Influence of the disorder on tracer dispersion in a flow channel

Tracer dispersion is studied experimentally in periodic or disordered arrays of beads in a capillary tube. Dispersion is measured from light absorption variations near the outlet following a steplike injection of dye at the inlet. Visualizations using dye and pure glycerol are also performed in similar geometries. Taylor dispersion is dominant both in an empty tube and for a periodic array of beads: the dispersivity $l\_d$ increases with the P\'eclet number $Pe$ respectively as $Pe$ and $Pe^{0.82}$ and is larger by a factor of 8 in the second case. In a disordered packing of smaller beads (1/3 of the tube diameter) geometrical dispersion associated to the disorder of the flow field is dominant with a constant value of $l\_d$ reached at high P\'eclet numbers. The minimum dispersivity is slightly higher than in homogeneous nonconsolidated packings of small grains, likely due heterogeneities resulting from wall effects. In a disordered packing with the same beads as in the periodic configuration, $l\_d$ is up to 20 times lower than in the latter and varies as $Pe^\alpha$ with $\alpha = 0.5$ or $= 0.69$ (depending on the fluid viscosity). A simple model accounting for this latter result is suggested.Comment: available online at http://www.edpsciences.org/journal/index.cfm?edpsname=epjap&niv1=contents&niv2=archive

AsaGEI2b: a new variant of a genomic island identified in the Aeromonas salmonicida subsp. salmonicida JF3224 strain isolated from a wild fish in Switzerland

Aeromonas salmonicida subsp. salmonicida is the causal agent of furunculosis in salmonids. We recently identified a group of genomic islands (AsaGEI) in this bacterium. AsaGEI2a, one of these genomic islands, has almost exclusively been identified in isolates from North America. To date, Aeromonas salmonicida subsp. salmonicida JF3224, a strain isolated from a wild brown trout (Salmo trutta) caught in Switzerland, was the only European isolate that appeared to bear AsaGEI2a. We analyzed the genome of JF3224 and showed that the genomic island in JF3224 is a new variant of AsaGEI, which we have called AsaGEI2b. While AsaGEI2b shares the same integrase gene and insertion site as AsaGEI2a, it is very different in terms of many other features. Additional genomic investigations combined with PCR genotyping revealed that JF3224 is sensitive to growth at 25°C, leading to insertion sequence-dependent rearrangement of the locus on the pAsa5 plasmid that encodes a type three secretion system, which is essential for the virulence of the bacterium. The analysis of the JF3224 genome confirmed that AsaGEIs are accurate indicators of the geographic origins of A. salmonicida subsp. salmonicida isolates and is another example of the susceptibility of the pAsa5 plasmid to DNA rearrangement

Ice-nucleating particles in Canadian Arctic sea-surface microlayer and bulk seawater

The sea-surface microlayer and bulk seawater can contain ice-nucleating particles (INPs) and these INPs can be emitted into the atmosphere. Our current understanding of the properties, concentrations, and spatial and temporal distributions of INPs in the microlayer and bulk seawater is limited. In this study we investigate the concentrations and properties of INPs in microlayer and bulk seawater samples collected in the Canadian Arctic during the summer of 2014. INPs were ubiquitous in the microlayer and bulk seawater with freezing temperatures in the immersion mode as high as −14 °C. A strong negative correlation (R = −0. 7, p = 0. 02) was observed between salinity and freezing temperatures (after correction for freezing depression by the salts). One possible explanation is that INPs were associated with melting sea ice. Heat and filtration treatments of the samples show that the INPs were likely heat-labile biological materials with sizes between 0.02 and 0.2 µm in diameter, consistent with previous measurements off the coast of North America and near Greenland in the Arctic. The concentrations of INPs in the microlayer and bulk seawater were consistent with previous measurements at several other locations off the coast of North America. However, our average microlayer concentration was lower than previous observations made near Greenland in the Arctic. This difference could not be explained by chlorophyll a concentrations derived from satellite measurements. In addition, previous studies found significant INP enrichment in the microlayer, relative to bulk seawater, which we did not observe in this study. While further studies are needed to understand these differences, we confirm that there is a source of INP in the microlayer and bulk seawater in the Canadian Arctic that may be important for atmospheric INP concentrations

