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2020
Zancajo, V. M. R. ; Lindtner, T. ; Eisele, M. ; Huber, A. J. ; Elbaum, R. ; Kneipp, J. FTIR Nanospectroscopy Shows Molecular Structures of Plant Biominerals and Cell Walls. Analytical ChemistryAnalytical Chemistry 2020, 92, 13694 - 13701. Publisher's VersionAbstract
Plant tissues are complex composite structures of organic and inorganic components whose function relies on molecular heterogeneity at the nanometer scale. Scattering-type near-field optical microscopy (s-SNOM) in the mid-infrared (IR) region is used here to collect IR nanospectra from both fixed and native plant samples. We compared structures of chemically extracted silica bodies (phytoliths) to silicified and nonsilicified cell walls prepared as a flat block of epoxy-embedded awns of wheat (Triticum turgidum), thin sections of native epidermis cells from sorghum (Sorghum bicolor) comprising silica phytoliths, and isolated cells from awns of oats (Avena sterilis). The correlation of the scanning-probe IR images and the mechanical phase image enables a combined probing of mechanical material properties together with the chemical composition and structure of both the cell walls and the phytolith structures. The data reveal a structural heterogeneity of the different silica bodies in situ, as well as different compositions and crystallinities of cell wall components. In conclusion, IR nanospectroscopy is suggested as an ideal tool for studies of native plant materials of varied origins and preparations and could be applied to other inorganic–organic hybrid materials.Plant tissues are complex composite structures of organic and inorganic components whose function relies on molecular heterogeneity at the nanometer scale. Scattering-type near-field optical microscopy (s-SNOM) in the mid-infrared (IR) region is used here to collect IR nanospectra from both fixed and native plant samples. We compared structures of chemically extracted silica bodies (phytoliths) to silicified and nonsilicified cell walls prepared as a flat block of epoxy-embedded awns of wheat (Triticum turgidum), thin sections of native epidermis cells from sorghum (Sorghum bicolor) comprising silica phytoliths, and isolated cells from awns of oats (Avena sterilis). The correlation of the scanning-probe IR images and the mechanical phase image enables a combined probing of mechanical material properties together with the chemical composition and structure of both the cell walls and the phytolith structures. The data reveal a structural heterogeneity of the different silica bodies in situ, as well as different compositions and crystallinities of cell wall components. In conclusion, IR nanospectroscopy is suggested as an ideal tool for studies of native plant materials of varied origins and preparations and could be applied to other inorganic–organic hybrid materials.
Biru, F. N. ; Cazzonelli, C. I. ; Elbaum, R. ; Johnson, S. N. Contrasting effects of Miocene and Anthropocene levels of atmospheric CO2 on silicon accumulation in a model grass. Biology Letters 2020, 16, 20200608. Publisher's VersionAbstract
Grasses are hyper-accumulators of silicon (Si), which they acquire from the soil and deposit in tissues to resist environmental stresses. Given the high metabolic costs of herbivore defensive chemicals and structural constituents (e.g. cellulose), grasses may substitute Si for these components when carbon is limited. Indeed, high Si uptake grasses evolved in the Miocene when atmospheric CO2 concentration was much lower than present levels. It is, however, unknown how pre-industrial CO2 concentrations affect Si accumulation in grasses. Using Brachypodium distachyon, we hydroponically manipulated Si-supply (0.0, 0.5, 1, 1.5, 2 mM) and grew plants under Miocene (200 ppm) and Anthropocene levels of CO2 comprising ambient (410 ppm) and elevated (640 ppm) CO2 concentrations. We showed that regardless of Si treatments, the Miocene CO2 levels increased foliar Si concentrations by 47% and 56% relative to plants grown under ambient and elevated CO2, respectively. This is owing to higher accumulation overall, but also the reallocation of Si from the roots into the shoots. Our results suggest that grasses may accumulate high Si concentrations in foliage when carbon is less available (i.e. pre-industrial CO2 levels) but this is likely to decline under future climate change scenarios, potentially leaving grasses more susceptible to environmental stresses.
