Sr and Nd isotope data for arc-related (meta) volcanics (SW Iberia)

In the southern sector of the Ossa-Morena Zone (Iberian Variscan Chain), along its boundaries with the Beja-Acebuches Ophiolite and the South-Portuguese Zone, Upper Palaeozoic igneous mafic and intermediate rocks, both intrusive and extrusive, are widely represented. The so-called Odivelas Unit (Andrade,1983), include (meta-) basalts and (meta-) andesites, which, according with previous studies, display low-K tholeiitic to calc-alkaline signatures and, therefore, are interpreted as remnants of an active margin volcanic arc. Santos et al. (1990) subdivided those volcanics into two groups: in Alfundão-Peroguarda, the tholeiitic nature is dominant; in Odivelas-Penique, the calc-alkaline signature becomes more pronounced. Intercalation of limestone layers provided some age constraints, showing that the subduction-related volcanic activity in the studied area began in the Lower Devonian and continued, at least, through the Middle Devonian (Conde & Andrade, 1974; Machado et al., 2010). In this work, samples previously studied by Santos et al. (1990) and Silva et al. (2011) were analysed for Sm-Nd and Rb-Sr isotopes. Considering that the volcanics were systematically affected by hydrothermal metamorphism, it is expected that the Sr signatures show significant disturbance. In contrast, Nd isotope ratios probably reflect the primary features. Alfundão-Peroguarda samples show a very limited range of positive initial εNd, from +5.1 to +4.3 (assuming 400 Ma), showing no evidence for significant crustal assimilation and, therefore, allowing the attribution of negative Nb and Ta anomalies to arc-related processes On the other hand, 87Sr/86Sr varies from 0.7044 to 0.7060 (for 400Ma). These samples rocks define a horizontal trend on the initial εNd vs. initial 87Sr/86Sr plot, typical of co-genetic rocks that underwent interaction with seawater. On the other hand, Odivelas-Penique volcanics show wide spectra for both initial 87Sr/86Sr (from 0.7038 to 0.7066) and εNd (from +4.6 to -4.1). Significantly, the highest εNd values for this group are within the narrow range defined by Alfundão-Peroguarda tholeiitic basalts, suggesting a common mantle source (or very similar sources) for the most mafic magmas of both sectors. The whole set of Nd isotope ratios supports the distinction previously proposed between the two groups of volcanics. In addition, the variation from positive to negative initial εNd values in the Odivelas-Penique suite shows that its geochemical features were likely influenced by assimilation of continental crustal material

Genomic and transcriptomic characterization of Pseudomonas aeruginosa small colony variants derived from a chronic infection model

Phenotypic change is a hallmark of bacterial adaptation during chronic infection. In the case of chronic Pseudomonas aeruginosa lung infection in patients with cystic fibrosis, well-characterized phenotypic variants include mucoid and small colony variants (SCVs). It has previously been shown that SCVs can be reproducibly isolated from the murine lung following the establishment of chronic infection with mucoid P. aeruginosa strain NH57388A. Using a combination of single-molecule real-time (PacBio) and Illumina sequencing we identify a large genomic inversion in the SCV through recombination between homologous regions of two rRNA operons and an associated truncation of one of the 16S rRNA genes and suggest this may be the genetic switch for conversion to the SCV phenotype. This phenotypic conversion is associated with large-scale transcriptional changes distributed throughout the genome. This global rewiring of the cellular transcriptomic output results in changes to normally differentially regulated genes that modulate resistance to oxidative stress, central metabolism and virulence. These changes are of clinical relevance because the appearance of SCVs during chronic infection is associated with declining lung function

Extreme Ultra-Violet Spectroscopy of the Lower Solar Atmosphere During Solar Flares

