A typical method for decellularization of plants as biomaterials

Decellularization is a process by which cells are removed from tissues or organs, leaving behind the extracellular matrix (ECM) structure. This process has gained interest in the fields of tissue engineering and regenerative medicine as a way to prepare suitable scaffolds for tissue reconstruction. Although the initial efforts come with the animal tissues, this technique can also be applied to various plant tissues with simple modifications, as plant-derived biomaterials have the benefit of being biocompatible and serving as a safe, all-natural substitute for synthetic or animal originated materials. Additionally, plant-derived biomaterials may help cells grow and differentiate, creating a three-dimensional environment for tissue regeneration and repair. Here we demonstrate a general method for plant tissue decellularization, including already experienced approaches and techniques.•Exhibit the basic steps for plant decellularization, which may be applied to several other plant tissues.•The proposed approach may be optimized considering various intended uses.•Gives basic information for the determination of decellularization efficiency.

Bioaccumulation and distribution of Pb, Ni, Zn and Fe in stinging nettle (Urtica dioica) tissues and heavy metal-contamination assessment in the industrial zone of smelter Ferronikeli (Drenas-Kosovo)

Here, we determined the concentrations of Pb, Ni, Zn and Fe in the soil and in vegetative organs of stinging nettle (Urtica dioica) collected from the banks of the Drenica River in the vicinity of the Ferronikeli smelter. The results were compared with samples collected from the banks 20 km (Shalë village) upriver. In addition, the bioaccumulation factor (BCF) and translocation factor (TF) were determined. Meanwhile, to evaluate the level of pollution in the study area was used the contamination factor (CF), potential ecological risk factor (Eri) and the potential ecological risk index (RI). The order of heavy metals according to their concentration in the soil samples at both sampling sites was as follows: Fe > Ni > Zn > Pb. Concentrations in excess of the limits allowed for soils in the samples collected in the vicinity of the smelter were recorded for Pb (173.13 mg kg^-1), Zn (1217.48 mg kg^-1), and Ni (1443.93 mg kg^-1), while at the control site, Zn (270.82 mg kg^-1) and Ni (375.47 mg kg^-1) were found in excess concentrations. But lead (Pb) level was under allowed limit. The data showed that the stinging nettle is not a hyperaccumulator because BCF < 1 at both sites for all metals under study. Furthermore, analysis of the translocation factor (TF_steam/root) showed that at low of heavy metal concentrations, their mobility was higher (TF > 1). The lowest mobility (TF < 1) was observed at site I (Poklek), where the concentration of heavy metals was higher, except for Fe. The opposite was shown for mobility of metals from stems to leaves (TF_leave/steam). The evaluation of CF showed that the area near the Ferronikeli smelter had low degree of Pb, moderate degree of Zn and considerable degree of Ni contamination. The values of RI indicate low potential ecological risk index.

Untargeted lipidomic profiling of grapes highlights the importance of modified lipid species beyond the traditional compound classes

The aim of this paper is to provide a detailed characterisation of grape lipidome. To achieve this objective, it starts by describing a pipeline implemented in R software to allow the semi-automatic annotation of the detected lipid species. It also provides an extensive description of the different properties of each molecule (such as retention time dependencies, mass accuracy, adduct formation and fragmentation patterns), which allowed the annotations to be made more accurately. Most annotated lipids in the grape samples were (lyso)glycerophospholipids and glycerolipids, although a few free fatty acids, hydroxyceramides and sitosterol esters were also observed. The proposed pipeline also allowed the identification of a series of methylated glycerophosphates never previously observed in grapes. The current results highlight the importance of expanding chemical analyses beyond the classical lipid categories.

The Use of Flow Cytometry for Estimating Genome Sizes and DNA Ploidy Levels in Plants

Flow cytometry has emerged as a uniquely flexible, accurate, and widely applicable technology for the analysis of plant cells. One of its most important applications centers on the measurement of nuclear DNA contents. This chapter describes the essential features of this measurement, outlining the overall methods and strategies, but going on to provide a wealth of technical details to ensure the most accurate and reproducible results. The chapter is aimed to be equally accessible to experienced plant cytometrists as well as those newly entering the field. Besides providing a step-by-step guide for estimating genome sizes and DNA-ploidy levels from fresh tissues, special attention is paid to the use of seeds and desiccated tissues for such purposes. Methodological aspects regarding field sampling, transport, and storage of plant material are also given in detail. Finally, troubleshooting information for the most common problems that may arise during the application of these methods is provided.

