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pepper heat shock protein 70a interacts with the type iii effector avrbst and triggers plant cell death and immunity.heat shock proteins (hsps) function as molecular chaperones and are essential for the maintenance and/or restoration of protein homeostasis. the genus xanthomonas type iii effector protein avrbst induces hypersensitive cell death in pepper (capsicum annuum). here, we report the identification of the pepper cahsp70a as an avrbst-interacting protein. bimolecular fluorescence complementation and coimmunoprecipitation assays confirm the specific interaction between cahsp70a and avrbst in planta. the ...201425491184
pepper heat shock protein 70a interacts with the type iii effector avrbst and triggers plant cell death and immunity.heat shock proteins (hsps) function as molecular chaperones and are essential for the maintenance and/or restoration of protein homeostasis. the genus xanthomonas type iii effector protein avrbst induces hypersensitive cell death in pepper (capsicum annuum). here, we report the identification of the pepper cahsp70a as an avrbst-interacting protein. bimolecular fluorescence complementation and coimmunoprecipitation assays confirm the specific interaction between cahsp70a and avrbst in planta. the ...201425491184
teaching fido new modification tricks. 201425255332
proteomics of effector-triggered immunity (eti) in plants.effector-triggered immunity (eti) was originally termed gene-for-gene resistance and dates back to fundamental observations of flax resistance to rust fungi by harold henry flor in the 1940s. since then, genetic and biochemical approaches have defined our current understanding of how plant "resistance" proteins recognize microbial effectors. more recently, proteomic approaches have expanded our view of the protein landscape during eti and contributed significant advances to our mechanistic under ...201425513776
pepper mitochondrial formate dehydrogenase1 regulates cell death and defense responses against bacterial pathogens.formate dehydrogenase (fdh; ec 1.2.1.2) is an nad-dependent enzyme that catalyzes the oxidation of formate to carbon dioxide. here, we report the identification and characterization of pepper (capsicum annuum) mitochondrial fdh1 as a positive regulator of cell death and defense responses. transient expression of fdh1 caused hypersensitive response (hr)-like cell death in pepper and nicotiana benthamiana leaves. the d-isomer -: specific 2-hydroxyacid dehydrogenase signatures of fdh1 were required ...201425237129
global analysis of the hrpl regulon in the plant pathogen pseudomonas syringae pv. tomato dc3000 reveals new regulon members with diverse functions.the type iii secretion system (t3ss) is required for virulence in the gram-negative plant pathogen pseudomonas syringae pv. tomato dc3000. the alternative sigma factor hrpl directly regulates expression of t3ss genes via a promoter sequence, often designated as the "hrp promoter." although the hrpl regulon has been extensively investigated in dc3000, it is not known whether additional regulon members remain to be found. to systematically search for hrpl-regulated genes, we used chromatin immunop ...201425170934
analysis of the pantoea ananatis pan-genome reveals factors underlying its ability to colonize and interact with plant, insect and vertebrate hosts.pantoea ananatis is found in a wide range of natural environments, including water, soil, as part of the epi- and endophytic flora of various plant hosts, and in the insect gut. some strains have proven effective as biological control agents and plant-growth promoters, while other strains have been implicated in diseases of a broad range of plant hosts and humans. by analysing the pan-genome of eight sequenced p. ananatis strains isolated from different sources we identified factors potentially ...201424884520
type iv secretion system is not involved in infection process in citrus.the type iv secretion system (t4ss) is used by gram-negative bacteria to translocate protein and dna substrates across the cell envelope and into target cells. xanthomonas citri subsp. citri contains two copies of the t4ss, one in the chromosome and the other is plasmid-encoded. to understand the conditions that induce expression of the t4ss in xcc, we analyzed, in vitro and in planta, the expression of 18 orfs from the t4ss and 7 hypothetical flanking genes by rt-qpcr. as a positive control, we ...201424707292
regulation of primary plant metabolism during plant-pathogen interactions and its contribution to plant defense.plants are constantly exposed to microorganisms in the environment and, as a result, have evolved intricate mechanisms to recognize and defend themselves against potential pathogens. one of these responses is the downregulation of photosynthesis and other processes associated with primary metabolism that are essential for plant growth. it has been suggested that the energy saved by downregulation of primary metabolism is diverted and used for defense responses. however, several studies have show ...201424575102
the cuticle and plant defense to pathogens.the cuticle provides a physical barrier against water loss and protects against irradiation, xenobiotics, and pathogens. components of the cuticle are perceived by invading fungi and activate developmental processes during pathogenesis. in addition, cuticle alterations of various types induce a syndrome of reactions that often results in resistance to necrotrophs. this article reviews the current knowledge on the role of the cuticle in relation to the perception of pathogens and activation of de ...201424982666
the kiwifruit emerging pathogen pseudomonas syringae pv. actinidiae does not produce ahls but possesses three luxr solos.pseudomonas syringae pv. actinidiae (psa) is an emerging phytopathogen causing bacterial canker disease in kiwifruit plants worldwide. quorum sensing (qs) gene regulation plays important roles in many different bacterial plant pathogens. in this study we analyzed the presence and possible role of n-acyl homoserine lactone (ahl) quorum sensing in psa. it was established that psa does not produce ahls and that a typical complete luxi/r qs system is absent in psa strains. psa however possesses thre ...201424498215
pathogenic adaptations to host-derived antibacterial copper.recent findings suggest that both host and pathogen manipulate copper content in infected host niches during infections. in this review, we summarize recent developments that implicate copper resistance as an important determinant of bacterial fitness at the host-pathogen interface. an essential mammalian nutrient, copper cycles between copper (i) (cu(+)) in its reduced form and copper (ii) (cu(2+)) in its oxidized form under physiologic conditions. cu(+) is significantly more bactericidal than ...201424551598
analysis of clonostachys rosea-induced resistance to tomato gray mold disease in tomato leaves.tomato gray mold disease, caused by botrytis cinerea, is a serious disease in tomato. clonostachys rosea is an antagonistic microorganism to b. cinerea. to investigate the induced resistance mechanism of c. rosea, we examined the effects of these microorganisms on tomato leaves, along with changes in the activities of three defense enzymes (pal, ppo, gst), second messengers (no, h2o2, o2(-)) and phytohormones (iaa, aba, ga3, zt, meja, sa and c2h4). compared to the control, all treatments induced ...201425061981
