Publications

arabidopsis membrane-associated acyl-coa-binding protein acbp1 is involved in stem cuticle formation.	the membrane-anchored arabidopsis thaliana acyl-coa-binding protein1 (atacbp1) plays important roles in embryogenesis and abiotic stress responses, and interacts with long-chain (lc) acyl-coa esters. here, atacbp1 function in stem cuticle formation was investigated. transgenic arabidopsis transformed with an atacbp1pro::gus construct revealed β-glucuronidase (gus) expression on the stem (but not leaf) surface, suggesting a specific role in stem cuticle formation. isothermal titration calorimetry ...	2014	25053648
long-term evolution of nucleotide-binding site-leucine-rich repeat genes: understanding gained from and beyond the legume family.	proper utilization of plant disease resistance genes requires a good understanding of their short- and long-term evolution. here we present a comprehensive study of the long-term evolutionary history of nucleotide-binding site (nbs)-leucine-rich repeat (lrr) genes within and beyond the legume family. the small group of nbs-lrr genes with an amino-terminal resistance to powdery mildew8 (rpw8)-like domain (referred to as rnl) was first revealed as a basal clade sister to both coiled-coil-nbs-lrr ( ...	2014	25052854
genomics and host specialization of honey bee and bumble bee gut symbionts.	gilliamella apicola and snodgrassella alvi are dominant members of the honey bee (apis spp.) and bumble bee (bombus spp.) gut microbiota. we generated complete genomes of the type strains g. apicola wkb1(t) and s. alvi wkb2(t) (isolated from apis), as well as draft genomes for four other strains from bombus. g. apicola and s. alvi were found to occupy very different metabolic niches: the former is a saccharolytic fermenter, whereas the latter is an oxidizer of carboxylic acids. together, they ma ...	2014	25053814
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 ...	2014	25101059
wrky45-dependent priming of diterpenoid phytoalexin biosynthesis in rice and the role of cytokinin in triggering the reaction.	plant activators such as benzothiadiazole (bth) protect plants against diseases by priming the salicylic acid (sa) signaling pathway. in rice, the transcription factor wrky45 plays a central role in this process. to investigate the mechanism involved in defense-priming by bth and the role of wrky45 in this process, we analyzed the transcripts of biosynthetic genes for diterpenoid phytoalexins (dps) during the rice-magnaporthe oryzae interaction. the dp biosynthetic genes were barely upregulated ...	2014	25033935
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, ...	2014	25036993
isolating fungal pathogens from a dynamic disease outbreak in a native plant population to establish plant-pathogen bioassays for the ecological model plant nicotiana attenuata.	the wild tobacco species nicotiana attenuata has been intensively used as a model plant to study its interaction with insect herbivores and pollinators in nature, however very little is known about its native pathogen community. we describe a fungal disease outbreak in a native n. attenuata population comprising 873 plants growing in an area of about 1500 m2. the population was divided into 14 subpopulations and disease symptom development in the subpopulations was monitored for 16 days, reveali ...	2014	25036191
lik1, a cerk1-interacting kinase, regulates plant immune responses in arabidopsis.	chitin, an integral component of the fungal cell wall, is one of the best-studied microbe-associated molecular patterns. previous work identified a lysm receptor-like kinase (lysm-rlk1/cerk1) as the primary chitin receptor in arabidopsis. in order to identify proteins that interact with cerk1, we conducted a yeast two-hybrid screen using the intracellular kinase domain of cerk1 as the bait. this screen identified 54 putative cerk1-interactors. screening mutants defective in 43 of these interacti ...	2014	25036661
the role of effectors and host immunity in plant-necrotrophic fungal interactions.	fungal diseases pose constant threats to the global economy and food safety. as the largest group of plant fungal pathogens, necrotrophic fungi cause heavy crop losses worldwide. the molecular mechanisms of the interaction between necrotrophic fungi and plants are complex and involve sophisticated recognition and signaling networks. here, we review recent findings on the roles of phytotoxin and proteinaceous effectors, pathogen-associated molecular patterns (pamps), and small rnas from necrotrop ...	2014	25513773
evolutionary relationship of disease resistance genes in soybean and arabidopsis specific for the pseudomonas syringae effectors avrb and avrrpm1.	in arabidopsis (arabidopsis thaliana), the pseudomonas syringae effector proteins avrb and avrrpm1 are both detected by the resistance to pseudomonas maculicola1 (rpm1) disease resistance (r) protein. by contrast, soybean (glycine max) can distinguish between these effectors, with avrb and avrrpm1 being detected by the resistance to pseudomonas glycinea 1b (rpg1b) and rpg1r r proteins, respectively. we have been using these genes to investigate the evolution of r gene specificity and have previo ...	2014	25034017
a multicopy srna of listeria monocytogenes regulates expression of the virulence adhesin lapb.	the multicopy srna lhrc of the intracellular pathogen listeria monocytogenes has been shown to be induced under infection-relevant conditions, but its physiological role and mechanism of action is not understood. in an attempt to pinpoint the exact terms of lhrc expression, cell envelope stress could be defined as a specific inducer of lhrc. in this process, the two-component system lisrk was shown to be indispensable for expression of all five copies of lhrc. lapb mrna, encoding a cell wall ass ...	2014	25034691
the beet cyst nematode heterodera schachtii modulates the expression of wrky transcription factors in syncytia to favour its development in arabidopsis roots.	cyst nematodes invade the roots of their host plants as second stage juveniles and induce a syncytium which is the only source of nutrients throughout their life. a recent transcriptome analysis of syncytia induced by the beet cyst nematode heterodera schachtii in arabidopsis roots has shown that thousands of genes are up-regulated or down-regulated in syncytia as compared to root segments from uninfected plants. among the down-regulated genes are many which code for wrky transcription factors. ...	2014	25033038
membrane-triggered plant immunity.	plants have evolved sophisticated defense mechanisms to resist pathogen invasion. upon the pathogen recognition, the host plants activate a variety of signal transduction pathways, and one of representative defense responses is systemic acquired resistance (sar) that provides strong immunity against secondary infections in systemic tissues. accumulating evidence has demonstrated that modulation of membrane composition contributes to establishing sar and disease resistance in arabidopsis, but und ...	2014	25763708
