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Urban greening can reduce concentrations of particulate matter (PM). However, most of the PM is deposited temporarily on foliage and can be removed by precipitation. Due to the unpredictability and randomness of natural rain and the complexity of environmental conditions, the effect of rainfall on PM removal from foliage is usually examined using simulated rain. The aim of this study was to compare the effects of natural and simulated rain on washing off PM deposited on the foliage of seventeen plant species (evergreen/deciduous trees and shrubs, herbaceous plants). Regardless of the PM fraction studied, simulated rain washed off a larger fraction of the PM than natural rain. A novel finding is the differential role played by various plant characteristics in determining the effectiveness of PM wash off under natural and simulated rain conditions, with their influence being more pronounced under natural rainfall. The type of rainfall and PM size fraction influenced the effectiveness of the PM wash-off from different plant groups. Natural rain was more effective at removing PM from evergreen trees, while simulated rainfall was more effective at removing PM from deciduous shrubs and herbaceous plants. The results obtained from this study suggest that simulated rain does not reflect the effects of natural precipitation on the processes removing PM from leaves, and therefore should not be used to explain phenomena that occur in realistic conditions., Competing Interests: Declarations Competing interests The authors declare no competing interests. Plant material statement The experiment (including field studies and harvest of plant material) complied with relevant institutional, national, and international guidelines and legislation., (© 2024. The Author(s).)

Cyanobacteria and chloroplasts of algae and plants harbor specialized thylakoid membranes (TMs) that convert sunlight into chemical energy. These membranes house PSII and I, the vital protein-pigment complexes that drive oxygenic photosynthesis. In the course of their evolution, TMs have diversified in structure. However, the core machinery for photosynthetic electron transport remained largely unchanged, with adaptations occurring primarily in the light-harvesting antenna systems. Whereas TMs in cyanobacteria are relatively simple, they become more complex in algae and plants. The chloroplasts of vascular plants contain intricate networks of stacked grana and unstacked stroma thylakoids. This review provides an in-depth view of TM architectures in phototrophs and the determinants that shape their forms, as well as presenting recent insights into the spatial organization of their biogenesis and maintenance. Its overall goal is to define the underlying principles that have guided the evolution of these bioenergetic membranes., Competing Interests: Conflict of interest statement: None declared., (© The Author(s) 2024. Published by Oxford University Press on behalf of American Society of Plant Biologists. All rights reserved. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.)

Competing Interests: Declaration of interests The authors have no interests to declare.

Capturing complete internal anatomies of plant organs and tissues within their relevant morphological context remains a key challenge in plant science. While plant growth and development are inherently multiscale, conventional light, fluorescence, and electron microscopy platforms are typically limited to imaging of plant microstructure from small flat samples that lack a direct spatial context to, and represent only a small portion of, the relevant plant macrostructures. We demonstrate technical advances with a lab-based X-ray microscope (XRM) that bridge the imaging gap by providing multiscale high-resolution three-dimensional (3D) volumes of intact plant samples from the cell to the whole plant level. Serial imaging of a single sample is shown to provide sub-micron 3D volumes co-registered with lower magnification scans for explicit contextual reference. High-quality 3D volume data from our enhanced methods facilitate sophisticated and effective computational segmentation. Advances in sample preparation make multimodal correlative imaging workflows possible, where a single resin-embedded plant sample is scanned via XRM to generate a 3D cell-level map, and then used to identify and zoom in on sub-cellular regions of interest for high-resolution scanning electron microscopy. In total, we present the methodologies for use of XRM in the multiscale and multimodal analysis of 3D plant features using numerous economically and scientifically important plant systems., (© The Author(s) 2021. Published by Oxford University Press on behalf of American Society of Plant Biologists.)

The study of plant mitochondria started in earnest around 1950 with the first isolations of mitochondria from animal and plant tissues. The first 35 years were spent establishing the basic properties of plant mitochondria and plant respiration using biochemical and physiological approaches. A number of unique properties (compared to mammalian mitochondria) were observed: (i) the ability to oxidize malate, glycine and cytosolic NAD(P)H at high rates; (ii) the partial insensitivity to rotenone, which turned out to be due to the presence of a second NADH dehydrogenase on the inner surface of the inner mitochondrial membrane in addition to the classical Complex I NADH dehydrogenase; and (iii) the partial insensitivity to cyanide, which turned out to be due to an alternative oxidase, which is also located on the inner surface of the inner mitochondrial membrane, in addition to the classical Complex IV, cytochrome oxidase. With the appearance of molecular biology methods around 1985, followed by genomics, further unique properties were discovered: (iv) plant mitochondrial DNA (mtDNA) is 10-600 times larger than the mammalian mtDNA, yet it only contains approximately 50% more genes; (v) plant mtDNA has kept the standard genetic code, and it has a low divergence rate with respect to point mutations, but a high recombinatorial activity; (vi) mitochondrial mRNA maturation includes a uniquely complex set of activities for processing, splicing and editing (at hundreds of sites); (vii) recombination in mtDNA creates novel reading frames that can produce male sterility; and (viii) plant mitochondria have a large proteome with 2000-3000 different proteins containing many unique proteins such as 200-300 pentatricopeptide repeat proteins. We describe the present and fairly detailed picture of the structure and function of plant mitochondria and how the unique properties make their metabolism more flexible allowing them to be involved in many diverse processes in the plant cell, such as photosynthesis, photorespiration, CAM and C4 metabolism, heat production, temperature control, stress resistance mechanisms, programmed cell death and genomic evolution. However, it is still a challenge to understand how the regulation of metabolism and mtDNA expression works at the cellular level and how retrograde signaling from the mitochondria coordinates all those processes., (© 2021 Society for Experimental Biology and John Wiley & Sons Ltd.)

The endoplasmic reticulum (ER) is a ubiquitous organelle that is vital to the life of eukaryotic cells. It synthesizes essential lipids and proteins and initiates the glycosylation of intracellular and surface proteins. As such, the ER is necessary for cell growth and communication with the external environment. The ER is also a highly dynamic organelle, whose structure is continuously remodeled through an interaction with the cytoskeleton and the action of specialized ER shapers. Recent and significant advances in ER studies have brought to light conserved and unique features underlying the structure and function of this organelle in plant cells. In this review, exciting developments in the understanding of the mechanisms for plant ER structural and functional homeostasis, particularly those that underpin ER network architecture and ER degradation, are presented and discussed., (Copyright © 2021 Elsevier Inc. All rights reserved.)

