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Publications

2022
Arun, P. V. ; Sadeh, R. ; Avneri, A. ; Tubul, Y. ; Camino, C. ; Buddhiraju, K. M. ; Porwal, A. ; Lati, R. N. ; Zarco-Tejada, P. J. ; Peleg, Z. ; et al. Multimodal Earth observation data fusion: Graph-based approach in shared latent space. 2022, 78, 20 - 39. Publisher's VersionAbstract
Multiple and heterogenous Earth observation (EO) platforms are broadly used for a wide array of applications, and the integration of these diverse modalities facilitates better extraction of information than using them individually. The detection capability of the multispectral unmanned aerial vehicle (UAV) and satellite imagery can be significantly improved by fusing with ground hyperspectral data. However, variability in spatial and spectral resolution can affect the efficiency of such dataset's fusion. In this study, to address the modality bias, the input data was projected to a shared latent space using cross-modal generative approaches or guided unsupervised transformation. The proposed adversarial networks and variational encoder-based strategies used bi-directional transformations to model the cross-domain correlation without using cross-domain correspondence. It may be noted that an interpolation-based convolution was adopted instead of the normal convolution for learning the features of the point spectral data (ground spectra). The proposed generative adversarial network-based approach employed dynamic time wrapping based layers along with a cyclic consistency constraint to use the minimal number of unlabeled samples, having cross-domain correlation, to compute a cross-modal generative latent space. The proposed variational encoder-based transformation also addressed the cross-modal resolution differences and limited availability of cross-domain samples by using a mixture of expert-based strategy, cross-domain constraints, and adversarial learning. In addition, the latent space was modelled to be composed of modality independent and modality dependent spaces, thereby further reducing the requirement of training samples and addressing the cross-modality biases. An unsupervised covariance guided transformation was also proposed to transform the labelled samples without using cross-domain correlation prior. The proposed latent space transformation approaches resolved the requirement of cross-domain samples which has been a critical issue with the fusion of multi-modal Earth observation data. This study also proposed a latent graph generation and graph convolutional approach to predict the labels resolving the domain discrepancy and cross-modality biases. Based on the experiments over different standard benchmark airborne datasets and real-world UAV datasets, the developed approaches outperformed the prominent hyperspectral panchromatic sharpening, image fusion, and domain adaptation approaches. By using specific constraints and regularizations, the network developed was less sensitive to network parameters, unlike in similar implementations. The proposed approach illustrated improved generalizability in comparison with the prominent existing approaches. In addition to the fusion-based classification of the multispectral and hyperspectral datasets, the proposed approach was extended to the classification of hyperspectral airborne datasets where the latent graph generation and convolution were employed to resolve the domain bias with a small number of training samples. Overall, the developed transformations and architectures will be useful for the semantic interpretation and analysis of multimodal data and are applicable to signal processing, manifold learning, video analysis, data mining, and time series analysis, to name a few.
2021
Hanhan, S. ; Goren, K. ; Rivkin, A. ; Saba, F. ; Nevo, H. ; Dar, N. ; Shilo, D. ; Liebergall, M. ; Shoseyov, O. ; Deutsch, D. ; et al. Regeneration of grade 3 ankle sprain, using the recombinant human amelogenin protein (rHAM+) in a rat model. Journal of Orthopaedic ResearchJournal of Orthopaedic ResearchJ Orthop Res 2021, 39, 1540 - 1547. Publisher's VersionAbstract
Abstract Lateral ligament tears, also known as high-grade ankle sprains, are common, debilitating, and usually heal slowly. Ten to thirty percent of patients continue to suffer from chronic pain and ankle instability even after 3 to 9 months. Previously, we showed that the recombinant human amelogenin (rHAM+) induced regeneration of fully transected rat medial collateral ligament, a common proof-of-concept model. Our aim was to evaluate whether rHAM+ can regenerate torn ankle calcaneofibular ligament (CFL), an important component of the lateral ankle stabilizers. Right CFLs of Sabra rats were transected and treated with 0, 0.5, or 1?µg/µL rHAM+ dissolved in propylene glycol alginate (PGA). Results were compared with the normal group, without surgery. Healing was evaluated 12 weeks after treatment by mechanical testing (ratio between the right and left, untransected ligaments of the same rat), and histology including immunohistochemical staining of collagen I and S100. The mechanical properties, structure, and composition of transected ligaments treated with 0.5??g/?L rHAM+ (experimental) were similar to untransected ligaments. PGA (control) treated ligaments were much weaker, lax, and unorganized compared with untransected ligaments. Treatment with 1??g/?L rHAM+ was not as efficient as 0.5??g/?L rHAM+. Normal arrangement of collagen I fibers and of proprioceptive nerve endings, parallel to the direction of the force, was detected in ligaments treated with 0.5??g/?L rHAM+, and scattered arrangement, resembling scar tissue, in control ligaments. In conclusion, we showed that rHAM+ induced significant mechanical and structural regeneration of torn rat CFLs, which might be translated into treatment for grades 2 and 3 ankle sprain injuries.
