SPIRE-a software tool for bicontinuous phase recognition: application for plastid cubic membranes.

Bicontinuous membranes in cell organelles epitomize nature's ability to create complex functional nanostructures. Like their synthetic counterparts, these membranes are characterized by continuous membrane sheets draped onto topologically complex saddle-shaped surfaces with a periodic network-like structure. Their structure sizes, (around 50-500 nm), and fluid nature make transmission electron microscopy (TEM) the analysis method of choice to decipher their nanostructural features. Here we present a tool, Surface Projection Image Recognition Environment (SPIRE), to identify bicontinuous structures from TEM sections through interactive identification by comparison to mathematical "nodal surface" models. The prolamellar body (PLB) of plant etioplasts is a bicontinuous membrane structure with a key physiological role in chloroplast biogenesis. However, the determination of its spatial structural features has been held back by the lack of tools enabling the identification and quantitative analysis of symmetric membrane conformations. Using our SPIRE tool, we achieved a robust identification of the bicontinuous diamond surface as the dominant PLB geometry in angiosperm etioplasts in contrast to earlier long-standing assertions in the literature. Our data also provide insights into membrane storage capacities of PLBs with different volume proportions and hint at the limited role of a plastid ribosome localization directly inside the PLB grid for its proper functioning. This represents an important step in understanding their as yet elusive structure-function relationship.

Multiscale characterization and micromechanical modeling of crop stem materials.

An essential prerequisite for the efficient biomechanical tailoring of crops is to accurately relate mechanical behavior to compositional and morphological properties across different length scales. In this article, we develop a multiscale approach to predict macroscale stiffness and strength properties of crop stem materials from their hierarchical microstructure. We first discuss the experimental multiscale characterization based on microimaging (micro-CT, light microscopy, transmission electron microscopy) and chemical analysis, with a particular focus on oat stems. We then derive in detail a general micromechanics-based model of macroscale stiffness and strength. We specify our model for oats and validate it against a series of bending experiments that we conducted with oat stem samples. In the context of biomechanical tailoring, we demonstrate that our model can predict the effects of genetic modifications of microscale composition and morphology on macroscale mechanical properties of thale cress that is available in the literature.

Anatomy of leaf apical hydathodes in four monocotyledon plants of economic and academic relevance.

Hydathode is a plant organ responsible for guttation in vascular plants, i.e. the release of droplets at leaf margin or surface. Because this organ connects the plant vasculature to the external environment, it is also a known entry site for several vascular pathogens. In this study, we present a detailed microscopic examination of leaf apical hydathodes in monocots for three crops (maize, rice and sugarcane) and the model plant Brachypodium distachyon. Our study highlights both similarities and specificities of those epithemal hydathodes. These observations will serve as a foundation for future studies on the physiology and the immunity of hydathodes in monocots.

Multiscale imaging of plant development by light-sheet fluorescence microscopy.

Light-sheet fluorescence microscopy (LSFM) methods collectively represent the major breakthrough in developmental bio-imaging of living multicellular organisms. They are becoming a mainstream approach through the development of both commercial and custom-made LSFM platforms that are adjusted to diverse biological applications. Based on high-speed acquisition rates under conditions of low light exposure and minimal photo-damage of the biological sample, these methods provide ideal means for long-term and in-depth data acquisition during organ imaging at single-cell resolution. The introduction of LSFM methods into biology extended our understanding of pattern formation and developmental progress of multicellular organisms from embryogenesis to adult body. Moreover, LSFM imaging allowed the dynamic visualization of biological processes under almost natural conditions. Here, we review the most important, recent biological applications of LSFM methods in developmental studies of established and emerging plant model species, together with up-to-date methods of data editing and evaluation for modelling of complex biological processes. Recent applications in animal models push LSFM into the forefront of current bio-imaging approaches. Since LSFM is now the single most effective method for fast imaging of multicellular organisms, allowing quantitative analyses of their long-term development, its broader use in plant developmental biology will likely bring new insights.

Characterization of crop residues from false banana /Ensete ventricosum/ in Ethiopia in view of a full-resource valorization.