Programmed cell death (PCD) is a process that plays a fundamental role in plant development and responses to biotic and abiotic stresses. Knowledge of plant PCD mechanisms is still very scarce and is incomparable to the large number of studies on PCD mechanisms in animals. Quick and accurate assays, e.g., the TUNEL assay, comet assay, and analysis of caspase-like enzyme activity, enable the differentiation of PCD from necrosis. Two main types of plant PCD, developmental (dPCD) regulated by internal factors, and environmental (ePCD) induced by external stimuli, are distinguished based on the differences in the expression of the conserved PCD-inducing genes. Abiotic stress factors, including heavy metals, induce necrosis or ePCD. Heavy metals induce PCD by triggering oxidative stress via reactive oxygen species (ROS) overproduction. ROS that are mainly produced by mitochondria modulate phytotoxicity mechanisms induced by heavy metals. Complex crosstalk between ROS, hormones (ethylene), nitric oxide (NO), and calcium ions evokes PCD, with proteases with caspase-like activity executing PCD in plant cells exposed to heavy metals. This pathway leads to very similar cytological hallmarks of heavy metal induced PCD to PCD induced by other abiotic factors. The forms, hallmarks, mechanisms, and genetic regulation of plant ePCD induced by abiotic stress are reviewed here in detail, with an emphasis on plant cell culture as a suitable model for PCD studies. The similarities and differences between plant and animal PCD are also discussed.

Chris Hawes had a lively fascination for the immensely complex organisation of the endomembrane system, including the process of endocytosis. This is the method by which eukaryotic cells internalise membrane proteins, lipids, carbohydrates, and cell wall enzymes from the cell surface through membrane bound vesicles. Endocytosis occurs progressively, starting with early membrane deformation, scission, and finally the release of the vesicle into the cytoplasm. Next to secretion, endocytosis allows the cell to control the proteome composition of its inner and outer surface membrane and as such, its communication with the outside world. Whereas endocytosis was initially considered theoretically impossible in plants due to their high turgor pressure, it is now established as essential for plant life. Furthermore, endocytosis remains a highly active field of research, both in yeast, animal, and plant model systems. Over the past three decades, the tools and techniques used to visualise, quantify, and characterise endocytosis have resulted in an increasingly higher spatiotemporal understanding of this process. Here we provide a brief history of plant endocytosis research from the time when Chris Hawes was investigating the process, to the current state-of-the-art in the field. We will end this chapter with a discussion on some promising future developments for plant endocytosis research. LAY DESCRIPTION: Endocytosis is a key process whereby eukaryotic cells can selectively take up membrane proteins, extracellular material and lipids. As this process controls the abundance and protein composition of the plasma membrane, it also controls the communication of the cell with the outside world. Whereas endocytosis was initially considered theoretically impossible in plants due to their high turgor pressure, it is now established as essential for plant life. Today, endocytosis remains a highly active field of research, both in yeast, animal, and plant model systems. Endocytosis was one of the favourite research topics of Chris Hawes, which is why this mini-review is part of the Festschrift issue in his honour. We provide here a brief history of plant endocytosis research from the time when Chris Hawes was investigating the process, to the current state-of-the-art in the field. Over the past three decades, the tools and techniques that were developed to visualise, quantify, and characterise endocytosis have allowed to achieve an increasingly higher spatiotemporal understanding of this process. We end this chapter with a discussion on some promising future developments for plant endocytosis research., (© 2020 Royal Microscopical Society.)

Sphingolipids are fundamental lipids involved in various cellular, developmental and stress-response processes. As such, they orchestrate not only vital molecular mechanisms of living cells but also act in diseases, thus qualifying as potential pharmaceutical targets. Sphingolipids are universal to eukaryotes and are also present in some prokaryotes. Some sphingolipid structures are conserved between animals, plants and fungi, whereas others are found only in plants and fungi. In plants, the structural diversity of sphingolipids, as well as their downstream effectors and molecular and cellular mechanisms of action, are of tremendous interest to both basic and applied researchers, as about half of all small molecules in clinical use originate from plants. Here, we review recent advances towards a better understanding of the biosynthesis of sphingolipids, the diversity in their structures as well as their functional roles in membrane architecture, cellular processes such as membrane trafficking and cell polarity, and cell responses to environmental or developmental signals., (© 2020 Federation of European Biochemical Societies.)

This survey paper contains a brief analysis of publications included in the special issue of the scientific journal Cell Biology International titled "Plant Cytoskeleton Structure, Dynamics and Functions". The manuscripts in this special issue reflect some new aspects of plant cytoskeleton organization, signaling and functioning, and results from different Ukrainian research groups, and focuses on bringing together scientists working across different instrumental scales., (© 2019 International Federation for Cell Biology.)

Although scanning electron microscopy (SEM) can generate high-resolution images of nanosized objects, it requires a high vacuum to do so, which precludes direct observations of living organisms and often produces unwanted structural changes. It has previously been reported that a simple surface modification gives rise to a nanoscale layer, termed the "NanoSuit", which can keep small animals alive under the high vacuum required for field-emission scanning electron microscopy (FE-SEM). We have previously applied this technique to plants, and successfully observed healthy petals in a fully hydrated state using SEM. The flower petals protected with the NanoSuit appeared intact, although we still lack a fundamental understanding of the images of other plants observed using FE-SEM. This report presents and evaluates a rich set of images, acquired using the NanoSuit, for a taxonomically diverse set of plant species. This dataset of images allows the surface features of various plants to be analyzed and thus provides a further complementary morphological profile. Image data can be accessed and viewed through Figshare (https://doi.org/10.6084/m9.figshare.c.4446026.v1)., Competing Interests: The authors have declared that no competing interests exist.

