Discovery of a large set of SNP and SSR genetic markers by high-throughput sequencing of pepper (Capsicum annuum)

Genetic markers based on single nucleotide polymorphisms (SNPs) are in increasing demand for genome mapping and fingerprinting of breeding populations in crop plants. Recent advances in high-throughput sequencing provide the opportunity for whole-genome resequencing and identification of allelic variants by mapping the reads to a reference genome. However, for many species, such as pepper (Capsicum annuum), a reference genome sequence is not yet available. To this end, we sequenced the C. annuum cv. "Yolo Wonder" transcriptome using Roche 454 pyrosequencing and assembled de novo 23,748 isotigs and 60,370 singletons. Mapping of 10,886,425 reads obtained by the Illumina GA II sequencing of C. annuum cv. "Criollo de Morclos 334" to the "Yolo Wonder" transcriptome allowed for SNP identification. By setting a threshold value that allows selecting reliable SNPs with minimal loss of information, 11,849 reliable SNPs spread across 5919 isotigs were identified. In addition, 853 single sequence repeats were obtained. This information has been made available online

COrE (Cosmic Origins Explorer) A White Paper

COrE (Cosmic Origins Explorer) is a fourth-generation full-sky, microwave-band satellite recently proposed to ESA within Cosmic Vision 2015-2025. COrE will provide maps of the microwave sky in polarization and temperature in 15 frequency bands, ranging from 45 GHz to 795 GHz, with an angular resolution ranging from 23 arcmin (45 GHz) and 1.3 arcmin (795 GHz) and sensitivities roughly 10 to 30 times better than PLANCK (depending on the frequency channel). The COrE mission will lead to breakthrough science in a wide range of areas, ranging from primordial cosmology to galactic and extragalactic science. COrE is designed to detect the primordial gravitational waves generated during the epoch of cosmic inflation at more than $3\sigma$ for $r=(T/S)>=10^{-3}$. It will also measure the CMB gravitational lensing deflection power spectrum to the cosmic variance limit on all linear scales, allowing us to probe absolute neutrino masses better than laboratory experiments and down to plausible values suggested by the neutrino oscillation data. COrE will also search for primordial non-Gaussianity with significant improvements over Planck in its ability to constrain the shape (and amplitude) of non-Gaussianity. In the areas of galactic and extragalactic science, in its highest frequency channels COrE will provide maps of the galactic polarized dust emission allowing us to map the galactic magnetic field in areas of diffuse emission not otherwise accessible to probe the initial conditions for star formation. COrE will also map the galactic synchrotron emission thirty times better than PLANCK. This White Paper reviews the COrE science program, our simulations on foreground subtraction, and the proposed instrumental configuration.Comment: 90 pages Latex 15 figures (revised 28 April 2011, references added, minor errors corrected

Planck intermediate results. XLI. A map of lensing-induced B-modes

The secondary cosmic microwave background (CMB) $B$-modes stem from the post-decoupling distortion of the polarization $E$-modes due to the gravitational lensing effect of large-scale structures. These lensing-induced $B$-modes constitute both a valuable probe of the dark matter distribution and an important contaminant for the extraction of the primary CMB $B$-modes from inflation. Planck provides accurate nearly all-sky measurements of both the polarization $E$-modes and the integrated mass distribution via the reconstruction of the CMB lensing potential. By combining these two data products, we have produced an all-sky template map of the lensing-induced $B$-modes using a real-space algorithm that minimizes the impact of sky masks. The cross-correlation of this template with an observed (primordial and secondary) $B$-mode map can be used to measure the lensing $B$-mode power spectrum at multipoles up to $2000$. In particular, when cross-correlating with the $B$-mode contribution directly derived from the Planck polarization maps, we obtain lensing-induced $B$-mode power spectrum measurement at a significance level of $12\,\sigma$, which agrees with the theoretical expectation derived from the Planck best-fit $\Lambda$CDM model. This unique nearly all-sky secondary $B$-mode template, which includes the lensing-induced information from intermediate to small ($10\lesssim \ell\lesssim 1000$) angular scales, is delivered as part of the Planck 2015 public data release. It will be particularly useful for experiments searching for primordial $B$-modes, such as BICEP2/Keck Array or LiteBIRD, since it will enable an estimate to be made of the lensing-induced contribution to the measured total CMB $B$-modes.Comment: 20 pages, 12 figures; Accepted for publication in A&A; The B-mode map is part of the PR2-2015 Cosmology Products; available as Lensing Products in the Planck Legacy Archive http://pla.esac.esa.int/pla/#cosmology; and described in the 'Explanatory Supplement' https://wiki.cosmos.esa.int/planckpla2015/index.php/Specially_processed_maps#2015_Lensing-induced_B-mode_ma

Response of Benthic Foraminifera to organic matter quantity and quality and bioavailable concentrations of metals in Aveiro Lagoon (Portugal)

