Untargeted metabolomics using liquid chromatography–mass spectrometry (LC–MS) is currently the gold-standard technique to determine the full chemical diversity in biological samples. However, this ...approach still has many limitations; notably, the difficulty of accurately estimating the number of unique metabolites profiled among the thousands of MS ion signals arising from chromatograms. Here, we describe a new workflow, MS-CleanR, based on the MS-DIAL/MS-FINDER suite, which tackles feature degeneracy and improves annotation rates. We show that implementation of MS-CleanR reduces the number of signals by nearly 80% while retaining 95% of unique metabolite features. Moreover, the annotation results from MS-FINDER can be ranked according to the database chosen by the user, which enhance identification accuracy. Application of MS-CleanR to the analysis of Arabidopsis thaliana grown in three different conditions fostered class separation resulting from multivariate data analysis and led to annotation of 75% of the final features. The full workflow was applied to metabolomic profiles from three strains of the leguminous plant Medicago truncatula that have different susceptibilities to the oomycete pathogen Aphanomyces euteiches. A group of glycosylated triterpenoids overrepresented in resistant lines were identified as candidate compounds conferring pathogen resistance. MS-CleanR is implemented through a Shiny interface for intuitive use by end-users (available at https://github.com/eMetaboHUB/MS-CleanR).
DNA-binding proteins (DNA-BPs) and RNA-binding proteins (RNA-BPs) have critical roles in living cells in all kingdoms of life. Various experimental approaches exist for the study of nucleic ...acid-protein interactions in vitro and in vivo, but the detection of such interactions at the subcellular level remains challenging. Here we describe how to detect nucleic acid-protein interactions in plant leaves by using a fluorescence resonance energy transfer (FRET) approach coupled to fluorescence lifetime imaging microscopy (FLIM). Proteins of interest (POI) are tagged with a GFP and transiently expressed in plant cells to serve as donor fluorophore. After sample fixation and cell wall permeabilization, leaves are treated with Sytox Orange, a nucleic acid dye that can function as a FRET acceptor. Upon close association of the GFP-tagged POI with Sytox-Orange-stained nucleic acids, a substantial decrease of the GFP lifetime due to FRET between the donor and the acceptor can be monitored. Treatment with RNase before FRET-FLIM measurements allows determination of whether the POI associates with DNA and/or RNA. A step-by-step protocol is provided for sample preparation, data acquisition and analysis. We describe how to calibrate the equipment and include a tutorial explaining the use of the FLIM software. To illustrate our approach, we provide experimental procedures to detect the interaction between plant DNA and two proteins (the AeCRN13 effector from the oomycete Aphanomyces euteiches and the AtWRKY22 defensive transcription factor from Arabidopsis). This protocol allows the detection of protein-nucleic acid interactions in plant cells and can be completed in <2 d.
Plant LysM proteins control the perception of microbial-derived N-acetylglucosamine compounds for the establishment of symbiosis or activation of plant immunity. This raises questions about how ...plants, and notably legumes, can differentiate friends and foes using similar molecular actors and whether any receptors can intervene in both symbiosis and resistance.
To study this question, nfp and lyk3 LysM-receptor like kinase mutants of Medicago truncatula that are affected in the early steps of nodulation, were analysed following inoculation with Aphanomyces euteiches, a root oomycete. The role of NFP in this interaction was further analysed by overexpression of NFP and by transcriptome analyses.
nfp, but not lyk3, mutants were significantly more susceptible than wildtype plants to A. euteiches, whereas NFP overexpression increased resistance. Transcriptome analyses on A. euteiches inoculation showed that mutation in the NFP gene led to significant changes in the expression of c. 500 genes, notably involved in cell dynamic processes previously associated with resistance to pathogen penetration. nfp mutants also showed an increased susceptibility to the fungus Colletotrichum trifolii.
These results demonstrate that NFP intervenes in M. truncatula immunity, suggesting an unsuspected role for NFP in the perception of pathogenic signals.
Streptomyces spp. constitute a major clade of the phylum Actinobacteria. These Gram-positive, filamentous prokaryotes are ubiquitous in soils and marine sediments, and are commonly found in the ...rhizosphere or inside plant roots. Plant-interacting Streptomyces have received limited attention, in contrast to Streptomyces spp. extensively investigated for decades in medicine given their rich potential for secondary metabolite biosynthesis. Recent genomic, metabolomic, and biotechnological advances have produced key insights into Streptomyces spp., paving the way to the use of their metabolites in agriculture. In this Opinion article we propose how Streptomyces spp. could dominate future aspects of crop nutrition and protection. Risks and benefits of the use of these microorganisms in agriculture are also discussed.
One of the current major scientific challenges is to ensure food security for a growing global population, with the assistance of safe and sustainable agronomic solutions.
Microbial communities of agronomic soils and endophytic microorganisms were largely ignored during the first green revolution, in the 1960s, and the beneficial functions for the crops fulfilled by these microbes have been taken over in recent decades by chemical applications. However, recent advances in omics and synthetic biology are now creating new opportunities to devise strategies aiming at reintroducing microbial genera into our agricultural system.