False banana /Ensete ventricosum [Welw.] Cheesman/ is exploited as a food crop in Ethiopia where it represents an important staple food. The plant is harvested and large amounts of biomass residues are originated, mainly from the pseudo stem (i.e., fiber bundles obtained from the leaf sheaths after being scrapped to produce starchy food) and the inflorescence stalk. These materials were studied in relation to their summative chemical composition, composition of lignin, lipophilic and polar extracts. Moreover, their structural characteristics, in view of their valorization, were scrutinized. The analytical studies were performed with the aid of FTIR, GC/MS, Py-GC/MS and SEM. The fiber bundles are aggregates of mainly long and slender fibers with low ash, extractives and lignin contents (3.8%. 4.4% and 10.5% respectively) and high holocellulose and α-cellulose contents (87.5% and 59.6% respectively). The hemicelluloses in the fibers are mostly highly acetylated xylans and the lignin is of the H-type (H:G:S, 1:0.7:0.8). This lignin composition is in line with the FTIR peaks at 1670 cm-1 and 1250 cm-1.The inflorescence stalk has high ash content (12.3% in the main stalk and 24.6% in fines) with a major proportion of potassium, high extractives (25.9%), and low lignin and α-cellulose contents (5.8% and 17.9% respectively). The stalk includes numerous starch granules in the cellular structure with the predominant presence of parenchyma. The potential valorization routes for these materials are clearly different. The fiber bundles could be used as a fiber source for paper pulp production with the possibility of a prior hemicelluloses removal while the inflorescence stalk has nutritional value for food and fodder. Furthermore, it can also be used for sugar fermentation products.

Morphology, composition, and mixing state of primary particles from combustion sources - crop residue, wood, and solid waste.

Morphology, composition, and mixing state of individual particles emitted from crop residue, wood, and solid waste combustion in a residential stove were analyzed using transmission electron microscopy (TEM). Our study showed that particles from crop residue and apple wood combustion were mainly organic matter (OM) in smoldering phase, whereas soot-OM internally mixed with K in flaming phase. Wild grass combustion in flaming phase released some Cl-rich-OM/soot particles and cardboard combustion released OM and S-rich particles. Interestingly, particles from hardwood (pear wood and bamboo) and softwood (cypress and pine wood) combustion were mainly soot and OM in the flaming phase, respectively. The combustion of foam boxes, rubber tires, and plastic bottles/bags in the flaming phase released large amounts of soot internally mixed with a small amount of OM, whereas the combustion of printed circuit boards and copper-core cables emitted large amounts of OM with Br-rich inclusions. In addition, the printed circuit board combustion released toxic metals containing Pb, Zn, Sn, and Sb. The results are important to document properties of primary particles from combustion sources, which can be used to trace the sources of ambient particles and to know their potential impacts in human health and radiative forcing in the air.

The Metabolite Pathway between Bundle Sheath and Mesophyll: Quantification of Plasmodesmata in Leaves of C3 and C4 Monocots.

C4 photosynthesis is characterized by a CO2-concentrating mechanism between mesophyll (M) and bundle sheath (BS) cells of leaves. This generates high metabolic fluxes between these cells, through interconnecting plasmodesmata (PD). Quantification of these symplastic fluxes for modeling studies requires accurate quantification of PD, which has proven difficult using transmission electron microscopy. Our new quantitative technique combines scanning electron microscopy and 3D immunolocalization in intact leaf tissues to compare PD density on cell interfaces in leaves of C3 (rice [Oryza sativa] and wheat [Triticum aestivum]) and C4 (maize [Zea mays] and Setaria viridis) monocot species. Scanning electron microscopy quantification of PD density revealed that C4 species had approximately twice the number of PD per pitfield area compared with their C3 counterparts. 3D immunolocalization of callose at pitfields using confocal microscopy showed that pitfield area per M-BS interface area was 5 times greater in C4 species. Thus, the two C4 species had up to nine times more PD per M-BS interface area (S. viridis, 9.3 PD µm(-2); maize, 7.5 PD µm(-2); rice 1.0 PD µm(-2); wheat, 2.6 PD µm(-2)). Using these anatomical data and measured photosynthetic rates in these C4 species, we have now calculated symplastic C4 acid flux per PD across the M-BS interface. These quantitative data are essential for modeling studies and gene discovery strategies needed to introduce aspects of C4 photosynthesis to C3 crops.

Effect of calcium chloride treatments on calcium content, anthracnose severity and antioxidant activity in papaya fruit during ambient storage.

BACKGROUND: There have been no reports on the effects of preharvest calcium application on anthracnose disease severity, antioxidant activity and cellular changes during ambient storage of papaya, and therefore the objective of this study was to investigate these effects. RESULTS: Higher calcium concentrations (1.5 and 2% w/v) increased calcium concentration in the peel and pulp tissues, maintained firmness, and reduced anthracnose incidence and severity. While leakage of calcium-treated fruit was lower for 1.5 and 2% calcium treatments compared to the control, microscopic results confirmed that pulp cell wall thickness was higher after 6 days in storage, for the 2% calcium treatment compared to the control. Calcium-treated fruit also had higher total antioxidant activity and total phenolic compounds during storage. CONCLUSION: Calcium chloride, especially at higher concentrations, is effective in maintaining papaya fruit quality during ambient storage. © 2015 Society of Chemical Industry.