killing two birds with one stone: trans-kingdom suppression of pamp/mamp-induced immunity by t3e from enteropathogenic bacteria.within the past decade, remarkable similarities between the molecular organization of animal and plant systems for non-self discrimination were revealed. obvious parallels exist between the molecular structures of the receptors mediating the recognition of pathogen- or microbe-associated molecular patterns (pamps/mamps) with plant pattern recognition receptors strikingly resembling mammalian toll-like receptors. mitogen-activated protein kinase cascades, leading to the transcriptional activation ...201425101059
interactions of seedborne bacterial pathogens with host and non-host plants in relation to seed infestation and seedling transmission.the ability of seed-borne bacterial pathogens (acidovorax citrulli, clavibacter michiganensis subsp. michiganensis, pseudomonas syringae pv. tomato, xanthomonas euvesicatoria, and pseudomonas syringae pv. glycinea) to infest seeds of host and non-host plants (watermelon, tomato, pepper, and soybean) and subsequent pathogen transmission to seedlings was investigated. a non-pathogenic, pigmented strain of serratia marcescens was also included to assess a null-interacting situation with the same pl ...201424936863
identification of novel coxiella burnetii icm/dot effectors and genetic analysis of their involvement in modulating a mitogen-activated protein kinase pathway.coxiella burnetii, the causative agent of q fever, is a human intracellular pathogen that utilizes the icm/dot type ivb secretion system to translocate effector proteins into host cells. to identify novel c. burnetii effectors, we applied a machine-learning approach to predict c. burnetii effectors, and examination of 20 such proteins resulted in the identification of 13 novel effectors. to determine whether these effectors, as well as several previously identified effectors, modulate conserved ...201424958706
the factors affecting effectiveness of treatment in phages therapy.in recent years, the use of lytic bacteriophages as antimicrobial agents controlling pathogenic bacteria has appeared as a promising new alternative strategy in the face of growing antibiotic resistance which has caused problems in many fields including medicine, veterinary medicine, and aquaculture. the use of bacteriophages has numerous advantages over traditional antimicrobials. the effectiveness of phage applications in fighting against pathogenic bacteria depends on several factors such as ...201424600439
small non-coding rnas in plant-pathogenic xanthomonas spp.the genus xanthomonas comprises a large group of plant-pathogenic bacteria. the infection and bacterial multiplication in the plant tissue depends on the type iii secretion system and other virulence determinants. recent studies revealed that bacterial virulence is also controlled at the post-transcriptional level by small non-coding rnas (srnas). in this review, we highlight our current knowledge about srnas and rna-binding proteins in xanthomonas species.201424667380
lamp assay and rapid sample preparation method for on-site detection of flavescence dorée phytoplasma in grapevine.in europe the most devastating phytoplasma associated with grapevine yellows (gy) diseases is a quarantine pest, flavescence dorée (fdp), from the 16srv taxonomic group. the on-site detection of fdp with an affordable device would contribute to faster and more efficient decisions on the control measures for fdp. therefore, a real-time isothermal lamp assay for detection of fdp was validated according to the eppo standards and miqe guidelines. the lamp assay was shown to be specific and extremely ...201426146413
lamp assay and rapid sample preparation method for on-site detection of flavescence dorée phytoplasma in grapevine.in europe the most devastating phytoplasma associated with grapevine yellows (gy) diseases is a quarantine pest, flavescence dorée (fdp), from the 16srv taxonomic group. the on-site detection of fdp with an affordable device would contribute to faster and more efficient decisions on the control measures for fdp. therefore, a real-time isothermal lamp assay for detection of fdp was validated according to the eppo standards and miqe guidelines. the lamp assay was shown to be specific and extremely ...201426146413
chp8, a diguanylate cyclase from pseudomonas syringae pv. tomato dc3000, suppresses the pathogen-associated molecular pattern flagellin, increases extracellular polysaccharides, and promotes plant immune evasion.the bacterial plant pathogen pseudomonas syringae causes disease in a wide range of plants. the associated decrease in crop yields results in economic losses and threatens global food security. competition exists between the plant immune system and the pathogen, the basic principles of which can be applied to animal infection pathways. p. syringae uses a type iii secretion system (t3ss) to deliver virulence factors into the plant that promote survival of the bacterium. the p. syringae t3ss is a ...201424846383
functionally redundant rxlr effectors from phytophthora infestans act at different steps to suppress early flg22-triggered immunity.genome sequences of several economically important phytopathogenic oomycetes have revealed the presence of large families of so-called rxlr effectors. functional screens have identified rxlr effector repertoires that either compromise or induce plant defense responses. however, limited information is available about the molecular mechanisms underlying the modes of action of these effectors in planta. the perception of highly conserved pathogen- or microbe-associated molecular patterns (pamps/mam ...201424763622
rapid and sensitive detection of candidatus liberibacter asiaticus by loop mediated isothermal amplification combined with a lateral flow dipstick.citrus huanglongbing (hlb) is the most devastating bacterial citrus disease worldwide. three candidatus liberibacter species are associated with different forms of the disease: candidatus liberibacter asiaticus, candidatus liberibacter americanus and candidatus liberibacter africanus. amongst them, candidatus liberibacter asiaticus is the most widespread and economically important. these gram-negative bacterial plant pathogens are phloem-limited and vectored by citrus psyllids. the current manag ...201424708539
salmonella enterica induces and subverts the plant immune system.infections with salmonella enterica belong to the most prominent causes of food poisoning and infected fruits and vegetables represent important vectors for salmonellosis. although it was shown that plants raise defense responses against salmonella, these bacteria persist and proliferate in various plant tissues. recent reports shed light into the molecular interaction between plants and salmonella, highlighting the defense pathways induced and the means used by the bacteria to escape the plant ...201424772109
an important role of the pepper phenylalanine ammonia-lyase gene (pal1) in salicylic acid-dependent signalling of the defence response to microbial pathogens.phenylalanine ammonia-lyase (pal) has a crucial role in secondary phenylpropanoid metabolism and is one of the most extensively studied enzymes with respect to plant responses to biotic and abiotic stress. here, we identified the pepper (capsicum annuum) pal (capal1) gene, which was induced in pepper leaves by avirulent xanthomonas campestris pv. vesicatoria (xcv) infection. capal1-silenced pepper plants exhibited increased susceptibility to virulent and avirulent xcv infection. reactive oxygen ...201424642849
