Cartography of cell morphology in tomato pericarp at the fruit scale

Development of a new bio-microscope for 3D geometry characterization of fruit single cells

Fruit cells are living irregular three-dimensional (3D) transparent objects which makes them challenging to determine their real 3D size and shape through only two-dimensional (2D) images using the existing biological microscope. This study deals with a newly self-developed biological microscope including a microscope imaging system, a light source system, a stage and a support base for the 3D size characterization of fruit single cells. The main design concept is based on two optical path systems set up at the front (x-axis) and bottom (z-axis) directions of a transparent chamber containing single cells that allow the front view and bottom view of the single cell to be observed. Performance indicators such as mass, size, observation range, objective magnification, total magnification, focal range, focal accuracy, and resolution of the developed biological microscope were estimated. Finally, the 3D geometry size of single tomato cells was measured by the new biological microscope to demonstrate the relative ease at which accurate real 3D geometry information of single fruit cells could be obtained, which echoes its scientific value.

Gastric devolution of transglutaminase-induced acid and rennet-induced casein gels using dynamic DIDGI® and static COST action INFOGEST protocols

Limited studies in the literature have compared in vitro dynamic and in vitro static protocols for modelling the gastric digestive process of food systems. This experiment explores the differences between two different in vitro approaches to the devolution of a transglutaminase-induced acid gel (TG, pH 5.1-5.3) and rennet-induced gel (RG, pH 6.5-6.7). Gels were exposed to a simulated oral phase, followed by either the dynamic DIDGI® or static COST action INFOGEST protocol to simulate gastric conditions. Protein hydrolysis was evident from 15 min onwards for TG exposed to the dynamic protocol where levels continued to increase at a steady rate. In contrast, RG exhibited a notable lag-phase before levels increased from around 60 min onwards. Under the static protocol, protein hydrolysis was observed for both TG and RG upon exposure to the gastric environment which continued to increase over time. Despite these differences, similar levels of protein hydrolysis were found for TG and RG at the gastric endpoint using either protocol demonstrating that both the dynamic DIDGI® and static COST action INFOGEST methods provide a suitable and comparable environment for the in vitro digestion of casein protein under simulated gastric conditions.

A comparison of fixation methods for SEM analysis of self-assembling peptide hydrogel nanoarchitecture

Determining the porosity of hydrogels is an important component of material characterisation. While scanning electron microscopy (SEM) is a widely used method to study hydrogel nanoarchitecture, it is well-established that SEM sample preparation methods can alter the structure of hydrogels. Herein we describe the impact of sample preparation on the SEM analysis of self-assembling β-peptide hydrogels. Three methods of hydrogel preparation for SEM were compared, and each method preserved distinctly different nanoarchitecture, specifically, different levels of fibre alignment and porosity. Comparison of conventional SEM preparation and our hybrid method, which comprises high pressure freezing, freeze substitution without fixative and critical point drying, showed a high degree of similarity at the nanometre scale and diverging architecture at the micron scale. This study quantified the impact of chemical fixation versus high pressure freezing on self-assembling β³-peptide hydrogels, demonstrated the effect of sample preparation on fibre alignment and porosity, and presents a novel hybrid preparation method where chemical fixation can be avoided when conventional SEM is desired.

Quantitative MRI analysis of structural changes in tomato tissues resulting from dehydration

A quantitative magnetic resonance imaging (MRI) analysis at 1.5T of the effects of different dehydration regimes on transverse relaxation parameters measured in tomato tissue is presented. Multi-exponential T₂ maps have been estimated for the first time, providing access to spatialized microstructural information at voxel scale. The objective was to provide a better understanding of the changes in the multi-exponential transverse relaxation parameters induced by dehydration in tomato tissues and to unravel the effects of microstructure and composition on relaxation parameters. The results led to the hypothesis that the multi-exponential relaxation signal reflects cell compartmentation and tissue heterogeneity, even at the voxel scale. Multi-exponential relaxation times provided information about water loss from specific cell compartments and seem to indicate that the dehydration process mainly affects large cells. By contrast, total signal intensity showed no sensitivity to variations in water content in the range investigated in the present study (between 95% [fresh tissue] and 90% [after dehydration]). The variation in relaxation times resulting from water loss was due to both changes in solute concentration and compartment size. The comparative analysis of the two contrasted tissues in terms of microporosity demonstrated that magnetic susceptibility effects, caused by the presence of air in the placenta tissue, significantly impact the effective relaxation and might be the dominant effect in the variations observed in relaxation times in this tissue.