'Laba' garlic processed by dense phase carbon dioxide: the relation between green colour generation and cellular structure, alliin consumption and alliinase activity.

BACKGROUND: 'Laba' garlic is usually processed by soaking garlic in vinegar for more than 1 week during winter. It is popular for its unique green colour and tasty flavour. Greening is desirable and required for this product as its characteristic. Dense phase carbon dioxide (DPCD) had a significant effect on the greening of intact garlic (Allium sativum L.) cloves. The relation between green colour generation and alliin consumption, alliinase activity and the cellular structure of garlic, respectively, were investigated in this work. The effects of treatment time, pressure and temperature of DPCD were also analysed and discussed. RESULTS: DPCD had a significant effect on the cellular structure of garlic cells. Garlic protoplast underwent greater morphological change after DPCD treatments at higher temperatures while the amount of precipitate increased with greater treatment time and temperature. Common trends on garlic greening and alliin consumption were observed except for DPCD treatment at 10 MPa and 65 °C. The alliinase activity decreased with increasing treatment time, pressure and temperature. It reached the lowest level at 13 MPa and 55 °C. CONCLUSION: The formation of the green colour was a comprehensive result of DPCD on changing cellular structure, alliin consumption and alliinase activity. DPCD treatment at 10 MPa and 55 °C was the optimum condition for the greening of 'Laba' garlic. This work further facilitated the application of DPCD in the industrial production of 'Laba' garlic. © 2015 Society of Chemical Industry.

Physical properties of root crops treated with novel softening technology capable of retaining the shape, color, and nutritional value of foods.

Hard, difficult-to-eat root crops (carrots and burdock roots) were homogeneously softened by an enzyme permeation method so that they could be mashed easily by the tongue while retaining appearance, flavor, and nutrients. The appearance, color, and nutritional value of these foods were equivalent to those of normally cooked root crops of the same type. The firmness of the softened root crops was at least 100 times as low as normally cooked root crops and lower than some care food products for patients with swallowing disorders. Compared with control root crops, which were treated with a freeze-thaw infusion method, the treated foods were 10 to 25 times as soft, with significantly lower rates of foodstuff syneresis and better preservation of color and nutritional value. Furthermore, the cell walls of the treated burdock roots resembled those of normally cooked ones, while the cells of freeze-thaw infusion burdock roots were destroyed and few cell walls remained. It was expected that these root crops softened by the enzymatic processing could be one of the best model foods for patients with masticatory disturbance or swallowing disorders or both.

Tissue-specific cell wall hydration in sugarcane stalks.

Plant cell walls contain water, especially under biological and wet processing conditions. The present work characterizes this water in tissues of sugarcane stalks. Environmental scanning electron microscopy shows tissue deformation upon drying. Dynamic vapor sorption determines the equilibrium and kinetics of moisture uptake. Thermoporometry by differential scanning calorimetry quantifies water in nanoscale pores. Results show that cell walls from top internodes of stalks are more deformable, slightly more sorptive to moisture, and substantially more porous. These differences of top internode are attributed to less lignified walls, which is confirmed by lower infrared spectral signal from aromatics. Furthermore, cell wall nanoscale porosity, an architectural and not directly compositional characteristic, is shown to be tissue-specific. Nanoscale porosities are ranked as follows: pith parenchyma > pith vascular bundles > rind. This ranking coincides with wall reactivity and digestibility in grasses, suggesting that nanoscale porosity is a major determinant of wall recalcitrance.

Micro-nanopores fabricated by high-energy electron beam irradiation: suitable structure for controlling pesticide loss.

Pesticide sprayed onto crop leaves tends to be washed off by rainwater and discharge into the environment through leaching and runoff, resulting in severe pollution to both soil and water. Here, to control pesticide loss, we developed a loss-control pesticide (LCP) by adding modified natural nanoclay (diatomite) through high-energy electron beam (HEEB) to traditional pesticide. After HEEB treatment, the originally clogged pores in diatomite opened, resulting in plenty of micro-nanopores in diatomite, which are beneficial for the pesticide molecules to access and be adsorbed. This pesticide-diatomite complex tended to be retained by the rough surface of crop leaves, displaying a high adhesion performance onto the leaves, so that the pesticide loss reduced, sufficient pesticide for crops was supplied, and the pollution risk of the pesticide could be substantially lowered.