physiological and molecular implications of plant polyamine metabolism during biotic interactions.during ontogeny, plants interact with a wide variety of microorganisms. the association with mutualistic microbes results in benefits for the plant. by contrast, pathogens may cause a remarkable impairment of plant growth and development. both types of plant-microbe interactions provoke notable changes in the polyamine (pa) metabolism of the host and/or the microbe, being each interaction a complex and dynamic process. it has been well documented that the levels of free and conjugated pas underg ...201424672533
peptidoglycan from fermentation by-product triggers defense responses in grapevine.plants are constantly under attack from a variety of microorganisms, and rely on a series of complex detection and response systems to protect themselves from infection. here, we found that a by-product of glutamate fermentation triggered defense responses in grapevine, increasing the expression of defense response genes in cultured cells, foliar chitinase activity, and resistance to infection by downy mildew in leaf explants. to identify the molecule that triggered this innate immunity, we frac ...201425427192
probing formation of cargo/importin-α transport complexes in plant cells using a pathogen effector.importin-αs are essential adapter proteins that recruit cytoplasmic proteins destined for active nuclear import to the nuclear transport machinery. cargo proteins interact with the importin-α armadillo repeat domain via nuclear localization sequences (nlss), short amino acids motifs enriched in lys and arg residues. plant genomes typically encode several importin-α paralogs that can have both specific and partially redundant functions. although some cargos are preferentially imported by a distin ...201425284001
probing formation of cargo/importin-α transport complexes in plant cells using a pathogen effector.importin-αs are essential adapter proteins that recruit cytoplasmic proteins destined for active nuclear import to the nuclear transport machinery. cargo proteins interact with the importin-α armadillo repeat domain via nuclear localization sequences (nlss), short amino acids motifs enriched in lys and arg residues. plant genomes typically encode several importin-α paralogs that can have both specific and partially redundant functions. although some cargos are preferentially imported by a distin ...201425284001
redundancy among phospholipase d isoforms in resistance triggered by recognition of the pseudomonas syringae effector avrrpm1 in arabidopsis thaliana.plants possess a highly sophisticated system for defense against microorganisms. so called mamp (microbe-associated molecular patterns) triggered immunity (mti) prevents the majority of non-adapted pathogens from causing disease. adapted plant pathogens use secreted effector proteins to interfere with such signaling. recognition of microbial effectors or their activity by plant resistance (r)-proteins triggers a second line of defense resulting in effector triggered immunity (eti). the latter us ...201425431578
a conserved peptide pattern from a widespread microbial virulence factor triggers pattern-induced immunity in arabidopsis.microbe- or host damage-derived patterns mediate activation of pattern-triggered immunity (pti) in plants. microbial virulence factor (effector)-triggered immunity (eti) constitutes a second layer of plant protection against microbial attack. various necrosis and ethylene-inducing peptide 1 (nep1)-like proteins (nlps) produced by bacterial, oomycete and fungal microbes are phytotoxic virulence factors that exert immunogenic activities through phytotoxin-induced host cell damage. we here show tha ...201425375108
novel cyclic di-gmp effectors of the yajq protein family control bacterial virulence.bis-(3',5') cyclic di-guanylate (cyclic di-gmp) is a key bacterial second messenger that is implicated in the regulation of many critical processes that include motility, biofilm formation and virulence. cyclic di-gmp influences diverse functions through interaction with a range of effectors. our knowledge of these effectors and their different regulatory actions is far from complete, however. here we have used an affinity pull-down assay using cyclic di-gmp-coupled magnetic beads to identify cy ...201425329577
expression profiling during arabidopsis/downy mildew interaction reveals a highly-expressed effector that attenuates responses to salicylic acid.plants have evolved strong innate immunity mechanisms, but successful pathogens evade or suppress plant immunity via effectors delivered into the plant cell. hyaloperonospora arabidopsidis (hpa) causes downy mildew on arabidopsis thaliana, and a genome sequence is available for isolate emoy2. here, we exploit the availability of genome sequences for hpa and arabidopsis to measure gene-expression changes in both hpa and arabidopsis simultaneously during infection. using a high-throughput cdna tag ...201425329884
apoplastic peroxidases are required for salicylic acid-mediated defense against pseudomonas syringae.reactive oxygen species (ros) generated by nadph oxidases or apoplastic peroxidases play an important role in the plant defense response. diminished expression of at least two arabidopsis thaliana peroxidase encoding genes, prx33 (at3g49110) and prx34 (at3g49120), as a consequence of anti-sense expression of a heterologous french bean peroxidase gene (asfbp1.1), were previously shown to result in reduced levels of ros following pathogen attack, enhanced susceptibility to a variety of bacterial a ...201425096754
apoplastic peroxidases are required for salicylic acid-mediated defense against pseudomonas syringae.reactive oxygen species (ros) generated by nadph oxidases or apoplastic peroxidases play an important role in the plant defense response. diminished expression of at least two arabidopsis thaliana peroxidase encoding genes, prx33 (at3g49110) and prx34 (at3g49120), as a consequence of anti-sense expression of a heterologous french bean peroxidase gene (asfbp1.1), were previously shown to result in reduced levels of ros following pathogen attack, enhanced susceptibility to a variety of bacterial a ...201425096754
interactions of salmonella with animals and plants.salmonella enterica species are gram-negative bacteria, which are responsible for a wide range of food- and water-borne diseases in both humans and animals, thereby posing a major threat to public health. recently, there has been an increasing number of reports, linking salmonella contaminated raw vegetables and fruits with food poisoning. many studies have shown that an essential feature of the pathogenicity of salmonella is its capacity to cross a number of barriers requiring invasion of a lar ...201425653644
sucrose and invertases, a part of the plant defense response to the biotic stresses.sucrose is the main form of assimilated carbon which is produced during photosynthesis and then transported from source to sink tissues via the phloem. this disaccharide is known to have important roles as signaling molecule and it is involved in many metabolic processes in plants. essential for plant growth and development, sucrose is engaged in plant defense by activating plant immune responses against pathogens. during infection, pathogens reallocate the plant sugars for their own needs forci ...201425002866
