It is probably fair to say that nature's design of cell walls is the product of a long evolutionary process, that helped in most effective species propagation, and as such a compromise between the different demands on cell wall function, including flexibility for remodelling. From the viewpoint of human use of plant biomass, cell wall design is not optimized. It seems likely that cell wall properties could be altered within limits to be better adaptated to environmental challenges posed by agriculture.
Hence, re-engineering of cell walls may be of enormous value in order for the plants to serve specific functions, such as becoming an ideal feedstock for lignocellulose-based biofuel production. Cell wall properties vary not only among different taxa of the plant kingdom, but also within the same plant and throughout the individual plant's life cycle. Variations in cell wall composition have been detected among different organs, different cell types within one tissue, and even within a single cell Knox, For example, the quantity and distribution of certain cell wall components in the triangular cell junctions between three cells differ significantly from the flat portions of the walls where two cells are adjoined.
Different layers of the cell wall, namely primary cell wall and secondary cell wall layers S1, S2, and S3 differ in composition and spatial 3D arrangement of wall components.
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Such diversity in cell walls clearly suggests that instead of a single model of cell walls, there will be a range of representative cell wall models that need to be determined. Plants have limited resources that they must use towards their growth, development, storage, defence, and reproduction, hence trade-offs became essential Herms and Mattson, ; Graham et al. It is therefore not a surprise that the allocation of resources for these various purposes depends on the status of the various tissues and the stage of life, and is reflected in the variability among cell walls within single individual plants.
The growth period requires plenty of resources and high flexibility to accommodate expansion. Hence, young plants have only primary cell walls, which are dynamic in nature. In contrast, secondary cell walls are less flexible and therefore their presence in young plants would probably hinder growth. At maturity, maintaining the physiological water and nutrient transport system and strengthening of the defence system inevitably becomes a higher priority for secondary cell walls.
Hence, secondary walls are formed in cells that have stopped growing in the mature parts of the plant. Plant growth can continue in the form of a vulnerable new branch if enough resources become available. Cells of such younger growing parts of the plant usually have only primary cell walls. So far we have depicted cell walls as being rigid structures that once laid down resist any modification. This picture is not entirely true.
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In fact, cell walls, in particular the primary cell walls, are highly dynamic in nature and are constantly being remodelled Knox, ; Pauly and Keegstra, Remodelling of cell walls occurs during cell growth, organ development, fruit ripening, and abscission of plant parts such as leaf, flower parts, and fruits at maturity Knox, ; Roberts et al.
Cell walls are modified by specific enzymes such as cellulases, hemicellulases, pectinases, and peroxidases. Small differences in cell wall ultrastructure and chemistry at different stages of the plant life cycle can have profound effects on the variety of functions that the cell walls perform. Cell wall ultrastructure has also been observed to change in response to different environmental conditions, such as during leaf abscission in winter Roberts et al. Changes in cell wall composition have been detected in response to chemical exposure Le Van et al.
Variations in cell wall composition and organization across plant species and within the same plant somewhat complicate the studies of cell walls, requiring statistical sampling and approaches that can detect the changes in composition and 3D architecture. Not too surprisingly, our knowledge about cell walls is still far from complete. It is anticipated that comprehensive imaging of a variety of cell walls, followed by careful comparisons of their similarities and differences, will allow the existing knowledge gaps to be filled with respect to cell wall design.
While plants have become increasingly successful in protecting themselves throughout evolution, the microbial world co-evolved with the plants and found novel ways to threaten the integrity of plant cell walls Walton, ; Warren, ; Cantu et al. For example, pathogens have evolved an array of cell wall-degrading enzymes including cellulases, hemicellulases, pectinases, and lignin-modifying enzymes LMEs.
The different enzymes degrade their respective cell wall components with a wide range of efficiency. While pectin and xylan can be degraded relatively easily, lignins prove to be the most resistant component of the cell wall Walton, , probably due to the complex organization of the lignin units. The degradability of the wall depends on the total concentration of lignin monomers in the cell wall, its hydrophobicity, as well as the exact nature of the covalent bonds of the cross-links Grabber, Occurrences of LMEs are less common than those of the polysaccharide-degrading enzymes. LMEs have been reported only in certain fungi and in some insects.
Due to the aromatic nature of the polymer, lignin degradation requires a lot of energy and hence is not a preferred food source. Even the organisms that can produce LMEs only degrade lignin under unfavourable conditions and at a very slow rate Ros Barcelo et al. Lignins are typically found to be most concentrated in cells located close to the dermal layers of a stem. Within individual cells, lignins are usually confined to the secondary walls. Such strategic placement towards the outer portion of plants probably evolved to retain protection while allowing the inner portion of the plants to undergo remodelling and continue their cellular and physiological functions Grabber, Cell wall degradation by depolymerizing enzymes results in the formation of so-called active oligosaccharins, which are thought to play important roles in signalling and activate the defence mechanisms of the cell Darvill et al.
