slotreck/pickle huggingface dataset:
A nonpathogenic rhizobacterium , Pseudomonas putida LSW17S , elicited systemic protection against Fusarium wilt and pith necrosis caused by Fusarium oxysporum f. sp. lycopersici and P. corrugata in tomato ( Lycopersicon esculentum L. ) . LSW17S also confers disease resistance against P. syringae pv . tomato DC3000 ( DC3000 ) on Arabidopsis ecotype Col-0 . To investigate mechanisms underlying disease protection , expression patterns of defense-related genes PR1 , PR2 , PR5 , and PDF1.2 and cellular defense responses such as hydrogen peroxide accumulation and callose deposition were investigated . LSW17S treatment exhibited the typical phenomena of priming . Strong and faster transcription of defense-related genes was induced and hydrogen peroxide or callose were accumulated in Arabidopsis treated with LSW17S and infected with DC3000 . In contrast , individual actions of LSW17S and DC3000 did not elicit rapid molecular and cellular defense responses . Priming by LSW17S was translocated systemically and retained for more than 10 days . Treatment with LSW17S reduced pathogen proliferation in Arabidopsis ecotype Col-0 expressing bacterial NahG ; however , npr1 , etr1 , and jar1 mutations impaired inhibition of pathogen growth . Cellular and molecular priming responses support these results . In sum , LSW17S primes Arabidopsis for NPR1- , ethylene- , and jasmonic acid-dependent disease resistance , and efficient molecular and cellular defense responses .
The abscisic acid (ABA)- , stress- , and ripening-induced ( ASR ) protein is a plant-specific hydrophilic transcriptional factor involved in fruit ripening and the abiotic stress response . To date , there have been no studies on the role of ASR genes in delayed flowering time . Here , we found that the ASR from banana , designated as MaASR , was preferentially expressed in the banana female flowers from the eighth , fourth , and first cluster of the inflorescence . MaASR transgenic lines ( L14 and L38 ) had a clear delayed-flowering phenotype . The number of rosette leaves , sepals , and pedicel trichomes in L14 and L38 was greater than in the wild type ( WT ) under long day ( LD ) conditions . The period of buds , mid-flowers , and full bloom of L14 and L38 appeared later than the WT . cDNA microarray and quantitative real-time PCR ( qRT-PCR ) analyses revealed that overexpression of MaASR delays flowering through reduced expression of several genes , including photoperiod pathway genes , vernalization pathway genes , gibberellic acid pathway genes , and floral integrator genes , under short days ( SD ) for 28 d ( from vegetative to reproductive transition stage ) ; however , the expression of the autonomous pathway genes was not affected . This study provides the first evidence of a role for ASR genes in delayed flowering time in plants .
This study was designed to examine the effects of NaCl pretreatment on the seed germination of white clover ( Trifolium repens cv . Ladino ) under water stress induced by 19 % polyethylene glycol ( PEG ) 6000 . Lower concentrations of NaCl ( 0.5 , 1 , and 2.5 mM ) pretreatment significantly alleviated stress-induced decreases in germination percentage , germination vigor , germination index , and radicle length of seedlings after seven days of germination under water stress . The soaking with 1 mM of NaCl exhibited most the pronounced effects on improving seed germination and alleviating stress damage . NaCl-induced seeds germination and growth could be associated with the increases in endogenous gibberellic acid ( GA ) and indole-3-acetic acid ( IAA ) levels through activating amylases leading to improved amylolysis under water stress . Seedlings pretreated with NaCl had a significantly lower osmotic potential than untreated seedlings during seed germination , which could be related to significantly higher soluble sugars and free proline content in NaCl-treated seedlings under water stress . For antioxidant metabolism , NaCl pretreatment mainly improved superoxide dismutase , peroxidase , ascorbate peroxidase , and glutathione reductase activities , transcript levels of FeSOD , APX , and DHAR , and the content of ascorbic acid , reduced glutathione , and oxidized glutathione during seed germination under water stress . The results indicated that seeds soaking with NaCl could remarkably enhance antioxidant metabolism , thereby decreasing the accumulation of reactive oxygen species and membrane lipid peroxidation during germination under water stress . In addition , NaCl-upregulated dehydrin-encoded genes SK2 expression could be another important mechanism of drought tolerance during seeds germination of white clover in response to water stress .