searchdogs bacteria, software that provides automated identification of potentially missed genes in annotated bacterial genomes.we report the development of searchdogs bacteria, software to automatically detect missing genes in annotated bacterial genomes by combining blast searches with comparative genomics. having successfully applied the approach to yeast genomes, we redeveloped searchdogs to function as a standalone, downloadable package, requiring only a set of genbank annotation files as input. the software automatically generates a homology structure using reciprocal blast and a synteny-based method; this is follo ...201424659774
image-based phenotyping of plant disease symptoms.plant diseases cause significant reductions in agricultural productivity worldwide. disease symptoms have deleterious effects on the growth and development of crop plants, limiting yields and making agricultural products unfit for consumption. for many plant-pathogen systems, we lack knowledge of the physiological mechanisms that link pathogen infection and the production of disease symptoms in the host. a variety of quantitative high-throughput image-based methods for phenotyping plant growth a ...201425601871
image-based phenotyping of plant disease symptoms.plant diseases cause significant reductions in agricultural productivity worldwide. disease symptoms have deleterious effects on the growth and development of crop plants, limiting yields and making agricultural products unfit for consumption. for many plant-pathogen systems, we lack knowledge of the physiological mechanisms that link pathogen infection and the production of disease symptoms in the host. a variety of quantitative high-throughput image-based methods for phenotyping plant growth a ...201425601871
structure of a diguanylate cyclase from thermotoga maritima: insights into activation, feedback inhibition and thermostability.large-scale production of bis-3'-5'-cyclic-di-gmp (c-di-gmp) would facilitate biological studies of numerous bacterial signaling pathways and phenotypes controlled by this second messenger molecule, such as virulence and biofilm formation. c-di-gmp constitutes also a potentially interesting molecule as a vaccine adjuvant. even though chemical synthesis of c-di-gmp can be done, the yields are incompatible with mass-production. tdgc, a stand-alone diguanylate cyclase (dgc or ggdef domain) from the ...201425360685
analysis of phaseolus vulgaris response to its association with trichoderma harzianum (all-42) in the presence or absence of the phytopathogenic fungi rhizoctonia solani and fusarium solani.the present study was carried out to evaluate the ability of trichoderma harzianum (all 42-isolated from brazilian cerrado soil) to promote common bean growth and to modulate its metabolism and defense response in the presence or absence of the phytopathogenic fungi rhizoctonia solani and fusarium solani using a proteomic approach. t. harzianum was able to promote common bean plants growth as shown by the increase in root/foliar areas and by size in comparison to plants grown in its absence. the ...201424878929
phenotypic and genotypic characterization of some lactic acid bacteria isolated from bee pollen: a preliminary study.in the present work, five hundred and sixty-seven isolates of lactic acid bacteria were recovered from raw bee pollen grains. all isolates were screened for their antagonistic activity against both gram-positive and gram-negative pathogenic bacteria. neutralized supernatants of 54 lactic acid bacteria (lab) cultures from 216 active isolates inhibited the growth of indicator bacteria. they were phenotypically characterized, based on the fermentation of 39 carbohydrates. using the simple matching ...201424936378
genetic diversity analysis in a set of caricaceae accessions using resistance gene analogues.in order to assess genetic diversity of a set of 41 caricaceae accessions, this study used 34 primer pairs designed from the conserved domains of bacterial leaf blight resistance genes from rice, in a pcr based approach, to identify and analyse resistance gene analogues from various accessions of carica papaya, vasconcellea goudotiana, v. microcarpa, v. parviflora, v. pubescens, v. stipulata and, v. quercifolia and jacaratia spinosa.201425491793
detection progress of selected drugs in tlc.this entry describes applications of known indicators and dyes as new visualizing reagents and various visualizing systems as well as photocatalytic reactions and bioautography method for the detection of bioactive compounds including drugs and compounds isolated from herbal extracts. broadening index, detection index, characteristics of densitometric band, modified contrast index, limit of detection, densitometric visualizing index, and linearity range of detected compounds were used for the ev ...201424551853
improving crop disease resistance: lessons from research on arabidopsis and tomato.one of the great challenges for food security in the 21st century is to improve yield stability through the development of disease-resistant crops. crop research is often hindered by the lack of molecular tools, growth logistics, generation time and detailed genetic annotations, hence the power of model plant species. our knowledge of plant immunity today has been largely shaped by the use of models, specifically through the use of mutants. we examine the importance of arabidopsis and tomato as ...201425520730
genomic analysis of xanthomonas translucens pathogenic on wheat and barley reveals cross-kingdom gene transfer events and diverse protein delivery systems.in comparison to dicot-infecting bacteria, only limited numbers of genome sequences are available for monocot-infecting and in particular cereal-infecting bacteria. herein we report the characterisation and genome sequence of xanthomonas translucens isolate dar61454 pathogenic on wheat and barley. based on phylogenetic analysis of the atp synthase beta subunit (atpd) gene, dar61454 is most closely related to other x. translucens strains and the sugarcane- and banana- infecting xanthomonas strain ...201424416331
the rise of the undead: pseudokinases as mediators of effector-triggered immunity.pathogens use effector proteins to suppress host immunity and promote infection. however, plants can recognize specific effectors and mount an effector-triggered immune response that suppresses pathogen growth. the yopj/hopz family of type iii secreted effector proteins is broadly distributed in bacterial pathogens of both animals and plants. these effectors can either suppress host immunity or elicit defense responses depending on the host genotype. in a recent report, we identified an arabidop ...201424398910
genomic insights into the evolutionary origin of xanthomonas axonopodis pv. citri and its ecological relatives.xanthomonas axonopodis pv. citri (xac) is the causal agent of citrus bacterial canker (cbc) and is a serious problem worldwide. like cbc, several important diseases in other fruits, such as mango, pomegranate, and grape, are also caused by xanthomonas pathovars that display remarkable specificity toward their hosts. while citrus and mango diseases were documented more than 100 years ago, the pomegranate and grape diseases have been known only since the 1950s and 1970s, respectively. interestingl ...201425085494
altered cultivar resistance of kimchi cabbage seedlings mediated by salicylic acid, jasmonic acid and ethylene.two cultivars buram-3-ho (susceptible) and cr-hagwang (moderate resistant) of kimchi cabbage seedlings showed differential defense responses to anthracnose (colletotrichum higginsianum), black spot (alternaria brassicicola) and black rot (xanthomonas campestris pv. campestris, xcc) diseases in our previous study. defense-related hormones salicylic acid (sa), jasmonic acid (ja) and ethylene led to different transcriptional regulation of pathogenesis-related (pr) gene expression in both cultivars. ...201425289020
