Arc magmas sourced from melange diapirs in subduction zones

Author Posting. © The Author(s), 2012. This is the author's version of the work. It is posted here by permission of Nature Publishing Group for personal use, not for redistribution. The definitive version was published in Nature Geoscience 5 (2012): 862-867, doi:10.1038/ngeo1634.At subduction zones, crustal material is recycled back into the mantle. A certain proportion, however, is returned to the overriding plate via magmatism. The magmas show a characteristic range of compositions that have been explained by three-component mixing in their source regions: hydrous fluids derived from subducted altered oceanic crust and components derived from the thin sedimentary veneer are added to the depleted peridotite in the mantle beneath the volcanoes. However, currently no uniformly accepted model exists for the physical mechanism that mixes the three components and transports them from the slab to the magma source. Here we present an integrated physico-chemical model of subduction zones that emerges from a review of the combined findings of petrology, modelling, geophysics, and geochemistry: Intensely mixed metamorphic rock formations, so-called mélanges, form along the slab-mantle interface and comprise the characteristic trace-element patterns of subduction-zone magmatic rocks. We consider mélange formation the physical mixing process that is responsible for the geochemical three-component pattern of the magmas. Blobs of low-density mélange material, so-called diapirs, rise buoyantly from the surface of the subducting slab and provide a means of transport for well-mixed materials into the mantle beneath the volcanoes, where they produce melt. Our model provides a consistent framework for the interpretation of geophysical, petrological and geochemical data of subduction zones.H.M. was funded by the J. LamarWorzel Assistant Scientist Fund and the Penzance Endowed Fund in Support of Assistant Scientists. Funding from NSF grant #1119403 (G. Harlow) is acknowledged.2013-05-1

The History, Relevance, and Applications of the Periodic System in Geochemistry

Geochemistry is a discipline in the earth sciences concerned with understanding the chemistry of the Earth and what that chemistry tells us about the processes that control the formation and evolution of Earth materials and the planet itself. The periodic table and the periodic system, as developed by Mendeleev and others in the nineteenth century, are as important in geochemistry as in other areas of chemistry. In fact, systemisation of the myriad of observations that geochemists make is perhaps even more important in this branch of chemistry, given the huge variability in the nature of Earth materials – from the Fe-rich core, through the silicate-dominated mantle and crust, to the volatile-rich ocean and atmosphere. This systemisation started in the eighteenth century, when geochemistry did not yet exist as a separate pursuit in itself. Mineralogy, one of the disciplines that eventually became geochemistry, was central to the discovery of the elements, and nineteenth-century mineralogists played a key role in this endeavour. Early “geochemists” continued this systemisation effort into the twentieth century, particularly highlighted in the career of V.M. Goldschmidt. The focus of the modern discipline of geochemistry has moved well beyond classification, in order to invert the information held in the properties of elements across the periodic table and their distribution across Earth and planetary materials, to learn about the physicochemical processes that shaped the Earth and other planets, on all scales. We illustrate this approach with key examples, those rooted in the patterns inherent in the periodic law as well as those that exploit concepts that only became familiar after Mendeleev, such as stable and radiogenic isotopes

MrkH, a Novel c-di-GMP-Dependent Transcriptional Activator, Controls Klebsiella pneumoniae Biofilm Formation by Regulating Type 3 Fimbriae Expression

Klebsiella pneumoniae causes significant morbidity and mortality worldwide, particularly amongst hospitalized individuals. The principle mechanism for pathogenesis in hospital environments involves the formation of biofilms, primarily on implanted medical devices. In this study, we constructed a transposon mutant library in a clinical isolate, K. pneumoniae AJ218, to identify the genes and pathways implicated in biofilm formation. Three mutants severely defective in biofilm formation contained insertions within the mrkABCDF genes encoding the main structural subunit and assembly machinery for type 3 fimbriae. Two other mutants carried insertions within the yfiN and mrkJ genes, which encode GGDEF domain- and EAL domain-containing c-di-GMP turnover enzymes, respectively. The remaining two isolates contained insertions that inactivated the mrkH and mrkI genes, which encode for novel proteins with a c-di-GMP-binding PilZ domain and a LuxR-type transcriptional regulator, respectively. Biochemical and functional assays indicated that the effects of these factors on biofilm formation accompany concomitant changes in type 3 fimbriae expression. We mapped the transcriptional start site of mrkA, demonstrated that MrkH directly activates transcription of the mrkA promoter and showed that MrkH binds strongly to the mrkA regulatory region only in the presence of c-di-GMP. Furthermore, a point mutation in the putative c-di-GMP-binding domain of MrkH completely abolished its function as a transcriptional activator. In vivo analysis of the yfiN and mrkJ genes strongly indicated their c-di-GMP-specific function as diguanylate cyclase and phosphodiesterase, respectively. In addition, in vitro assays showed that purified MrkJ protein has strong c-di-GMP phosphodiesterase activity. These results demonstrate for the first time that c-di-GMP can function as an effector to stimulate the activity of a transcriptional activator, and explain how type 3 fimbriae expression is coordinated with other gene expression programs in K. pneumoniae to promote biofilm formation to implanted medical devices

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

A young source for the Hawaiian plume

International audienceRecycling of oceanic crust through subduction, mantle upwelling, and remelting in mantle plumes is a widely accepted mechanism to explain ocean island volcanism1. The timescale of this recycling is important to our understanding of mantle circulation rates. Correlations of uranogenic lead isotopes in lavas from ocean islands such as Hawaii or Iceland, when interpreted as model isochrons, have yielded source differentiation ages between 1 and 2.5 billion years (Gyr)2,3,4,5. However, if such correlations are produced by mixing of unrelated mantle components6 they will have no direct age significance. Re-Os decay model ages take into account the mixing of sources with different histories7,8, but they depend on the assumed initial Re/Os ratio of the subducted crust, which is poorly constrained because of the high mobility of rhenium during subduction9. Here we report the first data on 87Sr/86Sr ratios for 138 melt inclusions in olivine phenocrysts from lavas of Mauna Loa shield volcano, Hawaii, indicating enormous mantle source heterogeneity. We show that highly radiogenic strontium in severely rubidium-depleted melt inclusions matches the isotopic composition of 200-650-Myr-old sea water. We infer that such sea water must have contaminated the Mauna Loa source rock, before subduction, imparting a unique 'time stamp' on this source. Small amounts of seawater-derived strontium in plume sources may be common but can be identified clearly only in ultra-depleted melts originating from generally highly (incompatible-element) depleted source components. The presence of 200-650-Myr-old oceanic crust in the source of Hawaiian lavas implies a timescale of general mantle circulation with an average rate of about 2 (±1) cm yr-1, much faster than previously thought