As the cell wall structure became ever more sophisticated, pathogens and herbivores evolved their own strategies to breach the protective barriers. A number of animals feed exclusively on grass or wood, with the best studied examples being cows and termites, respectively.
Animals themselves do not contain the enzymatic make-up for cell wall degradation, but instead entered symbiotic relationships with microbial communities specialized in anaerobic lignocellulose breakdown Flint et al. The host may even provide the community with reduced nitrogen and other essential minerals, which are low in the plant biomass. These communities can be of remarkable complexity. Only high-resolution spatial mapping of the individual species in the termite gut and the cow rumen communities can reveal their interactions and, together with the knowledge of their respective physiological repertoire, will illustrate their interdependencies.
The herbivore animal provides a mechanical and chemical pre-processing of the biomass that allows efficient microbial degradation, and provides a protected stable environment. One could argue that human evolution would not have been possible were it not for plants. Throughout the history of human civilization, plants have served as a source of energy firewood , building material, and medicine.
More recently, our civilization has come to recognize that energy production through the burning of fossil plants, such as coal or oil, is no longer sustainable and has led to climate change. Global warming, limited supplies of fossil fuels, and fluctuating fuel prices have resulted in a revived interest in renewable energies, with a new focus on various transportation fuels derived from lignocellulosic plant biomass Ragauskas et al. Ethanol as a transportation fuel is currently being produced in modest quantities from the readily extractable sugars of corn and sugar cane, but such efforts are not scalable and sustainable to meet the increasing need for carbon-neutral biofuels.
Plant cell walls represent one of the most abundant renewable resources on this planet. However, due to their recalcitrance and the low yields of fermentable sugars, biomass is currently not a viable alternative for biofuel production. Various physical and chemical pre-treatment steps are currently being explored to allow for subsequent enzymatic cell wall degradation, but such pre-treatment approaches often lead to undesired by-products that are toxic to microbial fermentation. One possible solution is the re-design of plant cell walls, e.
Therefore, it seems crucial to understand better the design principles that guide the many functions of cell walls Himmel et al. Both the increase in wall biomass by means of genetic modification, and rendering plants more susceptible to degradation without compromising the life cycle of a plant require a thorough integrative biophysical, developmental, and genetic knowledge of the composition as well as a molecular-resolution 3D structure of the plant cell wall Somerville et al. Armed with such detailed knowledge the large quantities of lignocellulosic waste created through forestry, agricultural activities, and industrial processes, such as breweries, paper-pulp, textile, and timber industries, could be turned into biodegradable biomass Levine, With appropriate technology, such biomass could be converted into valuable products such as biofuels, chemical precursors, and cheap energy sources for fermentation, as well as improved animal feeds and human nutrients Howard et al.
Fibres, which are traditionally used in the textile industry, have become of increasing interest in the development of agro-materials for the automobile and building industries. However, there is still a lack of a comprehensive understanding of the link between 3D structures and physicochemical characteristics of the fibres. Likewise, the increasing demands for paper further shows the need to understand the 3D structure of non-woody sources Khalil et al. Moreover, since fungal pathogens, and bacterial and virus infections are known to cause devastating annual crop losses worldwide, detailed knowledge about cell wall lignin and polysaccharide organization might help geneticists engineer less vulnerable cell walls Dey and Harborne, While attempts have been made to characterize the modification of the content of the cell wall during ripening of fruits, including the intricate genetically programmed biochemical pathways involved in this process Giovannoni, , there is still a lack of a detailed understanding about cell wall degradation in the process of fruit softening.
Detailed knowledge of the underlying enzymatic and regulatory mechanisms would greatly benefit the storage and transportation of fruits Tucker and Seymour, and would have significant commercial impact, as fruit ripening dictates the harvesting time and might allow subsequent handling without damage. Cell walls have been a prominent area of research for a long time, but most of the research has been concentrated on either biochemical analysis or genetic studies. Biochemical studies have been invaluable to provide detailed information about the chemical nature of the different types of cell wall components, typically by employing organic chemical or enzymatic reactions to break down the complex biopolymers, followed by separation and identification of the breakdown products, e.
While biochemical analysis can yield the composition as well as the stoichiometry of cell wall component monomers and oligomers, analysis of the intact polymers is complicated by polymer insolubility, hence rendering fractionation, purification, and chemical analysis more complicated. Biochemical analyses have been complemented by genetic analyses, which have identified a number of genes associated with cell wall synthesis and function. Because of the vast numbers of proteins involved in cell wall formation, genetic dissection of the regulation and breakdown pathways is daunting and on its own unlikely to succeed.