Kumar, S. ; Natalio, F. ; Elbaum, R. Protein-driven biomineralization: comparing silica formation in grass silica cells to other biomineralization processes. Journal of Structural Biology 2020, 107665. Publisher's VersionAbstract
Biomineralization is a common strategy adopted by organisms to support their body structure. Plants practice significant silicon and calcium based biomineralization in which silicon is deposited as silica in cell walls and intracellularly in various cell-types, while calcium is deposited mostly as calcium oxalate in vacuoles of specialized cells. In this review, we compare cellular processes leading to protein-dependent mineralization in plants, diatoms and sponges (phylum Porifera). The mechanisms of biomineralization in these organisms are inherently different. The composite silica structure in diatoms forms inside the cytoplasm in a membrane bound vesicle, which after maturation is exocytosed to the cell surface. In sponges, separate vesicles with the mineral precursor (silicic acid), an inorganic template, and organic molecules, fuse together and are extruded out. In plants, calcium oxalate precursors are concentrated in a vacuolar vesicle containing a protein matrix which is never exocytosed. Silica deposition in grass silica cells takes place outside the cell membrane when the cells secrete the mineralizing protein into the apoplasm rich with silicic acid (the mineral precursor molecules). Our review infers that the organism complexity and precursor reactivity (calcium and oxalate versus silicic acid) are main driving forces for the evolution of varied mineralization mechanisms.
Biru, F. N. ; Cazzonelli, C. I. ; Elbaum, R. ; Johnson, S. N. Contrasting effects of Miocene and Anthropocene levels of atmospheric CO2 on silicon accumulation in a model grass. Biology Letters 2020, 16, 20200608. Publisher's VersionAbstract
Grasses are hyper-accumulators of silicon (Si), which they acquire from the soil and deposit in tissues to resist environmental stresses. Given the high metabolic costs of herbivore defensive chemicals and structural constituents (e.g. cellulose), grasses may substitute Si for these components when carbon is limited. Indeed, high Si uptake grasses evolved in the Miocene when atmospheric CO2 concentration was much lower than present levels. It is, however, unknown how pre-industrial CO2 concentrations affect Si accumulation in grasses. Using Brachypodium distachyon, we hydroponically manipulated Si-supply (0.0, 0.5, 1, 1.5, 2 mM) and grew plants under Miocene (200 ppm) and Anthropocene levels of CO2 comprising ambient (410 ppm) and elevated (640 ppm) CO2 concentrations. We showed that regardless of Si treatments, the Miocene CO2 levels increased foliar Si concentrations by 47% and 56% relative to plants grown under ambient and elevated CO2, respectively. This is owing to higher accumulation overall, but also the reallocation of Si from the roots into the shoots. Our results suggest that grasses may accumulate high Si concentrations in foliage when carbon is less available (i.e. pre-industrial CO2 levels) but this is likely to decline under future climate change scenarios, potentially leaving grasses more susceptible to environmental stresses.
Kumar, S. ; Adiram-Filiba, N. ; Blum, S. ; Sanchez-Lopez, J. A. ; Tzfadia, O. ; Omid, A. ; Volpin, H. ; Heifetz, Y. ; Goobes, G. ; Elbaum, R. Siliplant1 (Slp1) protein precipitates silica in sorghum silica cells. Journal of Experimental Botany 2020. Publisher's VersionAbstract
Silicon is absorbed by plant roots as silicic acid. The acid moves with the transpiration stream to the shoot, and mineralizes as silica. In grasses, leaf epidermal cells called silica cells deposit silica in most of their volume by unknown mechanism. Using bioinformatics tools, we identified a previously uncharacterized protein in sorghum (Sorghum bicolor), which we named Siliplant1 (Slp1). Slp1 is a basic protein with seven repeat units rich in proline, lysine, and glutamic acid. We found Slp1 RNA in sorghum immature leaf and immature inflorescence. In leaves, transcription was highest just before the active silicification zone (ASZ). There, Slp1 was localized specifically to developing silica cells, packed inside vesicles and scattered throughout the cytoplasm or near the cell boundary. These vesicles fused with the membrane, releasing their content in the apoplastic space. A short peptide that is repeated five times in Slp1 precipitated silica in vitro at a biologically relevant silicic acid concentration. Transient overexpression of Slp1 in sorghum resulted in ectopic silica deposition in all leaf epidermal cell-types. Our results show that Slp1 precipitates silica in sorghum silica cells.