Influence of calcium and silicon supplementation into Pleurotus ostreatus substrates on quality of fresh and canned mushrooms.

Supplements of gypsum (calcium source), pumice (silicon source) and pumice sulfate (silicon and calcium source) into substrates for oyster mushrooms (Pleurotus ostreatus) were searched for their effects on production as well as qualities of fresh and canned mushrooms. The addition of pumice up to 30% had no effect on total yield, size distribution and cap diameters. The supplementation of gypsum at 10% decreased the total yield; and although gypsum at 5% did not affect total yield, the treatment increased the proportion of large-sized caps. High content (>10%) of pumice sulfate resulted in the lower yield. Calcium and silicon contents in the fruit bodies were not influenced by supplementations. The centrifugal drip loss values and solid content of fresh mushrooms, and the percentage of weight gained and firmness of canned mushrooms, cultivated in substrates supplemented with gypsum, pumice and pumice sulfate were significantly (p≤0.05) higher than those of the control. Scanning electron micrographs revealed the more compacted hyphae of mushroom stalks supplemented with silicon and/or calcium after heat treatment, compared to the control. Supplementation of P. ostreatus substrates with 20% pumice was the most practical treatment because it showed no effect on yield and the most cost-effective.

Evolution of the localisation and composition of phenolics in grape skin between veraison and maturity in relation to water availability and some climatic conditions.

BACKGROUND: Several studies have investigated the composition of phenolics in grape skin during grape maturation under various conditions of light exposure, water stress, nitrogen supply and mineral nutrition, but their localisation during berry development is not well known. In this study the composition and localisation of proanthocyanidins were monitored for three years on four plots known to induce a distinctive behaviour of the vine (Cabernet Franc). The composition of phenolics was determined by spectrophotometry; also, in one year, proanthocyanidins were determined by high-performance liquid chromatography. Further information was obtained histochemically by means of toluidine blue O staining and image analysis. RESULTS: The results indicated that clear differences in phenolic quantification existed between the biochemical and histochemical approaches; the proportion of cells without phenolics was not linked with the quantity determined by the analytical methods used. The histochemical method showed the evolution of the localisation and typology of cells with and without phenolics during ripening. The number of cells without any phenolic compounds appeared to be very dependent on the mesoclimatic conditions and only slightly dependent on the site water status. CONCLUSION: Clear differences in phenolic quantification existed between the biochemical and histochemical approaches; the proportion of cells with phenolics was not linked with the quantity determined by biochemistry. The histochemical method showed an evolution of the localisation and typology of cells with and without phenolics in which mesoclimatic conditions were the most influential factor. Finally, the study showed some advantages of the histochemical approach: it gives information about the anatomy of the tissue as well as the nature and distribution of some of the large macromolecules and allows reconstruction of the three-dimensional plant structure.

Preparation of activated carbons from agricultural residues for pesticide adsorption.

Activated carbons (ACs) can be used not only for liquid but also for vapour phase applications, such as water treatment, deodorisation, gas purification and air treatment. In the present study, activated carbons produced from agricultural residues (olive kernel, corn cobs, rapeseed stalks and soya stalks) via physical steam activation were tested for the removal of Bromopropylate (BP) from water. For the characterization of the activated carbons ICP, SEM, FTIR and XRD analyses were performed. Adsorption kinetics and equilibrium isotherms were investigated for all biomass activated carbons in aqueous solutions. Experimental data of BP adsorption have fitted best to the pseudo 2nd-order kinetic model and Langmuir isotherm. The study resulted that corn cobs showed better adsorption capacity than the other biomass ACs. Comparison among ACs from biomass and commercial ones (F400 and Norit GL50) revealed that the first can be equally effective for the removal of BP from water with the latter.

Leaf senescence and nutrient remobilisation in barley and wheat.

Extensive studies have been undertaken on senescence processes in barley and wheat and their importance for the nitrogen use efficiency of these crop plants. During the senescence processes, proteins are degraded and nutrients are re-mobilised from senescing leaves to other organs, especially the developing grain. Most of the proteins degraded reside in the chloroplasts, with Rubisco constituting the most dominant protein fraction. Despite intensive studies, the proteases responsible for Rubisco degradation have not yet been identified. Evidence for degradation of stromal proteins outside of chloroplasts is summarised. Rubisco is thought to be released from chloroplasts into vesicles containing stroma material (RCB = Rubisco-containing bodies). These vesicles may then take different routes for their degradation. Transcriptome analyses on barley and wheat senescence have identified genes involved in degradative, metabolic and regulatory processes that could be used in future strategies aimed at modifying the senescence process. The breeding of crops for characters related to senescence processes, e.g. higher yields and better nutrient use efficiency, is complex. Such breeding has to cope with the dilemma that delayed senescence, which could lead to higher yields, is correlated with a decrease in nutrient use efficiency. Pinpointing regulatory genes involved in senescence might lead to tools that could effectively overcome this dilemma.