A robust and efficient automatic method to segment maize FASGA stained stem cross section images to accurately quantify histological profile

BACKGROUND

Grasses internodes are made of distinct tissues such as vascular bundles, epidermis, rind and pith. The histology of grasses stem was largely revisited recently taking advantage of the development of microscopy combined with the development of computer-automated image analysis workflows. However, the diversity and complexity of the histological profile complicates quantification. Accurate and automated analysis of histological images thus remains challenging.

RESULTS

Herein, we present a workflow that automatically segments maize internode cross section images into 40 distinct tissues: two tissues in the epidermis, 19 tissues in the rind, 14 tissues in the pith and 5 tissues in the bundles. This level of segmentation is achieved by combining the Hue, Saturation and Value properties of each pixel and the location of each pixel in FASGA stained cross sectiona. This workflow is likewise able to highlight significant and subtle histological genotypic variations between maize internodes. The grain of precision provided by the workflow also makes it possible to demonstrate different levels of sensitivity to digestion by enzymatic cocktails of the tissues in the pith. The precision and strength of the workflow is all the more impressive because it is preserved on cross section images of other grasses such as miscanthus or sorghum.

CONCLUSIONS

The fidelity of this tool and its capacity to automatically identify variations of a large number of histological profiles among different genotypes pave the way for its use to identify genotypes of interest and to study the underlying genetic bases of variations in histological profiles in maize or other species.

Plant Tissue Parenchyma and Vascular Bundles Selectively Regulate Stem Cell Mechanosensing and Differentiation

Introduction

Plant tissues are plentiful, diverse, and due to convergent evolution are structurally similar to many animal tissues. Decellularized plant tissues feature microtopographies that resemble cancellous bone (porous parenchyma) and skeletal muscle (fibrous vascular bundles). However, the use of plant tissues as an inexpensive and abundant biomaterial for controlling stem cell behavior has not been widely explored.

Methods

Celery plant tissues were cut cross-sectionally (porous parenchyma) or longitudinally (fibrous vascular bundles) and decellularized. Human mesenchymal stem cells (MSCs) were then cultured atop plant tissues and confocal imaging of single cells was used to evaluate the early effects of microtopography on MSC adhesion, morphology, cytoskeletal alignment, Yes-associated protein (YAP) signaling, and downstream lineage commitment to osteogenic or myogenic phenotypes.

Results

Microtopography was conserved post plant tissue decellularization and MSCs attached and proliferated on plant tissues. MSCs cultured on porous parenchyma spread isotropically along the periphery of plant tissue pores. In contrast, MSCs cultured on vascular bundles spread anisotropically and aligned in the direction of fibrous vascular bundles. Differences in microtopography also influenced MSC nuclear YAP localization and actin anisotropy, with higher values observed on fibrous tissues. When exposed to osteogenic or myogenic culture medium, MSCs on porous parenchyma had a higher percentage of cells stain positive for bone biomarker alkaline phosphatase, whereas myoblast determination protein 1 (MyoD) was significantly upregulated for MSCs on fibrous vascular bundles.

Conclusions

Together, these results show that plant tissues are an abundant biomaterial with defined microarchitecture that can reproducibly regulate MSC morphology, mechanosensing, and differentiation.

Supplementary Information

The online version of this article contains supplementary material available 10.1007/s12195-022-00737-9.

Towards defining the core Saccharum microbiome: input from five genotypes

Background

Plant microbiome and its manipulation inaugurate a new era for plant biotechnology with the potential to benefit sustainable crop production. Here, we used the large-scale 16S rDNA sequencing analysis to unravel the dynamic, structure, and composition of exophytic and endophytic microbial communities in two hybrid commercial cultivars of sugarcane (R570 and SP80–3280), two cultivated genotypes (Saccharum officinarum and Saccharum barberi) and one wild species (Saccharum spontaneum).

Results

Our analysis identified 1372 amplicon sequence variants (ASVs). The microbial communities’ profiles are grouped by two, root and bulk soils and stem and leave when these four components are compared. However, PCoA-based data supports that endophytes and epiphytes communities form distinct groups, revealing an active host-derived mechanism to select the resident microbiota. A strong genotype-influence on the assembly of microbial communities in Saccharum ssp. is documented. A total of 220 ASVs persisted across plant cultivars and species. The ubiquitous bacteria are two potential beneficial bacteria, Acinetobacter ssp., and Serratia symbiotica.