This work analyses the distribution of living benthic foraminiferal assemblages of surface sediments in different intertidal areas of Ria de Aveiro (Portugal), a polihaline and anthropized coastal lagoon. The relationships among foraminiferal assemblages in association with environmental parameters (temperature, salinity, Eh and pH), grain size, the quantity and quality of organic matter (enrichment in carbohydrates, proteins and lipids), pollution caused by metals, and mineralogical data are studied in an attempt to identify indicators of adaptability to environmental stress. In particular, concentrations of selected metals in the surficial sediment are investigated to assess environmental pollution levels that are further synthetically parameterised by the Pollution Load Index (PLI). The PLI variations allowed the identification of five main polluted areas. Concentrations of metals were also analysed in three extracted phases to evaluate their possible mobility, bioavailability and toxicity in the surficial sediment. Polluted sediment in the form of both organic matter and metals can be found in the most confined zones. Whereas enrichment in organic matter and related biopolymers causes an increase in foraminifera density, pollution by metals leads to a decline in foraminiferal abundance and diversity in those zones. The first situation may be justified by the existence of opportunistic species (with high reproduction rate) that can live in low oxic conditions. The second is explained by the sensitivity of some species to pressure caused by metals. The quality of the organic matter found in these places and the option of a different food source should also explain the tolerance of several species to pollution caused by metals, despite their low reproductive rate in the most polluted areas. In this study, species that are sensitive and tolerant to organic matter and metal enrichment are identified, as is the differential sensitivity/tolerance of some species to metals enrichment.CNPq [401803/2010-4]; [PEst-OE/CTE/UI4035/2014]info:eu-repo/semantics/publishedVersio

Planck 2015 results: I. Overview of products and scientific results

The European Space Agency's Planck satellite, which is dedicated to studying the early Universe and its subsequent evolution, was launched on 14 May 2009. It scanned the microwave and submillimetre sky continuously between 12 August 2009 and 23 October 2013. In February 2015, ESA and the Planck Collaboration released the second set of cosmology products based ondata from the entire Planck mission, including both temperature and polarization, along with a set of scientific and technical papers and a web-based explanatory supplement. This paper gives an overview of the main characteristics of the data and the data products in the release, as well as the associated cosmological and astrophysical science results and papers. The data products include maps of the cosmic microwave background (CMB), the thermal Sunyaev-Zeldovich effect, diffuse foregrounds in temperature and polarization, catalogues of compact Galactic and extragalactic sources (including separate catalogues of Sunyaev-Zeldovich clusters and Galactic cold clumps), and extensive simulations of signals and noise used in assessing uncertainties and the performance of the analysis methods. The likelihood code used to assess cosmological models against the Planck data is described, along with a CMB lensing likelihood. Scientific results include cosmological parameters derived from CMB power spectra, gravitational lensing, and cluster counts, as well as constraints on inflation, non-Gaussianity, primordial magnetic fields, dark energy, and modified gravity, and new results on low-frequency Galactic foregrounds

Can Simply Answering Research Questions Change Behaviour? Systematic Review and Meta Analyses of Brief Alcohol Intervention Trials

BACKGROUND: Participant reports of their own behaviour are critical for the provision and evaluation of behavioural interventions. Recent developments in brief alcohol intervention trials provide an opportunity to evaluate longstanding concerns that answering questions on behaviour as part of research assessments may inadvertently influence it and produce bias. The study objective was to evaluate the size and nature of effects observed in randomized manipulations of the effects of answering questions on drinking behaviour in brief intervention trials. METHODOLOGY/PRINCIPAL FINDINGS: Multiple methods were used to identify primary studies. Between-group differences in total weekly alcohol consumption, quantity per drinking day and AUDIT scores were evaluated in random effects meta-analyses. Ten trials were included in this review, of which two did not provide findings for quantitative study, in which three outcomes were evaluated. Between-group differences were of the magnitude of 13.7 (-0.17 to 27.6) grams of alcohol per week (approximately 1.5 U.K. units or 1 standard U.S. drink) and 1 point (0.1 to 1.9) in AUDIT score. There was no difference in quantity per drinking day. CONCLUSIONS/SIGNIFICANCE: Answering questions on drinking in brief intervention trials appears to alter subsequent self-reported behaviour. This potentially generates bias by exposing non-intervention control groups to an integral component of the intervention. The effects of brief alcohol interventions may thus have been consistently under-estimated. These findings are relevant to evaluations of any interventions to alter behaviours which involve participant self-report

Assessment of Yellow Fever Epidemic Risk: An Original Multi-criteria Modeling Approach

This article describes the use of an original modeling approach to assess the risk of yellow fever (YF) epidemics. YF is a viral hemorrhagic fever responsible in past centuries for devastating outbreaks. Since the 1930s, a vaccine has been available that protects the individual for at least 10 years, if not for life. However, immunization of populations in African countries was gradually discontinued after the 1960s. With the decrease in immunity against YF in African populations the disease reemerged in the 1980s. In 2005, WHO, UNICEF, and the GAVI Alliance decided to support preventive vaccination of at-risk populations in West African endemic countries in order to tackle the reemergence of YF and reduce the risk of urban YF outbreaks. Financial resources were made available to scale up a global YF vaccine stockpile and to support countries with limited resources in the management of preventive vaccination campaigns. This article describes the process we used to determine the most at-risk populations using a mathematical model to prioritize targeted immunization campaigns. We believe that this approach could be useful for other diseases for which decision making process is difficult because of limited data availability, complex risk variables, and a need for rapid decisions and implementation