What is still lacking is a detailed understanding of how the identified gene products utilize the chemical components and arrange them spatially in order to achieve such multifunctional cell walls, in part due to limited knowledge about temporal and spatial patterns of protein and carbohydrate subcellular localization. Nevertheless, a consensus model of plant cell walls has emerged. Cellulose fibres act not unlike steel girders stabilizing a skyscraper's structure Somerville et al. Tracks of parallel cellulose microfibrils are laid down in a highly coordinated manner, presumably due to the interaction of the CeS with the underlying cortical microtubule network Paredez et al.
Though the causative relationship between microtubule organization and microfibril orientation is still hotly debated, many researchers hypothesize that a dynamic alteration of the microtubule network is responsible for a change in the directionality of the nascent microfibril scaffold Somerville, Recent data suggest that the microfibril's crystalline core is surrounded by a paracrystalline layer of cellulose, followed by hemicellulose, a ramified polymer composed of pentoses and hexoses Himmel et al.
In secondary cell walls, hemicellulose is thought also to form covalent links with lignin. Lignins are rigid aromatic polymers, whose 3D structure and organization is poorly defined due to the radical chemistry nature of lignin polymer formation. Both the highly organized crystalline structure of cellulose and its tight association with hemicellulose and lignin are physical, steric, and biochemical obstacles for cell wall breakdown.
The current model of cell walls represents an educated guess on the cell wall organization that presumably is not too far off from reality. However, if one wants to redesign cell walls for biofuel or agricultural applications, one requires models that are based on direct experimental data with respect to exact chemical composition and macromolecular 3D structural organization.
While invaluable, and clearly the foundation on which future cell wall models will stand, biochemical and genetic analyses alone do not suffice to describe the vast diversity in cell wall organization expected to be found to differ significantly between plant species, within the same plant, organ, tissue, cell, and even neighbouring portions of the same cell wall.
To gain direct experimental insight into cell wall composition and 3D architecture and to deal with the heterogeneity of cell wall designs, biochemical and genetic analyses need to be complemented with advanced microscopic imaging. To date, a small but important number of conventional electron microscopy EM and spectroscopy studies on cell walls have helped answer some of the coarse architectural questions, but still a huge knowledge gap persists with respect to the exact molecular organization of cell walls and its regulation Somerville et al.
To date, most studies have focused on the dimensions of cellulose microfibrils, whereas little is known about the structural relationship of cellulose, hemicellulose, and lignin within the different layers of the wall, which reflects the difficulties in studying such interaction with current technologies. Atomic force microcopy AFM imaging of the maize parenchyma cell wall surface in combination with earlier immuno-transmission electron microscopy TEM; Kimura et al. These 36 glucan chains are thought then to assemble into a crystalline core and a subcrystalline structure of the elementary fibril via hydrogen bonds and van der Waals forces.
However, it remains unclear whether and how the composition of the elementary fibrils changes during cell wall growth. TEM and nuclear magnetic resonance NMR of some angiosperms have estimated that the cellulose crystallites are 2—5 nm in diameter with disordered surface chains. Since TEM preparations involve solvent extractions that introduce disorder or may remove non-crystalline layers altogether, it is not yet confirmed that these structural disorders indeed exist in native plant cell wall microfibrils, or are a result of the sample preparation process.
Ding and Himmel visualized the parenchyma cell walls in different growth stages, and found that as the cells expand, more cell wall components are deposited on the inner faces in a directional way. Microfibril aggregates macrofibrils have been examined by NMR Hult et al. Donaldson visualized the organization of macrofibrils in different cell wall types comparing normal and reaction wood of radiata pine and poplar as examples of a typical softwood and hardwood respectively using a combination of FESEM and environmental scanning electron microscopy SEM.
They showed the size of macrofibrils to range typically from 10 nm to 60 nm in diameter and to vary between different cell wall types and even slightly between adjacent cells of the same cell wall type. Donaldson also observed that macrofibrils occur predominantly in a random arrangement, although radial and tangential lamellae may sometimes be seen in individual cells.
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Most of the imaging studies have focused on microfibrils, whereas visualization of hemicellulose and lignin remains to be accomplished. Biochemical and genetic studies of lignin mutants Hu et al. Since there is no single imaging technique—currently being deployed or foreseeable—that on its own can provide both chemical and architectural information at the same time, combining a variety of imaging approaches seems to be the most promising path forward to gain the desired molecular understanding of plant cell wall design.