Effect of clay and guishe-ash as substrate on Lycopersicon esculentum germination and production

The effect of biomass ash and clay on tomato plants (Lycopersicon esculentum) in greenhouse conditions from germination to production was studied. Biomass ash is a waste obtained from thermal treatment of guishe (a by-product of natural fiber), and clay is collected from local soils. Several trials were performed to assess the influence of the addition of clay and guishe-ash on seeds germination, seedling growth, and production yield. The decrease in the values of these variables was considered an indicator of toxicity. The obtained results showed that based clay/ash materials positively affect germination (average ∼90% and six materials allow obtaining 90%) and seedlings growth (an increase of ∼20% in height and more than 50% in fresh air corpuscular weight). However, applying these materials on the production stage induces minor positive effects on fruit diameter, locule number, pericarp thickness, and the number of seeds per fruit. Also, adverse effects (first harvest yield, number of fruits, fresh mass of ripe fruits, lycopene content) were observed. To valorize biomass ash, its combination with other materials such as clay could be an alternative to improve tomato production.

Investigating casein gel structure during gastric digestion using ultra-small and small-angle neutron scattering

This study aimed to understand the structural devolution of 10% w/w rennet-induced (RG) and transglutaminase-induced acid (TG) gels in H₂O and D₂O under in vitro gastric conditions with and without pepsin. The real-time devolution of structure at a nano- (e.g. colloidal calcium phosphate (CCP) and micelle) and micro- (gel network) level was determined using ultra-small (USANS) and small-angle neutron scattering (SANS) with electron microscopy. Results demonstrate that gel firmness or elasticity determines disintegration behaviour during simulated mastication and consequently the particle size entering the stomach. Shear of mixing in the stomach, pH, and enzyme activity will also affect the digestion process. Our results suggest that shear of mixing primarily results in erosion at the particle surface and governs gel disintegration behaviour during the early stages of digestion. Pepsin diffusivity, and hence action, occur more readily in the latter stages of gastric digestion via access to the particle interior. This occurs via the progressively larger pores of the looser gel network and channels created within the larger, less dense casein micelles of the RG gels. Gel firmness and brittleness were greater in the D₂O samples compared to H₂O, facilitating gel disintegration. Despite the higher strength and elasticity of RG compared to TG, the protein network strands of the RG gels become more compact when exposed to the acidic gastric environment with comparatively larger pores observed through SEM imaging. This led to a higher degree of digestibility in RG gels compared to TG gels. This is the first study to examine casein gel structure during simulated gastric digestion using scattering and highlights the benefits of neutron scattering to monitor structural changes during digestion at multiple length scales.

Spatial and temporal evolution of quantitative magnetic resonance imaging parameters of peach and apple fruit - relationship with biophysical and metabolic traits

Fruits are complex organs that are spatially regulated during development. Limited phenotyping capacity at cell and tissue levels is one of the main obstacles to our understanding of the coordinated regulation of the processes involved in fruit growth and quality. In this study, the spatial evolution of biophysical and metabolic traits of peach and apple fruit was investigated during fruit development. In parallel, the multi-exponential relaxation times and apparent microporosity were assessed by quantitative magnetic resonance imaging (MRI). The aim was to identify the possible relationships between MRI parameters and variations in the structure and composition of fruit tissues during development so that transverse relaxation could be proposed as a biomarker for the assessment of the structural and functional evolution of fruit tissues during growth. The study provides species-specific data on developmental and spatial variations in density, cell number and size distribution, insoluble and soluble compound accumulation and osmotic and water potential in the fruit mesocarp. Magnetic resonance imaging was able to capture tissue evolution and the development of pericarp heterogeneity by accessing information on cell expansion, water status and distribution at cell level, and microporosity. Changes in vacuole-related transverse relaxation rates were mostly explained by cell/vacuole size. The impact of cell solute composition, microporosity and membrane permeability on relaxation times is also discussed. The results demonstrate the usefulness of MRI as a tool to phenotype fruits and to access important physiological data during development, including information on spatial variability.