Understanding longterm deep tissue damage caused by UV radiation is imperative for ensuring the health and safety of living organisms that are regularly exposed to radiation sources. While existing UV dosimeters can quantify the cumulative amount of radiation to which an organism is exposed, these sensors cannot reveal the presence and extent of internal tissue damage caused by such exposure. Here we describe a method that uses conducting polymer tattoos to detect UV radiation-induced deep tissue damage in living organisms using bioimpedance analysis (BIA), which allows for noninvasive, real-time measurements of body composition and point-of-care assessment of clinical condition. To establish a performance baseline for this method, we quantify the effects of UVA radiation on live plant leaves. Low-energy UVA waves penetrate further into biological tissue, as compared to UVB, UVC and ionizing radiation, and cause longlasting deep tissue damage that cannot be immediately and readily detected using surface-sensitive techniques, such as photogrammetry and epidermal sensors. We show that single-frequency bioimpedance analysis allows for sensitive, real-time monitoring of UVA damage: as UVA dose increases, the bioimpedance of a plant leaf measured at a frequency of 1 kHz linearly decreases until the extent of radiation damage saturates and the specimen is effectively necrotized. We establish a strong correlation between radiation fluence, internal biological damage and the bioimpedance signal measured using our conducting polymer tattoos, which supports the efficacy of our method as a new type of internal biodosimetry., (Copyright © 2019 Elsevier B.V. All rights reserved.)

Decaying cyanobacterial blooms carry a potential risk for submerged macrophyte and periphyton biofilms in aquatic environments. This study comprehensively studied the responses in growth, oxidative response, detoxification pathway, and ultrastructure characteristics of aquatic plants to Microcystis aeruginosa (M. aeruginosa) exudates and extracts released during the decline phase. Particular emphasis was placed on the variation of extracellular polymeric substances (EPS) and quorum-sensing signaling molecules. The results showed that superoxide dismutase, peroxidase, and glutathione S-transferase were significantly induced as antioxidant response, and the malondialdehyde content increased. Increased content of MC-LR (1.129 μg L -1 ) and NH 4 + -N (1.35 mg L -1 ) were found in the decline phase of M. aeruginosa, which played a vital role in the damage to submerged plants. In addition, a change in the amount of osmiophilic granules and a variation of organelles and membranes was observed. A broad distribution of α-d-glucopyranose polysaccharides was dominant and aggregated into clusters in biofilm EPS in response to exposure to decaying M. aeruginosa. Furthermore, exposure to exudates and extracts changed the abundance and structure of the microbial biofilm community. Increased contents of N-acylated-L-homoserine lactone signal molecule might result in a variation of biofilm EPS production in response to decaying M. aeruginosa. These results expand the understanding of how submerged macrophyte and periphyton biofilms respond to environmental stress caused by exudates and extracts of decaying M. aeruginosa., (Copyright © 2019 Elsevier B.V. All rights reserved.)

Autophagy is a highly regulated bulk degradation process that plays a key role in the maintenance of cellular homeostasis. During autophagy, a double membrane-bound compartment termed the autophagosome is formed through de novo nucleation and assembly of membrane sources to engulf unwanted cytoplasmic components and targets them to the lysosome or vacuole for degradation. Central to this process are the autophagy-related (ATG) proteins, which play a critical role in plant fitness, immunity, and environmental stress response. Over the past few years, cryo-electron microscopy (cryo-EM) and single-particle analysis has matured into a powerful and versatile technique for the structural determination of protein complexes at high resolution and has contributed greatly to our current understanding of the molecular mechanisms underlying autophagosome biogenesis. Here we describe the plant-specific ATG proteins and summarize recent structural and mechanistic studies on the protein machinery involved in autophagy initiation with an emphasis on those by single-particle analysis., Competing Interests: The authors declare no conflict of interest.

Key Message: Short review focussing on the role and targeting of vacuolar substructure in plant immunity and pathogenesis. Plants lack specialized immune cells, therefore each plant cell must defend itself against invading pathogens. A typical plant defense strategy is the hypersensitive response that results in host cell death at the site of infection, a process largely regulated by the vacuole. In plant cells, the vacuole is a vital organelle that plays a central role in numerous fundamental processes, such as development, reproduction, and cellular responses to biotic and abiotic stimuli. It shows divergent membranous structures that are continuously transforming. Recent technical advances in visualization and live-cell imaging have significantly altered our view of the vacuolar structures and their dynamics. Understanding the active nature of the vacuolar structures and the mechanisms of vacuole-mediated defense responses is of great importance in understanding plant-pathogen interactions. In this review, we present an overview of the current knowledge about the vacuole and its internal structures, as well as their role in plant-microbe interactions. There is so far limited information on the modulation of the vacuolar structures by pathogens, but recent research has identified the vacuole as a possible target of microbial interference.

The present work describes the chemical characterization and the phytotoxicity assessment of essential oils (EOs) obtained from spent materials or pruning waste of four plant species: Zingiber officinale Roscoe used in the juicing industry, Pistacia vera L. var. Bronte used in the food industry, discarded material of industrial hemp ( Cannabis sativa L. var. Futura 75 ), and pruning waste from Cupressus sempervirens L. The phytochemical profile of the EOs was evaluated by gas chromatographic flame ionization detection (GC-FID) and GC-MS analyses, which highlighted the presence of several compounds with a wide range of biological activities. Among them, application possibilities in agriculture were evaluated by studying the phytotoxic activity in vitro against germination and initial radical growth of several seeds such as Raphanus sativus L., Lepidium sativum L., Lactuca sativa L., Solanum lycopersicum L., Lolium multiflorum Lam., and Portulaca oleracea L.