Fatiukha, A. ; Deblieck, M. ; Klymiuk, V. ; Merchuk-Ovnat, L. ; Peleg, Z. ; Ordon, F. ; Fahima, T. ; Korol, A. ; Saranga, Y. ; Krugman, T. Genomic Architecture of Phenotypic Plasticity in Response to Water Stress in Tetraploid Wheat. International Journal of Molecular Sciences 2021, 22. Publisher's VersionAbstract
Phenotypic plasticity is one of the main mechanisms of adaptation to abiotic stresses via changes in critical developmental stages. Altering flowering phenology is a key evolutionary strategy of plant adaptation to abiotic stresses, to achieve the maximum possible reproduction. The current study is the first to apply the linear regression residuals as drought plasticity scores while considering the variation in flowering phenology and traits under non-stress conditions. We characterized the genomic architecture of 17 complex traits and their drought plasticity scores for quantitative trait loci (QTL) mapping, using a mapping population derived from a cross between durum wheat (Triticum turgidum ssp. durum) and wild emmer wheat (T. turgidum ssp. dicoccoides). We identified 79 QTLs affected observed traits and their plasticity scores, of which 33 reflected plasticity in response to water stress and exhibited epistatic interactions and/or pleiotropy between the observed and plasticity traits. Vrn-B3 (TaTF1) residing within an interval of a major drought-escape QTL was proposed as a candidate gene. The favorable alleles for most of the plasticity QTLs were contributed by wild emmer wheat, demonstrating its high potential for wheat improvement. Our study presents a new approach for the quantification of plant adaptation to various stresses and provides new insights into the genetic basis of wheat complex traits under water-deficit stress.
Shumeiko, V. ; Hidas, G. ; Nowogrodski, C. ; Pinto, Y. ; Gofrit, O. ; Duvdevani, M. ; Shoseyov, O. BactoSpin: Novel Technology for Rapid Bacteria Detection and Antibiotic Susceptibility Testing. Sensors 2021, 21. Publisher's VersionAbstract
Inappropriate use of antibiotics is one of the leading causes of the increasing numbers of resistant bacteria strains, resulting in 700,000 deaths worldwide each year. Reducing unnecessary use of antibiotics and choosing the most effective antibiotics instead of broad-spectrum drugs will slow the arms race between germs and humans. Urinary tract infections (UTIs) are among the most common bacterial infections. Currently, accurate diagnosis of UTI requires approximately 48 h from the time of urine sample collection until antibiotic susceptibility test (AST) results. This work presents a rapid bacterial detection device that integrates a centrifuge, microscope, and incubator. Two disposable microfluidic chips were developed. The first chip was designed for bacteria concentration, detection, and medium exchange. A second multi-channel chip was developed for AST. This chip contains superhydrophobic and hydrophilic coatings to ensure liquid separation between the channels without the need for valves. The designed chips supported the detection of E. coli at a concentration as low as 5 × 103 cells/mL within 5 min and AST in under 2 h. AST was also successfully performed with Klebsiella pneumonia isolated from a human urine sample. In addition, machine-learning-based image recognition was shown to reduce the required time for AST and to provide results within 1 h for E. coli cells. Thus, the BactoSpin device can serve as an efficient and rapid platform for UTI diagnostics and AST.