engineering modular and tunable genetic amplifiers for scaling transcriptional signals in cascaded gene networks.	synthetic biology aims to control and reprogram signal processing pathways within living cells so as to realize repurposed, beneficial applications. here we report the design and construction of a set of modular and gain-tunable genetic amplifiers in escherichia coli capable of amplifying a transcriptional signal with wide tunable-gain control in cascaded gene networks. the devices are engineered using orthogonal genetic components (hrprs, hrpv and phrpl) from the hrp (hypersensitive response an ...	2014	25030903
exogenous application of histone demethylase inhibitor trans-2-phenylcyclopropylamine mimics fld loss-of-function phenotype in terms of systemic acquired resistance in arabidopsis thaliana.	plants often learn from previous infections to mount higher level of resistance during subsequent infections, a phenomenon referred to as systemic acquired resistance (sar). during primary infection, mobile signals generated at the infection site subsequently move to the rest of plant to activate sar. sar activation is associated with alteration in the nucleosomal composition at the promoters of several defense-related genes. however, genetic regulations of such epigenetic modifications are larg ...	2014	25763701
divergent evolution of potato immune receptor cc domain interactions with the ran gtpase-activating protein 2.	effector-triggered immunity mediated by immune receptors in plants provides powerful defense against specific pathogens. solanum tuberosum ran gtpase-activating protein 2 (strangap2) interacts with immune receptors rx and gpa2 through their coiled-coil (cc) domains. we assayed additional cc domains from other solanaceous immune receptors and observed interaction by co-immunoprecipitation between strangap2 and a novel immune receptor, str5. a cc domain very similar to rx and gpa2, str4, failed to ...	2014	25763710
arabidopsis lip5, a positive regulator of multivesicular body biogenesis, is a critical target of pathogen-responsive mapk cascade in plant basal defense.	multivesicular bodies (mvbs) play essential roles in many cellular processes. the mvb pathway requires reversible membrane association of the endosomal sorting complexes required for transports (escrts) for sustained protein trafficking. membrane dissociation of escrts is catalyzed by the aaa atpase skd1, which is stimulated by lyst-interacting protein 5 (lip5). we report here that lip5 is a target of pathogen-responsive mitogen-activated protein kinases (mpks) and plays a critical role in plant ...	2014	25010425
tomato nac transcription factor slsrn1 positively regulates defense response against biotic stress but negatively regulates abiotic stress response.	biotic and abiotic stresses are major unfavorable factors that affect crop productivity worldwide. nac proteins comprise a large family of transcription factors that play important roles in plant growth and development as well as in responses to biotic and abiotic stresses. in a virus-induced gene silencing-based screening to identify genes that are involved in defense response against botrytis cinerea, we identified a tomato nac gene slsrn1 (solanum lycopersicum stress-related nac1). slsrn1 is ...	2014	25010573
identification of cucurbitacins and assembly of a draft genome for aquilaria agallocha.	agarwood is derived from aquilaria trees, the trade of which has come under strict control with a listing in appendix ii of the convention on international trade in endangered species of wild fauna and flora. many secondary metabolites of agarwood are known to have medicinal value to humans, including compounds that have been shown to elicit sedative effects and exhibit anti-cancer properties. however, little is known about the genome, transcriptome, and the biosynthetic pathways responsible for ...	2014	25005802
closely related nac transcription factors of tomato differentially regulate stomatal closure and reopening during pathogen attack.	to restrict pathogen entry, plants close stomata as an integral part of innate immunity. to counteract this defense, pseudomonas syringae pv tomato produces coronatine (cor), which mimics jasmonic acid (ja), to reopen stomata for bacterial entry. it is believed that abscisic acid (aba) plays a central role in regulating bacteria-triggered stomatal closure and that stomatal reopening requires the ja/cor pathway, but the downstream signaling events remain unclear. we studied the stomatal immunity ...	2014	25005917
the legionella effector sidc defines a unique family of ubiquitin ligases important for bacterial phagosomal remodeling.	the activity of proteins delivered into host cells by the dot/icm injection apparatus allows legionella pneumophila to establish a niche called the legionella-containing vacuole (lcv), which is permissive for intracellular bacterial propagation. among these proteins, substrate of icm/dot transporter (sidc) anchors to the cytoplasmic surface of the lcv and is important for the recruitment of host endoplasmic reticulum (er) proteins to this organelle. however, the biochemical function underlying t ...	2014	25006264
stomata prioritize their responses to multiple biotic and abiotic signal inputs.	stomata are microscopic pores in leaf epidermis that regulate gas exchange between plants and the environment. being natural openings on the leaf surface, stomata also serve as ports for the invasion of foliar pathogenic bacteria. each stomatal pore is enclosed by a pair of guard cells that are able to sense a wide spectrum of biotic and abiotic stresses and respond by precisely adjusting the pore width. however, it is not clear whether stomatal responses to simultaneously imposed biotic and abi ...	2014	25003527
autophagy deficiency leads to accumulation of ubiquitinated proteins, er stress, and cell death in arabidopsis.	autophagy is a homeostatic degradation and recycling process that is also involved in defense against microbial pathogens and in certain forms of cellular suicide. autophagy has been proposed to negatively regulate plant immunity-associated cell death related to the hypersensitive response (hr), as older autophagy-deficient mutants are unable to contain this type of cell death 5 to 10 d after infection. such spreading cell death was found to require npr1 (nonexpressor of pr genes 1), but surpris ...	2014	25046116
root defense analysis against fusarium oxysporum reveals new regulators to confer resistance.	fusarium oxysporum is a root-infecting fungal pathogen that causes wilt disease on a broad range of plant species, including arabidopsis thaliana. investigation of the defense response against this pathogen had primarily been conducted using leaf tissue and little was known about the root defense response. in this study, we profiled the expression of root genes after infection with f. oxysporum by microarray analysis. in contrast to the leaf response, root tissue did not show a strong induction ...	2014	24998294
