Dengue Virus Type 3 Adaptive Changes during Epidemics in Sao Jose de Rio Preto, Brazil, 2006–2007

Global dengue virus spread in tropical and sub-tropical regions has become a major international public health concern. It is evident that DENV genetic diversity plays a significant role in the immunopathology of the disease and that the identification of polymorphisms associated with adaptive responses is important for vaccine development. The investigation of naturally occurring genomic variants may play an important role in the comprehension of different adaptive strategies used by these mutants to evade the human immune system. In order to elucidate this role we sequenced the complete polyprotein-coding region of thirty-three DENV-3 isolates to characterize variants circulating under high endemicity in the city of Sao Jose de Rio Preto, Brazil, during the onset of the 2006-07 epidemic. By inferring the evolutionary history on a local-scale and estimating rates of synonymous (dS) and nonsynonimous (dN) substitutions, we have documented at least two different introductions of DENV-3 into the city and detected 10 polymorphic codon sites under significant positive selection (dN/dS > 1) and 8 under significant purifying selection (dN/dS < 1). We found several polymorphic amino acid coding sites in the envelope (15), NS1 (17), NS2A (11), and NS5 (24) genes, which suggests that these genes may be experiencing relatively recent adaptive changes. Furthermore, some polymorphisms correlated with changes in the immunogenicity of several epitopes. Our study highlights the existence of significant and informative DENV variability at the spatio-temporal scale of an urban outbreak

A Factorization Law for Entanglement Decay

We present a simple and general factorization law for quantum systems shared by two parties, which describes the time evolution of entanglement upon passage of either component through an arbitrary noisy channel. The robustness of entanglement-based quantum information processing protocols is thus easily and fully characterized by a single quantity.Comment: 4 pages, 5 figure

Arabidopsis uses two gluconeogenic gateways for organic acids to fuel seedling establishment.

Gluconeogenesis is a fundamental metabolic process that allows organisms to make sugars from non-carbohydrate stores such as lipids and protein. In eukaryotes only one gluconeogenic route has been described from organic acid intermediates and this relies on the enzyme phosphoenolpyruvate carboxykinase (PCK). Here we show that two routes exist in Arabidopsis, and that the second uses pyruvate, orthophosphate dikinase (PPDK). Gluconeogenesis is critical to fuel the transition from seed to seedling. Arabidopsis pck1 and ppdk mutants are compromised in seed-storage reserve mobilization and seedling establishment. Radiolabelling studies show that PCK predominantly allows sugars to be made from dicarboxylic acids, which are products of lipid breakdown. However, PPDK also allows sugars to be made from pyruvate, which is a major product of protein breakdown. We propose that both routes have been evolutionarily conserved in plants because, while PCK expends less energy, PPDK is twice as efficient at recovering carbon from pyruvate.We thank the Biotechnology and Biology Sciences Research Council for funding J.M.H. (P18931 and a studentship to B.P.W.) and P.J.E. (BB/G009724/1 and BB/K002147/1), the Isaac Newton Trust and the Max-Planck Gesellschaft for funding and ATC for a CASE studentship to H.M.A.This is the final published version. It first appeared at http://www.nature.com/ncomms/2015/150410/ncomms7659/full/ncomms7659.html

Characterizing ancient and modern hydrothermal venting systems

Highlights • Ancient and modern hydrothermal venting systems occur offshore mid-Norway and Java. • They can share morphologies, eruptive behavior and develop similarly. • Modern hydrothermal venting systems are relevant analogues for ancient systems. Abstract Ancient hydrothermal vent complexes have released large volumes of greenhouse gases in the past causing global warming, and similar modern vent structures are potential geohazards. In the NE Atlantic, thousands of hydrothermal vent complexes were formed during the Paleocene-Eocene Thermal Maximum. In Java, Indonesia, the erupting Lusi sediment-hosted geothermal system caused the displacement of 40,000 people. In order to determine how ancient and modern hydrothermal venting systems are related, we map a well-defined buried hydrothermal vent complex offshore mid-Norway using 3D seismic reflection data and then compare it to the active Lusi eruption (since 2006) and the neighboring inactive Porong Structure. These are characterized using 2D seismic reflection data, borehole data and field observations. The venting structures are subcircular in plan-view and a few kilometers in diameter. They are funnel-shaped in profiles, with inward-dipping beds surrounding the conduits. The hydrothermal vent complex offshore mid-Norway reveals five seismically-distinct vent fill facies units. Importantly, two of the facies units are separated by an angular unconformity, clearly indicating that the depositional events within the vent fill were distinct. Hydrothermal fluids are interpreted to have led to the fluidization of mud-rich sediments which were erupted and deposited in and around the vent complex. Interpretation of a seismically transparent body along the conduit of the Norwegian venting structure, and the abrupt widening of the conduit at the Porong Structure, are interpreted to be caused by changes in fluid-flow dynamics as the fluids rise and get released from the host-rock. The hydrothermal venting systems in Java and offshore mid-Norway are found to be morphologically similar and are interpreted to form as the result of the transport and eruption of fluidized sediments

