(see also plant physiology)

Innate immune system

• wide temperature ranges, so a lot of germs won’t thrive with these temperature variations.
• lymph pressure is really high, so antigens have a harder time penetrating
• plant fluids travel slowly, so infection spreads slowly
• induced plant resistance traits are expressed in response to attack and occur throughout the plant kingdom.
• extrafloral nectar, a usually inducible trait, is constitutively secreted by Central American Acacia as an indirect resistance, attracting ants that defend plants against herbivores. Leaf damage induces extrafloral nectar secretion in several plant species; among these are various Acacia species and other Fabaceae investigated here. In contrast, Acacia species obligately inhabited by symbiotic ants nourish these ants by secreting extrafloral nectar constitutively at high rates that are not affected by leaf damage. The phylogeny of the genus Acacia and closely related genera indicate that the inducibility of extrafloral nectar is the plesiomorphic or 'original' state, whereas the constitutive extrafloral nectar flow is derived within Acacia. A constitutive resistance trait has evolved from an inducible one, obviously in response to particular functional demands^ref.
• plant defensins are ubiquitous, cationic, cysteine-rich plant peptides and have a folding pattern that shares high similarity to defense peptides of mammals and insects, with antifungal activity
• alfalfa antifungal peptide (alfAFP) defensin isolated from seeds of Medicago sativa displays strong activity against the agronomically important fungal pathogen Verticillium dahliae.
• antimicrobial protein from Mirabilis jalapa
• antimicrobial protein from Phytolacca americana AMP (Pa-AMP-1)
• saponins are soap-like chemicals that are toxic to different types of antigen.  Many saponins are rather sweet, such as the sweet tasting compounds of licorice (Glycyrrhiza spp.). However, there exist some saponins that block the sweet tastes of sugars. You can find these saponins in the roots of a Gymnema sylvestre plant. Beans contain a lot of saponin. When you prepare them, you will notice a little foam in the water. The foam is a result of the bean saponin. Because Medicago sativa (alfalfa) and Avena sativa (cultiuvated oat) saponins combine with bile chemicals (maybe cholesterin or bile salt), they somehow decrease re-absorption of bile cholesterol into the body. As a result, the alfalfa and oats may reduce a person’s cholesterol level slightly. Anyway they have hemolytic properties when introduced in excess.
• conipher resin contains antibiotic chemicals which are collected by bees and ants
• treatment of plants with flg22, a peptide representing the elicitor-active epitope of flagellin, induces the expression of numerous defence-related genes and triggers resistance to pathogenic bacteria in wild-type plants, but not in plants carrying mutations in the flagellin receptor gene FLS2. This induced resistance seems to be independent of salicylic acid, jasmonic acid and ethylene signalling. Wild-type and fls2 mutants both display enhanced resistance when treated with crude bacterial extracts, even devoid of elicitor-active flagellin, indicating the existence of functional perception systems for PAMPs other than flagellin. Although fls2 mutant plants are as susceptible as the wild type when bacteria are infiltrated into leaves, they are more susceptible to the pathogen Pseudomonas syringae pv. tomato DC3000 when it is sprayed on the leaf surface. Thus, flagellin perception restricts bacterial invasion, probably at an early step, and contributes to the plant's disease resistance^ref.
