New approach for precise computation of Lyman-alpha forest power spectrum with hydrodynamical simulations

Current experiments are providing measurements of the flux power spectrum from the Lyman-α forests observed in quasar spectra with unprecedented accuracy. Their interpretation in terms of cosmological constraints requires specific simulations of at least equivalent precision. In this paper, we present a suite of cosmological N-body simulations with cold dark matter and baryons, specifically aiming at modeling the low-density regions of the inter-galactic medium as probed by the Lyman-α forests at high redshift. The simulations were run using the GADGET-3 code and were designed to match the requirements imposed by the quality of the current SDSS-III/BOSS or forthcoming SDSS-IV/eBOSS data. They are made using either 2 × 7683 1 billion or 2 × 1923 14 million particles, spanning volumes ranging from (25 Mpc h−1)3 for high-resolution simulations to (100 Mpc h−1)3 for large-volume ones. Using a splicing technique, the resolution is further enhanced to reach the equivalent of simulations with 2 × 30723 58 billion particles in a (100 Mpc h−1)3 box size, i.e. a mean mass per gas particle of 1.2 × 105M⊙ h−1. We show that the resulting power spectrum is accurate at the 2% level over the full range from a few Mpc to several tens of Mpc. We explore the effect on the one-dimensional transmitted-flux power spectrum of four cosmological parameters (ns, σ8, Ωm and H0) and two astrophysical parameters (T0 and γ) that are related to the heating rate of the intergalactic medium. By varying the input parameters around a central model chosen to be in agreement with the latest Planck results, we built a grid of simulations that allows the study of the impact on the flux power spectrum of these six relevant parameters. We improve upon previous studies by not only measuring the effect of each parameter individually, but also probing the impact of the simultaneous variation of each pair of parameters. We thus provide a full second-order expansion, including cross-terms, around our central model. We check the validity of the second-order expansion with independent simulations obtained either with different cosmological parameters or different seeds. Finally, a comparison to the one-dimensional Lyman-α forest power spectrum obtained with BOSS by [1] shows an excellent agreement

Crossover recombination and synapsis are linked by adjacent regions within the N terminus of the Zip1 synaptonemal complex protein

Accurate chromosome segregation during meiosis relies on the prior establishment of at least one crossover recombination event between homologous chromosomes. Most meiotic recombination intermediates that give rise to interhomolog crossovers are embedded within a hallmark chromosomal structure called the synaptonemal complex (SC), but the mechanisms that coordinate the processes of SC assembly (synapsis) and crossover recombination remain poorly understood. Among known structural components of the budding yeast SC, the Zip1 protein is unique for its independent role in promoting crossover recombination; Zip1 is specifically required for the large subset of crossovers that also rely on the meiosis-specific MutSgamma complex. Here we report that adjacent regions within Zip1\u27s N terminus encompass its crossover and synapsis functions. We previously showed that deletion of Zip1 residues 21-163 abolishes tripartite SC assembly and prevents robust SUMOylation of the SC central element component, Ecm11, but allows excess MutSgamma crossover recombination. We find the reciprocal phenotype when Zip1 residues 2-9 or 10-14 are deleted; in these mutants SC assembles and Ecm11 is hyperSUMOylated, but MutSgamma crossovers are strongly diminished. Interestingly, Zip1 residues 2-9 or 2-14 are required for the normal localization of Zip3, a putative E3 SUMO ligase and pro-MutSgamma crossover factor, to Zip1 polycomplex structures and to recombination initiation sites. By contrast, deletion of Zip1 residues 15-20 does not detectably prevent Zip3\u27s localization at Zip1 polycomplex and supports some MutSgamma crossing over but prevents normal SC assembly and Ecm11 SUMOylation. Our results highlight distinct N terminal regions that are differentially critical for Zip1\u27s roles in crossing over and SC assembly; we speculate that the adjacency of these regions enables Zip1 to serve as a liaison, facilitating crosstalk between the two processes by bringing crossover recombination and synapsis factors within close proximity of one another

Constraint on neutrino masses from SDSS-III/BOSS Ly-alpha forest and other cosmological probes