Phytohormones , such as salicylic acid ( SA ) , ethylene ( ET ) and jasmonic acid ( JA ) , play key roles in plant defence following pathogen attack . The involvement of these hormones in susceptibility following Fusarium oxysporum ( Fo ) infection has mostly been studied in Arabidopsis thaliana . However , Fo causes vascular wilt disease in a broad range of crops , including tomato ( Solanum lycopersicum ) . Surprisingly little is known about the involvement of these phytohormones in the susceptibility of tomato towards Fo f. sp. lycopersici ( Fol ) . Here , we investigate their involvement by the analysis of the expression of ET , JA and SA marker genes following Fol infection , and by bioassays of tomato mutants affected in either hormone production or perception . Fol inoculation triggered the expression of SA and ET marker genes , showing the activation of these pathways . NahG tomato , in which SA is degraded , became hypersusceptible to Fol infection and showed stronger disease symptoms than wild-type . In contrast , ACD and Never ripe ( Nr ) mutants , in which ET biosynthesis and perception , respectively , are impaired , showed decreased disease symptoms and reduced fungal colonization on infection . The susceptibility of the def1 tomato mutant , and a prosystemin over-expressing line , in which JA signalling is compromised or constitutively activated , respectively , was unaltered . Our results show that SA is a negative and ET a positive regulator of Fol susceptibility . The SA and ET signalling pathways appear to act synergistically , as an intact ET pathway is required for the induction of an SA marker gene , and vice versa .
Germination of Amaranthus caudatus is inhibited by light , far-red being the most effective part of the spectrum . At temperatures of 25 ° and below there is a low final germination percentage under continuous far-red whereas above 25 ° there is only a delaying effect . In the presence of a saturating concentration of gibberellic acid ( GA3 ) at 25 ° seeds germinate under continuous far-red although they are delayed . At 25 ° seeds exposed to 48 hr far-red fail to germinate when transferred to darkness . This induced dormancy can be broken by a single short exposure to red light given at any time after the far-red illumination . This effect of short red can be reversed by a subsequent short period of far-red indicating that the seeds are phytochrome controlled . Although most seeds have escaped from the reversing effect of short far-red after an intervening dark period of 5 hours , germination is greatly reduced by continuous far-red at this time . Results of exposing seeds to varying periods of far-red before and after dark imbibition are interpreted in terms of a continual production of phytochrome in its active P fr form and a requirement for P fr action over a long period of time . Effects of intermittent and continuous low intensity far-red on the inhibition of germination provides further evidence for a low energy photoreaction involving phytochrome . Effects on Germination Index of continuous illumination with various light sources maintaining different P fr /P total ratios have been investigated . The results suggest that the proportion of phytochrome in the P fr form is the most important factor in the regulation of germination . A scheme for the phytochrome control of germination in Amaranthus caudatus is presented and possible explanations for the dependence on P fr /P total ratio are discussed .
In plants , ethylene and jasmonate control the defense responses to multiple stressors , including insect predation . Among the defense proteins known to be regulated by ethylene is maize insect resistance 1-cysteine protease ( Mir1-CP ) . This protein is constitutively expressed in the insect-resistant maize ( Zea mays ) genotype Mp708 ; however , its abundance significantly increases during fall armyworm ( Spodoptera frugiperda ) herbivory . Within 1 h of herbivory by fall armyworm , Mir1-CP accumulates at the feeding site and continues to increase in abundance until 24 h without any increase in its transcript ( mir1 ) levels . To resolve this discrepancy and elucidate the role of ethylene and jasmonate in the signaling of Mir1-CP expression , the effects of phytohormone biosynthesis and perception inhibitors on Mir1-CP expression were tested . Immunoblot analysis of Mir1-CP accumulation and quantitative reverse-transcriptase polymerase chain reaction examination of mir1 levels in these treated plants demonstrate that Mir1-CP accumulation is regulated by both transcript abundance and protein expression levels . The results also suggest that jasmonate functions upstream of ethylene in the Mir1-CP expression pathway , allowing for both low-level constitutive expression and a two-stage defensive response , an immediate response involving Mir1-CP accumulation and a delayed response inducing mir1 transcript expression .