Adiram-Filiba, N. ; Geiger, Y. ; Kumar, S. ; Keinan-Adamsky, K. ; Elbaum, R. ; Goobes, G. Peptides from diatoms and grasses harness phosphate ion binding to silica to help regulate biomaterial structure. Acta Biomaterialia 2020. Publisher's VersionAbstract
Many life forms generate intricate submicron biosilica structures with various important biological functions. The formation of such structures, from the silicic acid in the waters and in the soil, is thought to be regulated by unique proteins with high repeats of specific amino acids and unusual sidechain modifications. Some silicifying proteins are characterized by high prevalence of basic amino acids in their primary structures. Lysine-rich domains are found, for instance, in diatom silaffin proteins and in the sorghum grass siliplant protein. These domains exhibit catalytic activity in silica chain condensation, owing to molecular interactions of the lysine amine groups with the forming mineral. The use of amine chemistry by two very remote organisms has motivated us to seek other molecular biosilicification processes that may be common to the two life forms. In diatom silaffins, domains rich in phosphoserine residues are thought to assist the assembly of silaffin molecules into an organic supra-structure which serves as a template for the silica to precipitate on. This mold, held by salt bridges between serine phosphates and lysine amines, dictates the shape of the silica particles formed. Yet, silica synthesized with the dephosphorylated silaffin in phosphate buffer showed similar morphology to the one prepared with the native protein, suggesting that a defined spatial arrangement of serine phosphates is not required to generate silica with the desired shape. Concurrently, free phosphates enhanced the activity of siliplant1 in silica formation. It is therefore beneficial to characterize the involvement of these anions as co-factors in regulated silicification by functional peptides from the two proteins and to understand whether they play similar molecular role in the mechanism of mineralization. Here we analyze the molecular interactions of free phosphate ions with silica and the silaffin peptide PL12 and separately with silica and siliplant1 peptide SLP1 in the two biomimetic silica products generated by the two peptides. MAS NMR measurements show that the phosphate ions interact with the peptides and at the same time may be forming bonds with the silica mineral. This bridging capability may add another avenue by which the structure of the silica material is influenced. A model for the molecular/ionic interactions at the bio-inorganic interface is described, which may have bearings for the role of phosphorylated residues beyond the function as intermolecular cross linkers or free phosphate ions as co-factors in regulation of silicification.
Hodson, M. J. ; Song, Z. ; Ball, T. B. ; Elbaum, R. ; Struyf, E. Editorial: Frontiers in Phytolith Research. Frontiers in Plant Science 2020, 11, 454. Publisher's Version
2019
Zancajo, V. M. R. ; Diehn, S. ; Filiba, N. ; Goobes, G. ; Kneipp, J. ; Elbaum, R. Spectroscopic Discrimination of Sorghum Silica Phytoliths. Front Plant Sci 2019, 10, 1571.Abstract
Grasses accumulate silicon in the form of silicic acid, which is precipitated as amorphous silica in microscopic particles termed phytoliths. These particles comprise a variety of morphologies according to the cell type in which the silica was deposited. Despite the evident morphological differences, phytolith chemistry has mostly been analysed in bulk samples, neglecting differences between the varied types formed in the same species. In this work, we extracted leaf phytoliths from mature plants of (L.) Moench. Using solid state NMR and thermogravimetric analysis, we show that the extraction methods alter greatly the silica molecular structure, its condensation degree and the trapped organic matter. Measurements of individual phytoliths by Raman and synchrotron FTIR microspectroscopies in combination with multivariate analysis separated bilobate silica cells from prickles and long cells, based on the silica molecular structures and the fraction and composition of occluded organic matter. The variations in structure and composition of sorghum phytoliths suggest that the biological pathways leading to silica deposition vary between these cell types.