Particle export during the Southern Ocean Iron Experiment (SOFeX)

Author Posting. © The Authors, 2004. This is the author's version of the work. It is posted here by permission of American Society of Limnology and Oceanography for personal use, not for redistribution. The definitive version was published in Limnology and Oceanography 50 (2005): 311-327, doi:10.4319/lo.2005.50.1.0311.We studied the effect of iron addition on particle export in the Southern Ocean by measuring changes in the distribution of thorium-234 during a 4 week Fe enrichment experiment conducted in the high-silicate high-nitrate waters just south of the Southern Antarctic Circumpolar Current Front at 172.5°W. Decreases in 234Th activity with time in the fertilized mixed layer (0-50m) exceeded those in unfertilized waters, indicating enhanced export of 234Th on sinking particles after Fe enrichment. The addition of Fe also affected export below the fertilized patch by increasing the efficiency of particle export through the 100 m depth horizon. Extensive temporal and vertical Lagrangian sampling allowed us to make a detailed examination of the 234Th flux model, which was used to quantify the fluxes of particulate organic carbon (POC) and biogenic silica (bSiO2). Iron addition increased the flux of both POC and bSiO2 out of the mixed layer by about 300%. The flux at 100 m increased by more than 700% and 600% for POC and bSiO2, respectively. The absolute magnitude of the POC and bSiO2 fluxes were not large relative to natural blooms at these latitudes, or to those found in association with the termination of blooms in other ocean regions. Our results support the hypothesis that Fe addition leads directly to significant particle export and sequestration of C in the deep ocean. This is a key link between ocean Fe inputs and past changes in atmospheric CO2 and climate.This work was supported by the Division of Ocean Sciences at the U.S. National Science Foundation, the Biological and Environmental Research Office, Office of Science, U.S. Department of Energy, and for RIB Polar Star logistical support, Polar Programs at the U.S. National Science Foundation

Hsp-27 expression at diagnosis predicts poor clinical outcome in prostate cancer independent of ETS-gene rearrangement

BACKGROUND: This study was performed to test the hypothesis that expression of small heat shock protein Hsp-27 is, at diagnosis, a reliable predictive biomarker of clinically aggressive prostate cancer. METHODS: A panel of tissue microarrays constructed from a well-characterised cohort of 553 men with conservatively managed prostate cancer was stained immunohistochemically to detect Hsp-27 protein. Hsp-27 expression was compared with a series of pathological and clinical parameters, including outcome. RESULTS: Hsp-27 staining was indicative of higher Gleason score (P7, the presence of Hsp-27 retained its power to independently predict poor clinical outcome (P<0.002). Higher levels of Hsp-27 staining were almost entirely restricted to cancers lacking ERG rearrangements (chi2 trend=31.4, P<0.001), although this distribution did not have prognostic significance. INTERPRETATION: This study has confirmed that, in prostate cancers managed conservatively over a period of more than 15 years, expression of Hsp-27 is an accurate and independent predictive biomarker of aggressive disease with poor clinical outcome (P<0.001). These findings suggest that apoptotic and cell-migration pathways modulated by Hsp-27 may contain targets susceptible to the development of biologically appropriate chemotherapeutic agents that are likely to prove effective in treating aggressive prostate cancers

Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells

Post-transcriptional modification of RNA nucleosides occurs in all living organisms. Pseudouridine, the most abundant modified nucleoside in non-coding RNAs, enhances the function of transfer RNA and ribosomal RNA by stabilizing the RNA structure. Messenger RNAs were not known to contain pseudouridine, but artificial pseudouridylation dramatically affects mRNA function—it changes the genetic code by facilitating non-canonical base pairing in the ribosome decoding centre. However, without evidence of naturally occurring mRNA pseudouridylation, its physiological relevance was unclear. Here we present a comprehensive analysis of pseudouridylation in Saccharomyces cerevisiae and human RNAs using Pseudo-seq, a genome-wide, single-nucleotide-resolution method for pseudouridine identification. Pseudo-seq accurately identifies known modification sites as well as many novel sites in non-coding RNAs, and reveals hundreds of pseudouridylated sites in mRNAs. Genetic analysis allowed us to assign most of the new modification sites to one of seven conserved pseudouridine synthases, Pus1–4, 6, 7 and 9. Notably, the majority of pseudouridines in mRNA are regulated in response to environmental signals, such as nutrient deprivation in yeast and serum starvation in human cells. These results suggest a mechanism for the rapid and regulated rewiring of the genetic code through inducible mRNA modifications. Our findings reveal unanticipated roles for pseudouridylation and provide a resource for identifying the targets of pseudouridine synthases implicated in human disease.American Cancer Society (Robbie Sue Mudd Kidney Cancer Research Scholar Grant RSG-13-396-01-RMC)National Institutes of Health (U.S.) (GM094303)National Institutes of Health (U.S.) (GM081399)American Cancer Society. New England Division (Ellison Foundation Postdoctoral Fellowship)American Cancer Society (Postdoctoral Fellowship PF-13-319-01-RMC)National Institutes of Health (U.S.) (Pre-doctoral Training Grant T32GM007287

Coastal ocean and shelf-sea biogeochemical cycling of trace elements and isotopes: lessons learned from GEOTRACES

Continental shelves and shelf seas play a central role in the global carbon cycle. However, their importance with respect to trace element and isotope (TEI) inputs to ocean basins is less well understood. Here, we present major findings on shelf TEI biogeochemistry from the GEOTRACES programme as well as a proof of concept for a new method to estimate shelf TEI fluxes. The case studies focus on advances in our understanding of TEI cycling in the Arctic, transformations within a major river estuary (Amazon), shelf sediment micronutrient fluxes and basin-scale estimates of submarine groundwater discharge. The proposed shelf flux tracer is 228-radium (T1/2 = 5.75 yr), which is continuously supplied to the shelf from coastal aquifers, sediment porewater exchange and rivers. Model-derived shelf 228Ra fluxes are combined with TEI/ 228Ra ratios to quantify ocean TEI fluxes from the western North Atlantic margin. The results from this new approach agree well with previous estimates for shelf Co, Fe, Mn and Zn inputs and exceed published estimates of atmospheric deposition by factors of approximately 3–23. Lastly, recommendations are made for additional GEOTRACES process studies and coastal margin-focused section cruises that will help refine the model and provide better insight on the mechanisms driving shelf-derived TEI fluxes to the ocean. This article is part of the themed issue ‘Biological and climatic impacts of ocean trace element chemistry’

HPV16 E7-Dependent Transformation Activates NHE1 through a PKA-RhoA-Iinduced Inhibition of p38alpha

Background: Neoplastic transformation originates from a large number of different genetic alterations. Despite this genetic variability, a common phenotype to transformed cells is cellular alkalinization. We have previously shown in human keratinocytes and a cell line in which transformation can be turned on and followed by the inducible expression of the E7 oncogene of human papillomavirus type 16 (HPV16), that intracellular alkalinization is an early and essential physiological event driven by the up-regulation of the Na/H-+(+) exchanger isoform 1 (NHE1) and is necessary for the development of other transformed phenotypes and the in vivo tumor formation in nude mice.Methodology: Here, we utilize these model systems to elucidate the dynamic sequence of alterations of the upstream signal transduction systems leading to the transformation-dependent activation of NHE1.Principal Findings: We observe that a down-regulation of p38 MAPK activity is a fundamental step in the ability of the oncogene to transform the cell. Further, using pharmacological agents and transient transfections with dominant interfering, constitutively active, phosphorylation negative mutants and siRNA strategy to modify specific upstream signal transduction components that link HPV16 E7 oncogenic signals to up-regulation of the NHE1, we demonstrate that the stimulation of NHE1 activity is driven by an early rise in cellular cAMP resulting in the down-stream inhibition of p38 MAPK via the PKA-dependent phosphorylation of the small G-protein, RhoA, and its subsequent inhibition.Conclusions: All together these data significantly improve our knowledge concerning the basic cellular alterations involved in oncogene-driven neoplastic transformation