Conclusions

The results presented support the existence of common and cultivar-specific ASVs in two commercial hybrids, two cultivated canes and one species of Saccharum across tissues (leaves, stems, and roots). Also, evidence is provided that under the experimental conditions described here, each genotype bears its microbial community with little impact from the soil conditions, except in the root system. It remains to be demonstrated which aspect, genotype, environment or both, has the most significant impact on the microbial selection in sugarcane fields.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-022-02598-8.

Chemical and biological studies of Daphniphyllum oldhamii from Hunan Province, China

The fruits, twigs and leaves of Daphniphyllum oldhamii (Hemsl.) K. Rosenthal, collected from Longshan County, Hunan Province, China, were chemically investigated. Three undescribed daphniphyllum alkaloids, namely longshanoldhamines A‒C, and six known related ones have been isolated from the fruits, whereas two undescribed triterpenoids and one undescribed lignan, along with six known triterpenoids, were found in the twigs and leaves. Their structures were elucidated by extensive spectroscopic analysis, X-ray diffraction analysis and comparison with the reported data.

Determination of phosphorus compounds in plant tissues: from colourimetry to advanced instrumental analytical chemistry

Although the spectrum of effective methods and techniques that allow determination of inorganic or total phosphorus is impressive, more precise analysis of these substances in plant tissues is not a routine or trivial task. The complexity of chemical composition of plant tissues treated as the analytical matrices is thought to be the main cause why there is no one answer, how appropriate phosphorus compounds may be determined qualitatively and quantitatively. Even if more advanced spectrophotometric measurements and classical variants of absorption (FAAS) or emission (ICP-AES/ ICP-OES) spectrometry techniques are used, it is necessary at first to isolate various forms of phosphorus from the matrix, and then to mineralize them prior the determination. Significant progress in such a kind of analytical efforts was brought by implementation of combined methods e.g. ETV-ICP-AES or HR-ETAAS, does allow the isolation of the phosphorus analyte and its detection during a kind of "one step" analytical procedure, directly in plant tissues. Similar benefits, regarding sensitivity of determinations, are obtained when XRF, SIMS or nanoSIMS-more expensive techniques of imaging the presence of phosphorus in biological matrices have been used. Nowadays, obviously being aware of higher limit of detection, nuclear magnetic resonance spectroscopy, especially the ³¹P NMR technique, is thought to be the most universal analytical tool allowing to determine various chemical forms of plant phosphorus qualitatively and quantitatively, at the same time. Although ³¹P NMR provides valuable information about the phosphorus profile of plants, it should be emphasized that each analytical issue related to the determination of phosphorus compounds in plant tissues and organs, requires an individual approach to defined problem.

Organophosphate pesticides sequestered in tissues of a seagrass species - Zostera capensis from a polluted watershed

Organophosphate pesticides (OPPs) are persistent in the environment, but little information is available on their bioaccumulation in seagrass. In this study, the seagrass - Zostera capensis was collected from Swartkops Estuary in South Africa to investigate the bioaccumulation of OPPs from contaminated sediments and the water column. This plant was chosen because it grows abundantly in the estuary's intertidal zone, making it a viable phytoremediator in the urban environment. Extraction was performed by the QuEChERS method followed by GC-MS analysis. The mean concentration of ∑OPPs ranged from 0.01 to 0.03 μg/L for surface water; 6.20-13.35 μg/kg dw for deep-rooted sediments; 18.79-37.75 μg/kg dw for leaf tissues and 12.14-39.80 μg/kg dw for root tissues of Z. capensis. The biota-sediment accumulation factors (BSAFs) were greater than one, indicating the potential for Z. capensis to bioaccumulate and intercept the targeted pesticides. A weak insignificant correlation observed between log BSAFs and log Kow indicates that the bioaccumulation of OPPs in tissues of Z. capensis were not dependent on the Kow. Eight of the selected pesticides had root-leaf translocation factors (TFr-l) greater than 1, indicating that Z. capensis can transport these chemicals from roots to leaves. The results from this study implies that this plant species can clean up OPP contamination in the environment.