Leaf surface factors of transgenic Bt cotton associated with the feeding behaviors of cotton aphids: a case study on non-target effects.

The present paper reports case study results of the risk assessment of transgenic Bt cotton on a non-target pest, cotton aphid, Aphis gossypii. Several types of techniques, i.e., electrical penetration graph (EPG), light and electron microscopy, bioassays and chemical analysis, were applied to investigate physical and chemical leaf factors of 2 transgenic Bt cotton lines (GK12 and GK19) and their parental non-Bt cotton line (Simian3) associated with searching and feeding behaviors of cotton aphids on leaves or leaf extracts of cotton plants. EPG results showed that there were some differences among behaviors of cotton aphids on 2 Bt cotton and 1 non-Bt cotton lines. Cotton aphids performed similarly to leaf surface extracts from 3 cotton lines; and leaf surface chemicals, mainly volatiles and waxes, were almost identical in the components and concentrations among the cotton lines. However, three cotton lines were quite different from each other in the densities of certain kinds of covering trichomes. Therefore, the relationships between the physical characteristics and the searching behaviors of cotton aphids on the three cotton lines were constructed as the regression equations. Glandular trichomes and covering trichomes with 5 branches influenced the cotton aphids' searching behaviors effectively; and other trichomes with other branches affected aphids in varying ways. These results demonstrated that leaf surface physical factors of transgenic Bt cotton lines different from their parental non-Bt line could affect the penetration behaviors of non-target cotton aphids. Cotton aphids penetrate and feed more easily on two Bt cotton lines than on the non-Bt cotton line.

Retention and rainfastness of mancozeb as affected by physicochemical characteristics of adaxial apple leaf surface after enhanced UV-B radiation.

It is not clear so far whether alteration of leaf micromorphology and surface wax chemistry due to the impact of environmental factors, such as UV-B radiation, affects retention and rainfastness of applied pesticide solutions. In this study; UV-B treated and untreated adaxial leaf surfaces of apple seedlings (Malus domestica Borkh.) were characterized in terms of chemical composition, micromorphological fine structure, hydrophobicity, and wettability. Furthermore, the retention and rainfastness of applied fungicide mancozeb were studied. The samples were examined 0, 24 and 48 h after ultraviolet (UV)-B radiation (0.022 kW m(-2) for 150 min) The total wax mass, recovered from the adaxial leaf surface, amounted from 0.38 microg cm(-2) (control) up to 0.49 microg cm(-2) (24 h). Chemical composition of surface wax altered, whereas the contact angle of applied water droplets on leaf surface of UV-B treated plants did not change significantly compared to the control. The alteration of surface wax quantity and quality significantly affected retention of a.i.; it increased at a sampling time of 24 h after UV-B irradiation, whereas rainfastness of the fungicide spray solution was not significantly influenced.

Genotype-specific spatial distribution of starch molecules in the starch granule: a combined CLSM and SEM approach.

Starch granule types from a variety of botanical sources were selected to represent differences in crystalline polymorph, amylose and phosphate content, and amylopectin chain length distribution. Equimolar labeling of starch molecules with the fluorophore 8-amino-1,3,6-pyrenetrisulfonic acid (APTS) was used to construct a detailed map of the distribution of amylose and amylopectin within the granule by confocal laser scanning microscopy (CLSM) analysis. Medium- and high-resolution scanning electron microscopy (SEM) were used to provide detailed images of granule surface structures. By using a combined surface and internal imaging approach, interpretations of a number of previous structural observations is presented. In particular, internal images of high amylose maize and potato suggest that multiple initiations of new granules are responsible for the compound or elongated structures observed in these starches. CLSM optical sections of rice granules revealed an apparent altered distribution of amylose in relation to the proposed growth ring structure, hinting at a novel mechanism of starch molecule deposition. Well-described granule features, such as equatorial grooves, channels, cracks, and growth rings were documented and related to both the internal and external observations. A new method for probing the phosphate distribution in native granules was developed using a phosphate-binding fluorescent dye and CLSM.