Nissan, H. ; Blum, S. ; Shimoni, E. ; Elbaum, R. Characterization of Silicon Accumulation in Maize Cell Suspension Cultures. Silicon 2019, 11, 2377-2383. Publisher's VersionAbstract
Purpose: Silicon (Si) is an abundant element in the earth’s crust and is available to plants as silicic acid. Silicon uptake by plants is correlated with increased tolerance to various biotic and abiotic stresses. However, cellular mechanisms responsible for its beneficial effects are still unknown. Even its cellular import mechanisms are not well understood. We thus aimed to characterize silicon localization within minimally differentiated Zea mays (Black Mexican Sweet) cells in suspension. Methods: Cells were grown in a medium containing silicon, and the mRNA levels of silicon transporters were measured by real-time PCR. Cells were separated into an insoluble (mainly walls and starch) and a cytoplasmic fraction. Soluble and total silicon was measured by inductively-coupled-plasma – atomic-emission-spectroscopy. Silicon distribution was assessed by transmission electron microscopy. The cell walls were analyzed chemically, and by Raman micro-spectroscopy and thermal gravimetric analysis. Results: Silicon treatment reduced the levels of silicon transporters transcripts, without affecting cell proliferation. About 70 % of the silicon was localized in the cytoplasm, mostly in vesicles. We found indications that silicon affected the secondary structure of proteins and thermally stabilized starch. Silicon was loosely bound, and diffused out of the cells within 24 hours. Conclusions: Our results show that silicon binds spontaneously to cell walls/starch and accumulates in cytoplasm vesicles. These processes allow the cells to accumulate silicon against its concentration gradient in solution. However, cellular intake acts against reversible diffusion processes, probably through the aquaporin silicon channels (Lsi1, Lsi6) that exchange the cellular silicon with the surrounding medium. © 2015, Springer Science+Business Media Dordrecht.
2018
Heiner, Z. ; Zeise, I. ; Elbaum, R. ; Kneipp, J. Insight into plant cell wall chemistry and structure by combination of multiphoton microscopy with Raman imaging. Journal of Biophotonics 2018, 11, e201700164. Publisher's VersionAbstract
Spontaneous Raman scattering microspectroscopy, second harmonic generation (SHG) and 2-photon excited fluorescence (2PF) were used in combination to characterize the morphology together with the chemical composition of the cell wall in native plant tissues. As the data obtained with unstained sections of Sorghum bicolor root and leaf tissues illustrate, nonresonant as well as pre-resonant Raman microscopy in combination with hyperspectral analysis reveals details about the distribution and composition of the major cell wall constituents. Multivariate analysis of the Raman data allows separation of different tissue regions, specifically the endodermis, xylem and lumen. The orientation of cellulose microfibrils is obtained from polarization-resolved SHG signals. Furthermore, 2-photon autofluorescence images can be used to image lignification. The combined compositional, morphological and orientational information in the proposed coupling of SHG, Raman imaging and 2PF presents an extension of existing vibrational microspectroscopic imaging and multiphoton microscopic approaches not only for plant tissues.
Elbaum, R. Structural Principles in the Design of Hygroscopically Moving Plant Cells. In Plant Biomechanics: From Structure to Function at Multiple Scales; Geitmann, A. ; Gril, J., Ed. Plant Biomechanics: From Structure to Function at Multiple Scales; Springer International Publishing: Cham, 2018; pp. 235–246. Publisher's VersionAbstract
Plants do not have mineralized skeletons. Instead, each of the plant's cells has an envelope of a cellulose-based wall, which provides a mechanical support to the organism. This stiff wall enables plants to assume flexible body shapes. However, the wall interferes with proteinous muscle-like movements of cells and organs because it is too stiff to yield to forces generated by motor proteins. Nevertheless, plants move constantly. The movements rely on water translocations, which result in the swelling (or growth) of cells located strategically. Water may swell protoplasts in movements that require live cells, like tip growth, tropism, and gas exchange. Other movements are initiated by the swelling of cell walls. These occur in dead tissues that can afford drying. The hygroscopically based movement is very common in seed dispersal mechanisms. The seed that detaches from the mother plant is carried by a cellulosic device. This device was synthesized by the plant and programmed to do some mechanical work, like jumping, crawling, and sowing, in order to deliver the seed to a germination location. This nonliving device provides the seed with means to move away from its mother and siblings. The movement may utilize several types of cells, which differ in the arrangement of cell wall cellulose microfibrils. I present here three types of contracting cells that, together with stiff fiber cells resisting any contraction, create a variety of hygroscopic movements.