International audienceWe present constraints on the parameters of the $\Lambda$CDM cosmologicalmodel in the presence of massive neutrinos, using the one-dimensionalLy$\alpha$ forest power spectrum obtained with the Baryon OscillationSpectroscopic Survey (BOSS) of the Sloan Digital Sky Survey (SDSS) byPalanque-Delabrouille et al. (2013), complemented by additional cosmologicalprobes. The interpretation of the measured Ly$\alpha$ spectrum is done using asecond-order Taylor expansion of the simulated power spectrum. BOSS Ly$\alpha$ data alone provide better bounds than previous Ly$\alpha$ results,but are still poorly constraining, especially for the sum of neutrino masses$\sum m_\nu$, for which we obtain an upper bound of 1.1~eV (95\% CL), includingsystematics for both data and simulations. Ly$\alpha$ constraints on$\Lambda$CDM parameters and neutrino masses are compatible with CMB bounds fromthe Planck collaboration. Interestingly, the combination of Ly$\alpha$ with CMBdata reduces the uncertainties significantly, due to very different directionsof degeneracy in parameter space, leading to the strongest cosmological boundto date on the total neutrino mass, $\sum m_\nu < 0.15$~eV at 95\% CL (with abest-fit in zero). Adding recent BAO results further tightens this constraintto $\sum m_\nu < 0.14$~eV at 95\% CL. This bound is nearly independent of thestatistical approach used, and of the different combinations of CMB and BAOdata sets considered in this paper in addition to Ly$\alpha$. Given themeasured values of the two squared mass differences $\Delta m^2$, this resulttends to favor the normal hierarchy scenario against the inverted hierarchyscenario for the masses of the active neutrino species

A meiotic XPF-ERCC1-like complex recognizes joint molecule recombination intermediates to promote crossover formation

Meiotic crossover formation requires the stabilization of early recombination intermediates by a set of proteins and occurs within the environment of the chromosome axis, a structure important for the regulation of meiotic recombination events. The molecular mechanisms underlying and connecting crossover recombination and axis localization are elusive. Here, we identified the ZZS (Zip2–Zip4–Spo16) complex, required for crossover formation, which carries two distinct activities: one provided by Zip4, which acts as hub through physical interactions with components of the chromosome axis and the crossover machinery, and the other carried by Zip2 and Spo16, which preferentially bind branched DNA molecules in vitro. We found that Zip2 and Spo16 share structural similarities to the structure-specific XPF–ERCC1 nuclease, although it lacks endonuclease activity. The XPF domain of Zip2 is required for crossover formation, suggesting that, together with Spo16, it has a noncatalytic DNA recognition function. Our results suggest that the ZZS complex shepherds recombination intermediates toward crossovers as a dynamic structural module that connects recombination events to the chromosome axis. The identification of the ZZS complex improves our understanding of the various activities required for crossover implementation and is likely applicable to other organisms, including mammals

The Baryon Oscillation Spectroscopic Survey of SDSS-III

The Baryon Oscillation Spectroscopic Survey (BOSS) is designed to measure the scale of baryon acoustic oscillations (BAO) in the clustering of matter over a larger volume than the combined efforts of all previous spectroscopic surveys of large scale structure. BOSS uses 1.5 million luminous galaxies as faint as i=19.9 over 10,000 square degrees to measure BAO to redshifts z<0.7. Observations of neutral hydrogen in the Lyman alpha forest in more than 150,000 quasar spectra (g<22) will constrain BAO over the redshift range 2.15<z<3.5. Early results from BOSS include the first detection of the large-scale three-dimensional clustering of the Lyman alpha forest and a strong detection from the Data Release 9 data set of the BAO in the clustering of massive galaxies at an effective redshift z = 0.57. We project that BOSS will yield measurements of the angular diameter distance D_A to an accuracy of 1.0% at redshifts z=0.3 and z=0.57 and measurements of H(z) to 1.8% and 1.7% at the same redshifts. Forecasts for Lyman alpha forest constraints predict a measurement of an overall dilation factor that scales the highly degenerate D_A(z) and H^{-1}(z) parameters to an accuracy of 1.9% at z~2.5 when the survey is complete. Here, we provide an overview of the selection of spectroscopic targets, planning of observations, and analysis of data and data quality of BOSS.Comment: 49 pages, 16 figures, accepted by A