• systemic acquired resistance (SAR) : lower leaves of a plant, when inoculated with a necrotizing pathogen, will express typical symptoms in leaves of susceptible plants. At a later time (a few days) when newly developed upper leaves are inoculated with the same or a related pathogen, fewer lesions and/or reduced lesion size are observed, relative to control plants not previously inoculated. The inducing agent is considered to be salicylic acid (SA). SAR is associated with systemic expression of pathogenesis-related proteins (PR proteins) in infected plants. Moreover, application of exogenous SA induces both PR proteins and resistance to attack by pathogens^{ref1, ref2, ref3}
• resistance (R) proteins detect pathogens and initiate defense mechanisms including MAP kinase activation, oxygen radical formation, salicylate production, induced transcription of kinases and transcription factors, and rapid cell death. Many of these proteins have an NBD and LRRs and may represent the oldest examples of proteins using this CIITA-like domain arrangement, typical of CATERPILLER family members. Pathogen recognition by the plant immune system is governed by structurally related, polymorphic products of disease resistance (R) genes. RAR1 and/or SGT1b mediate the function of many R proteins. RAR1 controls pre-activation R protein accumulation by an unknown mechanism. Arabidopsis SGT1b has 2 distinct, genetically separable functions in the plant immune system: SGT1b antagonizes RAR1 to negatively regulate R protein accumulation before infection, and SGT1b has a RAR1-independent function that regulates programmed cell death during infection. The balanced activities of RAR1 and SGT1, in concert with cytosolic HSP90, modulate pre-activation R protein accumulation and signaling competence^ref
• self-incompatibility (SI) : in the plant kingdom, sophisticated self-recognition systems have evolved that allow plants with perfect (hermaphroditic) flowers to avoid inbreeding. SI encompasses several systems that are mechanistically distinct but have the same outcome, namely the inhibition of self-related pollen tube development and, consequently, the prevention of sperm cell delivery to the ovules. SI systems are said to discriminate between self and nonself because they produce different outcomes in self- and cross-pollinations. Specificity in SI is typically controlled by one or more highly polymorphic genetic loci. In the context of SI, self and nonself mean, respectively, genetic identity and nonidentity at the SI locus (or loci) in pistils and pollen. The outcome of this discrimination is the converse of that of the immune response, in which case self has been classically defined as those elements that are tolerated and do not elicit a response (although modified in the danger model). In SI, self, is the condition that elicits the response and is inhibited, whereas nonself is the condition that is ignored and does not elicit a response. As an advantageous outbreeding device, SI is widely distributed in flowering plants. It evolved indipendently in several lineages, and the SI systems adopted by different plant families vary with respect to site and mechanism of self inhibition.
• in self-incompatible species of the crucifer family (e.g. Brassica species and close relatives of Arabidopsis thaliana), SI disrupts hydration and germination of a pollen grain on the stigma epidermis, thus preventing growth of pollen tubes into the subepidermal tissues of the pistil. In this early-acting SI system recognition of pollen is mediated by a epidermal receptor (S-locus receptor protein kinase (SRK)) / pollen ligand (S-locus cysteine-ricj protein gene (SCR) / SP-11) system, with a signaling cascade being triggered within the stigma epidermis. This interaction occurs only between receptor and ligand variants encoded by the same S haplotype. : SRK ectodomains can diverge by as much as 35% (only 7 Cys residues and 1 Gly residue are conserved among the 22 SCR sequences isolated to date). A difficult issue to resolve is how multiple SI specificities evolve. In this 2-gene system, SRK an SCR proteins ecoded in 1 S haplotype must co-evolve to maintain their interaction. Therefore, a mutation in one component that disrupts their interaction will lead to the loss of SI, and a new specificity can arise only if a compensatory mutation in the second component within the same S haplotype restores the interaction. Schemes outlining how this process might have occurred repeatedly to evolve a multiplicity of SI specificities usually involve sequential mutations through self-compatible intermediate. Evolution through a dual-specificity intermediate has also been proposed, but this scheme has been criticized because it requires at least 3 mutations in a single S haplotype for each new specificity. The binding of self SCR to the SRK ectodomain apparently causes oligomerization, transphosphorylation of the receptor, and phosphorylation of specific substrates. One such substrate is the arm repeat-containing protein ARC1. A U-box in ARC1 suggests a role for ubiquitination in the SI response, but the immediate cause of inhibition of self pollen remains unknown. Nor it is known if events downstream of SRK activation are mediated by components shared with other signaling pathways. Another challenge is to explain how allelic polymorphism in SRK and SCR translate into the puzzling interactions of co-dominance, dominance, incomplete dominance, or mutual weakening that are exhibited by different S haplotypes. These interactions occur not only in stigmas but also in pollen, because in crucifers the SI specificity of a pollen grain is determined by the diploid genotype of the plant that produced it rather than by its own genotype. The SCR peptide exhibit some resemblance, but not sequence identity, to defensins, a ubiquitous class of small cysteine-rich antimicrobial peptides found in mammals, insects, and plants that function primarily in innate immunity, although some have functions unrelated to defense. Defensin-like proteins are gouped into highly diverged classes whose evolutionary relationships have been difficult to resolve, and it will be even more difficult to retrace the evolutionary path connecting the rapidly evolving SCR gene to defensins. Nevertheless, it can be speculated that a function directed at recognizing nonself patterns in microbial pathogens was co-opted for self recognition in the SI response.