A translocation analysis of organophosphate pesticides between surface water, sediments and tissues of common reed Phragmites australis

This study investigated the ability of common reed, Phragmites australis to take up organophosphate pesticides (OPPs). The study site was the agriculturally polluted Sundays Estuary in South Africa. Surface water, leaves, roots, and deep-rooted-sediments of P. australis were collected along the length of the estuary and analysed for 13 different OPPS. The extraction of OPPs in plant tissues was performed by QuEChERS method followed by GC-MS analysis. The highest concentration of OPPs was found in leaves (16.41-31.39 μg kg^-1 dw), followed by roots (13.92-30.88 μg kg^-1 dw), and sediments (3.30-8.07 μg kg^-1 dw). Of the 13 targeted OPPs, only one compound was not detected across the four sample matrices, thus reflecting widespread contamination in the Sundays Estuary. The biota sediment accumulation factor (BSAF) values of pyraclofos, quinalphos, fenitrothion, phosalone, EPN, diazinon, chlorpyrifos, pyrazophos, and isazophos were higher than one implying that P. australis possesses the ability to bioaccumulate these compounds. The root-leaf translocation factors (TF_r-l) of these pesticides were higher than 1, suggesting that P. australis possesses the capacity to move these pesticides from roots to leaves. The insignificant correlation observed between log BSAF and log K_ow and log TF_r-l and log K_ow implies that OPPs uptake by P. australis tissues were not dependent on log Kow. Our study demonstrates that P. australis possesses the potential to effectively remove OPPs from contaminated water and sediment.

Study of Potentially Toxic Elements Uptake into Organs of Quercus spp. from Copper Deposits in Slovakia, Italy and Portugal

The article is focused on the application of Energy dispersive micro X-ray fluorescence spectroscopy as a specific method to determine the contents of potentially toxic elements and its spread in plant tissues. As a model species, Quercus spp. were selected. In order to compare the obtained results with previous research, four well-described abandoned Cu-deposits were selected for sampling: Ľubietová (Slovakia), Libiola and Caporciano (Italy), and São Domingos (Portugal). The results of micro X-ray fluorescence spectrometry confirm the irregular contamination of Quercus spp. by potentially toxic elements. The level of contamination is the highest predominantly in the root cortex, where is also the highest Ca contents (with exception of São Domingos). At Ľubietová and Caporciano, high Ni content was described in branches cortex, in branches mesoderm also Fe, Cu and Zn. At the same time, the inhibition influence of Ca was also confirmed regarding the input of these elements into plants.

In Situ Localization of Plant Lipid Metabolites by Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging (MALDI-MSI)

Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) has emerged as a major analytical platform for the determination and localization of lipid metabolites directly from tissue sections. Unlike analysis of lipid extracts, where lipid localizations are lost due to homogenization and/ or solvent extraction, MALDI-MSI analysis is capable of revealing spatial localization of metabolites while simultaneously collecting high chemical resolution mass spectra. Important considerations for obtaining high quality MALDI-MS images include tissue preservation, section preparation, MS data collection and data processing. Errors in any of these steps can lead to poor quality metabolite images and increases the chance for metabolite misidentification and/ or incorrect localization. Here, we present detailed methods and recommendations for specimen preparation, MALDI-MS instrument parameters, software analysis platforms for data processing, and practical considerations for each of these steps to ensure acquisition of high-quality chemical and spatial resolution data for reconstructing MALDI-MS images of plant tissues.

SERS imaging analyses of bacteria cells among plant tissues

A chemical imaging method to mass surveil bacteria cells among plant tissues in situ is reported. Bacteria cells were pre-labeled with 3-mercaptophenylboronic acid for complexation with gold nanoparticles. Surface-enhanced Raman spectra were collated en masse to generate panoramic chemical images of bacteria populations. The approach was successfully employed to study the distribution of mass bacteria populations directly on and in selected plant tissues. This study demonstrates the great potential with which SERS imaging can be utilized for the study of bacterial cells among complex matrices, in some ways that are superior to electron and fluorescent microscopies.

Effects on anatomy of some abundantly growing herbs in the effluents contaminated soil of oil refinery

The soil contaminations from refinery effluents are still a burning problem in the oil-producing nations of the globe. In the present study, the effect of oil refinery effluents on anatomical characteristics of some selected herbs has been studied. The abundantly growing herb species of the contaminated sites that includes Ageratum conyzoides, Alternanthera paronychioides, and Cyperus brevifolius were selected for the anatomical investigation. The samplings site of these herbs was adjacent to Numaligarh oil refinery, Assam, India, where a huge amount of oil effluents are released every day. For comparison, the same plant species were collected from the control sites where effluent contamination was not evident. The results showed that anatomical sections of both shoots and roots of the studied herbs are adversely affected by oil refinery effluents contamination and showed various structural abnormalities. Dark/blackish depositions were traced in the different tissues that include the epidermis, cortex, vascular bundles and pith region in the plant samples collected from the effluents contaminated areas. The results also revealed widening, thickening, and reduction of different tissues of the studied plants besides affecting overall shoot diameter; cell sizes; and length of epidermis, cortex, vascular bundles, and pith as a defense mechanism against the adverse condition created due to effluent contamination. Such abnormalities were not observed in control plants.