From an understanding of design principles, it might be possible to predict and possibly alter cell wall properties. Naively spoken, the hope is that the task is similar to calculating the statics for a skyscraper building and to estimate what forces the various building materials and building designs can withstand. Although undoubtedly, given the diversity and dynamic nature of cell walls and the uncertainties associated with the precise mechanical properties of the cell wall components, calculating the physical properties of cell walls is far more complicated. Currently, we have substantial amounts of biochemical information with respect to overall cell wall composition, and relative molecular ratios of its constituents, but this information was derived from bulk measurements and therefore represents at best an average, and from different specimens, and tissues at different growth stages.
Moreover, biochemical analysis speaks little of the 3D organization of the polymers. What has not yet been accomplished, but is clearly needed, is the integration of biochemical, genetic, and imaging information. Since no single imaging technique can provide all of the desired information, it seems essential to image the same samples by multiple imaging modalities, at multiple levels of scale and resolution, followed by integration of the information obtained by each imaging modality.
It is believed that a target correlative multimodal, multiscale in situ imaging study as illustrated in Fig. In order to achieve integration of different imaging modalities, a variety of technical and organizational obstacles need to be overcome, including the development of common sample preparation methods for multimodal imaging, the development of cross-modality-specific labels, correlative widefield 2D and 3D imaging using optical microscopy Raman, UV, super-resolution and EM, data integration, and analysis.
Summary of the comprehensive, multiscale, multimodal approach that we think is needed to produce a realistic cell wall model and its implications. Integration of the data obtained from different image modalities on the exact same specimen will provide the exact chemical composition, as well as geometrical constraints that will yield cell wall models, which will reflect the expected diversity of cell walls. Clearly, both compositional and architectural information is needed from the same specimen. The inventories of molecular components, both carbohydrate polymers and proteins, are needed, but geometries are also needed to determine how the molecular components are arranged in 3D.
For precise modelling of cell wall architecture and prediction of cell wall properties, both the parts and the building instructions are needed, including spatial and temporal patterns of precise localization and molecular interactions. Compositional information can be obtained through a variety of optical imaging approaches such as diffraction-limited and super-resolution fluorescence microscopy, visible and UV optical, near infrared IR , Fourier transform infrared FT-IR , Raman spectroscopy, and imaging, as well as specific labelling approaches.
Architectural information can be obtained though polarization and second harmonic generation SHG microscopy, which exploits the effect of preferentially organized macromolecules such as the microfibrils on polarized light, possibly small-angle X-ray scattering analysis, as well as a variety of higher resolution surface scanning and transmission microscopies. AFM detects topological profiles, which with appropriate cantilever tip geometries can yield near-atomic resolution.
AFM has been successfully used for the study of Venericardia ventricosa cellulose microfibrils Hanley et al. SEM uses backscattering properties of heavy atom-coated surfaces to determine topologies, not unlike AFM, with nanometre resolution, and allows heavy atom elemental analysis. However, unlike AFM, SEM is highly invasive and cannot be done on living samples, and often requires extensive sample preparation. Freeze-fracture sample preparation as well as deep-etching elctron microscopy can overcome the problem of access to the cell interior and may be of particular interest for cell wall analysis; however, precise location of the fracture lines cannot be predicted, which then leaves TEM as the method of choice for ultrastructural analysis.
The disadvantage of TEM is that it requires extensive sample preparation, is a destructive technique, and cannot study live specimens, although in-depth analysis of certain time points allows detailed snapshots of a complex biological process to be obtained.
Pure ultrastructural analysis ideally is complemented by specific labelling approaches, with conventional immunoaffinity probes being the most commonly deployed. However, due to the shortcomings of affinity probes, including target accessibility and target affinity retention, and the often necessary compromises in ultrastructural preservation, multiple efforts are underway to develop genetically encoded tag-based approaches, which promise higher sensitivity and coverage and which are compatible with exquisite sample preservation.
TEM imaging approaches require sophisticated sample preparation, with biological samples being imaged either as whole mounts or as sections, depending on the size of the specimen. Whole-mount imaging is typically done in a frozen-hydrated state using rapid liquid ethane plunge-freezing of the sample on a microscope grid, although the less challenging alternative approaches such as negative and positive staining may also be sufficient. Often biological specimens need to be sectioned in order to allow the electron beam to penetrate the sample, and to avoid multiple scattering.
Samples are either sectioned in their frozen state or embedded in a hardened plastic resin. In either case, samples are typically ultra rapidly frozen, e.
Freeze-substitution and resin embedding is by far the easiest approach and allows the addition of staining reagents that provide higher contrast in the resulting EM image. Freeze-substitution typically avoids the issues often associated with conventional sample preparation, including aggregation and extraction due to the low temperature at which water-to-organic solvent exchange occurs. Lengthy resin-embedding protocols can also lead to extraction artefacts, and hence microwave-assisted sample preparation protocols in our hands have proven to be very valuable for cell walls, but not for retention of cytoplasmic ultrastructural details.