• in other families, SI acts after pollen germination and pollen tube ingress into the pistil (late-acting SI systems) and invading pollen tubes are actively destroyed
• within the stigmatic zone. In the poppy, a glycoprotein secreted by cells of the stigma somehow induces within self pollen tubes a signal transduction cascade manifested by increase in cytosolic calcium, disruption of the cytoskeleton, and cessation of growth.
• within the style (as in the tobacco, rose, and snapdragon families) : an RNas secreted by cells of the style enters pollen tubes and degrades cytoplasmic RNA selectively in self tubes.
A unique feature of plant SI system is that they are based on the recognition of self, whereas all other known recognition systems are based on the recognition of nonself. This distinction holds true, even in comparisons to other mate recognition systems that also prevent self-mating. For example, in basidiomycete fungi, multiallelic genes at 2 unlinked loci specify a large number of different mating types, and mating can only occur between individuals that differ at both loci. One of these loci contains genes for lipopeptide pheromone ligands and pheromone receptors and is therefore at least superficially analogoud to the crucifer S locus. A major difference, however, is that a given pheromone can only activate receptors encoded in a different haplotype and not a receptor encoded in the same haplotype. Additionally, a pheromone can activate several different receptors, and one receptor can be activated by more than one pheromone. This relaxed specificity is essential in such a non-self recognition system, because a one-to-one correspondence between receptor and ligand, which maximizes the number of compatible mates in self-incompatible crucifer populations, would instead have the unfavorable effect of severely restricting flexibility in mate choice in the fungal system. Despite their unique features, plant SI systems share important similarities with other eukaryotic self/nonself recognition systems, such as the vertebrate MHC, histocompatibility in colonial marine vertebrates, and mating type in Chlamydomonas and fungi. The striking parallels among these disparate systems, which have been noted by immunologist grappling with the origin of adaptive immunity are a consequence of similar selective pressures for diversification and co-evolution of recognition functions to retain affinity between interaction partners. A hallmark of these specific recognition systems is that their genes are subject to intense diverifying selection. Large numbers of alleles are commonly found, and extraordinarily high levels of intraspecific polymorphism are typically achieved, in some cases resulting from accelerated rates of evolution. Due to balancing selection, polymorphisms in these genes can persist for long periods of time and often predate species diversification. Trans-species polymorphism have been described in the MHC and in SI systems, and in both cases, divergence of some allelic lineages appears to have occurred at least 20 million years ago. Another emerging commonality between recognition loci is their structural heteromorphism, which apparently reduces intralocus recombination events and prevents disruption of the co-adapted gene complex. The crucifer S locus has been extensively restructured by expansion or contraction of the physical distance between SRK and SRC, gene duplication, as well as rearrangement of these 2 genes relative to each other and to flanking markers. Similarly, the MHC has undergone frequent gene duplications and deletions during its evolution, and the mating-type locus of Chlamydomonas contains a highly rearranged region that causes suppression of recombination over a 1-megabase chromosomal region.