Esca disease is one of the most destructive grapevine trunk diseases.
and
are two of the known fungal pathogens associated with this disease. Today, biocontrol agents against Esca are mainly based on ...the use of the strain of the mycoparasite fungal genus
such as the Vintec
product. The aim of this study was to investigate early response of woody tissues to Esca pathogens and identify metabolites that could be correlated with a biocontrol activity within a complex woody matrix. An untargeted liquid chromatography-high-resolution mass spectrometry metabolomic approach coupled to a spectral similarity network was used to highlight clusters of compounds associated with the plant response to pathogens and biocontrol. Dereplication highlighted the possible role of glycerophospholipids and polyphenol compounds, the latest mainly belonging to stilbenoids. Antifungal activity of some relevant biomarkers, evaluated
on
and
, suggests that some of these compounds can play a role to limit the development of Esca pathogens in planta.
Given their well-known antifungal abilities, species of the genus
are of significant interest in modern agriculture. Recent studies have shown that
species can induce plant resistance against ...different phytopathogens. To further extend this line of investigation, we investigate herein the transcriptomic response of grapevine trunk to Vintec
, which is a
SC1-based commercial formulation for biological control of grapevine trunk diseases and which reduces wood colonization. The aim of the study is to understand whether the biocontrol agent Vintec
modifies the trunk response to
and
, which are two esca-associated fungal pathogens. An analysis of transcriptional regulation identifies clusters of co-regulated genes whose transcriptomic reprogramming in response to infection depends on the absence or presence of Vintec
. On one hand, the results show that Vintec
differentially modulates the expression of putative genes involved in hormonal signaling, especially those involved in auxin signaling. On the other hand, most significant gene expression modifications occur among secondary-metabolism-related genes, especially regarding phenylpropanoid metabolism and stilbene biosynthesis. Taken together, these results suggest that the biocontrol agent Vintec
induces wood responses that counteract disease development.
To successfully colonize their host, pathogens produce effectors that can interfere with host cellular processes. Here we investigated the function of CRN13 candidate effectors produced by plant ...pathogenic oomycetes and detected in the genome of the amphibian pathogenic chytrid fungus Batrachochytrium dendrobatidis (BdCRN13). When expressed in Nicotiana, AeCRN13, from the legume root pathogen Aphanomyces euteiches, increases the susceptibility of the leaves to the oomycete Phytophthora capsici. When transiently expressed in amphibians or plant cells, AeCRN13 and BdCRN13 localize to the cell nuclei, triggering aberrant cell development and eventually causing cell death. Using Förster resonance energy transfer experiments in plant cells, we showed that both CRN13s interact with nuclear DNA and trigger plant DNA damage response (DDR). Mutating key amino acid residues in a predicted HNH‐like endonuclease motif abolished the interaction of AeCRN13 with DNA, the induction of DDR and the enhancement of Nicotiana susceptibility to P. capsici. Finally, H2AX phosphorylation, a marker of DNA damage, and enhanced expression of genes involved in the DDR were observed in A. euteiches‐infected Medicago truncatula roots. These results show that CRN13 from plant and animal eukaryotic pathogens promotes host susceptibility by targeting nuclear DNA and inducing DDR.
Pythium oligandrum
is a soil-borne oomycete associated with rhizosphere and root tissues. Its ability to enhance plant growth, stimulate plant immunity and parasitize fungal and oomycete preys has ...led to the development of agricultural biocontrol products. Meanwhile, the effect of
P. oligandrum
on mutualistic interactions and more generally on root microbial communities has not been investigated. Here, we developed a biological system comprising
P. oligandrum
interacting with two legume plants,
Medicago truncatula
and
Pisum sativum. P. oligandrum
activity was investigated at the transcriptomics level through an RNAseq approach, metabolomics and finally metagenomics to investigate the impact of
P. oligandrum
on root microbiota. We found that
P. oligandrum
promotes plant growth in these two species and protects them against infection by the oomycete
Aphanomyces euteiches
, a devastating legume root pathogen. In addition,
P. oligandrum
up-regulated more than 1000 genes in
M. truncatula
roots including genes involved in plant defense and notably in the biosynthesis of antimicrobial compounds and validated the enhanced production of
M. truncatula
phytoalexins, medicarpin and formononetin. Despite this activation of plant immunity, we found that root colonization by
P. oligandrum
did not impaired symbiotic interactions, promoting the formation of large and multilobed symbiotic nodules with
Ensifer meliloti
and did not negatively affect the formation of arbuscular mycorrhizal symbiosis. Finally, metagenomic analyses showed the oomycete modifies the composition of fungal and bacterial communities. Together, our results provide novel insights regarding the involvement of
P. oligandrum
in the functioning of plant root microbiota.
Implied Volatility Functions: Empirical Tests Dumas, Bernard; Fleming, Jeff; Whaley, Robert E.
The Journal of finance (New York),
December 1998, Letnik:
53, Številka:
6
Journal Article
Recenzirano
Odprti dostop
Derman and Kani (1994), Dupire (1994), and Rubinstein (1994) hypothesize that asset return volatility is a deterministic function of asset price and time, and develop a deterministic volatility ...function (DVF) option valuation model that has the potential of fitting the observed cross section of option prices exactly. Using S&P 500 options from June 1988 through December 1993, we examine the predictive and hedging performance of the DVF option valuation model and find it is no better than an ad hoc procedure that merely smooths Black-Scholes (1973) implied volatilities across exercise prices and times to expiration.
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