The morphology and structure of megaspores assigned to Lagenoisporites magnus from the Toregua Formation, Retama Group, mid-upper Tournaisian of Bolivia were studied. The analysis was performed with light, fluorescence and scanning electron microscopy. Megaspores were laterally compressed and presented a spherical body with a proximal gula, of the hologula type. Gula had verrucae ornamentation and the spore body presented complex processes consisting of a bulbous base and an internally partitioned projection with sharp apex. In addition to this main ornamentation, perforations were present throughout the spore surface. Megaspores showed well marked curvaturae perfectae due to the abrupt transition existing between the gula ornamentation and the spore body processes. These megaspores were assigned to heterosporous arborescent lycopsids of the Lepidocarpaceae family, as in section view, exospore structure presented a three-dimensional network of fused elements. Likewise, due to a similarity found between sporoderm and Isoetes L. structure, it is evident that megaspores structure has remained intact inside the heterosporous lycopsids. Therefore; the L. magnus structure not only would confirm its affinity with the Lycophyta fossils but also with the living ones.

The tracheary system of plant leaves is composed of a cellulose skeleton with diverse hierarchical structures. It is built of polygonally bent helical microfilaments of cellulose-based nanostructures coated by different layers, which provide them high compression resistance, elasticity, and roughness. Their function includes the transport of water and nutrients from the roots to the leaves. Unveiling details about local interactions of tracheary elements with surrounding material, which varies between plants due to adaptation to different environments, is crucial for understanding ascending fluid transport and for tracheary mechanical strength relevant to potential applications. Here we show that plant tracheary microfilaments, collected from Agapanthus africanus and Ornithogalum thyrsoides leaves, have different surface morphologies, revealed by nematic liquid crystal droplets. This results in diverse interactions among microfilaments and with the environment; the differences translate to diverse mechanical properties of entangled microfilaments and their potential applications. The presented study also introduces routes for accurate characterization of plants' microfilaments., Competing Interests: The authors declare no conflict of interest., (Copyright © 2019 the Author(s). Published by PNAS.)

The chloroplast organelle in mesophyll cells of higher plants represents a sunlight-driven metabolic factory that eventually fuels life on our planet. Knowledge of the ultrastructure and the dynamics of this unique organelle is essential to understanding its function in an ever-changing and challenging environment. Recent technological developments promise unprecedented insights into chloroplast architecture and its functionality. The review highlights these new methodical approaches and provides structural models based on recent findings about the plasticity of the thylakoid membrane system in response to different light regimes. Furthermore, the potential role of the lipid droplets plastoglobuli is discussed. It is emphasized that detailed structural insights are necessary on different levels ranging from molecules to entire membrane systems for a holistic understanding of chloroplast function., (© 2019 The Author. New Phytologist © 2019 New Phytologist Trust.)

Unravelling a chain of events in ultrasound-assisted extraction (UAE) of bioactive compounds from plants has to start with a detailed description of destructuration at macroscopic and microscopic scale. The present work aims to study the impacts and interactions of UAE on the extreme complexity and diversity of plants structures. Three plant species were selected for their difference in specialized structures and their spatial distribution of secondary metabolites: bitter orange leaf (C. aurantium L.), blackcurrant leaf (R. nigrum L.), and artichoke leaf (C. scolymus L.). Different microscopic techniques (Cyto-histochemistry, stereomicroscopic analysis, Scanning Electron Microscopy (SEM)) have been used to understand the complexity of plant structures and to highlight ultrasound-induced impacts especially on metabolites storage structures, with a neat comparison with conventional "silent" extraction procedure. The main results indicate that spatial UAE impacts are strongly related to plant structures' properties (morphology, thickness, etc.) and particularly to the nature and the chemical constitution of their storage specialized structures. From a temporal point of view, for all studied leaves, observed mechanisms followed a special order according to structures and their mechanical resistance level to ultrasound (US) treatment. Microscopic mapping of metabolites and structures should be considered as a decision tool during UAE to target intensification process., (Copyright © 2019 Elsevier B.V. All rights reserved.)

The endoplasmic reticulum (ER) is a highly dynamic polygonal membrane network composed of interconnected tubules and sheets (cisternae) that forms the first compartment in the secretory pathway involved in protein translocation, folding, glycosylation, quality control, lipid synthesis, calcium signalling, and metabolon formation. Despite its central role in this plethora of biosynthetic, metabolic and physiological processes, there is little quantitative information on ER structure, morphology or dynamics. Here we describe a software package (AnalyzER) to automatically extract ER tubules and cisternae from multi-dimensional fluorescence images of plant ER. The structure, topology, protein-localisation patterns, and dynamics are automatically quantified using spatial, intensity and graph-theoretic metrics. We validate the method against manually-traced ground-truth networks, and calibrate the sub-resolution width estimates against ER profiles identified in serial block-face SEM images. We apply the approach to quantify the effects on ER morphology of drug treatments, abiotic stress and over-expression of ER tubule-shaping and cisternal-modifying proteins.

In plants, the stacking of part of the photosynthetic thylakoid membrane generates two main subcompartments: the stacked grana core and unstacked stroma lamellae. However, a third distinct domain, the grana margin, has been postulated but its structural and functional identity remains elusive. Here, an optimized thylakoid fragmentation procedure combined with detailed ultrastructural, biochemical, and functional analyses reveals the distinct composition of grana margins. It is enriched with lipids, cytochrome b 6 f complex, and ATPase while depleted in photosystems and light-harvesting complexes. A quantitative method is introduced that is based on Blue Native Polyacrylamide Gel Electrophoresis (BN-PAGE) and dot immunoblotting for quantifying various photosystem II (PSII) assembly forms in different thylakoid subcompartments. The results indicate that the grana margin functions as a degradation and disassembly zone for photodamaged PSII. In contrast, the stacked grana core region contains fully assembled and functional PSII holocomplexes. The stroma lamellae, finally, contain monomeric PSII as well as a significant fraction of dimeric holocomplexes that identify this membrane area as the PSII repair zone. This structural organization and the heterogeneous PSII distribution support the idea that the stacking of thylakoid membranes leads to a division of labor that establishes distinct membrane areas with specific functions., (© 2018 The Authors The Plant Journal © 2018 John Wiley & Sons Ltd.)

Histochemical methods allow for identification and localization of various components within the tissue. Such information on the spatial heterogeneity is not available with biochemical methods. However, there is limitation of the specificity of such detection in context of complex tissue, which is important to consider, and interpretations of the results should regard suitable control treatments if possible. Such methods are valuable extension to specific optical and spectroscopic analytical methods. Here we present a set of selected simple methods of staining and histochemical tests with comments based on our laboratory experience.