evaluation of antibacterial and cytotoxic activity of artemisia nilagirica and murraya koenigii leaf extracts against mycobacteria and macrophages.artemisia nilagirica (asteraceae) and murraya koenigii (rutaceae) are widely distributed in eastern region of india. leaves of artemisia nilagirica plant are used to treat cold and cough by the local tribal population in east india. murraya koenigii is an edible plant previously reported to have an antibacterial activity. pathogenic strains of mycobacteria are resistant to most of the conventional antibiotics. therefore, it is imperative to identify novel antimycobacterial molecules to treat myc ...201424597853
the phytotoxin coronatine is a multifunctional component of the virulence armament of pseudomonas syringae.plant pathogens deploy an array of virulence factors to suppress host defense and promote pathogenicity. numerous strains of pseudomonas syringae produce the phytotoxin coronatine (cor). a major aspect of cor function is its ability to mimic a bioactive jasmonic acid (ja) conjugate and thus target the ja-receptor cor-insensitive 1 (coi1). biological activities of cor include stimulation of ja-signaling and consequent suppression of sa-dependent defense through antagonistic crosstalk, antagonism ...201425156488
hell's bels: bacterial e3 ligases that exploit the eukaryotic ubiquitin machinery. 201425121772
genome-wide identification of mapkk and mapkkk gene families in tomato and transcriptional profiling analysis during development and stress response.mitogen-activated protein kinase (mapk) cascades have important functions in plant growth, development, and response to various stresses. the mapkk and mapkkk gene families in tomato have never been systematically analyzed. in this study, we performed a genome-wide analysis of the mapkk and mapkkk gene families in tomato and identified 5 mapkk genes and 89 mapkkk genes. phylogenetic analyses of the mapkk and mapkkk gene families showed that all the mapkk genes formed four groups (groups a, b, c, ...201425036993
intervention of phytohormone pathways by pathogen effectors.the constant struggle between plants and microbes has driven the evolution of multiple defense strategies in the host as well as offense strategies in the pathogen. to defend themselves from pathogen attack, plants often rely on elaborate signaling networks regulated by phytohormones. in turn, pathogens have adopted innovative strategies to manipulate phytohormone-regulated defenses. tactics frequently employed by plant pathogens involve hijacking, evading, or disrupting hormone signaling pathwa ...201424920334
genome-wide identification of hfq-regulated small rnas in the fire blight pathogen erwinia amylovora discovered small rnas with virulence regulatory function.erwinia amylovora is a phytopathogenic bacterium and causal agent of fire blight disease in apples and pears. although many virulence factors have been characterized, the coordination of expression of these virulence factors in e. amylovora is still not clear. regulatory small rnas (srnas) are important post-transcriptional regulatory components in bacteria. a large number of srnas require the rna chaperone hfq for both stability and functional activation. in e. amylovora, hfq was identified as ...201424885615
growth-defense tradeoffs in plants: a balancing act to optimize fitness.growth-defense tradeoffs are thought to occur in plants due to resource restrictions, which demand prioritization towards either growth or defense, depending on external and internal factors. these tradeoffs have profound implications in agriculture and natural ecosystems, as both processes are vital for plant survival, reproduction, and, ultimately, plant fitness. while many of the molecular mechanisms underlying growth and defense tradeoffs remain to be elucidated, hormone crosstalk has emerge ...201424777989
measurement of ice nucleation-active bacteria on plants and in precipitation by quantitative pcr.ice nucleation-active (ina) bacteria may function as high-temperature ice-nucleating particles (inp) in clouds, but their effective contribution to atmospheric processes, i.e., their potential to trigger glaciation and precipitation, remains uncertain. we know little about their abundance on natural vegetation, factors that trigger their release, or persistence of their ice nucleation activity once airborne. to facilitate these investigations, we developed two quantitative pcr (qpcr) tests of th ...201424317082
tomato genomic resources database: an integrated repository of useful tomato genomic information for basic and applied research.tomato genomic resources database (tgrd) allows interactive browsing of tomato genes, micro rnas, simple sequence repeats (ssrs), important quantitative trait loci and tomato-expen 2000 genetic map altogether or separately along twelve chromosomes of tomato in a single window. the database is created using sequence of the cultivar heinz 1706. high quality single nucleotide polymorphic (snp) sites between the genes of heinz 1706 and the wild tomato s. pimpinellifolium la1589 are also included. ge ...201424466070
unravelling the diversity of grapevine microbiome.vitis vinifera is one of the most widely cultivated fruit crops with a great economic impact on the global industry. as a plant, it is naturally colonised by a wide variety of both prokaryotic and eukaryotic microorganisms that interact with grapevine, having either beneficial or phytopathogenic effects, who play a major role in fruit yield, grape quality and, ultimately, in the evolution of grape fermentation and wine production. therefore, the objective of this study was to extensively charact ...201424454903
transgenic expression of the rice xa21 pattern-recognition receptor in banana (musa sp.) confers resistance to xanthomonas campestris pv. musacearum.banana xanthomonas wilt (bxw), caused by the bacterium xanthomonas campestris pv. musacearum (xcm), is the most devastating disease of banana in east and central africa. the spread of bxw threatens the livelihood of millions of african farmers who depend on banana for food security and income. there are no commercial chemicals, biocontrol agents or resistant cultivars available to control bxw. here, we take advantage of the robust resistance conferred by the rice pattern-recognition receptor (pr ...201424612254
dissemination of 6s rna among bacteria.6s rna is a highly abundant small non-coding rna widely spread among diverse bacterial groups. by competing with dna promoters for binding to rna polymerase (rnap), the rna regulates transcription on a global scale. rnap produces small product rnas derived from 6s rna as template, which rearranges the 6s rna structure leading to dissociation of 6s rna:rnap complexes. although 6s rna has been experimentally analysed in detail for some species, such as escherichia coli and bacillus subtilis, and w ...201425483037
luxr solos in photorhabdus species.bacteria communicate via small diffusible molecules to mediate group-coordinated behavior, a process designated as quorum sensing. the basic molecular quorum sensing system of gram-negative bacteria consists of a luxi-type autoinducer synthase producing acyl-homoserine lactones (ahls) as signaling molecules, and a luxr-type receptor detecting the ahls to control expression of specific genes. however, many proteobacteria possess one or more unpaired luxr-type receptors that lack a cognate luxi-li ...201425478328
