustments suggest complex responses of plant communities to environmental changes, and potentially contrasting feedbacks of plant traits with ecosystem properties. We demonstrate that despite the growing evidence for broadly consistent resource-acquisition strategies at the whole plant level among species, plants also show partially decoupled, finely tuned strategies between above- and belowground parts at the intraspecific level in response to their environment. This decoupling within species suggests a need for many species-centred ecological theories on how plants respond to their environments (e.g. competitive/stress-tolerant/ruderal and response-effect trait frameworks) to be adapted to account for distinct plant-environment interactions among distinct individuals of the same species and parts of the same individual.

Transpiration rate relates to within‐ and across‐species variations in effective path length in a leaf water model of oxygen isotope enrichment

Stable oxygen isotope ratio of leaf water (δ(18)O(L)) yields valuable information on many aspects of plant-environment interactions. However, current understanding of the mechanistic controls on δ(18)O(L) does not provide complete characterization of effective path length (L) of the Péclet effect,--a key component of the leaf water model. In this study, we collected diurnal and seasonal series of leaf water enrichment and estimated L in six field-grown angiosperm and gymnosperm tree species. Our results suggest a pivotal role of leaf transpiration rate (E) in driving both within- and across-species variations in L. Our observation of the common presence of an inverse scaling of L with E in the different species therefore cautions against (1) the conventional treatment of L as a species-specific constant in leaf water or cellulose isotope (δ(18)O(p)) modelling; and (2) the use of δ(18)O(p) as a proxy for gs or E under low E conditions. Further, we show that incorporation of a multi-species L-E scaling into the leaf water model has the potential to both improve the prediction accuracy and simplify parameterization of the model when compared with the conventional approach. This has important implications for future modelling of oxygen isotope ratios.

Eigenvalues of Jacobian Matrices Report on Steps of Metabolic Reprogramming in a Complex Plant-Environment Interaction

Mathematical modeling of biochemical systems aims at improving the knowledge about complex regulatory networks. The experimental high-throughput measurement of levels of biochemical components, like metabolites and proteins, has become an integral part for characterization of biological systems. Yet, strategies of mathematical modeling to functionally integrate resulting data sets is still challenging. In plant biology, regulatory strategies that determine the metabolic output of metabolism as a response to changes in environmental conditions are hardly traceable by intuition. Mathematical modeling has been shown to be a promising approach to address such problems of plant-environment interaction promoting the comprehensive understanding of plant biochemistry and physiology. In this context, we recently published an inversely calculated solution for first-order partial derivatives, i.e. the Jacobian matrix, from experimental high-throughput data of a plant biochemical model system. Here, we present a biomathematical strategy, comprising 1) the inverse calculation of a biochemical Jacobian; 2) the characterization of the associated eigenvalues and 3) the interpretation of the results with respect to biochemical regulation. Deriving the real parts of eigenvalues provides information about the stability of solutions of inverse calculations. We found that shifts of the eigenvalue real part distributions occur together with metabolic shifts induced by short-term and long-term exposure to low temperature. This indicates the suitability of mathematical Jacobian characterization for recognizing perturbations in the metabolic homeostasis of plant metabolism. Together with our previously published results on inverse Jacobian calculation this represents a comprehensive strategy of mathematical modeling for the analysis of complex biochemical systems and plant-environment interactions from the molecular to the ecosystems level.