Abraham, Y. ; Dong, Y. ; Aharoni, A. ; Elbaum, R. Mapping of cell wall aromatic moieties and their effect on hygroscopic movement in the awns of stork’s bill. 2018, 25, 3827 - 3841. Publisher's VersionAbstract
The awn in stork’s bill (Erodium gruinum) seed dispersal units coils as it dries. This hygroscopic movement promotes the dissemination and sowing of the seeds. Here we aimed to understand the movement rate, by correlating water dynamics within the awn to the spatial variation in the chemical composition of the awn’s cell walls. We followed the hygroscopic movement visually and measured the kinetics of water adsorption–desorption in segments along the awn. We integrated data from white light, fluorescence, and Raman microscopy, and Matrix Assisted Laser Desorption Ionization imaging to characterize the micro chemical makeup of the awn. We hydrolyzed awns and followed the change in the cell walls’ composition and the effect on the movement. We found that the coil’s top segment is more sensitive to humidity changes than the coil’s base. At the top part of the coil, we found high concentration of modified lignin. In comparison, the base part of the awn contained lower concentration of mostly unmodified lignin. Ferulic acid concentration increased along the awn, apparently cross-linking hemicellulose and strengthening cell-to-cell adhesion. We propose that the high concentration of modified lignin at the coil’s top increased the hydrophobicity of the cell walls, allowed faster water molecules dynamics; thus inducing fast reaction to ambient humidity. Strong cell-to-cell adhesion in this region created a durable tissue required for the awn’s repeated movement that is induced by the diurnal humidity cycles.
Kumar, S. ; Elbaum, R. Interplay between silica deposition and viability during the life span of sorghum silica cells. New Phytol 2018, 217, 1137-1145.Abstract
Silica cells are specialized epidermal cells found on both surfaces of grass leaves, with almost the entire lumen filled with solid silica. The mechanism precipitating silicic acid into silica is not known. Here we investigate this process in sorghum (Sorghum bicolor) leaves. Using fluorescent confocal microscopy, we followed silica cells' ontogeny, aiming to understand the fate of vacuoles and nuclei. Correlating the confocal and scanning electron microscopy, we timed the initiation of silica deposition in relation to cell's viability. Contrary to earlier reports, silica cells did not lose their nucleus before silica deposition. Vacuoles in silica cells did not concentrate silicic acid. Instead, postmaturation silicification initiated at the cell periphery in live cells. Less than 1% silica cells showed characteristics of programmed cell death in the cell maturation zone. In fully elongated mature leaves, 2.4% of silica cells were nonsilicified and 1.6% were partially silicified. Silica deposition occurs in the paramural space of live silica cells. The mineral does not kill the cells. Instead, silica cells are genetically programmed to undergo cell death independent of silicification. Fully silicified cells seem to have nonsilicified voids containing membrane remains after the completion of the cell death processes.
2017
Kumar, S. ; Milstein, Y. ; Brami, Y. ; Elbaum, M. ; Elbaum, R. Mechanism of silica deposition in sorghum silica cells. New Phytologist 2017, 213, 791-798. Publisher's VersionAbstract
Summary Grasses take up silicic acid from soil and deposit it in their leaves as solid silica. This mineral, comprising 1–10% of the grass dry weight, improves plants' tolerance to various stresses. The mechanisms promoting stress tolerance are mostly unknown, and even the mineralization process is poorly understood. To study leaf mineralization in sorghum (Sorghum bicolor), we followed silica deposition in epidermal silica cells by in situ charring and air-scanning electron microscopy. Our findings were correlated to the viability of silica cells tested by fluorescein diacetate staining. We compared our results to a sorghum mutant defective in root uptake of silicic acid. We showed that the leaf silicification in these plants is intact by detecting normal mineralization in leaves exposed to silicic acid. Silica cells were viable while condensing silicic acid into silica. The controlled mineral deposition was independent of water evapotranspiration. Fluorescence recovery after photobleaching suggested that the forming mineral conformed to the cellulosic cell wall, leaving the cytoplasm well connected to neighboring cells. As the silicified wall thickened, the functional cytoplasm shrunk into a very small space. These results imply that leaf silica deposition is an active, physiologically regulated process as opposed to a simple precipitation.