Lindtner, T. ; Uzan, A. Y. ; Eder, M. ; Bar-On, B. ; Elbaum, R. Repetitive hygroscopic snapping movements in awns of wild oats. 2021. Publisher's VersionAbstract
Wild oat (Avena sterilis) is a very common annual plant species. Successful seed dispersion support its wide distribution in Africa, Asia and Europe. The seed dispersal units are made of two elongated stiff awns that are attached to a pointy compartment containing two seeds. The awns bend and twist with changes in humidity, pushing the seeds along and into the soil. The present work reveals the material structure of the awns, and models their functionality as two-link robotic arms. Based on nano-to-micro structure analyses the bending and twisting hygroscopic movements are explained. The coordinated movements of two sister awns attached to one dispersal unit were followed. Our work shows that sister awns intersect typically twice every wetting-drying cycle. Once the awns cross each other, epidermal silica hairs are suggested to lock subsequent movements, resulting in stress accumulation. Sudden release of the interlocked awns induces jumps of the dispersal unit and changes in its movement direction. Our findings propose a new role to epidermis silica hairs and a new facet of wild oat seed dispersion. Reversible jumping mechanism in multiple-awn seed dispersal units may serve as a blueprint for reversibly jumping robotic systems.Statement of significance The seed dispersal unit of wild oats carries two elongated stiff awns covered by unidirectional silica hairs. The awns bend and twist with changes in humidity, pushing the seed capsule along and into the ground. We studied structures constructing the movement mechanism and modeled the awn as a two-link robotic arm. We show that sister awns, attached to the same seed capsule, intersect twice every drying cycle. Once the awns cross each other, the epidermal silica hairs are suggested to lock any subsequent movements, causing stress accumulation. Sudden release of the interlocked awns may cause the dispersal unit to jump and change its direction. Our findings suggest a new role to silica hairs and a new dispersal mechanism in multiple-awn seed dispersal units.
Vaidya, A. S. ; Peterson, F. C. ; Eckhardt, J. ; Xing, Z. ; Park, S. - Y. ; Dejonghe, W. ; Takeuchi, J. ; Pri-Tal, O. ; Faria, J. ; Elzinga, D. ; et al. Click-to-lead design of a picomolar ABA receptor antagonist with potent activity in vivo. Proceedings of the National Academy of Sciences 2021, 118, e2108281118. Publisher's VersionAbstract
Abscisic acid (ABA) is a phytohormone that plants utilize to coordinate responses to abiotic stress, modulate seed dormancy, and is central to plant development in several contexts. Chemicals that activate or block ABA signaling are useful as research tools and as potential agrochemical leads. Many successes have been reported for ABA activators (agonists), but existing ABA blockers (antagonists) are limited by modest in vivo activity. Here we report antabactin (ANT), a potent ABA blocker developed using “click chemistry”–based diversification of a known ABA activator. Structural studies reveal, ANT disrupts signaling by stabilizing ABA receptors in an unproductive form. ANT can accelerate seed germination in multiple species, making it a chemical tool for improving germination.Abscisic acid (ABA) is a key plant hormone that mediates both plant biotic and abiotic stress responses and many other developmental processes. ABA receptor antagonists are useful for dissecting and manipulating ABA’s physiological roles in vivo. We set out to design antagonists that block receptor–PP2C interactions by modifying the agonist opabactin (OP), a synthetically accessible, high-affinity scaffold. Click chemistry was used to create an ∼4,000-member library of C4-diversified opabactin derivatives that were screened for receptor antagonism in vitro. This revealed a peptidotriazole motif shared among hits, which we optimized to yield antabactin (ANT), a pan-receptor antagonist. An X-ray crystal structure of an ANT–PYL10 complex (1.86 Å) reveals that ANT’s peptidotriazole headgroup is positioned to sterically block receptor–PP2C interactions in the 4′ tunnel and stabilizes a noncanonical closed-gate receptor conformer that partially opens to accommodate ANT binding. To facilitate binding-affinity studies using fluorescence polarization, we synthesized TAMRA–ANT. Equilibrium dissociation constants for TAMRA–ANT binding to Arabidopsis receptors range from ∼400 to 1,700 pM. ANT displays improved activity in vivo and disrupts ABA-mediated processes in multiple species. ANT is able to accelerate seed germination in Arabidopsis, tomato, and barley, suggesting that it could be useful as a germination stimulant in species where endogenous ABA signaling limits seed germination. Thus, click-based diversification of a synthetic agonist scaffold allowed us to rapidly develop a high-affinity probe of ABA–receptor function for dissecting and manipulating ABA signaling.The atomic coordinates and structure factors reported in this article have been deposited in the Protein Data Bank, https://www.wwpdb.org/ [PDB ID codes 7MLC (45) and 7MLD (46)].