• Numerous plant species have been known for decades that respond to herbivore attacks by systemically synthesizing defensive chemicals to protect themselves from predators. The nature of systemic wound signals remained obscure until 1991, when an 18-aa peptide called systemin was isolated from tomato leaves and shown to be a primary signal for systemic defense. More recently, 2 new hydroxyproline-rich, glycosylated peptide defense signals have been isolated from tobacco leaves, and three from tomato leaves. Because of their origins in plants, small sizes, hydroxyproline contents (tomato systemin is proline-rich), and defense-signaling activities, the new peptides are included in a functionally defined family of signals collectively called systemins. Systemin, the initial peptide signal found in plants, is an intracellular signaling molecule that is synthesized within the amino acid sequence of a 200-aa precursor, called prosystemin^{ref1, ref2}. Systemin induces proteinase inhibitor protein synthesis in leaves of young tomato plants when supplied for a few minutes through their cut stems at nanomolar concentrations^ref. Radioactively labeled systemin, when placed on wound sites on leaves, is found in the phloem^{ref1, ref2}. A key role for systemin in systemic signaling was established by showing that tomato plants expressing an antisense prosystemin gene become deficient in long-distance wound signaling and are more susceptible to insect attacks than wild-type plants^ref. In contrast to animal peptide hormones, the systemin precursor protein lacks a leader or signal sequence that is required for synthesis and processing through the secretory pathway^ref. Immunolocalization techniques revealed that prosystemin is localized in parenchyma cells of vascular bundles. This localization in the vicinity of the sieve tubes of the phloem may facilitate transport of systemin and the oxylipins it induces in response to wounding to distal cells. Systemin activates defensive genes by interacting with a cell-surface receptor, called SR160, a 160-kDa transmembrane protein with an extracellular leucinerich domain, and an intracellular receptor kinase domain^{ref1, ref2}. The interaction of systemin with the receptor is the first step of a complex intracellular signaling pathway that involves the activation of a mitogen-activated protein kinase (MAPK)^ref, the rapid alkalinization of the extracellular medium^{ref1, ref2}, the activation of a phospholipase^{ref1, ref2}, and the release of linolenic acid that is converted into oxylipins such as phytodienoic acid and jasmonic acid that are powerful signals for defense genes^{ref1, ref2}. The pathway exhibits analogies to the inflammatory response in animals^ref in which wounding activates MAPKs, phospholipases, the release of arachidonic acid from membranes, and its conversion to prostaglandins, which are analogs of phytodienoic acid and jasmonic acid. A simplified diagram of the systemin signaling pathway. The pathway shows several key steps of the signaling pathway, and in particular the steps leading to the blockage of a proton ATPase that leads to the alkalinization of the extracellular medium, which is the basis of the assay developed to identify signaling peptides.


The early alkalinization in response to systemin in tomato suspension cultures was the basis for the development of an assay system that led to the identification and characterization of the systemin receptor, SR160^ref. SR160 is homologous to the BRI1 receptor from Arabidopsis, with a high percentage of amino acid identity. This was the first indication that the systemin receptor may be a close relative of the BRI1 receptor. This possibility was confirmed by the identification and cloning of the tomato brassinolide receptor, BRI1^ref, which was found to be identical to the tomato SR160 receptor. The identity of a receptor with two functions, i.e., defense and development, was unique in plants, but examples are known in the animal kingdom. The dual function of the SR160/BRI1 receptor was supported by experiments in which the tomato SR160/BRI1 receptor cDNA was expressed in tobacco, which does not express a prosystemin gene and therefore does not produce systemin as a defense signal^ref. Transformed tobacco suspension-cultured cells synthesized the receptor and targeted it to the cell surface membranes of tobacco, where it displayed the identical binding characteristics with systemin as SR160 in tomato cells. The systemin–receptor interaction in tobacco cells induced the alkalinization response, indicating that signaling components for the early steps in the systemin signaling pathway were present in tobacco and could be activated by the tomato SR160 receptor when it interacted with systemin. Additionally, a tomato mutant cu-3, which was caused by a mutation in the BRI1 receptor and led to the isolation of the BRI1 gene^ref, is severely impaired in systemin signaling^ref. Because tobacco does not produce systemin, the presence of components in tobacco cells that react to the systemin–receptor interaction indicated that the BRI1 receptor may have, or may have had in the past, a defensive role in plants that was co-opted by systemin as the prosystemin gene evolved in species of the Solaneae subtribe of the Solanaceae family. Tobacco does exhibit a fairly strong systemic defense response to wounding in young plants, but it is much weaker in older plants. Wounded tobacco plants synthesize a trypsin inhibitor (TTI) that is a paralog of tomato inhibitor II^ref, which is induced in tomato leaves in response to wounding. The induction of TTI in tobacco leaves in response to wounding indicates a genetic link between the wound-signaling systems of tomato and tobacco, despite the absence of systemin in tobacco. The synthesis of TTI in young tobacco plants is strongly induced by jasmonic acid^ref, indicative of the early steps of signaling that result in the release of linolenic acid from membranes, similar to tomato plants. The roles of both systemin and jasmonate in systemic signaling have been the subject of considerable speculation^{ref1, ref2}. The evolution of the prosystemin gene in species of the Solaneae subtribe resulted in the production of systemin, a strong systemic signal that is not found in other plants, that amplifies the jasmonate signaling pathway. Prosystemin released from cells at the wound site is likely processed to systemin by proteinases also released from damaged cells. This would allow diffusion of systemin to the apoplast of nearby unwounded vascular cells to interact with its receptor and induce the synthesis of jasmonates. As jasmonates move through the plant, it would induce more prosystemin along with proteolytic enzymes that are known to be induced by jasmonate^ref that could process the nascent prosystemin to systemin to continue to amplify the jasmonate signal in nearby cells. A major source of jasmonates at wound sites is from linolenic acid that is produced by the degradation of membrane lipids within the cellular debris. This source of jasmonates would likely provide an important "kick-start" for defense signaling, as the oxylipins diffuse into the vascular system and are transported to parenchyma cells to up-regulate signaling pathway genes, including the prosystemin gene (in Solaneae species). This hypothetical scenario led us to suspect that other peptide signals that were not systemic may be present in tobacco and tomato plants that might help amplify wound signaling. Such peptides in tobacco, which lacks a systemic peptide signal, might contribute to a localized amplification of the synthesis of jasmonates in response to wounding, and to amplification of jasmonate synthesis in the absence of systemin.