Kumar, S. ; Soukup, M. ; Elbaum, R. Silicification in Grasses: Variation between Different Cell Types. Frontiers in Plant Science 2017, 8 438. Publisher's VersionAbstract
Plants take up silicon as mono-silicic acid, which is released to soil by the weathering of silicate minerals. Silicic acid can be taken up by plant roots passively or actively, and later it is deposited in its polymerized form as amorphous hydrated silica. Major silica depositions in grasses occur in root endodermis, leaf epidermal cells, and outer epidermal cells of inflorescence bracts. Debates are rife about the mechanism of silica deposition, and two contrasting scenarios are often proposed to explain it. According to the passive mode of silicification, silica deposition is a result of silicic acid condensation due to dehydration, such as during transpirational loss of water from the aboveground organs. In general, silicification and transpiration are positively correlated, and continued silicification is sometimes observed after cell and tissue maturity. The other mode of silicification proposes the involvement of some biological factors, and is based on observations that silicification is not necessarily coupled with transpiration. Here, we review evidence for both mechanisms of silicification, and propose that the deposition mechanism is specific to the cell type. Considering all the cell types together, our conclusion is that grass silica deposition can be divided into three modes: spontaneous cell wall silicification, directed cell wall silicification, and directed paramural silicification in silica cells.
Soukup, M. ; Martinka, M. ; Bosnić, D. ; Čaplovičová, M. ; Elbaum, R. ; Lux, A. Formation of silica aggregates in sorghum root endodermis is predetermined by cell wall architecture and development. Annals of Botany 2017, 120, 739-753. Publisher's VersionAbstract
Background and Aims Deposition of silica in plant cell walls improves their mechanical properties and helps plants to withstand various stress conditions. Its mechanism is still not understood and silica–cell wall interactions are elusive. The objective of this study was to investigate the effect of silica deposition on the development and structure of sorghum root endodermis and to identify the cell wall components involved in silicification.MethodsSorghum bicolor seedlings were grown hydroponically with (Si+) or without (Si−) silicon supplementation. Primary roots were used to investigate the transcription of silicon transporters by quantitative RT–PCR. Silica aggregation was induced also under in vitro conditions in detached root segments. The development and architecture of endodermal cell walls were analysed by histochemistry, microscopy and Raman spectroscopy. Water retention capability was compared between silicified and non-silicified roots. Raman spectroscopy analyses of isolated silica aggregates were also carried out.Key Results Active uptake of silicic acid is provided at the root apex, where silicon transporters Lsi1 and Lsi2 are expressed. The locations of silica aggregation are established during the development of tertiary endodermal cell walls, even in the absence of silicon. Silica aggregation takes place in non-lignified spots in the endodermal cell walls, which progressively accumulate silicic acid, and its condensation initiates at arabinoxylan–ferulic acid complexes. Silicification does not support root water retention capability; however, it decreases root growth inhibition imposed by desiccation.Conclusion A model is proposed in which the formation of silica aggregates in sorghum roots is predetermined by a modified cell wall architecture and takes place as governed by endodermal development. The interaction with silica is provided by arabinoxylan–ferulic acid complexes and interferes with further deposition of lignin. Due to contrasting hydrophobicity, silicification and lignification do not represent functionally equivalent modifications of plant cell walls.
Markovich, O. ; Steiner, E. ; Kouřil, Štěpán; Tarkowski, P. ; Aharoni, A. ; Elbaum, R. Silicon promotes cytokinin biosynthesis and delays senescence in Arabidopsis and Sorghum. Plant Cell Environ 2017, 40, 1189-1196.Abstract
Silicate minerals are dominant soil components. Thus, plant roots are constantly exposed to silicic acid. High silicon intake, enabled by root silicon transporters, correlates with increased tolerance to many biotic and abiotic stresses. However, the underlying protection mechanisms are largely unknown. Here, we tested the hypothesis that silicon interacts with the plant hormones, and specifically, that silicic acid intake increases cytokinin biosynthesis. The reaction of sorghum (Sorghum bicolor) and Arabidopsis plants, modified to absorb high versus low amounts of silicon, to dark-induced senescence was monitored, by quantifying expression levels of genes along the senescence pathway and measuring tissue cytokinin levels. In both species, detached leaves with high silicon content senesced more slowly than leaves that were not exposed to silicic acid. Expression levels of genes along the senescence pathway suggested increased cytokinin biosynthesis with silicon exposure. Mass spectrometry measurements of cytokinin suggested a positive correlation between silicon exposure and active cytokinin concentrations. Our results indicate a similar reaction to silicon treatment in distantly related plants, proposing a general function of silicon as a stress reliever, acting via increased cytokinin biosynthesis.