Shohat, H. ; Cheriker, H. ; Kilambi, H. V. ; Illouz Eliaz, N. ; Blum, S. ; Amsellem, Z. ; Tarkowská, D. ; Aharoni, A. ; Eshed, Y. ; Weiss, D. Inhibition of gibberellin accumulation by water deficiency promotes fast and long-term ‘drought avoidance’ responses in tomato. New PhytologistNew PhytologistNew Phytol 2021, n/a. Publisher's VersionAbstract
Summary Plants reduce transpiration to avoid dehydration during drought episodes by stomatal closure and inhibition of canopy growth. Previous studies have suggested that low gibberellin (GA) activity promotes these ?drought avoidance? responses. Using genome editing, molecular, physiological and hormone analyses, we examined if drought regulates GA metabolism in tomato (Solanum lycopersicum) guard cells and leaves, and studied how this affects water loss. Water deficiency inhibited the expression of the GA biosynthesis genes GA20 oxidase1 (GA20ox1) and GA20ox2 and induced the GA deactivating gene GA2ox7 in guard cells and leaf tissue, resulting in reduced levels of bioactive GAs. These effects were mediated by abscisic acid-dependent and abscisic acid-independent pathways, and by the transcription factor TINY1. The loss of GA2ox7 attenuated stomatal response to water deficiency and during soil dehydration, ga2ox7 plants closed their stomata later, and wilted faster than wild-type (WT) M82 cv. Mutations in GA20ox1 and GA20ox2, had no effect on stomatal closure, but reduced water loss due to the mutants? smaller canopy areas. The results suggested that drought-induced GA deactivation in guard cells, contributes to stomatal closure at the early stages of soil dehydration, whereas inhibition of GA synthesis in leaves suppresses canopy growth and restricts transpiration area.
Eshed Williams, L. Genetics of Shoot Meristem and Shoot Regeneration. Annual Review of GeneticsAnnual Review of Genetics 2021. Publisher's VersionAbstract
Plants exhibit remarkable lineage plasticity, allowing them to regenerate organs that differ from their respective origins. Such developmental plasticity is dependent on the activity of pluripotent founder cells or stem cells residing in meristems. At the shoot apical meristem (SAM), the constant flow of cells requires continuing cell specification governed by a complex genetic network, with the WUSCHEL transcription factor and phytohormone cytokinin at its core. In this review, I discuss some intriguing recent discoveries that expose new principles and mechanisms of patterning and cell specification acting both at the SAM and, prior to meristem organogenesis during shoot regeneration. I also highlight unanswered questions and future challenges in the study of SAM and meristem regeneration. Finally, I put forward a model describing stochastic events mediated by epigenetic factors to explain how the gene regulatory network might be initiated at the onset of shoot regeneration. Expected final online publication date for the Annual Review of Genetics, Volume 55 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.Plants exhibit remarkable lineage plasticity, allowing them to regenerate organs that differ from their respective origins. Such developmental plasticity is dependent on the activity of pluripotent founder cells or stem cells residing in meristems. At the shoot apical meristem (SAM), the constant flow of cells requires continuing cell specification governed by a complex genetic network, with the WUSCHEL transcription factor and phytohormone cytokinin at its core. In this review, I discuss some intriguing recent discoveries that expose new principles and mechanisms of patterning and cell specification acting both at the SAM and, prior to meristem organogenesis during shoot regeneration. I also highlight unanswered questions and future challenges in the study of SAM and meristem regeneration. Finally, I put forward a model describing stochastic events mediated by epigenetic factors to explain how the gene regulatory network might be initiated at the onset of shoot regeneration. Expected final online publication date for the Annual Review of Genetics, Volume 55 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Shivaraj, S. M. ; Mandlik, R. ; Bhat, J. A. ; Raturi, G. ; Elbaum, R. ; Alexander, L. ; Tripathi, D. K. ; Deshmukh, R. ; Sonah, H. Outstanding Questions on the Beneficial Role of Silicon in Crop Plants. Plant Cell Physiol 2021. Publisher's VersionAbstract
Silicon (Si) is widely accepted as a beneficial element for plants. Despite the substantial progress made in understanding Si transport mechanisms and modes of action in plants, several questions remain unanswered. In this review, we discuss such outstanding questions and issues commonly encountered by biologists studying the role of Si in plants in relation to Si bioavailability. In recent years, advances in our understanding of the role of Si-solubilizing bacteria and the efficacy of Si-nanoparticles have been made. However, there are many unknown aspects associated with structural and functional features of Si transporters, Si loading into the xylem, and the role of specialized cells like silica cells and compounds preventing Si polymerization in plant tissues. In addition, despite several thousand reports showing the positive effects of Si in high as well as low Si-accumulating plant species, the exact roles of Si at the molecular level are yet to be understood. Some evidence suggests that Si regulates hormonal pathways and nutrient uptake, thereby explaining various observed benefits of Si uptake. However, how Si modulates hormonal pathways or improves nutrient uptake remains to be explained. Finally, we summarize the knowledge gaps that will provide a roadmap for further research on plant silicon biology, leading to an exploration of the benefits of Si uptake to enhance crop production.