To achieve vitrification of the cellular ice, and therefore the avoidance of damaging ice crystal formation, one usually resorts to a cryo-protectant in addition to the high-pressure conditions present during flash-freezing. The presence of cryo-protectants can disturb tissue osmolarity and lead to unwanted effects. A special case of cryo-sectioning is the Tokuyasu approach where chemically fixed biomass is infiltrated with high levels of sucrose which acts as a cryo-protectant, frozen, and sectioned in a frozen-hydrated state only to be thawed afterwards and subjected to on-section labelling.
This approach can result in vastly improved epitope recognition, but suffers from overall lower ultrastructural preservation and lower contrast. There are multiple challenges of multiscale multimodal imaging of a single specimen. The development of sample preparation protocols that are compatible with the different imaging modalities and the development of probes that work across imaging platforms and modalities are two of the major problems.
Post-imaging includes overlay of the various imaging information, which requires image data visualization, data registration, geometrical image and data analysis, feature extraction and annotation, as well as data integration and subsequent derivation of models. However, if successful, realistic cell wall models based on qualitative and quantitative information will allow a fundamentally improved understanding of cell wall physiology and function, and will probably allow biologists to reconstruct the adaptive design changes that occurred throughout evolution.
Such models will result in a more rational design of cell wall properties of crops and fruits for agriculture and finally allow the re-design of plant cell walls for easier breakdown to enable biofuel production. A number of the technical components to achieve the ambitious goal of integrated imaging already exist and have been successfully deployed in the past to the study of cell walls.
For example, FTIR microspectroscopy has been used to determine the major chemical components present in plant cell walls Sene et al. Surface-enhanced Raman imaging promises to improve the resolution to 30—50 nm; however, the feasibility of this approach for biofuel research remains to be proven but is currently under development.
The main advantage of such spectrum-based approaches is that intact cell walls can be analysed and the spatial distribution of their components can be visualized albeit at somewhat low resolution without the need for affinity probes. Several studies identified chemical signatures of different cell wall types, including the localization of cellulose and lignin in Picea mariana , Pinus and Populus Agarwal, ; Gierlinger and Schwanninger, Another spectroscopic technique that has been successfully applied to the study of cell wall is solid-state cross-polarization magic-angle spinning 13 C - NMR spectroscopy.
Applied to primary cell walls from a range of angiosperm species, this technique showed that all of the cellulose is in a crystalline state in the form of cellulose I. The calculated cross-sectional dimensions of the cellulose I crystallites from all cell wall sources was found to be in the range of 2—3 nm Vieter et al.
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Both NMR and FTIR spectroscopy have suggested that the cellulose microfibrils contain both crystalline and paracrystalline regions, exhibiting highly disordered structures Kataoka and Kondo, ; Sturcova et al. However, the relationship between the crystalline cellulose structure and the non-cellulosic polysaccharides remains to be determined Ding and Himmel, Where available, affinity probes can be used for specific labelling of cell wall components which can be visualized by either optical or EM imaging.
Traditionally, histochemical stains have been employed to distinguish between different categories of cell wall components such as hemicellulose, pectin, lignin, and glycoproteins. However, in most cases the partial removal of cell wall components was needed to allow these reagents access to their respective target Krishnamurthy, By employing antibodies specific for certain cell wall components followed by EM analysis, one can localize the various molecules with high precision within the cell wall.
However, such immunohistochemical labelling methods often suffer from the fact that only a small fraction of all epitopes are accessible and recognized by the specific antibody, and optimization of the labelling protocols are tedious and error prone. For some components such as lignin there is no specific antibody, which may be due to the fact that lignin polymerizes through radical formation, which makes the formation of unique epitopes far less likely.
A promising set of affinity tools are the carbohydrate-binding modules CBMs , which are non-catalytic proteins collectively covering a wide range of cell wall polysaccharides. CBMs have been found to have the capacity of distinguishing between in vitro and in vivo forms of the same polysaccharides McCartney et al. CBMs nevertheless face challenges similar to antibodies, including accessibility to their substrate and low stoichiometry.
All these approaches allow one to probe for the presence of certain candidate components, with some diffraction-limited spatial localization, although recent attempts to use super-resolution microscopy, e.
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PALM imaging, with appropriately modified CBMs appear promising for molecular resolution imaging of the microfibril nextwork Liphardt et al. For the most part, in order to achieve molecular resolution, TEM is still unsurpassed. Hence, TEM has been the primary study method of in situ cell wall structure for many decades.