Deep-Sea Origin and In-Situ Diversification of Chrysogorgiid Octocorals

The diversity, ubiquity and prevalence in deep waters of the octocoral family Chrysogorgiidae Verrill, 1883 make it noteworthy as a model system to study radiation and diversification in the deep sea. Here we provide the first comprehensive phylogenetic analysis of the Chrysogorgiidae, and compare phylogeny and depth distribution. Phylogenetic relationships among 10 of 14 currently-described Chrysogorgiidae genera were inferred based on mitochondrial (mtMutS, cox1) and nuclear (18S) markers. Bathymetric distribution was estimated from multiple sources, including museum records, a literature review, and our own sampling records (985 stations, 2345 specimens). Genetic analyses suggest that the Chrysogorgiidae as currently described is a polyphyletic family. Shallow-water genera, and two of eight deep-water genera, appear more closely related to other octocoral families than to the remainder of the monophyletic, deep-water chrysogorgiid genera. Monophyletic chrysogorgiids are composed of strictly (Iridogorgia Verrill, 1883, Metallogorgia Versluys, 1902, Radicipes Stearns, 1883, Pseudochrysogorgia Pante & France, 2010) and predominantly (Chrysogorgia Duchassaing & Michelotti, 1864) deep-sea genera that diversified in situ. This group is sister to gold corals (Primnoidae Milne Edwards, 1857) and deep-sea bamboo corals (Keratoisidinae Gray, 1870), whose diversity also peaks in the deep sea. Nine species of Chrysogorgia that were described from depths shallower than 200 m, and mtMutS haplotypes sequenced from specimens sampled as shallow as 101 m, suggest a shallow-water emergence of some Chrysogorgia species

Planck intermediate results: XLVI. Reduction of large-scale systematic effects in HFI polarization maps and estimation of the reionization optical depth

© 2016 ESO. This paper describes the identification, modelling, and removal of previously unexplained systematic effects in the polarization data of the Planck High Frequency Instrument (HFI) on large angular scales, including new mapmaking and calibration procedures, new and more complete end-to-end simulations, and a set of robust internal consistency checks on the resulting maps. These maps, at 100, 143, 217, and 353 GHz, are early versions of those that will be released in final form later in 2016. The improvements allow us to determine the cosmic reionization optical depth τ using, for the first time, the low-multipole EE data from HFI, reducing significantly the central value and uncertainty, and hence the upper limit. Two different likelihood procedures are used to constrain τ from two estimators of the CMB E-and B-mode angular power spectra at 100 and 143 GHz, after debiasing the spectra from a small remaining systematic contamination. These all give fully consistent results. A further consistency test is performed using cross-correlations derived from the Low Frequency Instrument maps of the Planck 2015 data release and the new HFI data. For this purpose, end-to-end analyses of systematic effects from the two instruments are used to demonstrate the near independence of their dominant systematic error residuals. The tightest result comes from the HFI-based τ posterior distribution using the maximum likelihood power spectrum estimator from EE data only, giving a value 0.055 ± 0.009. In a companion paper these results are discussed in the context of the best-fit PlanckΛCDM cosmological model and recent models of reionization

Fractal Dimensions and Scaling Laws in the Interstellar Medium and Galaxy Distributions: a new Field Theory Approach

We develop a field theoretical approach to the cold interstellar medium (ISM) and large structure of the universe. We show that a non-relativistic self- gravitating gas in thermal equilibrium with variable number of atoms or fragments is exactly equivalent to a field theory of a scalar field phi(x) with exponential self-interaction. We analyze this field theory perturbatively and non-perturbatively through the renormalization group(RG).We show scaling behaviour (critical) for a continuous range of the physical parameters as the temperature. We derive in this framework the scaling relation M(R) \sim R^{d_H} for the mass on a region of size R, and Delta v \sim R^\frac12(d_H -1) for the velocity dispersion. For the density-density correlations we find a power-law behaviour for large distances \sim |r_1 - r_2|^{2D - 6}.The fractal dimension D turns to be related with the critical exponent \nu by D = 1/ \nu. Mean field theory yields \nu = 1/2, D = 2. Both the Ising and the mean field values are compatible with the present ISM observational data:1.4\leq D \leq 2. We develop a field theoretical approach to the galaxy distribution considering a gas of self-gravitating masses on the FRW background, in quasi-thermal equi- librium. We show that it exhibits scaling behaviour by RG methods. The galaxy correlations are computed without assuming homogeneity. We find \sim r^{D-3} $. The theory allows to compute the three and higher density correlators without any assumption.We find that the connected N-points density scales as r_1^{N(D-3)}, when$ r_1 >> r_i