Steiner, E. ; Triana, M. R. ; Kubasi, S. ; Blum, S. ; Paz-Ares, J. ; Rubio, V. ; Weiss, D. KISS ME DEADLY F-box proteins modulate cytokinin responses by targeting the transcription factor TCP14 for degradation. Plant Physiol 2021, 185, 1495 - 1499. Publisher's VersionAbstract
Dear Editor,TCPs are basic helix-loop-helix transcription factors. Arabidopsis (Arabidopsis thaliana) has 24 TCPs, 13 belong to Class I, and 11 to Class II (Martín-Trillo and Cubas, 2010). Class I TCPs promote, and Class II restrict, cell proliferation (Efroni et al., 2008). Previously, we showed that two Class I TCPs, TCP14 and TCP15 interact with the O-fucosyltransferase (OFT) SPINDLY (SPY) to promote cytokinin (CK) responses in young leaves and flowers (Steiner et al., 2012). SPY activity is required for TCP14 stability; the loss of SPY stimulates TCP14 proteolysis by the 26S proteasome and inhibits CK responses in flowers and leaves (Steiner et al., 2016). This is reversed by mutation in CULLIN1 (CUL1), suggesting a role for Skp, CUL1, F-box E3 ubiquitin ligase (SCF) complex in TCP14 proteolysis. OFT modify target proteins by transferring mono-fucose to serine and threonine residues (Holdener and Haltiwanger, 2019). SPY modifies the DELLA protein REPRESSOR OF ga1-3 (RGA) and increases its activity (Zentella et al., 2017). SPY also modifies PSEUDO RESPONSE REGULATOR5 (PRR5) and facilitates its proteolysis (Wang et al., 2020). Since mutation in the putative OFT catalytic domain of SPY (spy-3) is sufficient to reduce TCP14 stability, we suggested that O-fucosylation by SPY stabilizes TCP14. Here, we bring evidence that TCP14 interacts with the F-box proteins KISS ME DEADLY1 (KMD1), KMD2, and KMD4 (Kim et al., 2013) and this interaction promotes its degradation in the spy background. KMDs are negative regulators of CK signaling; they interact and destabilize the CK signaling components Type B RESPONSE REGULATOR (RR). Zhang et al. (2013) found that KMDs also target PHENYLALANINE AMMONIA LYASE (PAL) for degradation. Thus, although F-box proteins have high substrate specificity, KMDs seem to target several unrelated proteins.
Firsov, A. ; Shaloiko, L. ; Kozlov, O. ; Vainstein, A. ; Dolgov, S. Tomatoes expressing thaumatin II retain their sweet taste after salting and pickling processing. Journal of the Science of Food and Agriculture 2021, 101, 5286-5289. Publisher's VersionAbstract
Abstract BACKGROUND Thaumatin II, a supersweet protein from the African plant katemfe (Thaumatococcus daniellii Benth.), shows promise as a zero-calorie sweetener for use in the food and pharmaceutical industries and for improving the taste of fruit. RESULTS We report on the stability of thaumatin in salted and pickled tomatoes, as well as on the effect of thaumatin on the taste quality of processed tomatoes. Fruit of tomato cv. Yalf, transformed with the thaumatin II gene were salted and pickled and then stored for 6 months. Western blot analysis showed relative thaumatin II stability at salting; its content in processed fruits was 62–83% of the initial level depending in the studied line. In pickled tomatoes, thaumatin II content was decreased by up to 25% of the initial amount. Both salted and pickled tomatoes had a sweet taste with a typical thaumatin aftertaste. Salted tomatoes were characterized as being sweeter than pickled tomatoes. The overall taste of pickled tomatoes was rated by panellists as significantly better compared to that of salted or non-processed ones. CONCLUSION In the present study, we have shown that tomatoes expressing supersweet protein thaumatin II can be used for processing under mild conditions, including salting and pickling. © 2021 Society of Chemical Industry.