Tobacco Systemins I and II
The search for peptide signals in tobacco was facilitated by the development of a biological assay that is based on the alkalinization of the medium of tomato suspension-cultured cells in response to systemin, which is characterized by an increase in pH (up to 1 pH unit per 10 min) in the culture medium^ref. Suspension cultured tobacco cells do not exhibit an alkalinization response when supplied with tomato systemin, but do so in response to a crude peptide fraction obtained from tobacco leaves, suggesting that a peptide–receptor interaction may be occurring that is coupled to an intracellular response. The alkalinization of 1 ml of suspension cultured tobacco cells in response to 1-µl aliquots from fractions eluting from HPLC or other columns revealed the presence of two peptides that, when purified and characterized, were found to be 18-aa glycopeptides that contained multiple hydroxyproline residues^ref. The 2 peptides are active in the alkalinization assay with tobacco suspension cultures at nM concentrations, and both cause a rapid activation of a 48-kDa MAPK, similar to the 48-kDa MAPK activated by tomato systemin in tomato cells^ref (8). These peptides, supplied to young excised tobacco plants through their cut stems at nM concentrations, induce the synthesis of TTI in leaves. Because of their similarities to tomato systemin in signaling properties, the two peptides were called tobacco systemin I and II^ref. However, because of their hydroxyproline (O) contents, they are now named tobacco hydroxyproline-rich systemin (TobHypSys) I and II to identify them as members of a functionally related systemin family^ref. Neither peptide exhibits homology with tomato systemin, but -OOS-motifs found in the tobacco peptides are posttranslational modifications of the primary translation motif -PPS-that is found in tomato systemin^ref. The 2 new peptides are rich in P/O residues, and in S and T residues as well. These 3 amino acids make up 50% of each peptide and are likely involved in their recognition as defense signals. Mass spectroscopy of the 2 peptides revealed that the attached carbohydrate moieties consist of pentose residues; 9 in TobHypSys I and 6 in TobHypSys II. The structural properties of TobHypSys I and II (leader sequence, hydroxylation of -P-residues, and carbohydrate decorations) indicate that they are synthesized through the secretory system, unlike tomato systemin, which is not glycosylated, whose prolines are not hydroxylated, and whose precursor has no signal sequence^{ref1, ref2}. Both TobHypSys peptides originate from a single 165-aa-long preproprotein, including a signal sequence, with the TobHypSys I sequence near the N terminus and the TobHypSys II sequence near the C terminus^ref. The presence of multiple signaling peptides contained in a single preproprecursor is a characteristic of many animal peptide hormones, but the two tobacco systemins provide the first example in plants of a peptide hormone precursor harboring multiple peptide signals. Although tobacco does not use a tomato systemin homolog for systemic wound signaling, TobHypSys I and II appear to serve roles in defense signaling. Because proTobHypSys is hydroxylated and glycosylated, like well characterized hydroxyproline-rich glycoproteins^ref, it may be associated with cell walls, and may be processed from the precursor at wound sites to provide signals to amplifiy the synthesis of oxylipins during long distance wound signaling. Zhang and Baldwin^ref have elegantly shown that wounding of tobacco causes the synthesis of jasmonic acid that acts as a systemic signal from leaves to roots. It may be that the TobHypSys peptides help generate jasmonic acid that is targeted to the roots of the plant in response to wounds. The isolation of 18-aa, glycosylated, hydroxyproline-containing tobacco systemins led to an investigation of the possibility that tomato plants may also have peptide defense signals similar to the tobacco systemins. The alkalinization assay used to identify and isolate the two tobacco systemins was used to analyze tomato leaf extracts for peptide signals in addition to systemin. The assay identified several components from tomato leaf extracts that caused an alkalinization response. Purification and characterization of these components confirmed that one peptide was tomato systemin and identified three new peptides^ref. The novel peptides exhibit several properties similar to TobHypSys I and II, being hydroxyproline-rich glycopeptides, and ranging in size from 15 to 20 aa. Each of the