Biomonitoring of heavy metal contamination with roadside trees from metropolitan area of Hefei, China

Air and dust borne heavy metals can be deposited and bioaccumulated by plants; therefore, biomonitoring employing plants is an effective tool for environmental impact assessment in urban environments. In this study, in addition to road dust, leaves and bark were collected from four common tree species at roadside and urban park sampling sites within the metropolitan area of Hefei, China. A range of heavy metals were analyzed by ICP-MS and AFS. The metal accumulation index (MAI) was adopted to compare the bioaccumulation capacity. Results showed that Cd was highly enriched in road dust although its abundance was low in comparison with that of other elements. The MAI values presented a narrow range (1.8-2.7); however, significant differences (p < 0.05) were found for Al, Cu, Zn, and As among the tree species. Moreover, deciduous Platanus orientalis bioaccumulated more nonessential As than the other species and deserved further risk management. In addition, bark samples from Cinnamomum camphora bioaccumulated more heavy metals than the other species as a result of its morphological and anatomical characteristics. The distribution patterns of heavy metals in tree tissues showed obvious spatial heterogeneity, as impacted by anthropogenic activities to varying degrees. This study examined the biomonitoring potential of roadside trees and the distribution pattern of heavy metals in an urban area under rapid development. Results from the present study could provide baseline data for urban environmental impact assessment and the design of green belts.

Structural modifications of plant organs and tissues by metals and metalloids in the environment: A review

At the dawn of the industrial revolution, the exorbitant use of heavy metals and toxic elements by mankind unfurls a powerful and complex web of hazard all around the world that significantly contributed to unprecedented trends in environmental degradation. Plants as sessile organisms, that cannot escape from the stress directly, have adapted to this environment via concurrent configurations of several traits. Among them the anatomy has been identified as much more advanced field of research that brought the explosion of interest among the expertise and its prodigious importance in stress physiology is unavoidable. In conjunction with various other disciplines, like physiology, biochemistry, genomics and metabolomics, the plant anatomy provides a large data sets that are paving the way towards a comprehensive and holistic understanding of plant growth, development, defense and productivity under heavy metal and toxic element stress. Present paper advances our recent knowledge about structural alterations of plant tissues induced by metals and metalloids, like antimony (Sb), arsenic (As), aluminium (Al), copper (Cu), cadmium (Cd), chromium (Cr), lead (Pb), manganese (Mn), mercury (Hg), nickel (Ni) and zinc (Zn) and points on essential role of plant anatomy and its understanding for plant growth and development in changing environment. Understanding of anatomical adaptations of various plant organs and tissues to heavy metals and metalloids could greatly contribute to integral and modern approach for investigation of plants in changing environmental conditions. These findings are necessary for understanding of the whole spectra of physiological and biochemical reactions in plants and to maintain the crop productivity worldwide. Moreover, our holistic perception regarding the processes underlying the plant responses to metal(loids) at anatomical level are needed for improving crop management and breeding techniques.

Cotton stalk-derived hydrothermal carbon for methylene blue dye removal: investigation of the raw material plant tissues

Conversion of the abundant agricultural residual cotton stalk (CS) into useful chemicals or functional materials could alleviate the fossil fuels caused energy shortages and environmental crises. Although some advances have been achieved, less attention has been paid to the plant tissues effect. In this study, the plant tissue of CS was changed by part degradation of some components (hemicelluloses and lignin, for example) with the aid of acid/base (or both). The pretreated CS was transformed into hydrochar by hydrothermal carbonization (HTC) method. Morphological and chemical compositions of CS hydrochar were analyzed by various techniques, including elemental analysis, Fourier transform infrared (FTIR), BET analysis, X-ray photoelectron spectroscopy (XPS) and X-ray diffraction (XRD). Methylene blue (MB) removal of prepared CS hydrochar was used to evaluate CS hydrochar pollutions adsorption capacity. Results reveal acid/base (or both) pretreatment is beneficial for CS raw material to prepare high-quality CS hydrochar. The effects of some parameters, such as initial MB concentration, temperature, pH value and recyclability on the adsorption of MB onto both acid and base-pretreated CS hydrochar (CS-H2SO4 + NaOH-HTC) were studied. The present work exhibits the importance of agricultural waste biomass material plant tissues on its derived materials, which will have a positive effect on the direct utilization of waste biomass.