However, conventional 2D TEM imaging runs into two problems: i only small, ideally representative areas of the sample are imaged at high resolution, therefore preventing an adequate statistical analysis; and ii the areas imaged constitute a 2D projection of a 3D volume onto the 2D area of a film or CCD camera. Therefore, multiple molecular layers contribute to the final image that for this reason can be difficult to interpret.
The recently developed high-resolution wide-field imaging and EM tomography can overcome these two limitations of conventional EM, respectively. In both approaches, several hundred CCD images are collected and then either assembled into a 2D projection montage or used for a 3D reconstruction of the cellular volume, leading to large amounts of data that require sophisticated computational support for interactive visualization and semi-automated image analysis.
Moreover, in EM the entire cellular ultrastructure including microtubules, vesicles, mitochondria, chloroplasts, Golgi, and endoplasmic reticulum membrane systems as well as the size, shape, and distribution of large macromolecular machines are readily visible, resulting in high-content data sets that can be examined for a variety of biological questions.
EM tomography of resin-embedded samples has been successfully applied to study the 3D organization of the chloroplast thylakoid membranes in lettuce leaves Shimoni et al. Another challenge stems from the fact that the plant tissue needs to be exposed to the high vacuum of the electron microscope, resulting in the immediate evaporation of cellular water and hence the drying out of the plant tissue.
One solution to these two problems is to embed the biological specimen in a plastic resin, which is then polymerized into a hard block, which is then suitable for sectioning and resistant in the vacuum of the TEM. This approach typically requires a controlled dehydration of the tissue using organic solvents such as ethanol or acetone because resins are not directly miscible with aqueous solutions and hence would not infiltrate the tissue.
In our view, it is this step in the sample preparation that is the most detrimental to ultrastructural preservation as exposure to organic solvents denatures proteins and leads to aggregation artefacts often detectable in conventionally prepared probes. Samples are then infiltrated with resin at either low temperature or room temperature, and the resin is then polymerized either by UV light or thermally, respectively.
To enhance the contrast, heavy metal ion solutions can be applied at various steps of the protocol. Osmium tetroxide and uranyl acetate, which are standard EM stains, primarily stain proteins, membranes, and nucleic acids, but to a far lesser degree carbohydrates, resulting in very low contrast. While every specimen presents its own challenges, and therefore one cannot easily generalize, it has been found that plant cell walls are typically well preserved by either microwave-assisted room temperature sample preparation or the more sophisticated high-pressure freezing and freeze-substitution approach, whereas faithful preservation of the cytoplasm depends crucially on the latter.
Microwave-assisted processing speeds up fixation, dehydration, and infiltration, and therefore avoids lengthy exposure to extracting reagents. High-pressure freezing avoids aggregation artefacts, which otherwise dominate in the cytoplasm, but no systematic difference in microfibril organization between high-pressure frozen, freeze-substituted, and microwave-processed samples was found, except for a possibly higher rate of extraction in microwave-processing unpublished observation.
Also, it should be emphasized that contrast in resin-embedded samples arises from the binding of heavy metal atoms to macromolecules. As an alternative to chemical fixation, dehydration, and resin embedding, high-pressure frozen tissue samples can be sectioned in their frozen-hydrated state at 30— nm, and then kept at liquid nitrogen temperature for cryo-EM imaging Al-Amoudi et al. This approach, while having been successfully applied to a number of prokaryotes, yeast, and some mammalian tissue, is technically very challenging, yet promising, and, given the staining behaviour of cell wall polymers in conventional approaches, cryo-sectioning followed by cryo-tomography is of particular interest in the study of the cell wall 3D architecture.
Very recently yet another tool has been added that may allow electron microscopists to obtain ultrathin frozen-hydrated samples: vitrified samples can be subjected to focused ion beam milling, resulting in ultrathin cryo-sections Marko et al. Independently of the exact sample preparation protocol, electron microscopic 2D and 3D imaging will probably retain a dominant role for imaging cell walls. An alternative approach to resin embedding or cryo-sectioning is freeze-fracture, where frozen samples are fractured in a vacuum, typically along cellular discontinuities such as membranes or cell walls.
Onto the freshly exposed surface one typically evaporates a thin layer of carbon, followed by platinum. Once the organic material is digested away by acid, one is left with a replica of the fracture surface that can be examined by TEM. Freeze-fracture imaging, while rarely performed these days, has revealed the rosettes of the cellulose synthase Mueller and Brown, , which remains one of the key pieces of evidence for the presumed organization of the cellulose-forming protein complex. Given all these sophisticated approaches for cell wall characterization, why is it that we do not yet have a model that is grounded in direct ultrastructural evidence?