Growth, electronic and electrical characterization of Ge-Rich Ge-Sb-Te alloy

In this study, we deposit a Ge-rich Ge-Sb-Te alloy by physical vapor deposition (PVD) in the amorphous phase on silicon substrates. We study in-situ, by X-ray and ultraviolet photoemission spectroscopies (XPS and UPS), the electronic properties and carefully ascertain the alloy composition to be GST 29 20 28. Subsequently, Raman spectroscopy is employed to corroborate the results from the photoemission study. X-ray diffraction is used upon annealing to study the crystallization of such an alloy and identify the effects of phase separation and segregation of crystalline Ge with the formation of grains along the [111] direction, as expected for such Ge-rich Ge-Sb-Te alloys. In addition, we report on the electrical characterization of single memory cells containing the Ge-rich Ge-Sb-Te alloy, including I-V characteristic curves, programming curves, and SET and RESET operation performance, as well as upon annealing temperature. A fair alignment of the electrical parameters with the current state-of-the-art of conventional (GeTe)n-(Sb2Te3)m alloys, deposited by PVD, is found, but with enhanced thermal stability, which allows for data retention up to 230 °C

Inflammatory Adipokines, High Molecular Weight Adiponectin, and Insulin Resistance: A Population-Based Survey in Prepubertal Schoolchildren

BackgroundThe aim of this study was to investigate sex differences and associations of high molecular weight (HMW) adiponectin, leptin and proinflammatory adipokines, individually or in combinations, with adiposity and insulin resistance (IR) measures in prepubertal childhood.MethodologyWe studied 305 prepubertal children (boys/girls: 144/161; Tanner stage 1; age: 5-13 yr), included in a cohort of 44,231 adolescents who participated in an extensive Italian school-based survey. According to Cole's criteria, 105 individuals were lean (L; boys/girls: 59/46), 60 overweight (OW; boys/girls: 32/28) and 140 obese (OB; boys/girls: 70/70). Measurements comprised total and HMW adiponectin, leptin, as well as a panel of proinflammatory adipokines/chemokines associated with diabetes risk.Principal findingsLeptin-, and the leptin-to-HMW adiponectin ratio (L/HMW)-, increased progressively (pConclusionsIn prepubertal children, leptin emerges as a sex-independent discrimination marker of adiposity degree and as a useful, sex-associated predictor of the systemic insulin resistance

Harmonizing methods for wildlife abundance estimation and pathogen detection in Europe-a questionnaire survey on three selected host-pathogen combinations

__Background:__ The need for wildlife health surveillance as part of disease control in wildlife, domestic animals and humans on the global level is widely recognized. However, the objectives, methods and intensity of existing wildlife health surveillance programs vary greatly among European countries, resulting in a patchwork of data that are difficult to merge and compare. This survey aimed at evaluating the need and potential for data harmonization in wildlife health in Europe. The specific objective was to collect information on methods currently used to estimate host abundance and pathogen prevalence. Questionnaires were designed t

Windthrows control biomass patterns and functional composition of Amazon forests

Amazon forests account for ~25% of global land biomass and tropical tree species. In these forests, windthrows (i.e., snapped and uprooted trees) are a major natural disturbance, but the rates and mechanisms of recovery are not known. To provide a predictive framework for understanding the effects of windthrows on forest structure and functional composition (DBH ≥10 cm), we quantified biomass recovery as a function of windthrow severity (i.e., fraction of windthrow tree mortality on Landsat pixels, ranging from 0%–70%) and time since disturbance for terra-firme forests in the Central Amazon. Forest monitoring allowed insights into the processes and mechanisms driving the net biomass change (i.e., increment minus loss) and shifts in functional composition. Windthrown areas recovering for between 4–27 years had biomass stocks as low as 65.2–91.7 Mg/ha or 23%–38% of those in nearby undisturbed forests (~255.6 Mg/ha, all sites). Even low windthrow severities (4%–20% tree mortality) caused decadal changes in biomass stocks and structure. While rates of biomass increment in recovering vegetation were nearly double (6.3 ± 1.4 Mg ha− 1 year− 1) those of undisturbed forests (~3.7 Mg ha− 1 year− 1), biomass loss due to post-windthrow mortality was high (up to −7.5 ± 8.7 Mg ha− 1 year− 1, 8.5 years since disturbance) and unpredictable. Consequently, recovery to 90% of “pre-disturbance” biomass takes up to 40 years. Resprouting trees contributed little to biomass recovery. Instead, light-demanding, low-density genera (e.g., Cecropia, Inga, Miconia, Pourouma, Tachigali, and Tapirira) were favored, resulting in substantial post-windthrow species turnover. Shifts in functional composition demonstrate that windthrows affect the resilience of live tree biomass by favoring soft-wooded species with shorter life spans that are more vulnerable to future disturbances. As the time required for forests to recover biomass is likely similar to the recurrence interval of windthrows triggering succession, windthrows have the potential to control landscape biomass/carbon dynamics and functional composition in Amazon forests. ©2018 The Authors. Global Change Biology Published by John Wiley & Sons Lt