Isolation and Purification of DNA from Complicated Biological Samples

The isolation of nucleic acids from a biological sample is an important step for many molecular biology applications and medical diagnostic assays. This chapter describes an efficient protocol using established acidic CTAB (with a pH value of 5.0 to 6.8) based extraction method for isolation and/or purification of high molecular weight genomic DNA from a range of fresh and difficult sources from plant, animal, fungi, and soil material. This protocol is suitable for many sequencing and genotyping applications, including large-scale sample screening.

Trace analysis of 28 antibiotics in plant tissues (root, stem, leaf and seed) by optimized QuEChERS pretreatment with UHPLC-MS/MS detection

Phytoremediation has proven to be an effective in-situ treatment technique for antibiotic contamination. Due to the immature methods of extracting multi-antibiotics in different plant tissues, the antibiotic absorption and transportation mechanism in the phytoremediation process has yet to be resolved. Therefore, an improved Quick, Easy, Cheap, Effective, Rugged and Safe (QuEChERS) pretreatment with ultra-high-performance liquid chromatography tandem mass spectrometry (UHPLC-MS/MS) detection method for 28 antibiotics in different plant tissues (root, stem, leaf and seed) was developed in this study. The optimized method showed satisfactory performance with recoveries for most antibiotics ranging from 70% to 130% (except sulfadoxine with 138 ± 8.84% in root, sulfameter with 68.9 ± 1.87% and sulfadoxine with 141 ± 10.0% in seed). The limits of detection (LODs) of the target compounds in root, stem, leaf and seed were 0.04 ± 0.02 ~ 2.50 ± 1.14 ng/g, 0.05 ± 0.02 ~ 1.78 ± 0.42 ng/g, 0.06 ± 0.01 ~ 2.50 ± 0.14 ng/g and 0.13 ± 0.10 ~ 3.64 ± 0.74 ng/g, respectively. This developed method was successfully applied to the determination of antibiotics in different tissues of hydroponic wetland plants exposed to antibiotics-spiked water for one-month. Sixteen of 28 spiked antibiotics were detected in plant tissue samples. Overall, of these 16 antibiotics, all were detected in root samples (from < LOQ to 1478 ± 353 ng/g), eleven in stem samples (from < LOQ to 425 ± 47.0 ng/g), and nine in leaf samples (from < LOQ to 429 ± 84.5 ng/g). This developed analytical method provided a robust tool for the simultaneous screening and determination of antibiotics in different plant tissues.

Exploring the Milk-Clotting and Proteolytic Activities in Different Tissues of Vallesia glabra: a New Source of Plant Proteolytic Enzymes

Proteolytic enzymes are widely distributed in nature, playing essential roles in important biological functions. Recently, the use of plant proteases at the industrial level has mainly increased in the food industry (e.g., cheesemaking, meat tenderizing, and protein hydrolysate production). Current technological and scientific advances in the detection and characterization of proteolytic enzymes have encouraged the search for new natural sources. Thus, this work aimed to explore the milk-clotting and proteolytic properties of different tissues of Vallesia glabra. Aqueous extracts from the leaves, fruits, and seeds of V. glabra presented different protein profiles, proteolytic activity, and milk-clotting activity. The milk-clotting activity increased with temperature (30-65 °C), but this activity was higher in leaf (0.20 MCU/mL) compared with that in fruit and seed extracts (0.12 and 0.11 MCU/mL, respectively) at 50 °C. Proteolytic activity in the extracts assayed at different pH (2.5-12.0) suggested the presence of different types of active proteases, with maximum activity at acidic conditions (4.0-4.5). Inhibitory studies indicated that major activity in V. glabra extracts is related to cysteine proteases; however, the presence of serine, aspartic, and metalloproteases was also evident. The hydrolytic profile of caseins indicated that V. glabra leaves could be used as a rennet substitute in cheesemaking, representing a new and promising source of proteolytic enzymes.