BACKGROUND : Jasmonic acid ( JA ) and methyl jasmonate ( MeJA ) regulate plant development , resistance to stress , and insect attack by inducing specific gene expression . However , little is known about the mechanism of plant defense against herbivore attack at a protein level . Using a high-resolution 2-D gel , we identified 62 MeJA-responsive proteins and measured protein expression level changes . RESULTS : Among these 62 proteins , 43 proteins levels were increased while 11 proteins were decreased . We also found eight proteins uniquely expressed in response to MeJA treatment . Data are available via ProteomeXchange with identifier PXD001793 . The proteins identified in this study have important biological functions including photosynthesis and energy related proteins ( 38.4 % ) , protein folding , degradation and regulated proteins ( 15.0 % ) , stress and defense regulated proteins ( 11.7 % ) , and redox-responsive proteins ( 8.3 % ) . The expression levels of four important genes were determined by qRT-PCR analysis . The expression levels of these proteins did not correlate well with their translation levels . To test the defense functions of the differentially expressed proteins , expression vectors of four protein coding genes were constructed to express in-fusion proteins in E. coli . The expressed proteins were used to feed Ostrinia furnacalis , the Asian corn borer ( ACB ) . Our results demonstrated that the recombinant proteins of pathogenesis-related protein 1 ( PR1 ) and thioredoxin M-type , chloroplastic precursor ( TRXM ) showed the significant inhibition on the development of larvae and pupae . CONCLUSIONS : We found MeJA could not only induce plant defense mechanisms to insects , it also enhanced toxic protein production that potentially can be used for bio-control of ACB .
Jasmonic acid ( JA ) and nitric oxide ( NO ) are well-characterized signaling molecules in plant defense responses . However , their roles in plant defense against root-knot nematode ( RKN , Meloidogyne incognita ) infection are largely unknown . In this study , we found that the transcript levels of the JA- and NO-related biosynthetic and signaling component genes were induced after RKN infection . Application of exogenous JA and sodium nitroprusside ( SNP ; a NO donor ) significantly decreased the number of egg masses in tomato roots after RKN infection and partially alleviated RKN-induced decreases in plant fresh weight and net photosynthetic rate . These molecules also alleviated RKN-induced increases in root electrolyte leakage and membrane peroxidation . Importantly , NO scavenger partially inhibited JA-induced RKN defense . The pharmacological inhibition of JA biosynthesis significantly increased the plants ' susceptibility to RKNs , which was effectively alleviated by SNP application , showing that NO may be involved in the JA-dependent RKN defense pathway . Furthermore , both JA and SNP induced increases in protease inhibitor 2 ( PI2 ) gene expression after RKN infestation . Silencing of PI2 compromised both JA- and SNP-induced RKN defense responses , suggesting that the PI2 gene mediates JA- and NO-induced defense against RKNs . This work will be important for deepening the understanding of the mechanisms involved in basal defense against RKN attack in plants .
Beet necrotic yellow vein virus ( BNYVV ) and Beet soil-borne mosaic virus ( BSBMV ) are closely related species , but disease development induced in their host sugar beet displays striking differences . Beet necrotic yellow vein virus induces excessive lateral root ( LR ) formation , whereas BSBMV-infected roots appear asymptomatic . A comparative transcriptome analysis was performed to elucidate transcriptomic changes associated with disease development . Many differentially expressed genes ( DEGs ) were specific either to BNYVV or BSBMV , although both viruses shared a high number of DEGs . Auxin biosynthesis pathways displayed a stronger activation by BNYVV compared to BSBMV-infected plants . Several genes regulated by auxin signalling and required for LR formation were exclusively altered by BNYVV . Both viruses reprogrammed the transcriptional network , but a large number of transcription factors involved in plant defence were upregulated in BNYVV-infected plants . A strong activation of pathogenesis-related proteins by both viruses suggests a salicylic acid or jasmonic acid mediated-defence response , but the data also indicate that both viruses counteract the SA-mediated defence . The ethylene signal transduction pathway was strongly downregulated which probably increases the susceptibility of sugar beet to Benyvirus infection . Our study provides a deeper insight into the interaction of BNYVV and BSBMV with the economically important crop sugar beet .