The extreme ultraviolet portion of the solar spectrum contains a wealth of diagnostic tools for probing the lower solar atmosphere in response to an injection of energy, particularly during the impulsive phase of solar flares. These include temperature and density sensitive line ratios, Doppler shifted emission lines and nonthermal broadening, abundance measurements, differential emission measure profiles, and continuum temperatures and energetics, among others. In this paper I shall review some of the advances made in recent years using these techniques, focusing primarily on studies that have utilized data from Hinode/EIS and SDO/EVE, while also providing some historical background and a summary of future spectroscopic instrumentation.Comment: 34 pages, 8 figures. Submitted to Solar Physics as part of the Topical Issue on Solar and Stellar Flare

Propionic acid promotes the virulent phenotype of Crohn's disease-associated adherent-invasive Escherichia coli

Propionic acid (PA) is a bacterium-derived intestinal antimicrobial and immune modulator used widely in food production and agriculture. Passage of Crohn’s disease-associated adherent-invasive Escherichia coli (AIEC) through a murine model, in which intestinal PA levels are increased to mimic the human intestine, leads to the recovery of AIEC with significantly increased virulence. Similar phenotypic changes are observed outside the murine model when AIEC is grown in culture with PA as the sole carbon source; such PA exposure also results in AIEC that persists at 20-fold higher levels in vivo. RNA sequencing identifies an upregulation of genes involved in biofilm formation, stress response, metabolism, membrane integrity, and alternative carbon source utilization. PA exposure also increases virulence in a number of E. coli isolates from Crohn’s disease patients. Removal of PA is sufficient to reverse these phenotypic changes. Our data indicate that exposure to PA results in AIEC resistance and increased virulence in its presence

Antibiotics induce sustained dysregulation of intestinal T cell immunity by perturbing macrophage homeostasis

Macrophages in the healthy intestine are highly specialized and usually respond to the gut microbiota without provoking an inflammatory response. A breakdown in this tolerance leads to inflammatory bowel disease (IBD), but the mechanisms by which intestinal macrophages normally become conditioned to promote microbial tolerance are unclear. Strong epidemiological evidence linking disruption of the gut microbiota by antibiotic use early in life to IBD indicates an important role for the gut microbiota in modulating intestinal immunity. Here, we show that antibiotic use causes intestinal macrophages to become hyperresponsive to bacterial stimulation, producing excess inflammatory cytokines. Re-exposure of antibiotic-treated mice to conventional microbiota induced a long-term, macrophage-dependent increase in inflammatory T helper 1 (T 1) responses in the colon and sustained dysbiosis. The consequences of this dysregulated macrophage activity for T cell function were demonstrated by increased susceptibility to infections requiring T 17 and T 2 responses for clearance (bacterial and helminth infections), corresponding with increased inflammation. Short-chain fatty acids (SCFAs) were depleted during antibiotic administration; supplementation of antibiotics with the SCFA butyrate restored the characteristic hyporesponsiveness of intestinal macrophages and prevented T cell dysfunction. Butyrate altered the metabolic behavior of macrophages to increase oxidative phosphorylation and also promoted alternative macrophage activation. In summary, the gut microbiota is essential to maintain macrophage-dependent intestinal immune homeostasis, mediated by SCFA-dependent pathways. Oral antibiotics disrupt this process to promote sustained T cell-mediated dysfunction and increased susceptibility to infections, highlighting important implications of repeated broad-spectrum antibiotic use

Female chromosome X mosaicism is age-related and preferentially affects the inactivated X chromosome

To investigate large structural clonal mosaicism of chromosome X, we analysed the SNP microarray intensity data of 38,303 women from cancer genome-wide association studies (20,878 cases and 17,425 controls) and detected 124 mosaic X events42Mb in 97 (0.25%) women. Here we show rates for X-chromosome mosaicism are four times higher than mean autosomal rates; X mosaic events more often include the entire chromosome and participants with X events more likely harbour autosomal mosaic events. X mosaicism frequency increases with age (0.11% in 50-year olds; 0.45% in 75-year olds), as reported for Y and autosomes. Methylation array analyses of 33 women with X mosaicism indicate events preferentially involve the inactive X chromosome. Our results provide further evidence that the sex chromosomes undergo mosaic events more frequently than autosomes, which could have implications for understanding the underlying mechanisms of mosaic events and their possible contribution to risk for chronic diseases