carbohydrate metabolism in archaea: current insights into unusual enzymes and pathways and their regulation.the metabolism of archaea, the third domain of life, resembles in its complexity those of bacteria and lower eukarya. however, this metabolic complexity in archaea is accompanied by the absence of many "classical" pathways, particularly in central carbohydrate metabolism. instead, archaea are characterized by the presence of unique, modified variants of classical pathways such as the embden-meyerhof-parnas (emp) pathway and the entner-doudoroff (ed) pathway. the pentose phosphate pathway is only ...201424600042
the influence of flanking secondary structures on amino acid content and typical lengths of 3/10 helices.we used 3d structures of a highly redundant set of bacterial proteins encoded by genes of high, average, and low gc-content. four types of connecting bridges-regions situated between any of two major elements of secondary structure (alpha helices and beta strands)-containing a pure random coil were compared with connecting bridges containing 3/10 helices. we included discovered trends in the original "vvtak connecting bridges" algorithm, which is able to predict more probable conformation for a ...201425371821
identification of a cyclic-di-gmp-modulating response regulator that impacts biofilm formation in a model sulfate reducing bacterium.we surveyed the eight putative cyclic-di-gmp-modulating response regulators (rrs) in desulfovibrio vulgaris hildenborough that are predicted to function via two-component signaling. using purified proteins, we examined cyclic-di-gmp (c-di-gmp) production or turnover in vitro of all eight proteins. the two rrs containing only ggdef domains (dvu2067, dvu0636) demonstrated c-di-gmp production activity in vitro. of the remaining proteins, three rrs with hd-gyp domains (dvu0722, dvua0086, and dvu2933 ...201425120537
structure of a novel o-linked n-acetyl-d-glucosamine (o-glcnac) transferase, gtfa, reveals insights into the glycosylation of pneumococcal serine-rich repeat adhesins.protein glycosylation catalyzed by the o-glcnac transferase (ogt) plays a critical role in various biological processes. in streptococcus pneumoniae, the core enzyme gtfa and co-activator gtfb form an ogt complex to glycosylate the serine-rich repeat (srr) of adhesin psrp (pneumococcal serine-rich repeat protein), which is involved in the infection and pathogenesis. here we report the 2.0 å crystal structure of gtfa, revealing a β-meander add-on domain beyond the catalytic domain. it represents ...201424936067
superoxide dismutases and superoxide reductases. 201424684599
membrane lipids in agrobacterium tumefaciens: biosynthetic pathways and importance for pathogenesis.many cellular processes critically depend on the membrane composition. in this review, we focus on the biosynthesis and physiological roles of membrane lipids in the plant pathogen agrobacterium tumefaciens. the major components of a. tumefaciens membranes are the phospholipids (pls), phosphatidylethanolamine (pe), phosphatidylglycerol, phosphatidylcholine (pc) and cardiolipin, and ornithine lipids (ols). under phosphate-limited conditions, the membrane composition shifts to phosphate-free lipid ...201424723930
the acidic c-terminal tail of the gyra subunit moderates the dna supercoiling activity of bacillus subtilis gyrase.gyrase is a type ii dna topoisomerase that introduces negative supercoils into dna in an atp-dependent reaction. it consists of a topoisomerase core, formed by the n-terminal domains of the two gyra subunits and by the two gyrb subunits, that catalyzes double-stranded dna cleavage and passage of a second double-stranded dna through the gap in the first. the c-terminal domains (ctds) of the gyra subunits form a β-pinwheel and bind dna around their positively charged perimeter. as a result, dna is ...201424563461
microbial peptidyl-prolyl cis/trans isomerases (ppiases): virulence factors and potential alternative drug targets.initially discovered in the context of immunomodulation, peptidyl-prolyl cis/trans isomerases (ppiases) were soon identified as enzymes catalyzing the rate-limiting protein folding step at peptidyl bonds preceding proline residues. intense searches revealed that ppiases are a superfamily of proteins consisting of three structurally distinguishable families with representatives in every described species of prokaryote and eukaryote and, recently, even in some giant viruses. despite the clear-cut ...201425184565
polybacterial human disease: the ills of social networking.polybacterial diseases involve multiple organisms that act collectively to facilitate disease progression. although this phenomenon was highlighted early in the 20th century, recent technological advances in diagnostics have led to the appreciation that many infections are far more complex than originally believed. furthermore, it is apparent that although most treatments focus on the dominant bacterial species in an infection, other microbes, including commensals, can have a profound impact on ...201424938173
unique aspects of fiber degradation by the ruminal ethanologen ruminococcus albus 7 revealed by physiological and transcriptomic analysis.bacteria in the genus ruminococcus are ubiquitous members of the mammalian gastrointestinal tract. in particular, they are important in ruminants where they digest a wide range of plant cell wall polysaccharides. for example, ruminococcus albus 7 is a primary cellulose degrader that produces acetate usable by its bovine host. moreover, it is one of the few organisms that ferments cellulose to form ethanol at mesophilic temperatures in vitro. the mechanism of cellulose degradation by r. albus 7 i ...201425477200
substrate specificity of cytoplasmic n-glycosyltransferase.n-linked protein glycosylation is a very common post-translational modification that can be found in all kingdoms of life. the classical, highly conserved pathway entails the assembly of a lipid-linked oligosaccharide and its transfer to an asparagine residue in the sequon nx(s/t) of a secreted protein by the integral membrane protein oligosaccharyltransferase. a few species in the class of γ-proteobacteria encode a cytoplasmic n-glycosylation system mediated by a soluble n-glycosyltransferase ( ...201424962585
a brief review: the z-curve theory and its application in genome analysis.in theoretical physics, there exist two basic mathematical approaches, algebraic and geometrical methods, which, in most cases, are complementary. in the area of genome sequence analysis, however, algebraic approaches have been widely used, while geometrical approaches have been less explored for a long time. the z-curve theory is a geometrical approach to genome analysis. the z-curve is a three-dimensional curve that represents a given dna sequence in the sense that each can be uniquely reconst ...201424822026
comparative genomics of closely related salmonella enterica serovar typhi strains reveals genome dynamics and the acquisition of novel pathogenic elements.typhoid fever is an infectious disease of global importance that is caused by salmonella enterica subsp. enterica serovar typhi (s. typhi). this disease causes an estimated 200,000 deaths per year and remains a serious global health threat. s. typhi is strictly a human pathogen, and some recovered individuals become long-term carriers who continue to shed the bacteria in their faeces, thus becoming main reservoirs of infection.201425412680