This chapter gives examples of basic procedures of quantification of plant structures with use of image analysis, which are commonly employed to describe differences among experimental treatments or phenotypes of plant material. Tasks are demonstrated with the use of ImageJ, a widely used public domain Java image processing program. Principles of sampling design based on systematic uniform random sampling for quantitative studies of anatomical parameters are given to obtain their unbiased estimations and simplified "rules of thumb" are presented. The basic procedures mentioned in the text are: (1) sampling, (2) calibration, (3) manual length measurement, (4) leaf surface area measurement, (5) estimation of particle density demonstrated on an example of stomatal density, and (6) analysis of epidermal cell shape.

Confocal Raman spectroscopy (RS) enables obtaining molecular information from the nondestructive analysis of plant material in situ. It can thereby be a useful method to investigate spatial distribution and heterogeneity of cell-wall polymers. The authors' intention is to present some examples of RS application and its capabilities for investigations of nonwoody plants. In this context, we present protocols for qualitative analysis of main polymers of plant wall and application of RS in a semiquantitative study of the arrangement of selected polymers in the wall in its native state.

In this chapter, conventional techniques are described for the preparation of plant samples at room temperature before examination in the high resolution scanning electron microscopy. Protocols are given on how to collect, to fix, to dehydrate, and to dry plant samples. Subsequently, it is described how to stick them to stubs and cover with a thin conductive layer. These methods are suitable for a wide variety of plant specimens, ranging from microalgae to higher plants.

There are various preparatory techniques for light microscopy permitting access to the inner structure of plant body and its development. Minute objects might be processed as whole-mount preparations, while voluminous ones should be separated into smaller pieces. Here we summarize some of the "classical" techniques to cut more voluminous objects into slices and access their inner structure either for simple anatomical analysis or for further processing (e.g., histochemistry, immunohistochemistry, in situ hybridization, enzyme histochemistry).

Knowledge about the spatiotemporal distribution patterns of proteins and other molecules of the cell is essential for understanding their function. A widely used technique is immunolabeling which uses specific antibodies to reveal the distribution of molecular components at various structural levels. Immunofluorescence gives an overview about the distribution of molecules at the level of the fluorescence or confocal laser scanning microscope. Electron microscopy offers the highest resolution of morphological techniques and is thus an indispensable tool for the analysis of molecule distribution patterns at the subcellular level. In this chapter we describe selected routine methods for immunofluorescence and for labeling ultrathin sections of resin-embedded material with antibodies conjugated to colloidal gold, including protocols for chemical fixation, embedding, and sectioning.

Optical tweezers allow for noninvasive manipulation of subcellular compartments to study their physical interactions and attachments. By measuring (delay of) displacements, (semi)quantitative force measurements within a living cell can be performed. In this chapter, we provide practical tips for setting up such experiments paying special attention to the technical considerations for integrating optical tweezers into a confocal microscope. Next, we describe experimental approaches we have taken to trap intracellular structures in plant cells.

Fluorescence is a versatile property of many molecules called fluorophores. In plant cell walls, fluorescence is generally attributed to aromatic molecules such as lignin. In contrary to fluorescence intensity, fluorescence lifetime is independent from fluorophore concentration. So mapping fluorescence lifetime of plant cell walls represents a complementary approach to acquire chemical and structural information of cell wall components and interactions.

Contents Summary 982 I. Introduction 982 II. The portraits of our ancestors: a gallery of ideas from more than 100 years of mycorrhizal research 983 III. Mycorrhizal fungi in the 'omics' era: first puzzle, how to name mycorrhizal fungi 985 IV. Signalling: a central question of our time? 987 V. The colonization process: how cellular studies predicted future 'omics' data 989 VI. The genetics underlying colonization events 991 VII. Concluding thoughts: chance and needs in mycorrhizal symbioses 992 Acknowledgements 992 References 992 SUMMARY: Our knowledge of mycorrhizas dates back to at least 150 years ago, when the plant pathologists A. B. Frank and G. Gibelli described the surprisingly morphology of forest tree roots surrounded by a fungal mantle. Compared with this history, our molecular study of mycorrhizas remains a young science. To trace the history of mycorrhizal research, from its roots in the distant past, to the present and the future, this review outlines a few topics that were already central in the 19 th century and were seminal in revealing the biological meaning of mycorrhizal associations. These include investigations of nutrient exchange between partners, plant responses to mycorrhizal fungi, and the identity and evolution of mycorrhizal symbionts as just a few examples of how the most recent molecular studies of mycorrhizal biology sprouted from the roots of past research. In addition to clarifying the ecological role of mycorrhizas, some of the recent results have changed the perception of the relevance of mycorrhizas in the scientific community, and in the whole of society. Looking to past knowledge while foreseeing strategies for the next steps can help us catch a glimpse of the future of mycorrhizal research., (© 2018 The Author. New Phytologist © 2018 New Phytologist Trust.)

Contents Summary 996 I. Introduction 996 II. An ancient, and diverse, symbiosis 998 III. Structural diversity in ancient plant-fungal partnerships 1000 IV. Mycorrhizal unity in host plant nutrition 1002 V. Plant-to-fungus carbon transfer 1003 VI. From individuals to networks 1003 VII. Diverse responses of mycorrhizal functioning to dynamic environments 1006 VIII. Summary of future research direction 1007 Acknowledgements 1006 References 1006 SUMMARY: Mycorrhizal symbiosis is an ancient and widespread mutualism between plants and fungi that facilitated plant terrestrialisation > 500 million years ago, with key roles in ecosystem functioning at multiple scales. Central to the symbiosis is the bidirectional exchange of plant-fixed carbon for fungal-acquired nutrients. Within this unifying role of mycorrhizas, considerable diversity in structure and function reflects the diversity of the partners involved. Early diverging plants form mutualisms not only with arbuscular mycorrhizal Glomeromycotina fungi, but also with poorly characterised Mucoromycotina, which may also colonise the roots of 'higher' plants as fine root endophytes. Functional diversity in these symbioses depends on both fungal and plant life histories and is influenced by the environment. Recent studies have highlighted the roles of lipids/fatty acids in plant-to-fungus carbon transport and potential contributions of Glomeromycotina fungi to plant nitrogen nutrition. Together with emerging appreciation of mycorrhizal networks as multi-species resource-sharing systems, these insights are broadening our views on mycorrhizas and their roles in nutrient cycling. It is crucial that the diverse array of biotic and abiotic factors that together shape the dynamics of carbon-for-nutrient exchange between plants and fungi are integrated, in addition to embracing the unfolding and potentially key role of Mucoromycotina fungi in these processes., (© 2018 The Authors. New Phytologist © 2018 New Phytologist Trust.)