the long-term maintenance of a resistance polymorphism through diffuse interactions.	plant resistance (r) genes are a crucial component in plant defence against pathogens. although r genes often fail to provide durable resistance in an agricultural context, they frequently persist as long-lived balanced polymorphisms in nature. standard theory explains the maintenance of such polymorphisms through a balance of the costs and benefits of resistance and virulence in a tightly coevolving host-pathogen pair. however, many plant-pathogen interactions lack such specificity. whether, an ...	2014	25043057
insect-induced daidzein, formononetin and their conjugates in soybean leaves.	in response to attack by bacterial pathogens, soybean (gylcine max) leaves accumulate isoflavone aglucones, isoflavone glucosides, and glyceollins. in contrast to pathogens, the dynamics of related insect-inducible metabolites in soybean leaves remain poorly understood. in this study, we analyzed the biochemical responses of soybean leaves to spodoptera litura (lepidoptera: noctuidae) herbivory and also s. litura gut contents, which contain oral secretion elicitors. following s. litura herbivory ...	2014	25000357
differential secretome analysis of pseudomonas syringae pv tomato using gel-free ms proteomics.	the plant pathogen pseudomonas syringae pv.tomato (dc3000) causes virulence by delivering effector proteins into host plant cells through its type three secretion system (t3ss). in response to the plant environment dc3000 expresses hypersensitive response and pathogenicity genes (hrp). pathogenesis depends on the ability of the pathogen to manipulate the plant metabolism and to inhibit plant immunity, which depends to a large degree on the plant's capacity to recognize both pathogen and microbia ...	2014	25071788
callose biosynthesis in arabidopsis with a focus on pathogen response: what we have learned within the last decade.	(1,3)-β-glucan callose is a cell wall polymer that is involved in several fundamental biological processes, ranging from plant development to the response to abiotic and biotic stresses. despite its importance in maintaining plant integrity and plant defence, knowledge about the regulation of callose biosynthesis at its diverse sites of action within the plant is still limited. the moderately sized family of gsl (glucan synthase-like) genes is predicted to encode callose synthases with a specifi ...	2014	24984713
dynamic changes in the subcellular distribution of the tobacco ros-producing enzyme rbohd in response to the oomycete elicitor cryptogein.	plant nadph oxidases, also known as respiratory burst oxidase homologues (rbohs), have been identified as a major source of reactive oxygen species (ros) during plant-microbe interactions. the subcellular localization of the tobacco (nicotiana tabacum) ros-producing enzyme rbohd was examined in bright yellow-2 cells before and after elicitation with the oomycete protein cryptogein using electron and confocal microscopy. the plasma membrane (pm) localization of rbohd was confirmed and immuno-elec ...	2014	24987013
comparison of five bacteriophages as models for viral aerosol studies.	bacteriophages are perceived to be good models for the study of airborne viruses because they are safe to use, some of them display structural features similar to those of human and animal viruses, and they are relatively easy to produce in large quantities. yet, only a few studies have investigated them as models. it has previously been demonstrated that aerosolization, environmental conditions, and sampling conditions affect viral infectivity, but viral infectivity is virus dependent. thus, se ...	2014	24795379
modulation of endogenous indole-3-acetic acid biosynthesis in bacteroids within medicago sativa nodules.	to evaluate the dose-response effects of endogenous indole-3-acetic acid (iaa) on medicago plant growth and dry weight production, we increased the synthesis of iaa in both free-living and symbiosis-stage rhizobial bacteroids during rhizobium-legume symbiosis. for this purpose, site-directed mutagenesis was applied to modify an 85-bp promoter sequence, driving the expression of iaam and tms2 genes for iaa biosynthesis. a positive correlation was found between the higher expression of iaa biosynt ...	2014	24814784
functional analysis of arabidopsis immune-related mapks uncovers a role for mpk3 as negative regulator of inducible defences.	mitogen-activated protein kinases (mapks) are key regulators of immune responses in animals and plants. in arabidopsis, perception of microbe-associated molecular patterns (mamps) activates the mapks mpk3, mpk4 and mpk6. increasing information depicts the molecular events activated by mamps in plants, but the specific and cooperative contributions of the mapks in these signalling events are largely unclear.	2014	24980080
pseudomonas cremoricolorata strain nd07 produces n-acyl homoserine lactones as quorum sensing molecules.	quorum sensing (qs) is a bacterial cell-to-cell communication system controlling qs-mediated genes which is synchronized with the population density. the regulation of specific gene activity is dependent on the signaling molecules produced, namely n-acyl homoserine lactones (ahls). we report here the identification and characterization of ahls produced by bacterial strain nd07 isolated from a malaysian fresh water sample. molecular identification showed that strain nd07 is clustered closely to p ...	2014	24984061
jasmonate-triggered plant immunity.	the plant hormone jasmonate (ja) exerts direct control over the production of chemical defense compounds that confer resistance to a remarkable spectrum of plant-associated organisms, ranging from microbial pathogens to vertebrate herbivores. the underlying mechanism of ja-triggered immunity (jati) can be conceptualized as a multi-stage signal transduction cascade involving: i) pattern recognition receptors (prrs) that couple the perception of danger signals to rapid synthesis of bioactive ja; i ...	2014	24973116
effector biology during biotrophic invasion of plant cells.	several obligate biotrophic phytopathogens, namely oomycetes and fungi, invade and feed on living plant cells through specialized structures known as haustoria. deploying an arsenal of secreted proteins called effectors, these pathogens balance their parasitic propagation by subverting plant immunity without sacrificing host cells. such secreted proteins, which are thought to be delivered by haustoria, conceivably reprogram host cells and instigate structural modifications, in addition to the mo ...	2014	25513771