defining the metabolic requirements for the growth and colonization capacity of campylobacter jejuni.during the last decade campylobacter jejuni has been recognized as the leading cause of bacterial gastroenteritis worldwide. this facultative intracellular pathogen is a member of the epsilonproteobacteria and requires microaerobic atmosphere and nutrient rich media for efficient proliferation in vitro. its catabolic capacity is highly restricted in contrast to salmonella typhimurium and other enteropathogenic bacteria because several common pathways for carbohydrate utilization are either missi ...201425325018
the interaction of human enteric pathogens with plants.there are an increasing number of outbreaks of human pathogens related to fresh produce. thus, the growth of human pathogens on plants should be explored. human pathogens can survive under the harsh environments in plants, and can adhere and actively invade plants. plant-associated microbiota or insects contribute to the survival and transmission of enteric pathogens in plants. human enteric pathogens also trigger plant innate immunity, but some pathogens-such as salmonella-can overcome this def ...201425288993
characterization of bacteriophages cp1 and cp2, the strain-typing agents for xanthomonas axonopodis pv. citri.the strains of xanthomonas axonopodis pv. citri, the causative agent of citrus canker, are historically classified based on bacteriophage (phage) sensitivity. nearly all x. axonopodis pv. citri strains isolated from different regions in japan are lysed by either phage cp1 or cp2; cp1-sensitive (cp1(s)) strains have been observed to be resistant to cp2 (cp2(r)) and vice versa. in this study, genomic and molecular characterization was performed for the typing agents cp1 and cp2. morphologically, c ...201424123743
exopolysaccharide biosynthesis enables mature biofilm formation on abiotic surfaces by herbaspirillum seropedicae.h. seropedicae associates endophytically and epiphytically with important poaceous crops and is capable of promoting their growth. the molecular mechanisms involved in plant colonization by this microrganism are not fully understood. exopolysaccharides (eps) are usually necessary for bacterial attachment to solid surfaces, to other bacteria, and to form biofilms. the role of h. seropedicae smr1 exopolysaccharide in biofilm formation on both inert and plant substrates was assessed by characteriza ...201425310013
biological roles of the o-methyl phosphoramidate capsule modification in campylobacter jejuni.campylobacter jejuni is a major cause of bacterial gastroenteritis worldwide, and the capsular polysaccharide (cps) of this organism is required for persistence and disease. c. jejuni produces over 47 different capsular structures, including a unique o-methyl phosphoramidate (meopn) modification present on most c. jejuni isolates. although the meopn structure is rare in nature it has structural similarity to some synthetic pesticides. in this study, we have demonstrated, by whole genome comparis ...201424498018
mechanisms of post-transcriptional gene regulation in bacterial biofilms.biofilms are characterized by a dense multicellular community of microorganisms that can be formed by the attachment of bacteria to an inert surface and to each other. the development of biofilm involves the initial attachment of planktonic bacteria to a surface, followed by replication, cell-to-cell adhesion to form microcolonies, maturation, and detachment. mature biofilms are embedded in a self-produced extracellular polymeric matrix composed primarily of bacterial-derived exopolysaccharides, ...201424724055
the arable ecosystem as battleground for emergence of new human pathogens.disease incidences related to escherichia coli and salmonella enterica infections by consumption of (fresh) vegetables, sprouts, and occasionally fruits made clear that these pathogens are not only transmitted to humans via the "classical" routes of meat, eggs, and dairy products, but also can be transmitted to humans via plants or products derived from plants. nowadays, it is of major concern that these human pathogens, especially the ones belonging to the taxonomical family of enterobacteriace ...201424688484
roles of a solo luxr in the biological control agent lysobacter enzymogenes strain oh11.lysobacter enzymogenes is a ubiquitous plant-associated and environmentally friendly bacterium emerging as a novel biological control agent of plant disease. this bacterium produces diverse antifungal factors, such as lytic enzymes and a secondary metabolite (heat-stable antifungal factor [hsaf]) having antifungal activity with a novel structure and mode of action. the regulatory mechanisms for biosynthesis of antifungal factors is largely unknown in l. enzymogenes. the solo luxr proteins have b ...201424111575
emra1 membrane fusion protein of francisella tularensis lvs is required for resistance to oxidative stress, intramacrophage survival and virulence in mice.francisella tularensis is a category a biodefence agent that causes a fatal human disease known as tularaemia. the pathogenicity of f. tularensis depends on its ability to persist inside host immune cells primarily by resisting an attack from host-generated reactive oxygen and nitrogen species (ros/rns). based on the ability of f. tularensis to resist high ros/rns levels, we have hypothesized that additional unknown factors act in conjunction with known antioxidant defences to render ros resista ...201424397487
tssar: tss annotation regime for drna-seq data.differential rna sequencing (drna-seq) is a high-throughput screening technique designed to examine the architecture of bacterial operons in general and the precise position of transcription start sites (tss) in particular. hitherto, drna-seq data were analyzed by visualizing the sequencing reads mapped to the reference genome and manually annotating reliable positions. this is very labor intensive and, due to the subjectivity, biased.201424674136
melanin-templated rapid synthesis of silver nanostructures.as a potent antimicrobial agent, silver nanostructures have been used in nanosensors and nanomaterial-based assays for the detection of food relevant analytes such as organic molecules, aroma, chemical contaminants, gases and food borne pathogens. in addition silver based nanocomposites act as an antimicrobial for food packaging materials. in this prospective, the food grade melanin pigment extracted from sponge associated actinobacterium nocardiopsis alba msa10 and melanin mediated synthesis of ...201424885756
a system to automatically classify and name any individual genome-sequenced organism independently of current biological classification and nomenclature.a broadly accepted and stable biological classification system is a prerequisite for biological sciences. it provides the means to describe and communicate about life without ambiguity. current biological classification and nomenclature use the species as the basic unit and require lengthy and laborious species descriptions before newly discovered organisms can be assigned to a species and be named. the current system is thus inadequate to classify and name the immense genetic diversity within s ...201424586551