Lipid signaling in plants

Membrane lipids provide both the structural basis for cell membranes and a rich source of cellular mediators that regulate many aspects of plant development and environmental interactions. Over recent years, lipids as hormones and signaling messengers have gained increasing attention in the plant biology community. This volume collected 20 articles, including both primary research articles and several timely reviews on lipid signaling pathways, from active researchers addressing various fundamental questions in lipid signaling in plants (Ibrahim et al., 2011; Alford et al., 2012; Benning et al., 2012; Berkey et al., 2012; Dave and Graham, 2012; Dieck et al., 2012; Ge et al., 2012; Guo and Wang, 2012; Jung et al., 2012; Koo and Howe, 2012; Lorenc-Kukula et al., 2012; Maatta et al., 2012; Pleskot et al., 2012; Scherer et al., 2012; Stenzel et al., 2012; Strawn et al., 2012; Teaster et al., 2012; Wager and Browse, 2012; Xia et al., 2012; Arisz et al., 2013). One important question addressed is what lipids act as mediators in plants, and several classes of lipids and their related metabolites have been described, including phosphatidic acid, oxylipins, phosphoinositides, sphingolipids, free fatty acids, lysophospholipids, N-acylethanolamines, oxidatively modified galactolipids, and others. In addition, advances in mass spectrometry-based analysis, which allow sensitive identification of lipids with structural information, have raised many new questions: How many lipids are there in plants? How do plant lipidomes change in response to growth, developmental, and stress cues? As a result, many lipid mediators remain to be identified, and this volume provides a current, baseline knowledge on lipid signaling molecules and their actions in plants. Signaling lipids are produced and metabolized by a number of enzymes described in this volume, including phospholipase Ds, phospholipase As, acyl hydrolases, phytosphingosine kinases, diacylglcerol kinases, fatty acid amide hydrolases. Each enzyme class has multiple members, which contribute to the spatial and temporal production of lipid mediators, as well as to the influence of specific molecular species for selected actions. Additional molecular complexity is afforded by the fact that each class of lipid mediators may be produced by different enzymes. Different approaches, such as genetic ablation of specific genes, enzymatic kinetics, lipid profiling, or differential metabolic labeling, have been applied. Deciphering the complexity of lipid molecular signals and their metabolism has been a challenge. Lipid signaling plays diverse roles in various cellular and physiological processes. The involvement of lipid mediators has been discussed here in plant responses to hormones (e.g., abscisic acid and auxin), abiotic stresses, plant-microbe interactions, and in plant growth and development. Some intriguing aspects of plant lipid mediators are also addressed, such as how lipids might play roles as long distance mobile signals in addition to their localized actions, contributing to processes such as flowering and defense against pathogens. One major challenge has been to elucidate mechanistically how lipid mediators carry out their functions. Recent advances in oxylipins, particularly metabolites in the jasmonate pathway, provide an excellent example of how some key players in the signaling cascade that have been identified and interact directly with target proteins to influence changes in gene transcription. At the same time, these articles on oxylipins emphasize the difficulty of assigning functions to lipid mediators when multiple metabolites within a pathway have biological actions (i.e., OPDA, jasmonate and jasmonyl-leu, and probably others). Identifying lipid-interacting proteins represents an exciting area for future research that will improve our understanding of how different signaling networks in plant cells are integrated. However, translating the milieu of lipid metabolite changes in cells into the mechanisms for regulation of physiological processes in plants will remain a formidable challenge in the coming years. Elsewhere in the volume, the contribution of lipid head-group differences and their potential for selective actions are suggested. The potential roles of phosphoinositides in nuclear function and in the dynamics of membrane trafficking and cell expansion are discussed. In addition, head-group modifications and their metabolites, like the myo-inositol phosphates, appear to play a role in energy homeostasis in plants. Furthermore, biophysical studies have provided information on how PA and its phosphorylated product, diacylglycerol pyrophosphate, interact with proteins and/or cell membranes, suggesting a means for different cellular effects of these two metabolically related classes of signaling lipids. The publication of this book would not have been possible without the efforts of many people. First and foremost are the authors who responded enthusiastically to the call to contribute to the special volume. And the essential critical comments from the many peer reviewers are gratefully acknowledged which provided valuable feedback to ensure the highest quality, and up-to-date information in the articles.

Pectin Methylesterase Activity Assay for Plant Material

Homogalacturonans, the most abundant pectins of the plant cell wall, can be methylesterified at the C-6 position of the galacturonic acid residues. Demethylesterification of cell wall pectins is catalyzed by apoplastic pectin methylesterases (PMEs). Several plant developmental processes and plant-environment interactions involve PME-mediated cell wall modification, as it promotes the formation of Ca2+cross-links along the stretches of the demethylesterified galacturonic acid residues (Wolf et al., 2009; Müller et al., 2013), and thus influences the biophysical properties of plant cell walls. Here, we describe a protocol that can be used to estimate the activity of PMEs in a total soluble protein extract from plant or seed tissues. Soluble protein is extracted from the plant/seed materials, and a coupled enzyme assay is performed, according to a procedure modified from Grsic-Rausch and Rausch (2004). The methanol released from methylesterified pectins as a result of PME activity is oxidized to formaldehyde by alcohol oxidase. The formaldehyde is then used as an electron donor by formaldehyde dehydrogenase to reduce NAD+ to NADH. The formation of NADH from NAD+ is followed spectrophotometrically, and used to estimate the PME activity in the protein extract., 同聚半乳糖醛酸，植物细胞壁中最丰富的果胶，可以在半乳糖醛酸残基的C-6位置被甲基酯化。细胞壁果胶的脱甲基酯化由外切纤维果胶甲酯酶（PME）催化。几种植物发育过程和植物 - 环境相互作用涉及PME介导的细胞壁修饰，因为其促进沿着脱甲基酯化的半乳糖醛酸残基的延伸形成Ca 2+ 2 + et al。，2009;Mülleret al。，2013），因此影响植物细胞壁的生物物理性质。在这里，我们描述一个协议，可以用于估计PMEs在植物或种子组织的总可溶性蛋白质提取物的活性。从植物/种子材料中提取可溶性蛋白质，并根据从Grsic-Rausch和Rausch（2004）修改的程序进行偶联酶测定。作为PME活性的结果从甲基酯化果胶释放的甲醇被醇氧化酶氧化成甲醛。然后通过甲醛脱氢酶将甲醛用作电子供体，以将NAD +还原为NADH。通过分光光度法跟踪从NAD +形成NADH，并用于估计蛋白质提取物中的PME活性。