Grunwald, Y. ; Wigoda, N. ; Sade, N. ; Yaaran, A. ; Torne, T. ; Gosa, S. C. ; Moran, N. ; Moshelion, M. Arabidopsis leaf hydraulic conductance is regulated by xylem sap pH, controlled, in turn, by a P-type H+-ATPase of vascular bundle sheath cells. The Plant Journal 2021, 106, 301-313. Publisher's VersionAbstract
SUMMARY The leaf vascular bundle sheath cells (BSCs) that tightly envelop the leaf veins, are a selective and dynamic barrier to xylem sap water and solutes radially entering the mesophyll cells. Under normal conditions, xylem sap pH below 6 is presumably important for driving and regulating the transmembranal solute transport. Having discovered recently a differentially high expression of a BSC proton pump, AHA2, we now test the hypothesis that it regulates the xylem sap pH and leaf radial water fluxes. We monitored the xylem sap pH in the veins of detached leaves of wild-type Arabidopsis, AHA mutants and aha2 mutants complemented with AHA2 gene solely in BSCs. We tested an AHA inhibitor (vanadate) and stimulator (fusicoccin), and different pH buffers. We monitored their impact on the xylem sap pH and the leaf hydraulic conductance (Kleaf), and the effect of pH on the water osmotic permeability (Pf) of isolated BSCs protoplasts. We found that AHA2 is necessary for xylem sap acidification, and in turn, for elevating Kleaf. Conversely, AHA2 knockdown, which alkalinized the xylem sap, or, buffering its pH to 7.5, reduced Kleaf, and elevating external pH to 7.5 decreased the BSCs Pf. All these showed a causative link between AHA2 activity in BSCs and leaf radial hydraulic water conductance.
Salam, B. B. ; Barbier, F. ; Danieli, R. ; Teper-Bamnolker, P. ; Ziv, C. ; Spíchal, L. ; Aruchamy, K. ; Shnaider, Y. ; Leibman, D. ; Shaya, F. ; et al. Sucrose promotes stem branching through cytokinin. Plant Physiol 2021, 185, 1708 - 1721. Publisher's VersionAbstract
Shoot branching is an important aspect of plant architecture because it substantially affects plant biology and agricultural performance. Sugars play an important role in the induction of shoot branching in several species, including potato (Solanum tuberosum L.). However, the mechanism by which sugars affect shoot branching remains mostly unknown. In the present study, we addressed this question using sugar-mediated induction of bud outgrowth in potato stems under etiolated conditions. Our results indicate that sucrose feeding to detached stems promotes the accumulation of cytokinin (CK), as well as the expression of vacuolar invertase (VInv), an enzyme that contributes to sugar sink strength. These effects of sucrose were suppressed by CK synthesis and perception inhibitors, while CK supplied to detached stems induced bud outgrowth and VInv activity in the absence of sucrose. CK-induced bud outgrowth was suppressed in vinv mutants, which we generated by genome editing. Altogether, our results identify a branching-promoting module, and suggest that sugar-induced lateral bud outgrowth is in part promoted by the induction of CK-mediated VInv activity.
Israeli, A. ; Burko, Y. ; Shleizer-Burko, S. ; Zelnik, I. D. ; Sela, N. ; Hajirezaei, M. R. ; Fernie, A. R. ; Tohge, T. ; Ori, N. ; Bar, M. Coordinating the morphogenesis-differentiation balance by tweaking the cytokinin-gibberellin equilibrium. PLOS Genetics 2021, 17, 1-25. Publisher's VersionAbstract
Morphogenesis and differentiation are important stages in organ development and shape determination. However, how they are balanced and tuned during development is not fully understood. In the compound leaved tomato, an extended morphogenesis phase allows for the initiation of leaflets, resulting in the compound form. Maintaining a prolonged morphogenetic phase in early stages of compound-leaf development in tomato is dependent on delayed activity of several factors that promote differentiation, including the CIN-TCP transcription factor (TF) LA, the MYB TF CLAU and the plant hormone Gibberellin (GA), as well as on the morphogenesis-promoting activity of the plant hormone cytokinin (CK). Here, we investigated the genetic regulation of the morphogenesis-differentiation balance by studying the relationship between LA, CLAU, TKN2, CK and GA. Our genetic and molecular examination suggest that LA is expressed earlier and more broadly than CLAU and determines the developmental context of CLAU activity. Genetic interaction analysis indicates that LA and CLAU likely promote differentiation in parallel genetic pathways. These pathways converge downstream on tuning the balance between CK and GA. Comprehensive transcriptomic analyses support the genetic data and provide insights into the broader molecular basis of differentiation and morphogenesis processes in plants.
Elbaum, R. ; Elbaum, M. A tough 3D puzzle in the walnut shell. J Exp Bot 2021, 72, 4593 - 4595. Publisher's VersionAbstract
Plant organs initiate as a group of tiny meristematic cells. After expansion, three basic shapes of organs may be defined: cylindrical, laminar, and spherical (Trinh et al., 2021). The development of a lamina can be followed by various surface and subsurface microscopy methods. However, organs shaped as opaque spheres are most conveniently studied in sections.Antreich et al. (2021) applied 3D reconstructions based on optical and scanning electron microscopy to study the development of cells building the walnut shell. Restricted by cellulose, the growing cells bulge and interdigitate with neighboring cells, leaving gaps at the regions of high curvature. Examining the cell interfaces with Raman microspectroscopy, they show that these gaps are lined with pectin.