hopw1 from pseudomonas syringae disrupts the actin cytoskeleton to promote virulence in arabidopsis.	a central mechanism of virulence of extracellular bacterial pathogens is the injection into host cells of effector proteins that modify host cellular functions. hopw1 is an effector injected by the type iii secretion system that increases the growth of the plant pathogen pseudomonas syringae on the columbia accession of arabidopsis. when delivered by p. syringae into plant cells, hopw1 causes a reduction in the filamentous actin (f-actin) network and the inhibition of endocytosis, a known actin- ...	2014	24968323
genome-wide analysis of the nadk gene family in plants.	nad(h) kinase (nadk) is the key enzyme that catalyzes de novo synthesis of nadp(h) from nad(h) for nadp(h)-based metabolic pathways. in plants, nadks form functional subfamilies. studies of these families in arabidopsis thaliana indicate that they have undergone considerable evolutionary selection; however, the detailed evolutionary history and functions of the various nadks in plants are not clearly understood.	2014	24968225
cerato-platanin induces resistance in arabidopsis leaves through stomatal perception, overexpression of salicylic acid- and ethylene-signalling genes and camalexin biosynthesis.	microbe-associated molecular patterns (mamps) lead to the activation of the first line of plant defence. few fungal molecules are universally qualified as mamps, and proteins belonging to the cerato-platanin protein (cpp) family seem to possess these features. cerato-platanin (cp) is the name-giving protein of the cpp family and is produced by ceratocystis platani, the causal agent of the canker stain disease of plane trees (platanus spp.). on plane tree leaves, the biological activity of cp has ...	2014	24968226
botrytis-induced kinase1 modulates arabidopsis resistance to green peach aphids via phytoalexin deficient4.	botrytis-induced kinase1 (bik1) plays important roles in induced defense against fungal and bacterial pathogens in arabidopsis (arabidopsis thaliana). its tomato (solanum lycopersicum) homolog is required for host plant resistance to a chewing insect herbivore. however, it remains unknown whether bik1 functions in plant defense against aphids, a group of insects with a specialized phloem sap-feeding style. in this study, the potential role of bik1 was investigated in arabidopsis infested with th ...	2014	24963070
environmental history modulates arabidopsis pattern-triggered immunity in a histone acetyltransferase1-dependent manner.	in nature, plants are exposed to a fluctuating environment, and individuals exposed to contrasting environmental factors develop different environmental histories. whether different environmental histories alter plant responses to a current stress remains elusive. here, we show that environmental history modulates the plant response to microbial pathogens. arabidopsis thaliana plants exposed to repetitive heat, cold, or salt stress were more resistant to virulent bacteria than arabidopsis grown ...	2014	24963055
transcriptomic analysis of prunus domestica undergoing hypersensitive response to plum pox virus infection.	plum pox virus (ppv) infects prunus trees around the globe, posing serious fruit production problems and causing severe economic losses. one variety of prunus domestica, named 'jojo', develops a hypersensitive response to viral infection. here we compared infected and non-infected samples using next-generation rna sequencing to characterize the genetic complexity of the viral population in infected samples and to identify genes involved in development of the resistance response. analysis of vira ...	2014	24959894
preparing to fight back: generation and storage of priming compounds.	immune-stimulated plants are able to respond more rapidly and adequately to various biotic stresses allowing them to efficiently combat an infection. during the priming phase, plant are stimulated in absence of a challenge, and can accumulate and store conjugates or precursors of molecules as well as other compounds that play a role in defense. these molecules can be released during the defensive phase following stress. these metabolites can also participate in the first stages of the stress per ...	2014	25009546
plasma membrane localization is essential for oryza sativa pto-interacting protein 1a-mediated negative regulation of immune signaling in rice.	oryza sativa pto-interacting protein 1a (ospti1a), an ortholog of tomato (solanum lycopersicum) slpti1, functions as a negative regulator of innate immunity in rice (oryza sativa). in ospti1a mutants, the activation of immune responses, including hypersensitive response-like cell death, is caused by loss of the ospti1a protein; however, it is as yet unclear how ospti1a suppresses immune responses. here, we report that ospti1a localizes to detergent-resistant membrane fractions of the plasma memb ...	2014	24958714
host-induced bacterial cell wall decomposition mediates pattern-triggered immunity in arabidopsis.	peptidoglycans (pgns) are immunogenic bacterial surface patterns that trigger immune activation in metazoans and plants. it is generally unknown how complex bacterial structures such as pgns are perceived by plant pattern recognition receptors (prrs) and whether host hydrolytic activities facilitate decomposition of bacterial matrices and generation of soluble prr ligands. here we show that arabidopsis thaliana, upon bacterial infection or exposure to microbial patterns, produces a metazoan lyso ...	2014	24957336
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 ...	2014	25002866
the potential for give and take in plant-microbiome relationships.	mutualistic microbes present in plant-associate microbial communities provide a variety of benefits for their host, including reciprocal exchange of nutrients and/or protection from biotic and abiotic environmental stresses. plant microbiomes have remarkably robust composition in comparison to the complex and dynamic microbial environments from which they form, suggesting finely tuned discrimination by the plant host. here the intersection between the plant immune system and microbiomes will be ...	2014	24999348
circadian redox signaling in plant immunity and abiotic stress.	plant crops are critically important to provide quality food and bio-energy to sustain a growing human population. circadian clocks have been shown to deliver an adaptive advantage to plants, vastly increasing biomass production by efficient anticipation to the solar cycle. plant stress, on the other hand, whether biotic or abiotic, prevents crops from reaching maximum productivity.	2014	23941583
interplay among pseudomonas syringae hrpr, hrps and hrpv proteins for regulation of the type iii secretion system.	pseudomonas syringae pv. tomato dc3000, a plant pathogenic gram-negative bacterium, employs the type iii secretion system (t3ss) to cause disease in tomato and arabidopsis and to induce the hypersensitive response in nonhost plants. the expression of t3ss is regulated by the hrpl extracytoplasmic sigma factor. expression of hrpl is controlled by transcriptional activators hrpr and hrps and negative regulator hrpv. in this study, we analysed the organization of hrprs and hrpv regulatory proteins ...	2014	24863420