Flux balance analysis of metabolism during growth by osmotic cell expansion and its application to tomato fruits

Cell expansion is a significant contributor to organ growth and is driven by the accumulation of osmolytes to increase cell turgor pressure. Metabolic modelling has the potential to provide insights into the processes that underpin osmolyte synthesis and transport, but the main computational approach for predicting metabolic network fluxes, flux balance analysis, often uses biomass composition as the main output constraint and ignores potential changes in cell volume. Here we present growth-by-osmotic-expansion flux balance analysis (GrOE-FBA), a framework that accounts for both the metabolic and ionic contributions to the osmotica that drive cell expansion, as well as the synthesis of protein, cell wall and cell membrane components required for cell enlargement. Using GrOE-FBA, the metabolic fluxes in dividing and expanding cells were analysed, and the energetic costs for metabolite biosynthesis and accumulation in the two scenarios were found to be surprisingly similar. The expansion phase of tomato fruit growth was also modelled using a multiphase single-optimization GrOE-FBA model and this approach gave accurate predictions of the major metabolite levels throughout fruit development, as well as revealing a role for transitory starch accumulation in ensuring optimal fruit development.

Parametric mapping of cellular morphology in plant tissue sections by gray level granulometry

BACKGROUND

The cellular morphology of plant organs is strongly related to other physical properties such as shape, size, growth, mechanical properties or chemical composition. Cell morphology often vary depending on the type of tissue, or on the distance to a specific tissue. A common challenge in quantitative plant histology is to quantify not only the cellular morphology, but also its variations within the image or the organ. Image texture analysis is a fundamental tool in many areas of image analysis, that was proven efficient for plant histology, but at the scale of the whole image.

RESULTS

This work presents a method that generates a parametric mapping of cellular morphology within images of plant tissues. It is based on gray level granulometry from mathematical morphology for extracting image texture features, and on Centroidal Voronoi Diagram for generating a partition of the image. Resulting granulometric curves can be interpreted either through multivariate data analysis or by using summary features corresponding to the local average cell size. The resulting parametric maps describe the variations of cellular morphology within the organ.

CONCLUSIONS

We propose a methodology for the quantification of cellular morphology and of its variations within images of tissue sections. The results should help understanding how the cellular morphology is related to genotypic and / or environmental variations, and clarify the relationships between cellular morphology and chemical composition of cell walls.

Organ-wide and ploidy-dependent regulation both contribute to cell-size determination: evidence from a computational model of tomato fruit

The development of a new organ is the result of coordinated events of cell division and expansion, in strong interaction with each other. This study presents a dynamic model of tomato fruit development that includes cell division, endoreduplication, and expansion processes. The model is used to investigate the potential interactions among these developmental processes within the context of the neo-cellular theory. In particular, different control schemes (either cell-autonomous or organ-controlled) are tested and compared to experimental data from two contrasting genotypes. The model shows that a pure cell-autonomous control fails to reproduce the observed cell-size distribution, and that an organ-wide control is required in order to get realistic cell-size variations. The model also supports the role of endoreduplication as an important determinant of the final cell size and suggests that a direct effect of endoreduplication on cell expansion is needed in order to obtain a significant correlation between size and ploidy, as observed in real data.

Quantitative imaging of plants: multi-scale data for better plant anatomy

This article comments on: Staedler YM, Kreisberger T, Manafzadeh S, Chartier M, Handschuh S, Pamperl S, Sontag S, Paun O, Schönenberger J. 2017. Novel computed tomography-based tools reliably quantify plant reproductive investment. Journal of Experimental Botany 69, 525–535.