Fast probing of glucose and fructose in plant tissues via plasmonic affinity sandwich assay with molecularly-imprinted extraction microprobes

Determination of specific target compounds in agriculture food and natural plant products is essential for many purposes; however, it is often challenging due to the complexity of the sample matrices. Herein we present a new approach called plasmonic affinity sandwich assay for the facile and rapid probing of glucose and fructose in plant tissues. The approach mainly relies on molecularly imprinted plasmonic extraction microprobes, which were prepared on gold-coated acupuncture needles via boronate affinity controllable oriented surface imprinting with the target monosaccharide as the template molecules. An extraction microprobe was inserted into plant tissues under investigation, which allowed for the specific extraction of glucose or fructose from the tissues. The glucose or fructose molecules extracted on the microprobe were labeled with boronic acid-functionalized Raman-active silver nanoparticles, and thus affinity sandwich complexes were formed on the microprobes. After excess Raman nanotags were washed away, the microprobe was subjected to Raman detection. Upon being irradiated with a laser beam, surface plasmon on the gold-coated microprobes was generated, which further produced plasmon-enhanced Raman scattering of the silver-based nanotags and thereby provided sensitive detection. Apple fruits, which contain abundant glucose and fructose, were used as a model of plant tissues. The approach exhibited high specificity, good sensitivity (limit of detection, 1 μg mL^-1), and fast speed (the whole procedure required only 20 min). The spatial distribution profiles of glucose and fructose within an apple were investigated by the developed approach.

Grapevine tissues and phenology differentially affect soluble carbohydrates determination by capillary electrophoresis

Soluble carbohydrates distribution depends on plant physiology and, among other important factors, determines fruit yield and quality. In plant biology, the analysis of sugars is useful for many purposes, including metabolic studies. Capillary electrophoresis (CE) proved to be a powerful green separation technique with minimal sample preparation, even in complex plant tissues, that can provide high-resolution efficiency. Matrix effect refers to alterations in the analytical response caused by components of a sample other than the analyte of interest. Thus, the assessment and reduction of the matrix factor is fundamental for metabolic studies in different matrices. The present study evaluated the source and levels of matrix effects in the determination of most abundant sugars in grapevine tissues (mature and young leaves, berries and roots) at two phenological growth stages. Sucrose was the sugar that showed the least matrix effects, while fructose was the most affected analyte. Based on plant tissues, young leaves presented the smaller matrix effects, irrespectively of the phenology. These changes may be attributed to considerable differences at chemical composition of grapevine tissues with plant development. Therefore, matrix effect should be an important concern for plant metabolomics.

Analysis of 3D Cellular Organization of Fixed Plant Tissues Using a User-guided Platform for Image Segmentation

The advent of non-invasive, high-resolution microscopy imaging techniques and computational pipelines for high-throughput image processing has contributed to gain insights in plant organ morphogenesis at the cellular level. Confocal scanning laser microscopy (CSLM) allows the generation of three dimensional images constituted of serial optical sections reporting on stained subcellular structures. Fluorescent labels of cell walls or cell membranes, either chemically or through reporter proteins, are particularly useful for the analyses of tissue organization and cellular shapes in 3D. Image segmentation based on cell boundary signals is used as an input to generate 3D-segments representing cells. These digitalized, 3D objects provide quantitative data on cell shape, size, geometry, position or on (intercellular) intensity signals if additional reporters are used. Herein, we report a detailed, annotated workflow for image segmentation using microscopic data. We used it in the context of a study of tissue patterning during ovule primordium development in Arabidopsis thaliana. Whole carpels are stained for cell boundaries using a modified pseudo-Schiff propidium iodide (mPS-PI) protocol, 3D images are acquired at high resolution by CSLM, segmented and annotated for individual cell types using ImarisCell. This allows for quantitative analyses of cell shape and cell number that are relevant for tissue morphodynamic studies.

iTRAQ-Based Shotgun Proteomics Approach for Relative Protein Quantification

Shotgun proteomics has a key role in quantitative estimation of proteins from biological systems under different conditions, which is crucial in the understanding of their functional roles. Isobaric tagging for relative and absolute quantitation (iTRAQ) mass spectrometry is based on pre-labeling of peptides with mass tags which allows the multiplex analysis of up to eight proteomes simultaneously. We describe here a detailed protocol for sample preparation and iTRAQ 4-plex labeling for relative quantification of multiple samples from human and plant tissues. We also present two strategies for peptide fractionation after the iTRAQ labeling protocol.