genome-wide identification of pathogenicity factors of the free-living amoeba naegleria fowleri.	the free-living amoeba naegleria fowleri is the causative agent of the rapidly progressing and typically fatal primary amoebic meningoencephalitis (pam) in humans. despite the devastating nature of this disease, which results in > 97% mortality, knowledge of the pathogenic mechanisms of the amoeba is incomplete. this work presents a comparative proteomic approach based on an experimental model in which the pathogenic potential of n. fowleri trophozoites is influenced by the compositions of diffe ...	2014	24950717
interaction of cpr5 with cell cycle regulators uvi4 and osd1 in arabidopsis.	the impact of cell cycle on plant immunity was indicated by the enhancement of disease resistance with overexpressing osd1 and uvi4 genes that are negative regulators of cell cycle controller apc (anaphase promoting complex). cpr5 is another gene that is implicated in cell cycle regulation and plant immunity, but its mode of action is not known. here we report the analysis of genetic requirement for the function of uvi4 and osd1 in cell cycle progression control and in particular the involvement ...	2014	24945150
dominance effects of deleterious and beneficial mutations in a single gene of the rna virus ϕ6.	most of our knowledge of dominance stems from studies of deleterious mutations. from these studies we know that most deleterious mutations are recessive, and that this recessivity arises from a hyperbolic relationship between protein function (i.e., protein concentration or activity) and fitness. here we investigate whether this knowledge can be used to make predictions about the dominance of beneficial and deleterious mutations in a single gene. we employed a model system--the bacteriophage φ6- ...	2014	24945910
bacterial type iii secretion systems: specialized nanomachines for protein delivery into target cells.	one of the most exciting developments in the field of bacterial pathogenesis in recent years is the discovery that many pathogens utilize complex nanomachines to deliver bacterially encoded effector proteins into target eukaryotic cells. these effector proteins modulate a variety of cellular functions for the pathogen's benefit. one of these protein-delivery machines is the type iii secretion system (t3ss). t3sss are widespread in nature and are encoded not only by bacteria pathogenic to vertebr ...	2014	25002086
agrobest: an efficient agrobacterium-mediated transient expression method for versatile gene function analyses in arabidopsis seedlings.	transient gene expression via agrobacterium-mediated dna transfer offers a simple and fast method to analyze transgene functions. although arabidopsis is the most-studied model plant with powerful genetic and genomic resources, achieving highly efficient and consistent transient expression for gene function analysis in arabidopsis remains challenging.	2014	24987449
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 ...	2014	24936863
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 ...	2014	24982666
salicylic acid signaling controls the maturation and localization of the arabidopsis defense protein accelerated cell death6.	accelerated cell death6 (acd6) is a multipass membrane protein with an ankyrin domain that acts in a positive feedback loop with the defense signal salicylic acid (sa). this study implemented biochemical approaches to infer changes in acd6 complexes and localization. in addition to forming endoplasmic reticulum (er)- and plasma membrane (pm)-localized complexes, acd6 forms soluble complexes, where it is bound to cytosolic hsp70, ubiquitinated, and degraded via the proteasome. thus, acd6 constitu ...	2014	24923602
the extent of genome flux and its role in the differentiation of bacterial lineages.	horizontal gene transfer (hgt) and gene loss are key processes in bacterial evolution. however, the role of gene gain and loss in the emergence and maintenance of ecologically differentiated bacterial populations remains an open question. here, we use whole-genome sequence data to quantify gene gain and loss for 27 lineages of the plant-associated bacterium pseudomonas syringae. we apply an extensive error-control procedure that accounts for errors in draft genome data and greatly improves the a ...	2014	24923323
the role of abiotic environmental conditions and herbivory in shaping bacterial community composition in floral nectar.	identifying the processes that drive community assembly has long been a central theme in ecology. for microorganisms, a traditional prevailing hypothesis states that "everything is everywhere, but the environment selects". although the bacterial community in floral nectar may be affected by both atmosphere (air-borne bacteria) and animals as dispersal vectors, the environmental and geographic factors that shape microbial communities in floral nectar are unknown. we studied culturable bacterial c ...	2014	24922317
interaction specificity and coexpression of rice npr1 homologs 1 and 3 (nh1 and nh3), tga transcription factors and negative regulator of resistance (nrr) proteins.	the nonexpressor of pathogenesis-related genes 1, npr1 (also known as nim1 and sai1), is a key regulator of sa-mediated systemic acquired resistance (sar) in arabidopsis. in rice, the npr1 homolog 1 (nh1) interacts with tga transcriptional regulators and the negative regulator of resistance (nrr) protein to modulate the sar response. though five npr1 homologs (nhs) have been identified in rice, only nh1 and nh3 enhance immunity when overexpressed. to understand why nh1 and nh3, but not nh2, nh4, ...	2014	24919709
an arabidopsis mutant impaired in intracellular calcium elevation is sensitive to biotic and abiotic stress.	ca2+, a versatile intracellular second messenger in various signaling pathways, initiates many responses involved in growth, defense and tolerance to biotic and abiotic stress. endogenous and exogenous signals induce cytoplasmic ca2+ ([ca2+]cyt) elevation, which are responsible for the appropriate downstream responses.	2014	24920452
structural diversity in the dandelion (taraxacum officinale) polyphenol oxidase family results in different responses to model substrates.	polyphenol oxidases (ppos) are ubiquitous type-3 copper enzymes that catalyze the oxygen-dependent conversion of o-diphenols to the corresponding quinones. in most plants, ppos are present as multiple isoenzymes that probably serve distinct functions, although the precise relationship between sequence, structure and function has not been addressed in detail. we therefore compared the characteristics and activities of recombinant dandelion ppos to gain insight into the structure-function relation ...	2014	24918587