Brassinosteroids ( BRs ) and jasmonates ( JAs ) regulate plant growth , development , and defense responses , but how these phytohormones mediate the growth-defense tradeoff is unclear . Here , we identified the Arabidopsis ( Arabidopsis thaliana ) dwarf at early stages1 ( dwe1 ) mutant , which exhibits enhanced expression of defensin genes PLANT DEFENSIN1.2a ( PDF1.2a ) and PDF1.2b The dwe1 mutant showed increased resistance to herbivory by beet armyworms ( Spodoptera exigua ) and infection by botrytis ( Botrytis cinerea ) . DWE1 encodes ROTUNDIFOLIA3 , a cytochrome P450 protein essential for BR biosynthesis . The JA-inducible transcription of PDF1.2a and PDF1.2b was significantly reduced in the BRASSINOSTEROID INSENSITIVE1-ETHYL METHANESULFONATE-SUPPRESSOR1 ( BES1 ) gain-of-function mutant bes1- D , which was highly susceptible to S. exigua and B. cinerea BES1 directly targeted the terminator regions of PDF1.2a/PDF1.2b and suppressed their expression . PDF1.2a overexpression diminished the enhanced susceptibility of bes1- D to B. cinerea but did not improve resistance of bes1- D to S. exigua In response to S. exigua herbivory , BES1 inhibited biosynthesis of the JA-induced insect defense-related metabolite indolic glucosinolate by interacting with transcription factors MYB DOMAIN PROTEIN34 ( MYB34 ) , MYB51 , and MYB122 and suppressing expression of genes encoding CYTOCHROME P450 FAMILY79 SUBFAMILY B POLYPEPTIDE3 ( CYP79B3 ) and UDP-GLUCOSYL TRANSFERASE 74B1 ( UGT74B1 ) . Thus , BR contributes to the growth-defense tradeoff by suppressing expression of defensin and glucosinolate biosynthesis genes .
BACKGROUND : The valuable medicinal plant Panax ginseng has high pharmaceutical efficacy because it produces ginsenosides . However , its yields decline because of a root-rot disease caused by Ilyonectria mors-panacis . Because species within Ilyonectria showed variable aggressiveness by altering ginsenoside concentrations in inoculated plants , we investigated how such infections might regulate the biosynthesis of ginsenosides and their related signaling molecules . METHODS : Two-year-old ginseng seedlings were treated with I.   mors-panacis and I.   robusta . Roots from infected and pathogen-free plants were harvested at 4 and 16 days after inoculation . We then examined levels or/and expression of genes of ginsenosides , salicylic acid ( SA ) , jasmonic acid ( JA ) , and reactive oxygen species ( ROS ) . We also checked the susceptibility of those pathogens to ROS . RESULTS : Ginsenoside biosynthesis was significantly suppressed and increased in response to infection by I.   mors-panacis and I.   robusta , respectively . Regulation of JA was significantly higher in I.   robusta-infected roots , while levels of SA and ROS were significantly higher in I.   mors-panacis-infected roots . Catalase activity was significantly higher in I.   robusta-infected roots followed in order by mock roots and those infected by I.   mors-panacis . Moreover , I.   mors-panacis was resistant to ROS compared with I.   robusta . CONCLUSION : Infection by the weakly aggressive I.   robusta led to the upregulation of ginsenoside production and biosynthesis , probably because only a low level of ROS was induced . In contrast , the more aggressive I.   mors-panacis suppressed ginsenoside biosynthesis , probably because of higher ROS levels and subsequent induction of programmed cell death pathways . Furthermore , I.   mors-panacis may have increased its virulence by resisting the cytotoxicity of ROS .
Mitogen-activated protein kinases ( MAPKs ) play an important role in defense responses to biotic and abiotic stresses . In order to investigate the role of SlMAPK3 in tomato plant resistance to Botrytis cinerea , two lines of slmapk3 mutants and wild-type ( WT ) tomato plants were used . The results showed that slmapk3 mutants were more susceptible to B. cinerea and that knockout of SlMAPK3 reduced the activities of defense enzymes and enhanced the accumulation of reactive oxygen species ( ROS ) . Furthermore , we detected the expressions of salicylic acid ( SA ) and jasmonic acid ( JA ) signaling-related genes and found that knockout of SlMAPK3 enhanced the expressions of SlPR1 , SlPAD4 and SlEDS1 , whereas   reduced the expressions of SlLoxC , SlPI I   and SlPI II and enhanced the expressions of SlJAZ1 and SlMYC2 . We postulate that SlMAPK3 plays a positive role in tomato plant resistance to B. cinerea through regulating ROS accumulation and SA and JA defense signaling pathways .