Contrast-enhanced 3D micro-CT of plant tissues using different impregnation techniques

BACKGROUND

X-ray micro-CT has increasingly been used for 3D imaging of plant structures. At the micrometer resolution however, limitations in X-ray contrast often lead to datasets with poor qualitative and quantitative measures, especially within dense cell clusters of plant tissue specimens. The current study developed protocols for delivering a cesium based contrast enhancing solution to varying plant tissue specimens for the purpose of improving 3D tissue structure characterization within plant specimens, accompanied by new image processing workflows to extract the additional data generated by the contrast enhanced scans.

RESULTS

Following passive delivery of a 10% cesium iodide contrast solution, significant increases of 85.4 and 38.0% in analyzable cell volumes were observed in pear fruit hypanthium and tomato fruit outer mesocarp samples. A significant increase of 139.6% in the number of analyzable cells was observed in the pear fruit samples along the added ability to locate and isolate better brachysclereids and vasculature in the sample volume. Furthermore, contrast enhancement resulted in significant improvement in the definition of collenchyma and parenchyma in the petiolule of tomato leaflets, from which both qualitative and quantitative data can be extracted with respect to cell measures. However, contrast enhancement was not achieved in leaf vasculature and mesophyll tissue due to fundamental limitations. Active contrast delivery to apple fruit hypanthium samples did yield a small but insignificant increase in analyzable volume and cells, but data on vasculature can now be extracted better in correspondence to the pear hypanthium samples. Contrast delivery thus improved visualization and analysis the most in dense tissue types.

CONCLUSIONS

The cesium based contrast enhancing protocols and workflows can be utilized to obtain detailed 3D data on the internal microstructure of plant samples, and can be adapted to additional samples of interest with minimal effort. The resulting datasets can therefore be utilized for more accurate downstream studies that requires 3D data.

Use of Natural Diversity and Biotechnology to Increase the Quality and Nutritional Content of Tomato and Grape

Improving fruit quality has become a major goal in plant breeding. Direct approaches to tackling fruit quality traits specifically linked to consumer preferences and environmental friendliness, such as improved flavor, nutraceutical compounds, and sustainability, have slowly been added to a breeder priority list that already includes traits like productivity, efficiency, and, especially, pest and disease control. Breeders already use molecular genetic tools to improve fruit quality although most advances have been made in producer and industrial quality standards. Furthermore, progress has largely been limited to simple agronomic traits easy-to-observe, whereas the vast majority of quality attributes, specifically those relating to flavor and nutrition, are complex and have mostly been neglected. Fortunately, wild germplasm, which is used for resistance against/tolerance of environmental stresses (including pathogens), is still available and harbors significant genetic variation for taste and health-promoting traits. Similarly, heirloom/traditional varieties could be used to identify which genes contribute to flavor and health quality and, at the same time, serve as a good source of the best alleles for organoleptic quality improvement. Grape (Vitis vinifera L.) and tomato (Solanum lycopersicum L.) produce fleshy, berry-type fruits, among the most consumed in the world. Both have undergone important domestication and selection processes, that have dramatically reduced their genetic variability, and strongly standardized fruit traits. Moreover, more and more consumers are asking for sustainable production, incompatible with the wide range of chemical inputs. In the present paper, we review the genetic resources available to tomato/grape breeders, and the recent technological progresses that facilitate the identification of genes/alleles of interest within the natural or generated variability gene pool. These technologies include omics, high-throughput phenotyping/phenomics, and biotech approaches. Our review also covers a range of technologies used to transfer to tomato and grape those alleles considered of interest for fruit quality. These include traditional breeding, TILLING (Targeting Induced Local Lesions in Genomes), genetic engineering, or NPBT (New Plant Breeding Technologies). Altogether, the combined exploitation of genetic variability and innovative biotechnological tools may facilitate breeders to improve fruit quality tacking more into account the consumer standards and the needs to move forward into more sustainable farming practices.