phosphoinositide-signaling is one component of a robust plant defense response.	the phosphoinositide pathway and inositol-1,4,5-triphosphate (insp3) have been implicated in plant responses to many abiotic stresses; however, their role in response to biotic stress is not well characterized. in the current study, we show that both basal defense and systemic acquired resistance responses are affected in transgenic plants constitutively expressing the human type i inositol polyphosphate 5-phosphatase (insp 5-ptase) which have greatly reduced insp3 levels. flagellin induced ca(2 ...	2014	24966862
phytochrome b-mediated activation of lipoxygenase modulates an excess red light-induced defence response in arabidopsis.	lipoxygenase (lox), a non-haem-iron-containing dioxygenase, is activated under various biotic or abiotic stresses to trigger a series resistance response, but the molecular mechanism of lox activation remains unclear. this work investigated the activation of lox during the plant defence response induced by excess red light (rl). in conditions of rl-induced defence, arabidopsis lox activity and transcription levels of lox2, lox3, and lox4 were both upregulated. under rl, phytochrome b promoted th ...	2014	24916071
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 ...	2014	24920334
alternative splicing in plant immunity.	alternative splicing (as) occurs widely in plants and can provide the main source of transcriptome and proteome diversity in an organism. as functions in a range of physiological processes, including plant disease resistance, but its biological roles and functional mechanisms remain poorly understood. many plant disease resistance (r) genes undergo as, and several r genes require alternatively spliced transcripts to produce r proteins that can specifically recognize pathogen invasion. in the fin ...	2014	24918296
an optimized method for the extraction of bacterial mrna from plant roots infected with escherichia coli o157:h7.	analysis of microbial gene expression during host colonization provides valuable information on the nature of interaction, beneficial or pathogenic, and the adaptive processes involved. isolation of bacterial mrna for in planta analysis can be challenging where host nucleic acid may dominate the preparation, or inhibitory compounds affect downstream analysis, e.g., quantitative reverse transcriptase pcr (qpcr), microarray, or rna-seq. the goal of this work was to optimize the isolation of bacter ...	2014	25018749
role of intron-mediated enhancement on accumulation of an arabidopsis nb-lrr class r-protein that confers resistance to cucumber mosaic virus.	the accumulation of rcy1 protein, which is encoded by resistance to cmv(y) (rcy1), a cc-nb-lrr class r-gene, is tightly correlated with the strength of the resistance to a yellow strain of cucumber mosaic virus [cmv(y)] in arabidopsis thaliana. in order to enhance resistance to cmv by overexpression of rcy1, a. thaliana was transformed with intron-less rcy1 cdna construct under the control of strong camv35s promoter. remarkably, a relative amount of rcy1 protein accumulation in the transformants ...	2014	24915153
the hnrnp-q protein lif2 participates in the plant immune response.	eukaryotes have evolved complex defense pathways to combat invading pathogens. here, we investigated the role of the arabidopsis thaliana heterogeneous nuclear ribonucleoprotein (hnrnp-q) lif2 in the plant innate immune response. we show that lif2 loss-of-function in a. thaliana leads to changes in the basal expression of the salicylic acid (sa)- and jasmonic acid (ja)- dependent defense marker genes pr1 and pdf1.2, respectively. whereas the expression of genes involved in sa and ja biosynthesis ...	2014	24914891
assessment of genetic variation in bulgarian tomato (solanum lycopersicum l.) genotypes, using fluorescent ssr genotyping platform.	genetic variability in modern crops is limited due to domestication and selection processes. genetic variation in eight bulgarian tomato varieties and breeding lines (variety plovdivska karotina, variety izk alya, l21β, l53β, l1140, l1116, l975, l984) differing in their morphological and biochemical composition was assessed using a highly efficient and low-cost fluorescent simple sequence repeat (ssr) genotyping platform. genotyping was conducted with 165 publicly available microsatellite marker ...	2014	26019490
salicylic acid signaling inhibits apoplastic reactive oxygen species signaling.	reactive oxygen species (ros) are used by plants as signaling molecules during stress and development. given the amount of possible challenges a plant face from their environment, plants need to activate and prioritize between potentially conflicting defense signaling pathways. until recently, most studies on signal interactions have focused on phytohormone interaction, such as the antagonistic relationship between salicylic acid (sa)-jasmonic acid and cytokinin-auxin.	2014	24898702
plant secretomics: identification, isolation, and biological significance under environmental stress.	plant secretomes are the proteins secreted by the plant cells and are involved in the maintenance of cell wall structure, relationship between host and pathogen, communication between different cells in the plant, etc. amalgamation of methodologies like bioinformatics, biochemical, and proteomics are used to separate, classify, and outline secretomes by means of harmonizing in planta systems and in vitro suspension cultured cell system (sscs). we summed up and explained the meaning of secretome, ...	2014	25763623
expression-based network biology identifies immune-related functional modules involved in plant defense.	plants respond to diverse environmental cues including microbial perturbations by coordinated regulation of thousands of genes. these intricate transcriptional regulatory interactions depend on the recognition of specific promoter sequences by regulatory transcription factors. the combinatorial and cooperative action of multiple transcription factors defines a regulatory network that enables plant cells to respond to distinct biological signals. the identification of immune-related modules in la ...	2014	24888606
uncovering plant-pathogen crosstalk through apoplastic proteomic studies.	plant pathogens have evolved by developing different strategies to infect their host, which in turn have elaborated immune responses to counter the pathogen invasion. the apoplast, including the cell wall and extracellular space outside the plasma membrane, is one of the first compartments where pathogen-host interaction occurs. the plant cell wall is composed of a complex network of polysaccharides polymers and glycoproteins and serves as a natural physical barrier against pathogen invasion. th ...	2014	24917874
multiple recognition of rxlr effectors is associated with nonhost resistance of pepper against phytophthora infestans.	nonhost resistance (nhr) is a plant immune response to resist most pathogens. the molecular basis of nhr is poorly understood, but recognition of pathogen effectors by immune receptors, a response known as effector-triggered immunity, has been proposed as a component of nhr. we performed transient expression of 54 phytophthora infestansrxlr effectors in pepper (capsicum annuum) accessions. we used optimized heterologous expression methods and analyzed the inheritance of effector-induced cell dea ...	2014	24889686