Part mounting revisited

Having been involved with single point diamond turning since the 1960's; I share with others of my age, a unique perspective of the craft. I am amazed at how the fundamentals seem to be forgotten or misplaced, and need to be re emphasized and re learned. Each new precision machine operator not only needs to re learn (many times the hard way), these fundamentals, but seems to inherit all the folklore; good and bad, from his predecessor. Let me explain. I spend some of my time as a consultant to the shops' division at the Los Alamos National Laboratory, at which there are five precision turning machines divided between two buildings. The main shop area houses an old friction way (hydrodynamic) turning Machine. The base of this turning machine is made from the base of an old Moore measuring machine. The air bearing spindle, a Red Head'' was made by the Heald Machine Tool Co. With the addition of an Allen-Bradley Numerical control system, this machine has become a work horse, used primarily to make smooth flat surfaces in the fly-cutting mode. Recently, I became involved in the evaluation and repair of the machine as it no longer produced smooth surfaces. Smooth surfaces are not the point of this narrative, accurate geometry however is

Response By Dairy Cows Grazing Tropical Grass Pasture To Barley or Sorghum Grain Based Concentrates and Lucerne Hay

This study investigated the responses by dairy cows grazing Callide Rhodes grass (Chloris gayana cv. Callide) pasture to supplementation with barley or sorghum based concentrates (5 grain:1 cotton seed meal) or barley concentrate plus lucerne (Medicago sativa) hay. It was conducted in summer - autumn 1999 with 20 spring calved cows in 4 treatments in 3 consecutive periods of 4 weeks. Rain grown pastures, heavily stocked at 4.4 cows/ha, provided 22 to 35 kg green DM and 14 to 16 kg green leaf DM/cow.day in periods 1 to 3. Supplements were fed individually twice daily after milking. Cows received 6 kg concentrate/day in period 1, increased by 1 kg/day as barley, sorghum or lucerne chaff in each of periods 2 and 3. The Control treatment received 6 kg barley concentrate in all 3 periods. Milk yields by cows fed sorghum were lower than for cows fed equivalent levels of barley-based concentrate (P0.05). Increased concentrate supplementation did not alleviate the problem of low protein in milk produced by freshly calved Holstein-Friesian cows grazing tropical grass pasture in summer. Animal production for a consuming world : proceedings of 9th Congress of the Asian-Australasian Association of Animal Production Societies [AAAP] and 23rd Biennial Conference of the Australian Society of Animal Production [ASAP] and 17th Annual Symposium of the University of Sydney, Dairy Research Foundation, [DRF]. 2-7 July 2000, Sydney, Australia

GCM compareR: A web application to assess differences and assist in the selection of general circulation models for climate change research

Climate change research often relies on downscaled general circulation models (GCM), projections of future scenarios that are used to build ecological and evolutionary models. With more than 35 different GCMs widely available at a resolution of 10 km and finer, standardized methods to understand the differences among GCM projections in a region of interest and to choose which GCM to use for analysis are essential to maximize relevance to policy and to assure a proper treatment of uncertainty. To help researchers and policymakers understand and select form the range of available GCM scenarios, we have developed GCM compareR, an open-source web application written in r using shiny. GCM compareR is freely accessible with an easy interactive user interface, has preloaded climate scenario data to increase the speed of analysis and is fully documented to ensure reproducibility. Users of the application need no prior experience in coding. GCM compareR is designed to compare GCMs and different climate change scenarios to provide full, documented exploration of the possible alternative futures from within the range of projections in CMIP5 climate models. Designed with a wide group of users in mind, including ecologists, conservationists and policymakers, the application is designed to adapt analyses to any geographic area of interest. Results are provided as figures, tables and maps that clearly communicate the differences among model projections for the region. Additionally, the tool allows for the export of a report that records the parameter choices and results of a session, along with contextual information, to make the analysis fully transparent and replicable