Dragon-kings: mechanisms, statistical methods and empirical evidence

This introductory article presents the special Discussion and Debate volume "From black swans to dragon-kings, is there life beyond power laws?" published in Eur. Phys. J. Special Topics in May 2012. We summarize and put in perspective the contributions into three main themes: (i) mechanisms for dragon-kings, (ii) detection of dragon-kings and statistical tests and (iii) empirical evidence in a large variety of natural and social systems. Overall, we are pleased to witness significant advances both in the introduction and clarification of underlying mechanisms and in the development of novel efficient tests that demonstrate clear evidence for the presence of dragon-kings in many systems. However, this positive view should be balanced by the fact that this remains a very delicate and difficult field, if only due to the scarcity of data as well as the extraordinary important implications with respect to hazard assessment, risk control and predictability.Comment: 20 page

The genome of the seagrass <i>Zostera marina</i> reveals angiosperm adaptation to the sea

Seagrasses colonized the sea on at least three independent occasions to form the basis of one of the most productive and widespread coastal ecosystems on the planet. Here we report the genome of Zostera marina (L.), the first, to our knowledge, marine angiosperm to be fully sequenced. This reveals unique insights into the genomic losses and gains involved in achieving the structural and physiological adaptations required for its marine lifestyle, arguably the most severe habitat shift ever accomplished by flowering plants. Key angiosperm innovations that were lost include the entire repertoire of stomatal genes, genes involved in the synthesis of terpenoids and ethylene signalling, and genes for ultraviolet protection and phytochromes for far-red sensing. Seagrasses have also regained functions enabling them to adjust to full salinity. Their cell walls contain all of the polysaccharides typical of land plants, but also contain polyanionic, low-methylated pectins and sulfated galactans, a feature shared with the cell walls of all macroalgae and that is important for ion homoeostasis, nutrient uptake and O2/CO2 exchange through leaf epidermal cells. The Z. marina genome resource will markedly advance a wide range of functional ecological studies from adaptation of marine ecosystems under climate warming, to unravelling the mechanisms of osmoregulation under high salinities that may further inform our understanding of the evolution of salt tolerance in crop plants

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

Use of a MU bacteriophage derivative to construct mutants of Erwinia amylovora altered in pathogenicity

Fire BlightInternational audienc

Acylcyclohexanediones and biological control: combining complementary strategies to control fire blight

Acylcyclohexanediones and antagonistic bacteria sprayed alone or in combination have been shown to suppress fire blight of apple and pear. Acylcyclohexanediones, such as prohexadione-calcium and trinexapac-ethyl, increase plant resistance and are effective against the shoot blight phase of the disease. Antagonistic bacteria, such as Pantoea agglomerans, compete with the pathogen (Erwinia amylovora) for space and nutrients on stigmas, which prevents blossom blight. Potential synergistic effects of acylcyclohexanediones with P. agglomerans for fire blight suppression were investigated on leaves and flowers of apple and pear. Acylcyclohexanediones modified the composition of apple nectar and stigmatic secretions which resulted in moderately higher epiphytic populations of P. agglomerans strain P10c. In experiments in apple orchards, the combination of acylcyclohexanediones and P. agglomerans gave the greatest protection against blossom blight and shoot blight. In pear orchards, under natural infection conditions, a similar result was obtained for the three of the four years of the experiment

Potential of the electronic nose for the diagnosis of bacterial and fungal diseases in fruit trees

The electronic-nose instrumentation has advanced rapidly during the past decade, since the need for highly sensitive, fast and accurate analytical measurements have considerably stimulated the interest in developing these sensors as diagnostic tools. Given that the pathogen-induced plant responses also include changes in emission of volatiles, the electronic-nose may represent a powerful and operator-friendly alternative for rapid and reliable screening of asymptomatic plant material. In the present study, the electronic nose EOS835 (Sacmi, Imola - Italy), based on metal oxide semiconductors, was used. EOS835 was able to detected asymptomatic apple and pear plants experimentally infected with Erwinia amylovora (fire blight). The electronic nose was also successfully tested for discriminating Botrytis and Sclerotinia rots on both green and yellow kiwifruits. Even if the electronic-nose can be successfully used in experimental conditions for early diagnosis of both pre- and post-harvest diseases, its practical application in open fields, nurseries and packing houses still requires further studies

Real time monitoring of the interactions between Pseudomonas syringae pv actinidiae and Actinidia species.

To elucidate the infection process and the colonization of plant tissues by P.syringae pv actinidiae, different strains of the bacterium were transformed with a stable and broad-host-range plasmid vector (pDSK-GFPuv) that strongly expresses the GFPuv protein. In comparison with the wild-type GFP, GFPuv produces 45-fold brighter green fluorescence in bacterial cells, while it retains the same excitation and emission maxima. In addition, GFPuv is a more soluble protein and does not produce, like wtGFP, nonfluorescent inclusion bodies. Finally, GFPuv has lower toxicity to bacteria than wtGFP. For these reasons, the use of GFPuv may potentially allow the direct observation of the bacterial colonization directly with naked eye under long-wavelength UV light (395 nm). The plasmid stability and the possible effect on P. syrinage actinidiae growth and virulence were tested both in vitro and in vivo. Successively, the use colonization of the plant tissue was monitored in planta on intact, viable plant tissues without any kind of staining of the specimens. The described methodology allows a non invasive observation of the plant-pathogen interaction both at the cell and whole plant level. Therefore, it may also be applied for investigating the influence of agricultural and phytosanitary practices on the host susceptibility and disease developmen

GROWTH-REGULATING ACYLCYCLOHEXANEDIONES, TRINEXAPAC-ETHYL AND PROHEXADIONE-CALCIUM DECREASE BLOSSOM BLIGHT INCIDENCE IN POME FRUITS

The growth-regulating acylcyclohexanediones, trinexapac-ethyl and prohexadione-calcium reduced fire blight infection on apple and pear flowers inoculated with Erwinia amylovora. A reduction of up to 50% of blossom blight was observed in treated plants. In addition, treatment with one of these compounds significantly reduced the percentage of flower infections that successively developed into shoot blight. The acylcyclohexanediones have also been combined with a biological control agent: Pantoea agglomerans EhC9-1. Treatments with such a combination resulted in 75% less flower infections developing into shoot blight than when treated with water. This level of reduction was higher than that observed for either EhC9-1 or an acylcyclohexanedione by itself. This synergic effect could be the result of combining complementary modes of actio

Gli induttori di resistenza nel controllo della Psa del kiwi

Per salvaguardare il pi\uf9 possibile le coltivazioni di kiwi, sempre pi\uf9 minacciate dal cancro batterico, \ue8 necessario comprendere i meccanismi attivati dalla pianta per contrastare l'infezione. Grazie a questi studi si \ue8 visto che alcuni prodotti attivatori delle difese delle piante hanno ridotto i livelli di infezione..