Identification and characterization of the Non-race specific Disease Resistance 1 (NDR1) orthologous protein in coffee

<p>Abstract</p> <p>Background</p> <p>Leaf rust, which is caused by the fungus <it>Hemileia vastatrix </it>(Pucciniales), is a devastating disease that affects coffee plants (<it>Coffea arabica </it>L.). Disadvantages that are associated with currently developed phytoprotection approaches have recently led to the search for alternative strategies. These include genetic manipulations that constitutively activate disease resistance signaling pathways. However, molecular actors of such pathways still remain unknown in <it>C. arabica</it>. In this study, we have isolated and characterized the coffee <it>NDR1 </it>gene, whose <it>Arabidopsis </it>ortholog is a well-known master regulator of the hypersensitive response that is dependent on coiled-coil type R-proteins.</p> <p>Results</p> <p>Two highly homologous cDNAs coding for putative NDR1 proteins were identified and cloned from leaves of coffee plants. One of the candidate coding sequences was then expressed in the <it>Arabidopsis </it>knock-out null mutant <it>ndr1-1</it>. Upon a challenge with a specific strain of the bacterium <it>Pseudomonas syringae </it>(DC3000::<it>AvrRpt2</it>), analysis of both macroscopic symptoms and <it>in planta </it>microbial growth showed that the coffee cDNA was able to restore the resistance phenotype in the mutant genetic background. Thus, the cDNA was dubbed <it>CaNDR1a </it>(standing for <it>Coffea arabica Non-race specific Disease Resistance 1a</it>). Finally, biochemical and microscopy data were obtained that strongly suggest the mechanistic conservation of the <it>NDR1</it>-driven function within coffee and <it>Arabidopsis </it>plants. Using a transient expression system, it was indeed shown that the CaNDR1a protein, like its <it>Arabidopsis </it>counterpart, is localized to the plasma membrane, where it is possibly tethered by means of a GPI anchor.</p> <p>Conclusions</p> <p>Our data provide molecular and genetic evidence for the identification of a novel functional <it>NDR1 </it>homolog in plants. As a key regulator initiating hypersensitive signalling pathways, <it>CaNDR1 </it>gene(s) might be target(s) of choice for manipulating the coffee innate immune system and achieving broad spectrum resistance to pathogens. Given the potential conservation of <it>NDR1</it>-dependent defense mechanisms between <it>Arabidopsis </it>and coffee plants, our work also suggests new ways to isolate the as-yet-unidentified <it>R</it>-gene(s) responsible for resistance to <it>H. vastatrix</it>.</p

Antioxidant actions of ovothiol-derived 4-mercaptoimidazoles: glutathione peroxidase activity and protection against peroxynitrite-induced damage

Abstract4-Mercaptoimidazoles derived from the naturally occurring antioxidants, ovothiols, were tested for their glutathione peroxidase-like (GSH Px-like) activity and protection against peroxynitrite-induced damage. All the thiol compounds displayed similar significant GSH Px-like activities, which are however weaker than that of the reference compound, ebselen. The inhibitions of the peroxynitrite-dependent oxidation of Evans blue dye and dihydrorhodamine 123 showed that the thiol compounds substituted on position 5 of the imidazole ring were nearly as effective as ebselen while the C-2 substituted ones were less effective. Both assays corroborate the large superiority of mercaptoimidazoles over glutathione as inhibitors of peroxynitrite-dependent oxidation

Identification and characterization of the Non- race specific Disease Resistance 1 (NDR1) orthologous protein in coffee

Abstract Background: Leaf rust, which is caused by the fungus Hemileia vastatrix (Pucciniales), is a devastating disease that affects coffee plants (Coffea arabica L.). Disadvantages that are associated with currently developed phytoprotection approaches have recently led to the search for alternative strategies. These include genetic manipulations that constitutively activate disease resistance signaling pathways. However, molecular actors of such pathways still remain unknown in C. arabica. In this study, we have isolated and characterized the coffee NDR1 gene, whose Arabidopsis ortholog is a well-known master regulator of the hypersensitive response that is dependent on coiledcoil type R-proteins