2016
Nida, H. ; Blum, S. ; Zielinski, D. ; Srivastava, D. A. ; Elbaum, R. ; Xin, Z. ; Erlich, Y. ; Fridman, E. ; Shental, N. Highly efficient de novo mutant identification in a Sorghum bicolor TILLING population using the ComSeq approach. The Plant JournalThe Plant JournalPlant J 2016, 86, 349 - 359. Publisher's VersionAbstract
Summary Screening large populations for carriers of known or de novo rare single nucleotide polymorphisms (SNPs) is required both in Targeting induced local lesions in genomes (TILLING) experiments in plants and in screening of human populations. We previously suggested an approach that combines the mathematical field of compressed sensing with next-generation sequencing to allow such large-scale screening. Based on pooled measurements, this method identifies multiple carriers of heterozygous or homozygous rare alleles while using only a small fraction of resources. Its rigorous mathematical foundations allow scalable and robust detection, and provide error correction and resilience to experimental noise. Here we present a large-scale experimental demonstration of our computational approach, in which we targeted a TILLING population of 1024 Sorghum bicolor lines to detect carriers of de novo SNPs whose frequency was less than 0.1%, using only 48 pools. Subsequent validation confirmed that all detected lines were indeed carriers of the predicted mutations. This novel approach provides a highly cost-effective and robust tool for biologists and breeders to allow identification of novel alleles and subsequent functional analysis.
AU - Fridman, Y. ; AU - Holland, N. ; Elbaum, R. ; AU - Savaldi-Goldstein, S. High Resolution Quantification of Crystalline Cellulose Accumulation in Arabidopsis Roots to Monitor Tissue-specific Cell Wall Modifications. 2016, e53707. Publisher's VersionAbstract
Plant cells are surrounded by a cell wall, the composition of which determines their final size and shape. The cell wall is composed of a complex matrix containing polysaccharides that include cellulose microfibrils that form both crystalline structures and cellulose chains of amorphous organization. The orientation of the cellulose fibers and their concentrations dictate the mechanical properties of the cell. Several methods are used to determine the levels of crystalline cellulose, each bringing both advantages and limitations. Some can distinguish the proportion of crystalline regions within the total cellulose. However, they are limited to whole-organ analyses that are deficient in spatiotemporal information. Others relying on live imaging, are limited by the use of imprecise dyes. Here, we report a sensitive polarized light-based system for specific quantification of relative light retardance, representing crystalline cellulose accumulation in cross sections of Arabidopsis thaliana roots. In this method, the cellular resolution and anatomical data are maintained, enabling direct comparisons between the different tissues composing the growing root. This approach opens a new analytical dimension, shedding light on the link between cell wall composition, cellular behavior and whole-organ growth.
Shtein, I. ; Elbaum, R. ; Bar-On, B. The Hygroscopic Opening of Sesame Fruits Is Induced by a Functionally Graded Pericarp Architecture. Frontiers in Plant Science 2016, 7 1501. Publisher's VersionAbstract
To enhance the distribution of their seeds, plants often utilize hygroscopic deformations that actuate dispersal mechanisms. Such movements are based on desiccation-induced shrinkage of tissues in predefined directions. The basic hygroscopic deformations are typically actuated by a bi-layer configuration, in which shrinking of an active tissue layer is resisted by a stiff layer, generating a set of basic movements including bending, coiling, and twisting. In this study, we investigate a new type of functionally graded hygroscopic movement in the fruit (capsule) of sesame (Sesamum indicum L.). Microscopic observations of the capsules showed that the inner stiff endocarp layer is built of a bilayer of transverse (i.e., circumferential) and longitudinal fiber cells with the layers positioned in a semi-circle, one inside the other. The outer mesocarp layer is made of soft parenchyma cells. The thickness of the fibrous layers and of the mesocarp exhibits a graded architecture, with gradual changes in their thickness around the capsule circumference. The cellulose microfibrils in the fiber cell walls are lying parallel to the cell long axis, rendering them stiff. The outer mesocarp layer contracted by 300% as it dried. Removal of this outer layer inhibited the opening movement, indicating that it is the active tissue. A biomechanical hygro-elastic model based on the relative thicknesses of the layers successfully simulated the opening curvature. Our findings suggest that the sesame capsules possess a functionally graded architecture, which promotes a non-uniform double-curvature hygroscopic bending movement. In contrast to other hygroscopic organs described in the literature, the sesame capsule actuating and resisting tissues are not uniform throughout the device, but changing gradually. This newly described mechanism can be exploited in bio-inspired designs of novel actuating platforms.