glutamate receptor-like channels in plants: a role as amino acid sensors in plant defence?	plant glutamate receptor-like genes (glrs) are homologous to the genes for mammalian ionotropic glutamate receptors (iglurs), after which they were named, but in the 16 years since their existence was first revealed, progress in elucidating their biological role has been disappointingly slow. recently, however, studies from a number of laboratories focusing on the model plant species arabidopsis thaliana (l.) have thrown new light on the functional properties of some members of the glr gene fami ...	2014	24991414
characterization and mapping of a spotted leaf mutant in rice (oryza sativa).	spotted leaf mutant belongs to a class of mutants that can produce necrotic lesions spontaneously in plants without any attack by pathogens. these mutants have no beneficial effect on plant productivity but provide a unique opportunity to study programmed cell death in plant defense responses. a novel rice spotted leaf mutant (spl30) was isolated through low-energy heavy ion irradiation. lesion expression was sensitive to light and humidity. the spl30 mutant caused a decrease in chlorophyll and ...	2014	25071406
production of proteasome inhibitor syringolin a by the endophyte rhizobium sp. strain ap16.	syringolin a, the product of a mixed nonribosomal peptide synthetase/polyketide synthase encoded by the syl gene cluster, is a virulence factor secreted by certain pseudomonas syringae strains. together with the glidobactins produced by a number of beta- and gammaproteobacterial human and animal pathogens, it belongs to the syrbactins, a structurally novel class of proteasome inhibitors. in plants, proteasome inhibition by syringolin a-producing p. syringae strains leads to the suppression of ho ...	2014	24727275
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 ...	2014	24659774
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 ...	2014	24885615
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 ...	2014	24878929
disruption of the ammonium transporter amt1.1 alters basal defenses generating resistance against pseudomonas syringae and plectosphaerella cucumerina.	disruption of the high-affinity nitrate transporter nrt2.1 activates the priming defense against pseudomonas syringae, resulting in enhanced resistance. in this study, it is demonstrated that the high-affinity ammonium transporter amt1.1 is a negative regulator of arabidopsis defense responses. the t-dna knockout mutant amt1.1 displays enhanced resistance against plectosphaerella cucumerina and reduced susceptibility to p. syringae. the impairment of amt1.1 induces significant metabolic changes ...	2014	24910636
ethylene signalling affects susceptibility of tomatoes to salmonella.	fresh fruits and vegetables are increasingly recognized as important reservoirs of human pathogens, and therefore, significant attention has been directed recently to understanding mechanisms of the interactions between plants and enterics, like salmonella. a screen of tomato cultivars for their susceptibility to salmonella revealed significant differences in the ability of this human pathogen to multiply within fruits; expression of the salmonella genes (cysb, agfb, fadh) involved in the intera ...	2014	24888884
intercellular salicylic acid accumulation during compatible and incompatible arabidopsis-pseudomonas syringae interactions.	the phytohormone salicylic acid (sa) plays an important role in several disease resistance responses. during the age-related resistance (arr) response that occurs in mature arabidopsis responding to pseudomonas syringae pv tomato (pst), sa accumulates in the intercellular space where it may act as an antimicrobial agent. recently we measured intracellular and intercellular sa levels in young, arr-incompetent plants responding to virulent and avirulent strains of pst to determine if intercellular ...	2014	25763618
polyphosphate, cyclic amp, guanosine tetraphosphate, and c-di-gmp reduce in vitro lon activity.	lon protease is conserved from bacteria to humans and regulates cellular processes by degrading different classes of proteins including antitoxins, transcriptional activators, unfolded proteins, and free ribosomal proteins. since we found that lon has several putative cyclic diguanylate (c-di-gmp) binding sites and since lon binds polyphosphate (polyp) and lipid polysaccharide, we hypothesized that lon has an affinity for phosphate-based molecules that might regulate its activity. hence we teste ...	2014	24874800
comparative analysis of klebsiella pneumoniae genomes identifies a phospholipase d family protein as a novel virulence factor.	klebsiella pneumoniae strains are pathogenic to animals and humans, in which they are both a frequent cause of nosocomial infections and a re-emerging cause of severe community-acquired infections. k. pneumoniae isolates of the capsular serotype k2 are among the most virulent. in order to identify novel putative virulence factors that may account for the severity of k2 infections, the genome sequence of the k2 reference strain kp52.145 was determined and compared to two k1 and k2 strains of low ...	2014	24885329
synchronization of developmental processes and defense signaling by growth regulating transcription factors.	growth regulating factors (grfs) are a conserved class of transcription factor in seed plants. grfs are involved in various aspects of tissue differentiation and organ development. the implication of grfs in biotic stress response has also been recently reported, suggesting a role of these transcription factors in coordinating the interaction between developmental processes and defense dynamics. however, the molecular mechanisms by which grfs mediate the overlaps between defense signaling and de ...	2014	24875638
enhanced disease susceptibility1 mediates pathogen resistance and virulence function of a bacterial effector in soybean.	enhanced disease susceptibility1 (eds1) and phytoalexin deficient4 (pad4) are well-known regulators of both basal and resistance (r) protein-mediated plant defense. we identified two eds1-like (gmeds1a/gmeds1b) proteins and one pad4-like (gmpad4) protein that are required for resistance signaling in soybean (glycine max). consistent with their significant structural conservation to arabidopsis (arabidopsis thaliana) counterparts, constitutive expression of gmeds1 or gmpad4 complemented the patho ...	2014	24872380