Re-visiting Meltsner: Policy Advice Systems and the Multi-Dimensional Nature of Professional Policy Analysis

10.2139/ssrn.15462511-2

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

The GenTree Platform: growth traits and tree-level environmental data in 12 European forest tree species

Background: Progress in the field of evolutionary forest ecology has been hampered by the huge challenge of phenotyping trees across their ranges in their natural environments, and the limitation in high-resolution environmental information. Findings: The GenTree Platform contains phenotypic and environmental data from 4,959 trees from 12 ecologically and economically important European forest tree species: Abies alba Mill. (silver fir), Betula pendula Roth. (silver birch), Fagus sylvatica L. (European beech), Picea abies (L.) H. Karst (Norway spruce), Pinus cembra L. (Swiss stone pine), Pinus halepensis Mill. (Aleppo pine), Pinus nigra Arnold (European black pine), Pinus pinaster Aiton (maritime pine), Pinus sylvestris L. (Scots pine), Populus nigra L. (European black poplar), Taxus baccata L. (English yew), and Quercus petraea (Matt.) Liebl. (sessile oak). Phenotypic (height, diameter at breast height, crown size, bark thickness, biomass, straightness, forking, branch angle, fructification), regeneration, environmental in situ measurements (soil depth, vegetation cover, competition indices), and environmental modeling data extracted by using bilinear interpolation accounting for surrounding conditions of each tree (precipitation, temperature, insolation, drought indices) were obtained from trees in 194 sites covering the species’ geographic ranges and reflecting local environmental gradients. Conclusion: The GenTree Platform is a new resource for investigating ecological and evolutionary processes in forest trees. The coherent phenotyping and environmental characterization across 12 species in their European ranges allow for a wide range of analyses from forest ecologists, conservationists, and macro-ecologists. Also, the data here presented can be linked to the GenTree Dendroecological collection, the GenTree Leaf Trait collection, and the GenTree Genomic collection presented elsewhere, which together build the largest evolutionary forest ecology data collection available

Between but not within species variation in the distribution of fitness effects

New mutations provide the raw material for evolution and adaptation. The distribution of fitness effects (DFE) describes the spectrum of effects of new mutations that can occur along a genome, and is therefore of vital interest in evolutionary biology. Recent work has uncovered striking similarities in the DFE between closely related species, prompting us to ask whether there is variation in the DFE among populations of the same species, or among species with different degrees of divergence, i.e., whether there is variation in the DFE at different levels of evolution. Using exome capture data from six tree species sampled across Europe we characterised the DFE for multiple species, and for each species, multiple populations, and investigated the factors potentially influencing the DFE, such as demography, population divergence and genetic background. We find statistical support for there being variation in the DFE at the species level, even among relatively closely related species. However, we find very little difference at the population level, suggesting that differences in the DFE are primarily driven by deep features of species biology, and that evolutionarily recent events, such as demographic changes and local adaptation, have little impact

Étangs d'eau industrielle : simulation dynamique.

L'objet de cette simulation dynamique est l 'identification des paramètres de design d'un bassin de rejet des eaux us é e s e t surchauffées. Un modèle dynamique à caractère prédictif visualisera le comportement de trois variables d'état considérées, soit: a) La variation de température de l'eau du bassin artificiel dans le but de prévoir la période de gel, lors d'une tel éventualité; B) la variation de la masse i.e. de la hauteur libre du niveau de l'eau afin de conjecturer les débordements intempestifs; C) la variation de la concentration d'un polluant en solution dans les eaux du bassin pour prédire et éviter des concentrations accidentelles excessives. L'information recueillie sur le comportement transitoire de l'étang de rejet, suggère l'approche de réalisation à poursuivre et permet de satisfaire les contraintes environnementales