Understanding the distribution of elements within plant tissues is important across a range of fields in plant science. In this review, we examine synchrotron-based x-ray fluorescence microscopy (XFM) as an elemental imaging technique in plant sciences, considering both its historical and current uses as well as discussing emerging approaches. XFM offers several unique capabilities of interest to plant scientists, including in vivo analyses at room temperature and pressure, good detection limits (approximately 1-100 mg kg -1 ), and excellent resolution (down to 50 nm). This has permitted its use in a range of studies, including for functional characterization in molecular biology, examining the distribution of nutrients in food products, understanding the movement of foliar fertilizers, investigating the behavior of engineered nanoparticles, elucidating the toxic effects of metal(loid)s in agronomic plant species, and studying the unique properties of hyperaccumulating plants. We anticipate that continuing technological advances at XFM beamlines also will provide new opportunities moving into the future, such as for high-throughput screening in molecular biology, the use of exotic metal tags for protein localization, and enabling time-resolved, in vivo analyses of living plants. By examining current and potential future applications, we hope to encourage further XFM studies in plant sciences by highlighting the versatility of this approach., (© 2018 American Society of Plant Biologists. All rights reserved.)

Premise of the Study: The apical meristem generates indeterminate apical growth of the stem and root of vascular plants. Our previous examination showed that shoot apical meristems (SAMs) can be classified into two types based on plasmodesmatal networks (PNs), which are important elements in symplasmic signaling pathways within the apical meristem. Here, we examined the PNs of root apical meristems (RAMs) in comparison with those of SAMs., Methods: Root apical meristems of 18 families and 22 species of lycophytes and euphyllophytes were analyzed. Plasmodesmata (PD) in cell walls in median longitudinal sections of RAMs were enumerated using transmission electron micrographs, and the PD density per 1 μm 2 of each cell wall was calculated., Key Results: Root apical meristems with prominent apical cells of monilophytes (euphyllophytes) and Selaginellaceae (lycophytes) had high PD densities, while RAMs with plural initial cells of gymnosperms and angiosperms (euphyllophytes), and of Lycopodiaceae and Isoetaceae (lycophytes) had low PD densities. This correlation between structures of apical meristems and PD densities is identical to that in SAMs already described., Conclusions: Irrespective of their diversified structures, the RAMs of vascular plants can be classified into two types with respect to PNs: the fern (monilophyte) type, which has a lineage-specific PN with only primary PD, and the seed-plant type, which has an interspecific PN with secondary PD in addition to primary PD. PNs may have played a key role in the evolution of apical meristems in vascular plants., (© 2018 Botanical Society of America.)

A detailed study of the external and internal surfaces of the cuticle of Orestovia and Schuguria using scanning electron microscopy and confocal laser microscopy has shown that the structures formerly interpreted as stomata or reproductive organs are most likely to be gland cells producing mucilage. Each structure represents a single large cell with a complex aperture on the external wall. In addition, a reproductive organ similar to multilocular sporangia known in brown algae of the order Ectocarpales has been found in attachment to a compression fossil of Orestovia. These data suggest similarity of the genera studied with brown algae.

Silymarin, an extract from milk thistle ( Silybum marianum ) fruits, is consumed in various food supplements. The metabolism of silymarin flavonolignans in mammals is complex, the exact structure of their metabolites still remains partly unclear and standards are not commercially available. This work is focused on the preparation of sulfated metabolites of silymarin flavonolignans. Sulfated flavonolignans were prepared using aryl sulfotransferase from Desulfitobacterium hafniense and p -nitrophenyl sulfate as a sulfate donor and characterized by high-resolution mass spectrometry (HRMS) and nuclear magnetic resonance (NMR). Their 1,1-diphenyl-2-picrylhydrazyl (DPPH), 2,2'-azinobis-(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS), and N , N -dimethyl- p -phenylenediamine (DMPD) radical scavenging; ferric (FRAP) and Folin⁻Ciocalteu reagent (FCR) reducing activity; anti-lipoperoxidant potential; and effect on the nuclear erythroid 2-related factor 2 (Nrf2) signaling pathway were examined. Pure silybin A 20- O -sulfate, silybin B 20- O -sulfate, 2,3-dehydrosilybin-20- O -sulfate, 2,3-dehydrosilybin-7,20-di- O -sulfate, silychristin-19- O -sulfate, 2,3-dehydrosilychristin-19- O -sulfate, and silydianin-19- O -sulfate were prepared and fully characterized. Sulfated 2,3-dehydroderivatives were more active in FCR and FRAP assays than the parent compounds, and remaining sulfates were less active chemoprotectants. The sulfated flavonolignans obtained can be now used as authentic standards for in vivo metabolic experiments and for further research on their biological activity.