control of foliar pathogens of spring barley using a combination of resistance elicitors.	the ability of the resistance elicitors acibenzolar-s-methyl (asm), β-aminobutyric acid (baba), cis-jasmone (cj), and a combination of the three products, to control infection of spring barley by rhynchosporium commune was examined under glasshouse conditions. significant control of r. commune was provided by asm and cj, but the largest reduction in infection was obtained with the combination of the three elicitors. this elicitor combination was found to up-regulate the expression of pr-1b, whic ...	2014	24904629
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 ...	2014	24884520
comparative genome analysis of pathogenic and non-pathogenic clavibacter strains reveals adaptations to their lifestyle.	the genus clavibacter harbors economically important plant pathogens infecting agricultural crops such as potato and tomato. although the vast majority of clavibacter strains are pathogenic, there is an increasing number of non-pathogenic isolates reported. non-pathogenic clavibacter strains isolated from tomato seeds are particularly problematic because they affect the current detection and identification tests for clavibacter michiganensis subsp. michiganensis (cmm), which is regulated with a ...	2014	24885539
the roles of anion channels in arabidopsis immunity.	anion efflux is one of the most immediate responses of plant cells to pathogen attacks, suggesting that anion channels may play a role in plant defense. recently we reported that the chloride channel atclcd negatively regulates arabidopsis pathogen-associated molecular pattern-triggered immunity (pti), probably by affecting trafficking of the pattern recognition receptors (prrs). since atclcd is localized to the trans-golgi network, it is not likely to be directly involved in anion flux across t ...	2014	25763497
effector missp7 of the mutualistic fungus laccaria bicolor stabilizes the populus jaz6 protein and represses jasmonic acid (ja) responsive genes.	ectomycorrhizal fungi, such as laccaria bicolor, support forest growth and sustainability by providing growth-limiting nutrients to their plant host through a mutualistic symbiotic relationship with host roots. we have previously shown that the effector protein missp7 (mycorrhiza-induced small secreted protein 7) encoded by l. bicolor is necessary for the establishment of symbiosis with host trees, although the mechanistic reasoning behind this role was unknown. we demonstrate here that missp7 i ...	2014	24847068
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 ...	2014	24846383
alternative functions of arabidopsis yellow stripe-like3: from metal translocation to pathogen defense.	yellow stripe-like1 (ysl1) and ysl3 are involved in iron (fe) and copper (cu) translocation. previously, we reported that upregulation of ysl1 and ysl3 under excess cu caused high accumulation of cu in the siz1 mutant, impaired in small ubiquitin-like modifier (sumo) e3 ligase. interestingly, the siz1 mutant contains high levels of salicylic acid (sa), involved in plant defense against biotrophic pathogens. in this study, we found that ysl1 and ysl3 were upregulated by sa. sa-regulated ysl3 but ...	2014	24845074
the phytotoxin coronatine induces abscission-related gene expression and boll ripening during defoliation of cotton.	defoliants can increase machine harvest efficiency of cotton (gossypium hirusutum l.), prevent lodging and reduce the time from defoliation to harvest. coronatine (cor) is a chlorosis-inducing non-host-specific phytotoxin that induces leaf and/or fruit abscission in some crops. the present study investigates how cor might induce cotton leaf abscission by modulating genes involved in cell wall hydrolases and acc (ethylene precursor) in various cotton tissues. the effects of cor on cotton boll rip ...	2014	24845465
enhancing crop resilience to combined abiotic and biotic stress through the dissection of physiological and molecular crosstalk.	plants growing in their natural habitats are often challenged simultaneously by multiple stress factors, both abiotic and biotic. research has so far been limited to responses to individual stresses, and understanding of adaptation to combinatorial stress is limited, but indicative of non-additive interactions. omics data analysis and functional characterization of individual genes has revealed a convergence of signaling pathways for abiotic and biotic stress adaptation. taking into account that ...	2014	24904607
modest: a web-based design tool for oligonucleotide-mediated genome engineering and recombineering.	recombineering and multiplex automated genome engineering (mage) offer the possibility to rapidly modify multiple genomic or plasmid sites at high efficiencies. this enables efficient creation of genetic variants including both single mutants with specifically targeted modifications as well as combinatorial cell libraries. manual design of oligonucleotides for these approaches can be tedious, time-consuming, and may not be practical for larger projects targeting many genomic sites. at present, t ...	2014	24838561
the cysteine2/histidine2-type transcription factor zinc finger of arabidopsis thaliana6 modulates biotic and abiotic stress responses by activating salicylic acid-related genes and c-repeat-binding factor genes in arabidopsis.	the cysteine2/histidine2-type zinc finger proteins are a large family of transcription regulators, and some of them play essential roles in plant responses to biotic and abiotic stress. in this study, we found that expression of c2h2-type zinc finger of arabidopsis thaliana6 (atzat6) was transcriptionally induced by salt, dehydration, cold stress treatments, and pathogen infection, and atzat6 was predominantly located in the nucleus. atzat6-overexpressing plants exhibited improved resistance to ...	2014	24834923
response to long-term nahco3-derived alkalinity in model lotus japonicus ecotypes gifu b-129 and miyakojima mg-20: transcriptomic profiling and physiological characterization.	the current knowledge regarding transcriptomic changes induced by alkalinity on plants is scarce and limited to studies where plants were subjected to the alkaline salt for periods not longer than 48 h, so there is no information available regarding the regulation of genes involved in the generation of a new homeostatic cellular condition after long-term alkaline stress. lotus japonicus is a model legume broadly used to study many important physiological processes including biotic interactions a ...	2014	24835559
edr1 physically interacts with mkk4/mkk5 and negatively regulates a map kinase cascade to modulate plant innate immunity.	mitogen-activated protein (map) kinase signaling cascades play important roles in the regulation of plant defense. the raf-like map kinase kinase kinase (mapkkk) edr1 negatively regulates plant defense responses and cell death. however, how edr1 functions, and whether it affects the regulation of mapk cascades, are not well understood. here, we showed that edr1 negatively regulates the mkk4/mkk5-mpk3/mpk6 kinase cascade in arabidopsis. we found that edr1 mutants have highly activated mpk3/mpk6 k ...	2014	24830651