Few effects of invasive plants Reynoutria japonica, Rudbeckia laciniata and Solidago gigantea on soil physical and chemical properties

Biological invasions are an important problem of human-induced changes at a global scale. Invasive plants can modify soil nutrient pools and element cycling, creating feedbacks that potentially stabilize current or accelerate further invasion, and prevent re-establishment of native species. The aim of this study was to compare the effects of Reynoutria japonica, Rudbeckia laciniata and Solidago gigantea, invading non-forest areas located within or outside river valleys, on soil physical and chemical parameters, including soil moisture, element concentrations, organic matter content and pH. Additionally, invasion effects on plant species number and total plant cover were assessed. The concentrations of elements in shoots and roots of invasive and native plants were also measured. Split-plot ANOVA revealed that the invasions significantly reduced plant species number, but did not affect most soil physical and chemical properties. The invasions decreased total P concentration and increased N-NO₃ concentration in soil in comparison to native vegetation, though the latter only in the case of R. japonica. The influence of invasion on soil properties did not depend on location (within- or outside valleys). The lack of invasion effects on most soil properties does not necessarily imply the lack of influence of invasive plants, but may suggest that the direction of the changes varies among replicate sites and there are no general patterns of invasion-induced alterations for these parameters. Tissue element concentrations, with the exception of Mg, did not differ between invasive and native plants, and were not related to soil element concentrations.

Arsenic in rice agrosystems (water, soil and rice plants) in Guayas and Los Ríos provinces, Ecuador

Geogenic arsenic (As) can accumulate and reach high concentrations in rice grains, thus representing a potential threat to human health. Ecuador is one of the main consumers of rice in South America. However, there is no information available about the concentrations of As in rice agrosystems, although some water bodies are known to contain high levels of the element. We carried out extensive sampling of water, soil, rice plants and commercial rice (obtained from local markets). Water samples were analysed to determine physico-chemical properties and concentrations of dissolved arsenic. Soil samples were analysed to determine total organic C, texture, total Fe and amorphous Fe oxyhydroxides (Fe_Ox), total arsenic (tAs) and the bioavailable fraction (As_Me). The different plant parts were analysed separately to determine total (tAs), inorganic (iAs) and organic arsenic (oAs). Low concentrations of arsenic were found in samples of water (generally <10μgl^-1) and soil (4.48±3mgkg^-1). The tAs in the rice grains was within the usual range (0.042-0.125mgkg^-1 dry weight, d.w.) and was significantly lower than in leaves (0.123-0.286mgkg^-1 d.w.) and stems (0.091-0.201mgkg^-1 d.w.). The Fe_Ox and tAs and also As_Me in flood water were negatively correlated with tAs in the plants. However, the concentrations of As in stems and leaves were linearly correlated with tAs in the soil and flood water. The relationship between tAs and arsenic in the grain fitted a logarithmic function, as did that between tAs in the grain and the stem. The findings seem to indicate that high concentrations of arsenic in the environment (soil or water) or in the rice stem do not necessarily imply accumulation of the element in the grain. The iAs form was dominant (>80%) in all parts of the rice plants.

The accumulation of elements in plants growing spontaneously on small heaps left by the historical Zn-Pb ore mining

The study evaluated the levels of nine metals, namely Ca, Cd, Fe, K, Mg, Mn, Pb, Tl, and Zn, in soils and tissues of ten plant species growing spontaneously on heaps left by historical mining for Zn-Pb ores. The concentrations of Cd, Pb, Tl, and Zn in heap soils were much higher than in control soils. Plants growing on heaps accumulated excessive amounts of these elements in tissues, on average 1.3-52 mg Cd kg(-1), 9.4-254 mg Pb kg(-1), 0.06-23 mg Tl kg(-1) and 134-1479 mg Zn kg(-1) in comparison to 0.5-1.1 mg Cd kg(-1), 2.1-11 mg Pb kg(-1), 0.02-0.06 mg Tl kg(-1), and 23-124 mg Zn kg(-1) in control plants. The highest concentrations of Cd, Pb, and Zn were found in the roots of Euphorbia cyparissias, Fragaria vesca, and Potentilla arenaria, and Tl in Plantago lanceolata. Many species growing on heaps were enriched in K and Mg, and depleted in Ca, Fe, and Mn. The concentrations of all elements in plant tissues were dependent on species, organ (root vs. shoot), and species-organ interactions. Average concentrations of Ca, K, and Mg were generally higher in shoots than in roots or similar in the two organs, whereas Cd, Fe, Pb, Tl, and Zn were accumulated predominantly in the roots. Our results imply that heaps left by historical mining for Zn-Pb ores may pose a potential threat to the environment and human health.