Nature has long offered human beings with useful materials. Herein, plant materials including flowers and leaves have been directly used as the dielectric material in flexible capacitive electronic skin (e-skin), which simply consists of a dried flower petal or leaf sandwiched by two flexible electrodes. The plant material is a 3D cell wall network which plays like a compressible metamaterial that elastically collapses upon pressing plus some specific surface structures, and thus the device can sensitively respond to pressure. The device works over a broad-pressure range from 0.6 Pa to 115 kPa with a maximum sensitivity of 1.54 kPa -1 , and shows high stability over 5000 cyclic pressings or bends. The natural-material-based e-skin has been applied in touch sensing, motion monitoring, gas flow detection, and the spatial distribution of pressure. As the foam-like structure is ubiquitous in plants, a general strategy for a green, cost-effective, and scalable approach to make flexible e-skins is offered here., (© 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

The complex form of higher plants requires continuous, balanced transport of nutrients in the phloem. The initial step of transferring sugars, amino acids, and other materials from photosynthetic cells to the conducting sieve tubes is known as phloem loading. Three phloem loading mechanisms have been described. The first involves release of sucrose into the apoplast and subsequent retrieval by the phloem. The initial release step in this process is now known to be mediated by a new class of transporters, the SWEET proteins. In the other two loading mechanisms, polymer trapping and diffusion, sucrose passes into the phloem through cytoplasmic channels, the plasmodesmata. Recent models have shed additional light on these mechanisms and their ability to sustain the growth of even the tallest trees., (Copyright © 2018 Elsevier Ltd. All rights reserved.)

Endosymbiotically originated chloroplast DNA (cpDNA) encodes part of the genetic information needed to fulfill chloroplast function, including fundamental processes such as photosynthesis. In the last two decades, advances in genome analysis led to the identification of a considerable number of cpDNA sequences from various species. While these data provided the consensus features of cpDNA organization and chloroplast evolution in plants, how cpDNA is maintained through development and is inherited remains to be fully understood. In particular, the fact that cpDNA exists as multiple copies despite its limited genetic capacity raises the important question of how copy number is maintained or whether cpDNA is subjected to quantitative fluctuation or even developmental degradation. For example, cpDNA is abundant in leaves, where it forms punctate structures called nucleoids, which seemingly alter their morphologies and numbers depending on the developmental status of the chloroplast. In this review, we summarize our current understanding of 'cpDNA dynamics', focusing on the changes in DNA abundance. A special focus is given to the cpDNA degradation mechanism, which appears to be mediated by Defective in Pollen organelle DNA degradation 1 (DPD1), a recently discovered organelle exonuclease. The physiological significance of cpDNA degradation in flowering plants is also discussed.

Lignocellulosic plant biomass is the most abundant carbon source in the planet, which makes it a potential substrate for biorefinery. It consists of polysaccharides and other molecules with applications in pharmaceutical, food and feed, cosmetics, paper and textile industries. The exploitation of these resources requires the hydrolysis of the plant cell wall, which is a complex process. Aiming to discover novel fungal natural isolates with lignocellulolytic capacities, a screening for feruloyl esterase activity was performed in samples taken from different metal surfaces. An extracellular enzyme extract from the most promising candidate, the natural isolate Alternaria alternata PDA1, was analyzed. The feruloyl esterase activity of the enzyme extract was characterized, determining the pH and temperature optima (pH 5.0 and 55-60 °C, respectively), thermal stability and kinetic parameters, among others. Proteomic analyses derived from two-dimensional gels allowed the identification and classification of 97 protein spots from the extracellular proteome. Most of the identified proteins belonged to the carbohydrates metabolism group, particularly plant cell wall degradation. Enzymatic activities of the identified proteins (β-glucosidase, cellobiohydrolase, endoglucanase, β-xylosidase and xylanase) of the extract were also measured. These findings confirm A. alternata PDA1 as a promising lignocellulolytic enzyme producer., Significance: Although plant biomass is an abundant material that can be potentially utilized by several industries, the effective hydrolysis of the recalcitrant plant cell wall is not a straightforward process. As this hydrolysis occurs in nature relying almost solely on microbial enzymatic systems, it is reasonable to infer that further studies on lignocellulolytic enzymes will discover new sustainable industrial solutions. The results included in this paper provide a promising fungal candidate for biotechnological processes to obtain added value from plant byproducts and analogous substrates. Moreover, the proteomic analysis of the secretome of a natural isolate of Alternaria sp. grown in the presence of one of the most used vegetal substrates on the biofuels industry (sugar beet pulp) sheds light on the extracellular enzymatic machinery of this fungal plant pathogen, and can be potentially applied to developing new industrial enzymatic tools. This work is, to our knowledge, the first to analyze in depth the secreted enzyme extract of the plant pathogen Alternaria when grown on a lignocellulosic substrate, identifying its proteins by means of MALDI-TOF/TOF mass spectrometry and characterizing its feruloyl esterase, cellulase and xylanolytic activities., (Copyright © 2018 Elsevier B.V. All rights reserved.)

Oxygenic phototrophs typically utilize visible light (400-700 nm) to drive photosynthesis. However, a large fraction of the energy in sunlight is contained in the far-red region, which encompasses light beyond 700 nm. In nature, certain niche environments contain high levels of this far-red light due to filtering by other phototrophs, and in these environments, organisms with photosynthetic antenna systems adapted to absorbing far-red light are able to thrive. We used selective far-red light conditions to isolate such organisms in environmental samples. One cultured organism, the Eustigmatophyte alga Forest Park Isolate 5 (FP5), is able to absorb far-red light using a chlorophyll (Chl) a-containing antenna complex, and is able to grow under solely far-red light. Here we characterize the antenna system from this organism, which is able to shift the absorption of Chl a to >705 nm.

Cytoplasmic lipid droplets (LDs) of neutral lipids (triacylglycerols [TAGs], sterylesters, etc.) are reserves of high-energy metabolites and other constituents for future needs. They are present in diverse cells of eukaryotes and prokaryotes. An LD has a core of neutral lipids enclosed with a monolayer of phospholipids and proteins, which play structural and/or metabolic roles. During the past 3 decades, studies of LDs in diverse organisms have blossomed after they were found to be involved in prevalent human diseases and industrial uses. LDs in plant seeds were studied before those in mammals and microbes, and the latter studies have since moved forward. Plant LDs carry a hallmark protein called oleosin, which has a long hydrophobic hairpin penetrating the TAG core and stabilizing the LD. The oleosin gene first appeared in green algae and has evolved in enhancing promoter strength, tandem repeats, and/or expression specificity, leading to the appearance of new LD organelles, such as tapetosomes in Brassicaceae. The synthesis of LDs occurs with TAG-synthesizing enzymes on the endoplasmic reticulum (ER), and nascent TAGs are sequestered in the acyl moiety region between the bilayers of phospholipids, which results in ER-LD swelling. Oleosin is synthesized on the cytosol side of the ER and extracts the LD from the ER-LD to cytosol. This extraction of LD to the cytosol is controlled solely by the innate properties of oleosin, and modified oleosin can redirect the LD to the ER lumen and then vacuoles. The breakdown of LDs requires lipase associating with core retromer and binding to peroxisomes, which then send the enzyme to LDs via tubular extensions. Two groups of LD-associated proteins, caleosin/dioxygenase/steroleosin and LD/oil body-associated proteins, participate in cellular stress defenses via enzymic activities and binding, respectively. The surface of LDs in all plant cells may be an inert refuge for these and other proteins, which exert functions on diverse cell components. Oleosin-LDs have been explored for commercial applications; successes in their uses will rely on overcoming conceptual and technical difficulties., (© 2018 American Society of Plant Biologists. All Rights Reserved.)