Singh, T. ; Yadav, S. K. ; Vainstein, A. ; Kumar, V. Genome recoding strategies to improve cellular properties: mechanisms and advances. 2021, 2 79 - 95. Publisher's VersionAbstract
The genetic code, once believed to be universal and immutable, is now known to contain many variations and is not quite universal. The basis for genome recoding strategy is genetic code variation that can be harnessed to improve cellular properties. Thus, genome recoding is a promising strategy for the enhancement of genome flexibility, allowing for novel functions that are not commonly documented in the organism in its natural environment. Here, the basic concept of genetic code and associated mechanisms for the generation of genetic codon variants, including biased codon usage, codon reassignment, and ambiguous decoding, are extensively discussed. Knowledge of the concept of natural genetic code expansion is also detailed. The generation of recoded organisms and associated mechanisms with basic targeting components, including aminoacyl-tRNA synthetase–tRNA pairs, elongation factor EF-Tu and ribosomes, are highlighted for a comprehensive understanding of this concept. The research associated with the generation of diverse recoded organisms is also discussed. The success of genome recoding in diverse multicellular organisms offers a platform for expanding protein chemistry at the biochemical level with non-canonical amino acids, genetically isolating the synthetic organisms from the natural ones, and fighting viruses, including SARS-CoV2, through the creation of attenuated viruses. In conclusion, genome recoding can offer diverse applications for improving cellular properties in the genome-recoded organisms.
Pandey, A. K. ; Jiang, L. ; Moshelion, M. ; Gosa, S. C. ; Sun, T. ; Lin, Q. ; Wu, R. ; Xu, P. Functional physiological phenotyping with functional mapping: A general framework to bridge the phenotype-genotype gap in plant physiology. iScience 2021, 24, 102846. Publisher's VersionAbstract
Summary The recent years have witnessed the emergence of high-throughput phenotyping techniques. In particular, these techniques can characterize a comprehensive landscape of physiological traits of plants responding to dynamic changes in the environment. These innovations, along with the next-generation genomic technologies, have brought plant science into the big-data era. However, a general framework that links multifaceted physiological traits to DNA variants is still lacking. Here, we developed a general framework that integrates functional physiological phenotyping (FPP) with functional mapping (FM). This integration, implemented with high-dimensional statistical reasoning, can aid in our understanding of how genotype is translated toward phenotype. As a demonstration of method, we implemented the transpiration and soil-plant-atmosphere measurements of a tomato introgression line population into the FPP-FM framework, facilitating the identification of quantitative trait loci (QTLs) that mediate the spatiotemporal change of transpiration rate and the test of how these QTLs control, through their interaction networks, phenotypic plasticity under drought stress.
Ackerman-Lavert, M. ; Fridman, Y. ; Matosevich, R. ; Khandal, H. ; Friedlander-Shani, L. ; Vragović, K. ; El, R. B. ; Horev, G. ; Tarkowská, D. ; Efroni, I. ; et al. Auxin requirements for a meristematic state in roots depend on a dual brassinosteroid function. Current Biology 2021. Publisher's VersionAbstract
Summary Root meristem organization is maintained by an interplay between hormone signaling pathways that both interpret and determine their accumulation and distribution. The interacting hormones Brassinosteroids (BR) and auxin control the number of meristematic cells in the Arabidopsis root. BR was reported both to promote auxin signaling input and to repress auxin signaling output. Whether these contradicting molecular outcomes co-occur and what their significance in meristem function is remain unclear. Here, we established a dual effect of BR on auxin, with BR simultaneously promoting auxin biosynthesis and repressing auxin transcriptional output, which is essential for meristem maintenance. Blocking BR-induced auxin synthesis resulted in rapid BR-mediated meristem loss. Conversely, plants with reduced BR levels were resistant to a critical loss of auxin biosynthesis, maintaining their meristem morphology. In agreement, injured root meristems, which rely solely on local auxin synthesis, regenerated when both auxin and BR synthesis were inhibited. Use of BIN2 as a tool to selectively inhibit BR signaling yielded meristems with distinct phenotypes depending on the perturbed tissue: meristem reminiscent either of BR-deficient mutants or of high BR exposure. This enabled mapping of the BR-auxin interaction that maintains the meristem to the outer epidermis and lateral root cap tissues and demonstrated the essentiality of BR signaling in these tissues for meristem response to BR. BR activity in internal tissues however, proved necessary to control BR levels. Together, we demonstrate a basis for inter-tissue coordination and how a critical ratio between these hormones determines the meristematic state.