Remodeling of pectin and hemicelluloses in tomato pericarp during fruit growth

Tomato fruit texture depends on histology and cell wall architecture, both under genetic and developmental controls. If ripening related cell wall modifications have been well documented with regard to softening, little is known about cell wall construction during early fruit development. Identification of key events and their kinetics with regard to tissue architecture and cell wall development can provide new insights on early phases of texture elaboration. In this study, changes in pectin and hemicellulose chemical characteristics and location were investigated in the pericarp tissue of tomato (Solanum lycopersicon var Levovil) at four stages of development (7, 14 and 21day after anthesis (DPA) and mature green stages). Analysis of cell wall composition and polysaccharide structure revealed that both are continuously modified during fruit development. At early stages, the relative high rhamnose content in cell walls indicates a high synthesis of rhamnogalacturonan I next to homogalacturonan. Fine tuning of rhamnogalacturonan I side chains appears to occur from the cell expansion phase until prior to the mature green stage. Cell wall polysaccharide remodelling also concerns xyloglucans and (galacto)glucomannans, the major hemicelluloses in tomato cell walls. In situ localization of cell wall polysaccharides in pericarp tissue revealed non-ramified RG-I rich pectin and XyG at cellular junctions and in the middle lamella of young fruit. Blocks of non-methyl esterified homogalacturonan are detected as soon as 14 DPA in the mesocarp and remained restricted to cell corner and middle lamella whatever the stages. These results point to new questions about the role of pectin RGI and XyG in cell adhesion and its maintenance during cell expansion.

Analysis of microstructures and macrotextures for different apple cultivars based on parenchyma morphology

Fuji, Golden Delicious, and Jonagold parenchyma were imaged by confocal laser scanning microscopy to be extracted morphology characteristics, which were used to analyze the relationship with macrotexture of apples tested by penetration and compression. Before analyzing the relationship, the significantly different morphology parameters were reduced in dimensions by principal component analysis and were proved to be availably used for distinguishing the different apple cultivars. For compression results, cell did not absolutely determine the hardness in different apple cultivars, and the pore should also be taken into consideration. With the same size in cell feret diameter, the bigger the pore feret diameter was, the softer the apple became. If no difference existed in pore feret diameter size, the cultivar became harder with a narrower distribution in cell feret diameter. The texture parameters were compared with the roundness parameters in the same or inverse changing trends to explore the relationship. High correlations were found between the texture parameters (energy required in whole penetration (Wt), fracture force (Fp), crispness) and pore solidity (R(2)  > 0.924, P < 0.001). Compactness of parenchyma played an important role in fruit texture. This research could provide the comprehension about relationship between microstructure and macrotexture of apple cultivars and morphological values for modeling apple parenchyma, contributing to numerical simulation for constitutive relation of fruit.

Micron-scale phenotyping quantification and three-dimensional microstructure reconstruction of vascular bundles within maize stalks based on micro-CT scanning

Vascular bundles within maize (Zea mays L.) stalks play a key role in the mechanical support of plant architecture as well as in water and nutrient transportation. Convenient and accurate phenotyping of vascular bundles may help phenotypic identification of germplasm resources for breeding. Based on practical sample preparation procedures for maize stalks, we acquired serials of cross-sectional images using a micro-computed tomography (CT) imaging device. An image processing pipeline dedicated to the phenotyping of vascular bundles was also developed to automatically segment and validate vascular bundles from the cross-sectional images of maize stalks, from which phenotypic traits of vascular bundles, i.e. number, area, and spatial distribution, were calculated. More profound quantification of spatial distribution was given as area ratio of vascular bundles, which described the distribution of vascular bundles associated with the centroid of maize stalks. In addition, three-dimensional visualisation was performed to reveal the spatial configuration and distribution of vascular bundles. The proposed method significantly improves computation accuracy for the phenotypic traits of vascular bundles compared with previous methods, and is expected to be useful for illustrating relationships between phenotypic traits of vascular bundles and their function.

Automatic analysis of the 3-D microstructure of fruit parenchyma tissue using X-ray micro-CT explains differences in aeration

BACKGROUND

3D high-resolution X-ray imaging methods have emerged over the last years for visualising the anatomy of tissue samples without substantial sample preparation. Quantitative analysis of cells and intercellular spaces in these images has, however, been difficult and was largely based on manual image processing. We present here an automated procedure for processing high-resolution X-ray images of parenchyma tissues of apple (Malus × domestica Borkh.) and pear (Pyrus communis L.) as a rapid objective method for characterizing 3D plant tissue anatomy at the level of single cells and intercellular spaces.