The answer may lie in the complexity and diversity of plant cell walls as well as the small number of investigators and suitable techniques, some of which are very recent or still in the process of being developed. With the renewed interest in lignocellulosic biofuels and the resulting surge in funding, more investigators have become interested in the problem, and hence it is very likely that enormous progress will be made within the next couple of years. However, we think that there is another reason why progress has been slow.
Since no single technique can give all the information necessary for a comprehensive cell wall model, it requires the teamwork of a variety of imaging and computer science experts. They must strive to integrate the information from various imaging modalities by subjecting the exact same sample to different imaging approaches, and superimpose and integrate the complementary data sets into a model.
Through sample preparation that is compatible with all the different imaging modalities, the details that are needed for a sophisticated model as well as statistics of the homogeneous and therefore representative data will be obtained. For example, we will need to determine the range of cellulose microfibril dimensions and distances, the range of their next neighbour angles, as well as the degree of order and organization of the cell wall components on a local, regional, or global scale.
Such integrative multiscale, multimodal imaging combined with sophisticated modelling lies at the heart of our quest for a realistic cell wall model, and we are just beginning now to put the pieces of the puzzle together. Preliminary widefield TEM imaging of different plant species suggests that there is not a single design that fits all plant cell walls, but instead that we are even likely to find differences within one cell wall, between neighbouring cells, between different tissues, between different plants, and at different times in the life cycle of the plant.
Nevertheless, it now seems that we are within reach of having the first model of plant cell walls and its building principles derived from direct experimental data. This work has been authored by a contractor of the U. Government under Contract No. Accordingly, the U. Government retains a nonexclusive royalty-free license to publish or reproduce the published form of this contribution, or allow others to do so, for U.
Government purposes. Oxford University Press is a department of the University of Oxford. It furthers the University's objective of excellence in research, scholarship, and education by publishing worldwide. Sign In or Create an Account. Sign In. Advanced Search. Article Navigation. Close mobile search navigation Article Navigation. Volume Article Contents.
Trends in evolution of cell walls. Changes in cell wall compositions throughout plant evolution. Remodelling and reconstruction of cell walls. Cell wall deconstruction. Economic importance of cell wall deconstruction. The quest for realistic cell wall models. Contribution and shortcomings of current imaging approaches. Towards realistic models of the plant cell wall through integrated imaging. Roadblocks and future outlook.
Plant cell walls throughout evolution: towards a molecular understanding of their design principles Purbasha Sarkar. Oxford Academic. Google Scholar. Elena Bosneaga. Manfred Auer. Cite Citation. Permissions Icon Permissions. Abstract Throughout their life, plants typically remain in one location utilizing sunlight for the synthesis of carbohydrates, which serve as their sole source of energy as well as building blocks of a protective extracellular matrix, called the cell wall.
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Open in new tab Download slide. Diagram showing changes in cell wall composition during the course of evolution. Raman imaging to investigate ultrastructure and composition of plant cell walls: distribution of lignin and cellulose in black spruce wood Picea mariana. Search ADS. An oscillating cryo-knife reduces cutting-induced deformation of vitreous ultrathin sections. Deposition of glucuronoxylans on the secondary cell wall of Japanese beech as observed by immuno-scanning electron microscopy. High-resolution atomic force microscopy of native Valonia cellulose I microcrystals.
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The intersection between cell wall disassembly, ripening, and fruit susceptibility to Botrytis cinerea. Distribution of cell-wall xylans in bryophytes and tracheophytes: new insights into basal interrelationships of land plants. Structural models of primary cell walls in flowering plants: consistency of molecular structure with the physical properties of the walls during growth. Host—microbe interactions: shaping the evolution of the plant immune response. Structural similarities between the surface layers of selected Charophycean algae and bryophytes and the cuticles of vascular plants.
High-pressure freezing for the preservation of biological structure. Theory and practice. Revealing the surface ultrastructure of spruce pulp fibres using field emission-SEM. The surface and intracellular nanostructure of wood fibres: electron microscope methods and observations.
Proceedings of COST action: wood fibre cell walls: methods to study their formation, structure and properties. Oligosaccharins—oligosaccharides that regulate growth, development and defense responses in plants. The maize primary cell wall microfibril: a new model derived from direct visualization. Cellulose microfibril aggregates and their size variation with cell wall type. The ultrastructure of wood fibre surfaces as shown by a variety of microscopical methods—a review. Uronic acid-containing oligosaccharins: their biosynthesis, degradation and signalling roles in non-diseased plant tissues.
Cross-sectional structure of the secondary cell wall of wood fibres as affected by processing. Polysaccharide utilization by gut bacteria: potential for new insights from genomic analysis. Poplar carbohydrate-active enzymes. Gene identification and expression analyses. How do lignin composition, structure, and cross-linking affect degradability? A review of cell wall model studies. The origin of plants: body plan changes contributing to a major evolutionary radiation. Rapid changes in cell wall pectic polysaccharides are closely associated with early stages of aerenchyma formation, a spatially localized form of programmed cell death in roots of maize Zea mays L.