peptides contains an internal continuous sequence of from 5 to 11 aa variously composed of O, P, S, or T residues, and all are flanked by various charged residues. The peptides are decorated with variable numbers of pentose residues, but their identities and locations on the peptides have not been determined. The amino acid sequences of tomato hydroxyproline-rich systemin (TomHypSys) II and III indicated that they shared limited amino acid sequence homology and were likely products of gene duplication-elongation events. The three tomato peptides exhibit similar biological activities as tomato systemin, indicating that they are defense signals^ref. They all exhibit similar specific activities in the alkalinization assays, and all are effective inducers of proteinase inhibitors I and II synthesis when supplied to young tomato plants. The tomato peptides were therefore included in the functionally defined systemin family and named tomato hydroxyproline-rich systemins, i.e., TomHypSys I (18 amino acid residues), TomHypSys II (20 amino acid residues), and TomHypSys III (15 amino acid residues). Although the three TomHypSys peptides are powerful inducers of defense genes when supplied to excised tomato plants, they do not serve as primary systemic signals, because tomato plants transformed with an antisense prosystemin gene were incapable of systemic signaling in response to wounding^ref. Isolation and characterization of cDNAs coding for the tomato peptides revealed that all three were derived from the same 146-aa preproprotein precursor that includes a signal sequence. This precursor, along with the precursor of the TobHypSys peptides, provides the only examples in plants of polyprotein hormone precursors. A comparison of the amino acid sequences of the TomHypSys precursor with the TobHypSys precursor revealed a 10-aa sequence at their N termini that were identical at eight residues. The nucleotide sequence identity of this sequence was 90%. The significance of this identity is not clear, but does suggest that the two precursor genes may have a common ancient precursor, and that this sequence may have an important function that has been conserved. No homology was evident between prosystemin and either of the two preproprecursor proteins. However, it is of interest that the sequence of tomato systemin contains 7 of 18 residues that are P, S, and T^ref. Because prosystemin has been found only in species of the Solaneae subtribe of the Solanaceae family, we speculate that prosystemin may have been a member of the TomHypSys family and that some mutational event may have caused the loss of the leader sequence that resulted in the synthesis of the nascent precursor peptide to shift from a secretory pathway origin to a cytoplasmic origin, providing a powerful systemic defense signal (systemin) that was retained in the evolving species of the Solaneae subtribe. The multiple P, O, S, and T residues in all six members of the systemin family in tomato and tobacco plants suggest that these residues have important structural roles for interacting with receptors. The P residues confer polyproline II structures (PP II) that have distinct kinks that may be the key to receptor recognition^{ref1, ref2}. PP II structures are commonly found in peptide ligands of animals, where they appear to be important for recognition by receptors^ref. In all 5 HypSys peptides, the central P and O residues are flanked by basic or acidic amino acids, either internally or near both the N and C termini. The discovery of the HypSys defense signals in tomato and tobacco raise many questions about wound signaling in these and other plant species. The relationship of the systemins to local and systemic signaling and whether the HypSys peptides interact with homologs of the systemin receptor or have entirely different receptors for each peptide remain to be determined. Also of interest is whether the different peptides in tomato plants can activate the same complement of defense genes as systemin in response to wounding. The presence of a family of functionally similar HypSys defense signaling peptides in tomato and tobacco that are derived from parologous precursors introduces the possibility that, in other plant families, related defense signaling peptides may be present that share a common ancestral origin. A search for such signals is now possible by using the same strategies that led to the discovery of the defense signaling peptides and their genes in tomato and tobacco that are described herein.

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