Goldberg, K. ; Herrmann, I. ; Hochberg, U. ; Rozenstein, O. Generating Up-to-Date Crop Maps Optimized for Sentinel-2 Imagery in Israel. Remote Sensing 2021, 13. Publisher's VersionAbstract
The overarching aim of this research was to develop a method for deriving crop maps from a time series of Sentinel-2 images between 2017 and 2018 to address global challenges in agriculture and food security. This study is the first step towards improving crop mapping based on phenological features retrieved from an object-based time series on a national scale. Five main crops in Israel were classified: wheat, barley, cotton, carrot, and chickpea. To optimize the object-based classification process, different characteristics and inputs of the mean shift segmentation algorithm were tested, including vegetation indices, three-band combinations, and high/low emphasis on the spatial and spectral characteristics. Four known vegetation indices (VIs)-based time series were tested. Additionally, we compared two widely used machine learning methods for crop classification, support vector machine (SVM) and random forest (RF), in addition to a newer classifier, extreme gradient boosting (XGBoost). Lastly, we examined two accuracy measures—overall accuracy (OA) and area under the curve (AUC)—in order to optimally estimate the accuracy in the case of imbalanced class representation. Mean shift best performed when emphasizing both the spectral and spatial characteristics while using the green, red, and near-infrared (NIR) bands as input. Both accuracy measures showed that RF and XGBoost classified different types of crops with significantly greater success than achieved by SVM. Nevertheless, AUC was better able to represent the significant differences between the classification algorithms than OA was. None of the VIs showed a significantly higher contribution to the classification. However, normalized difference infrared index (NDII) with XGBoost classifier showed the highest AUC results (88%). This study demonstrates that the short-wave infrared (SWIR) band with XGBoost improves crop type classification results. Furthermore, the study emphasizes the importance of addressing imbalanced classification datasets by using a proper accuracy measure. Since object-based classification and phenological features derived from a VI-based time series are widely used to produce crop maps, the current study is also relevant for operational agricultural management and informatics at large scales.
Mishra, P. ; Sadeh, R. ; Bino, E. ; Polder, G. ; Boer, M. P. ; Rutledge, D. N. ; Herrmann, I. Complementary chemometrics and deep learning for semantic segmentation of tall and wide visible and near-infrared spectral images of plants. Computers and Electronics in Agriculture 2021, 186, 106226. Publisher's VersionAbstract
Close range spectra imaging of agricultural plants is widely performed to support digital plant phenotyping, a task where physicochemical changes in plants are monitored in a non-destructive way. A major step before analyzing the spectral images of plants is to distinguish the plant from the background. Usually, this is an easy task and can be performed using mathematical operations on the combinations of selected spectral bands, such as estimating the normalized difference vegetative index (NDVI). However, when the background of plants contains objects with similar spectral properties as plant then the segmentation based on the threshold of NDVI images can suffer. Another common approach is to train pixel classifiers on spectra extracted from selected locations in the spectral image, but such an approach does not take the spatial information about the plant structure into account. From a technical perspective, plant spectral imaging for digital phenotyping applications usually involves imaging several plants together for a comparative purpose, hence, the imaging scene is relatively big in terms of memory. To solve the challenge of plant segmentation and handling the memory challenge, this study proposes a novel approach, which combines chemometrics with advanced deep learning (DL) based semantic segmentation. The approach has four key steps. As a first step, the spectral image is pre-processed to reduce illumination effects present in the close-range spectral images of plants resulting from the interaction of light with complex plant geometry. Different chemometric pre-processing methods were explored to find possible improvements in the segmentation performance of the DL model. The second step was to perform a principal components analysis (PCA) to reduce the dimensionality of the images, thus drastically reducing their size so that they can be handled more easily using the available computer memory during the training of the DL model. As the third step, small random images (128 × 128) were subsampled from the tall and wide image matrices to generate the training and validation sets for training the DL models. In the last step, a U-net based deep semantic segmentation model was trained and validated on the sub-sampled spectral images. The results showed that the proposed approach allowed efficient handling and training of the DL segmentation model. The intersection over union (IoU) scores for the segmentation was 0.96 for the independent test set image. The segmentation based on variable sorting for normalization and standard normal variate pre-processed data achieved the highest IoU scores. A combination of chemometrics and DL led to an efficient segmentation of tall and wide spectral images which otherwise would have given out-of-memory errors. The developed method can facilitate digital phenotyping tasks where close-range spectral imaging is used to estimate the physicochemical properties of plants.