A general prediction of the specialist/generalist paradigm indicates that plant responses to insect herbivores may depend on the degree of ecological specialization of the insect attacker . However , results from a single greenhouse experiment evaluating the responses of the model plant Arabidopsis thaliana to three specialist ( Plutella xylostella , Pieris rapae , and Brevicoryne brassicae ) and three generalist ( Trichoplusia ni , Spodoptera exigua , and Myzus persicae ) insect species did not support the previous prediction . Using an ecological genomic approach , we assessed plant responses in terms of herbivore-induced changes in genome-wide gene expression , defense-related pathways , and concentrations of glucosinolates ( i.e. , secondary metabolites that are ubiquitously present in cruciferous plants ) . Our results showed that plant responses were not influenced by the degree of specialization of insect herbivores . In contrast , responses were more strongly shaped by insect taxa ( i.e. , aphid vs. lepidopteran species ) , likely due to their different feeding modes . Interestingly , similar patterns of plant responses were induced by the same insect herbivore species in terms of defense signaling ( jasmonic acid pathway ) , aliphatic glucosinolate metabolism ( at both the gene expression and phenotypic levels ) and genome-wide responses . Furthermore , plant responses to insect herbivores belonging to the same taxon ( i.e. , four lepidopteran species ) were not explained by herbivore specialization or phylogenetic history . Overall , this study suggests that different feeding modes of insect taxa as well as herbivore-specific plant responses , which may result from distinct ecological/evolutionary interactions between A. thaliana ( or a close relative ) and each of the lepidopteran species , may explain why observed responses deviate from those predicted by the specialist/generalist paradigm .
A multiscaled ecophysiological model of barley ( Hordeum vulgare ) development is presented here . The model is based on the new formalism of relational growth grammars ( RGG ) , an extension of L-systems , and implemented using the new modelling language XL . It is executable in the interactive modelling platform GroIMP . The model consists of a set of morphogenetic rules , combined with a metabolic regulatory network , which simulates the biosynthesis of gibberellic acid ( GA1 ) . GA1 and two of its metabolic precursors are transported along the developing simulated structure . Local concentrations of GA1 determine internode elongation . Furthermore , virtual barley individuals are chosen interactively from a population , based on genotype , and ( sexual or asexual ) reproduction is simulated . Genotype and phenotype of the population are visualized . Seven Mendelian genes have been implemented in the model so far ; some of these directly influence the GA-regulation network . The model exemplifies and validates the new formalism and modelling language . RGG have the capability to represent genetic , metabolic and morphological aspects of plant development and reproduction , all within the same framework .
OBJECTIVES : This study investigated , whether the growth rate of Lemna gibba L. ( duckweed ) can be influenced by the application of homeopathic potencies of gibberellic acid , kinetin , argentum nitricum , and lemna minor . METHODS : Duckweed was grown in either potencies ( 14x-30x , decimal steps ) or water controls ( unsuccussed and succussed ) over seven days . Frond ( leaf-like structure ) growth was measured using a non-destructive image analysis system . Growth rates were calculated for three time intervals ( 0 - 7 , 0 - 3 , 3 - 7 days ) . Five to six independent , randomized and blinded experiments were analysed for each of the four tested substances . Water control experiments were performed repeatedly to test the reliability of the experimental set-up ( systematic negative controls ) . RESULTS : The systematic negative control experiments did not yield any significant effects . Hence , false positive results could be excluded . The test system had a low coefficient of variation ( 1.5 % ) . Out of the four tested substances gibberellic acid had the most pronounced effect ( p=0.0002 , F-test ) on the main outcome parameter frond growth rate ( r(area ) day 0 - 7 ) . Potency levels 15x , 17x , 18x , 23x and 24x reduced growth rate of Lemna gibba ( p<0.05 against the pooled water control , LSD test ) . CONCLUSIONS : Lemna gibba may be considered as a suitable test organism for further studies on the efficacy of homeopathic potencies . Evidence accumulates , that adjacent potency levels may strongly differ in their biological activity . Potential consequences for therapeutical application might be worth investigating .
Two-week-old dwarf peas ( Pisum sativum cv Little Marvel ) were sprayed with gibberellic acid ( GA(3 ) ) , and after 3 or 4 days the upper stem and young leaf samples were analyzed for indole-3-acetic acid ( IAA ) and indole-3-acetyl aspartic acid by an isotope dilution high performance liquid chromatography method . GA(3 ) increased IAA levels as much as 8-fold and decreased indole-3-acetyl aspartic acid levels .