RESULTS

We isolated neighboring cells in 3D images of apple and pear cortex tissues, and constructed a virtual sieve to discard incorrectly segmented cell particles or unseparated clumps of cells. Void networks were stripped down until their essential connectivity features remained. Statistical analysis of structural parameters showed significant differences between genotypes in the void and cell networks that relate to differences in aeration properties of the tissues.

CONCLUSIONS

A new model for effective oxygen diffusivity of parenchyma tissue is proposed that not only accounts for the tortuosity of interconnected voids, but also for significant diffusion across cells where the void network is not connected. This will significantly aid interpretation and analysis of future tissue aeration studies. The automated image analysis methodology will also support pheno- and genotyping studies where the 3D tissue anatomy plays a role.

Statistical mapping of maize bundle intensity at the stem scale using spatial normalisation of replicated images

The cellular structure of plant tissues is a key parameter for determining their properties. While the morphology of cells can easily be described, few studies focus on the spatial distribution of different types of tissues within an organ. As plants have various shapes and sizes, the integration of several individuals for statistical analysis of tissues distribution is a difficult problem. The aim of this study is to propose a method that quantifies the average spatial organisation of vascular bundles within maize stems, by integrating information from replicated images. In order to compare observations made on stems of different sizes and shapes, a spatial normalisation strategy was used. A model of average stem contour was computed from the digitisation of several stem slab images. Point patterns obtained from individual stem slices were projected onto the average stem to normalise them. Group-wise analysis of the spatial distribution of vascular bundles was applied on normalised data through the construction of average intensity maps. A quantitative description of average bundle organisation was obtained, via a 3D model of bundle distribution within a typical maize internode. The proposed method is generic and could easily be extended to other plant organs or organisms.

Automated image mosaics by non-automated light microscopes: the MicroMos software tool

Light widefield microscopes and digital imaging are the basis for most of the analyses performed in every biological laboratory. In particular, the microscope's user is typically interested in acquiring high-detailed images for analysing observed cells and tissues, meanwhile being representative of a wide area to have reliable statistics. The microscopist has to choose between higher magnification factor and extension of the observed area, due to the finite size of the camera's field of view. To overcome the need of arrangement, mosaicing techniques have been developed in the past decades for increasing the camera's field of view by stitching together more images. Nevertheless, these approaches typically work in batch mode and rely on motorized microscopes. Or alternatively, the methods are conceived just to provide visually pleasant mosaics not suitable for quantitative analyses. This work presents a tool for building mosaics of images acquired with nonautomated light microscopes. The method proposed is based on visual information only and the mosaics are built by incrementally stitching couples of images, making the approach available also for online applications. Seams in the stitching regions as well as tonal inhomogeneities are corrected by compensating the vignetting effect. In the experiments performed, we tested different registration approaches, confirming that the translation model is not always the best, despite the fact that the motion of the sample holder of the microscope is apparently translational and typically considered as such. The method's implementation is freely distributed as an open source tool called MicroMos. Its usability makes building mosaics of microscope images at subpixel accuracy easier. Furthermore, optional parameters for building mosaics according to different strategies make MicroMos an easy and reliable tool to compare different registration approaches, warping models and tonal corrections.

Color quantification of stained maize stem section describes lignin spatial distribution within the whole stem

This work presents a method to quantify the lignification of maize tissues by automated color image analysis of stained maize stem cross sections. Safranin and Alcian blue staining makes lignified tissues appear red, and nonlignified tissues appear blue. Lignification is assessed by the ratio of red intensity over blue intensity. A rough quantification of global lignification is computed as the surface ratio of lignified tissues. A more precise quantification is obtained by computing profiles of red/blue intensity ratio in relation to the distance to the epidermis, depicting the spatial distribution of lignified walls within the stem. Lignification profiles are analyzed through summary parameters describing the evolution of lignification in three specific regions. The distribution of lignification can be quickly assessed depending on the position and the development stage, allowing the screening of genetic variations to be envisioned.