In situ nucleus and chromatin analyses rely on microscopy imaging that benefits from versatile, efficient fluorescent probes and proteins for static or live imaging. Yet the broad choice in imaging instruments offered to the user poses orientation problems. Which imaging instrument should be used for which purpose? What are the main caveats and what are the considerations to best exploit each instrument's ability to obtain informative and high-quality images? How to infer quantitative information on chromatin or nuclear organization from microscopy images? In this review, we present an overview of common, fluorescence-based microscopy systems and discuss recently developed super-resolution microscopy systems, which are able to bridge the resolution gap between common fluorescence microscopy and electron microscopy. We briefly present their basic principles and discuss their possible applications in the field, while providing experience-based recommendations to guide the user toward best-possible imaging. In addition to raw data acquisition methods, we discuss commercial and noncommercial processing tools required for optimal image presentation and signal evaluation in two and three dimensions.

Cryopreservation encompasses several interconnect disciplines including physiology and cryophysics. This chapter reviews the current techniques for cryopreservation of plant genetic resources (PGRs). Vitrification is an effective ice crystal avoidance mechanism for hydrated cells and tissues. With any cryopreservation method, whole or partial parts of specimens which are sufficiently dehydrated can be vitrified by rapid cooling in liquid nitrogen (LN). Techniques discussed are the vitrification protocol, encapsulation-vitrification protocol, droplet vitrification protocol (DV), vitrification protocol using cryo-plates (V cryo-plate), and air dehydration protocol using cryo-plates (D cryo-plate). In these DV, V, and D cryo-plate protocols, specimens to be cryopreserved are immersed directly into LN on aluminum foil strips or cryo-plates; removal from LN to rewarming solution results in a high level of plant regrowth with ultrarapid cooling and warming. The protocols were applied to a wide array of plant species including wild and multi-ploid species, although fine tuning of the protocols was required for successful application to specific plant species and lines. These three protocols efficiently complement each other and appear highly promising to facilitate large-scale cryobanking of PGRs in genebanks. Cryo-scanning electron microscopy makes it possible to examine the cellular and water behavior in plant tissues when immersed in LN. It has been verified that tissues cryopreserved by the process of vitrification and the cryo-plate protocols are cryopreservation methods for reliable long-term preservation of PGRs.

Xyloglucan has been hypothesized to bind extensively to cellulose microfibril surfaces and to tether microfibrils into a load-bearing network, thereby playing a central role in wall mechanics and growth, but this view is challenged by newer results. Here we combined high-resolution imaging by field emission scanning electron microscopy (FESEM) with nanogold affinity tags and selective endoglucanase treatments to assess the spatial location and conformation of xyloglucan in onion cell walls. FESEM imaging of xyloglucanase-digested cell walls revealed an altered microfibril organization but did not yield clear evidence of xyloglucan conformations. Backscattered electron detection provided excellent detection of nanogold affinity tags in the context of wall fibrillar organization. Labelling with xyloglucan-specific CBM76 conjugated with nanogold showed that xyloglucans were associated with fibril surfaces in both extended and coiled conformations, but tethered configurations were not observed. Labelling with nanogold-conjugated CBM3, which binds the hydrophobic surface of crystalline cellulose, was infrequent until the wall was predigested with xyloglucanase, whereupon microfibril labelling was extensive. When tamarind xyloglucan was allowed to bind to xyloglucan-depleted onion walls, CBM76 labelling gave positive evidence for xyloglucans in both extended and coiled conformations, yet xyloglucan chains were not directly visible by FESEM. These results indicate that an appreciable, but still small, surface of cellulose microfibrils in the onion wall is tightly bound with extended xyloglucan chains and that some of the xyloglucan has a coiled conformation., (© 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd.)

The investigation of autophagy particularly when observed during programmed cell death (PCD) is strongly based on the morphological features recorded with transmission electron microscope (TEM). Here we describe methods to induce and to inhibit autophagy in plants. Also some tips for obtaining better preservation of biological membranes, crucial for the investigation of autophagy, are provided together with information about plant autophagic mutants, use of antibodies and methods for 3D reconstruction of large membrane-bound objects that are commonly formed during autophagic processes leading to PCD in plants.

In vitro plant regeneration systems have turned into invaluable tools to plant biotechnology. Despite being poorly understood, the molecular mechanisms underlying the control of both morphogenetic pathways, de novo organogenesis and somatic embryogenesis, have been supported by recent findings involving proteome-, metabolome-, and transcriptome-based profiles. Notwithstanding, the integration of molecular data with structural aspects has been an important strategy of study attempting to elucidate the basis of the cell competence acquisition to further follow commitment and determination to specific a particular in vitro regeneration pathway. In that sense, morpho-histological tools have allowed to recognize cellular markers and patterns of gene expression at cellular level and this way have collaborated in the identification of the cell types with high regenerative capacity. This chapter ties together up those fundamental and important microscopy techniques that help to elucidate that regeneration occurs, most of the time, from epidermis or subepidermal cells and from the procambial cells (pericycle and vascular parenchyma). Important findings are discussed toward ultrastructural differences observed in the nuclear organization among pluripotent and totipotent cells, implying that regeneration occurs from two cellular mechanisms based on cellular reprogramming or reactivation.