Ideas about heredity and evolution are undergoing a revolutionary change. New findings in molecular biology challenge the gene-centered version of Darwinian theory according to which adaptation occurs only through natural selection of chance DNA variations. These systems, they argue, can all provide variations on which natural selection can act. Evolution in Four Dimensions offers a richer, more complex view of evolution than the gene-based, one-dimensional view held by many today.
The new synthesis advanced by Jablonka and Lamb makes clear that induced and acquired changes also play a role in evolution. They consider how each may have originated and guided evolutionary history and they discuss the social and philosophical implications of the four-dimensional view of evolution. James A. Shapiro proposes an important new paradigm for understanding biological evolution, the core organizing principle of biology. Shapiro integrates advances in symbiogenesis, epigenetics, and saltationism into a unified approach that views evolutionary change as an active cell process, regulated epigenetically and capable of making rapid large changes by horizontal DNA transfer, inter-specific hybridization, whole genome doubling, symbiogenesis, or massive genome restructuring.
Evolution marshals extensive evidence in support of a fundamental reinterpretation of evolutionary processes, including more than 1, references to the scientific literature. It also has major implications for evolutionary computation, information science, and the growing synthesis of the physical and biological sciences.
What is Life? Decades of research have resulted in the full mapping of the human genome — three billion pairs of code whose functions are only now being understood. But for a physiologist, working with the living organism, the view is a very different one. Denis Noble is a world renowned physiologist, and sets out an alternative view to the question — one that becomes deeply significant in terms of the living, breathing organism.
The genome is not life itself. Noble argues that far from genes building organisms, they should be seen as prisoners of the organism. The view of life presented in this little, modern, post-genome project reflection on the nature of life, is that of the systems biologist: to understand what life is, we must view it at a variety of different levels, all interacting with each other in a complex web.
It is that emergent web, full of feedback between levels, from the gene to the wider environment, that is life. It is a kind of music. Epigenetics can potentially revolutionize our understanding of the structure and behavior of biological life on Earth. Surveying the twenty-year history of the field while also highlighting its latest findings and innovations, this volume provides a readily understandable introduction to the foundations of epigenetics.
Reaching beyond biology, epigenetics now informs work on drug addiction, the long-term effects of famine, and the physical and psychological consequences of childhood trauma. Carey concludes with a discussion of the future directions for this research and its ability to improve human health and well-being. As a result, evolutionary theory today includes concepts and even entire new fields that were not part of the foundational structure of the Modern Synthesis. Most of the contributors to Evolution, the Extended Synthesis accept many of the tenets of the classical framework but want to relax some of its assumptions and introduce significant conceptual augmentations of the basic Modern Synthesis structure — just as the architects of the Modern Synthesis themselves expanded and modulated previous versions of Darwinism.
This biographical study illuminates one of the most important yet misunderstood figures in the history of science. Barbara McClintock , a geneticist who integrated classical genetics with microscopic observations of the behavior of chromosomes, was regarded as a genius and as an unorthodox, nearly incomprehensible thinker. Since then, McClintock has become an emblem of feminine scientific thinking and the tragedy of narrow-mindedness and bias in science. Nor was McClintock marginalized by scientists; throughout the decades of her alleged rejection, she remained a distinguished figure in her field.
In BEEM, author and engineer Raju Pookottil boldly diverges from the Darwinian theory of natural selection and offers a thought provoking counter-hypothesis for the evolution of all living organisms. He proposes that every species, be it single cells, plants or animals, are equipped with the fundamental mechanisms that allows them to generate intelligent and logical decisions that they could then utilize in directing their own evolution. Whereas natural selection depends on random mutations followed by selection, Pookottil argues that species are capable of deciding how to logically construct themselves to near perfection over many generations, making modifications to their own genes where necessary.
The principles of emergence, swarm intelligence and signal networks, which he proposes are available to all living organisms, could in fact be the real forces that cleverly and logically drive the evolution of every species on earth. Our brains work by exploiting these very same principles. It is proposed that the complex signal networks that exist between the millions of protein molecules in a cell, or the billions of cells that make up larger organisms, are also capable of generating intelligent solutions, albeit at a slower pace.
Thus, species meaningfully assess their environment, create ingenious solutions, and crucially, pass them on to subsequent generations. Using observable examples, BEEM builds up a strong case supporting these arguments. For much of her life she worked alone, brilliant but eccentric, with ideas that made little sense to her colleagues. Nearly forty years later, her insights would bring her a MacArthur Foundation grant, the Nobel Prize, and long overdue recognition.