a linkage between smeijk efflux pump, cell envelope integrity, and σe-mediated envelope stress response in stenotrophomonas maltophilia.resistance nodulation division (rnd) efflux pumps, such as the smeijk pump of stenotrophomonas maltophilia, are known to contribute to the multidrug resistance in gram-negative bacteria. however, some rnd pumps are constitutively expressed even though no antimicrobial stresses occur, implying that there should be some physical implications for these rnd pumps. in this study, the role of smeijk in antimicrobials resistance, envelope integrity, and σe-mediated envelope stress response (esr) of s. ...201425390933
transcriptional regulation of bacterial virulence gene expression by molecular oxygen and nitric oxide.molecular oxygen (o2) and nitric oxide (no) are diatomic gases that play major roles in infection. the host innate immune system generates reactive oxygen species and no as bacteriocidal agents and both require o2 for their production. furthermore, the ability to adapt to changes in o2 availability is crucial for many bacterial pathogens, as many niches within a host are hypoxic. pathogenic bacteria have evolved transcriptional regulatory systems that perceive these gases and respond by reprogra ...201425603427
structural and biochemical analysis of a unique phosphatase from bdellovibrio bacteriovorus reveals its structural and functional relationship with the protein tyrosine phosphatase class of phytase.bdellovibrio bacteriovorus is an unusual δ-proteobacterium that invades and preys on other gram-negative bacteria and is of potential interest as a whole cell therapeutic against pathogens of man, animals and crops. ptps (protein tyrosine phosphatases) are an important class of enzyme involved in desphosphorylating a variety of substrates, often with implications in cell signaling. the b. bacteriovorus open reading frame bd1204 is predicted to encode a ptp of unknown function. bd1204 is both str ...201424718691
type iv pilus biogenesis, twitching motility, and dna uptake in thermus thermophilus: discrete roles of antagonistic atpases pilf, pilt1, and pilt2.natural transformation has a large impact on lateral gene flow and has contributed significantly to the ecological diversification and adaptation of bacterial species. thermus thermophilus hb27 has emerged as the leading model organism for studies of dna transporters in thermophilic bacteria. recently, we identified a zinc-binding polymerization nucleoside triphosphatase (ntpase), pilf, which is essential for the transport of dna through the outer membrane. here, we present genetic evidence that ...201424212586
transcriptomic analysis reveals new regulatory roles of clp signaling in secondary metabolite biosynthesis and surface motility in lysobacter enzymogenes oh11.lysobacter enzymogenes is a bacterial biological control agent emerging as a new source of antibiotic metabolites, such as heat-stable antifungal factor (hsaf) and the antibacterial factor wap-8294a2. the regulatory mechanism(s) for antibiotic metabolite biosynthesis remains largely unknown in l. enzymogenes. clp, a cyclic adenosine monophosphate (camp)-receptor-like protein, is shown to function as a global regulator in modulating biocontrol-associated traits in l. enzymogenes. however, the gen ...201425236801
homogalacturonan-modifying enzymes: structure, expression, and roles in plants.understanding the changes affecting the plant cell wall is a key element in addressing its functional role in plant growth and in the response to stress. pectins, which are the main constituents of the primary cell wall in dicot species, play a central role in the control of cellular adhesion and thereby of the rheological properties of the wall. this is likely to be a major determinant of plant growth. how the discrete changes in pectin structure are mediated is thus a key issue in our understa ...201425056773
identification of the catalytic triad of family s46 exopeptidases, closely related to clan pa endopeptidases.the exopeptidases of family s46 are exceptional, as the closest homologs of these enzymes are the endopeptidases of clan pa. the three-dimensional structure of s46 enzymes is unknown and only one of the catalytic residues, the serine, has been identified. the catalytic histidine and aspartate residues are not experimentally identified. here we present phylogenetic and experimental data that identify all residues of the catalytic triad of s46 peptidase, dipeptidyl aminopeptidase bii (dap bii) fro ...201424598890
prediction and characterization of enzymatic activities guided by sequence similarity and genome neighborhood networks.metabolic pathways in eubacteria and archaea often are encoded by operons and/or gene clusters (genome neighborhoods) that provide important clues for assignment of both enzyme functions and metabolic pathways. we describe a bioinformatic approach (genome neighborhood network; gnn) that enables large scale prediction of the in vitro enzymatic activities and in vivo physiological functions (metabolic pathways) of uncharacterized enzymes in protein families. we demonstrate the utility of the gnn a ...201424980702
the role of bacterial protein tyrosine phosphatases in the regulation of the biosynthesis of secreted polysaccharides.tyrosine phosphorylation and associated protein tyrosine phosphatases are gaining prominence as critical mechanisms in the regulation of fundamental processes in a wide variety of bacteria. in particular, these phosphatases have been associated with the control of the biosynthesis of capsular polysaccharides and extracellular polysaccharides, critically important virulence factors for bacteria.201424295407
fha interaction with phosphothreonine of tssl activates type vi secretion in agrobacterium tumefaciens.the type vi secretion system (t6ss) is a widespread protein secretion system found in many gram-negative bacteria. t6sss are highly regulated by various regulatory systems at multiple levels, including post-translational regulation via threonine (thr) phosphorylation. the ser/thr protein kinase ppka is responsible for this thr phosphorylation regulation, and the forkhead-associated (fha) domain-containing fha-family protein is the sole t6ss phosphorylation substrate identified to date. here we d ...201424626341
identification and biosynthesis of a novel xanthomonadin-dialkylresorcinol-hybrid from azoarcus sp. bh72.a novel xanthomonadin-dialkylresorcinol hybrid named arcuflavin was identified in azoarcus sp. bh72 by a combination of feeding experiments, hplc-ms and maldi-ms and gene clusters encoding the biosynthesis of this non-isoprenoid aryl-polyene containing pigment are reported. a chorismate-utilizing enzyme from the xanb2-type producing 3- and 4-hydroxybenzoic acid and an amp-ligase encoded by these gene clusters were characterized, that might perform the first two steps of the polyene biosynthesis. ...201424618669
pseudomonas aeruginosa isolates from dental unit waterlines can be divided in two distinct groups, including one displaying phenotypes similar to isolates from cystic fibrosis patients.pseudomonas aeruginosa displays broad genetic diversity, giving it an astonishing capacity to adapt to a variety of environments and to infect a wide range of hosts. while many p. aeruginosa isolates of various origins have been analyzed, isolates from cystic fibrosis (cf) patients have received the most attention. less is known about the genetic and phenotypic diversity of p. aeruginosa isolates that colonize other environments where flourishing biofilms can be found. in the present study, 29 p ...201425653647
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