The Ninth Data Release of the Sloan Digital Sky Survey: First Spectroscopic Data from the SDSS-III Baryon Oscillation Spectroscopic Survey

The Sloan Digital Sky Survey III (SDSS-III) presents the first spectroscopic data from the Baryon Oscillation Spectroscopic Survey (BOSS). This ninth data release (DR9) of the SDSS project includes 535,995 new galaxy spectra (median z=0.52), 102,100 new quasar spectra (median z=2.32), and 90,897 new stellar spectra, along with the data presented in previous data releases. These spectra were obtained with the new BOSS spectrograph and were taken between 2009 December and 2011 July. In addition, the stellar parameters pipeline, which determines radial velocities, surface temperatures, surface gravities, and metallicities of stars, has been updated and refined with improvements in temperature estimates for stars with T_eff<5000 K and in metallicity estimates for stars with [Fe/H]>-0.5. DR9 includes new stellar parameters for all stars presented in DR8, including stars from SDSS-I and II, as well as those observed as part of the SDSS-III Sloan Extension for Galactic Understanding and Exploration-2 (SEGUE-2). The astrometry error introduced in the DR8 imaging catalogs has been corrected in the DR9 data products. The next data release for SDSS-III will be in Summer 2013, which will present the first data from the Apache Point Observatory Galactic Evolution Experiment (APOGEE) along with another year of data from BOSS, followed by the final SDSS-III data release in December 2014.Comment: 9 figures; 2 tables. Submitted to ApJS. DR9 is available at http://www.sdss3.org/dr

Clustering heterochromatin: Sir3 promotes telomere clustering independently of silencing in yeast

Arrays of Sir3 binding sites at telomeres are sufficient to promote long-range trans-telomere interactions

The Sloan Digital Sky Survey quasar catalog: tenth data release

We present the Data Release 10 Quasar (DR10Q) catalog from the Baryon Oscillation Spectroscopic Survey (BOSS) of the Sloan Digital Sky Survey III. The catalog includes all BOSS objects that were targeted as quasar candidates during the first 2.5 years of the survey and that are confirmed as quasars via visual inspection of the spectra, have luminosities M-i[z = 2] 2.15 (117 668) is similar to 5 times greater than the number of z > 2.15 quasars known prior to BOSS. Redshifts and FWHMs are provided for the strongest emission lines (C IV, C III, Mg II). The catalog identifies 16 461 broad absorption line quasars and gives their characteristics. For each object, the catalog presents five-band (u, g, r, i, z) CCD-based photometry with typical accuracy of 0.03 mag and information on the optical morphology and selection method. The catalog also contains X-ray, ultraviolet, near-infrared, and radio emission properties of the quasars, when available, from other large-area surveys. The calibrated digital spectra cover the wavelength region 3600-10 500 angstrom at a spectral resolution in the range 1300 < R < 2500; the spectra can be retrieved from the SDSS Catalog Archive Server. We also provide a supplemental list of an additional 2376 quasars that have been identified among the galaxy targets of the SDSS-III/BOSS

A High Throughput Genetic Screen Identifies New Early Meiotic Recombination Functions in Arabidopsis thaliana

Meiotic recombination is initiated by the formation of numerous DNA double-strand breaks (DSBs) catalysed by the widely conserved Spo11 protein. In Saccharomyces cerevisiae, Spo11 requires nine other proteins for meiotic DSB formation; however, unlike Spo11, few of these are conserved across kingdoms. In order to investigate this recombination step in higher eukaryotes, we took advantage of a high-throughput meiotic mutant screen carried out in the model plant Arabidopsis thaliana. A collection of 55,000 mutant lines was screened, and spo11-like mutations, characterised by a drastic decrease in chiasma formation at metaphase I associated with an absence of synapsis at prophase, were selected. This screen led to the identification of two populations of mutants classified according to their recombination defects: mutants that repair meiotic DSBs using the sister chromatid such as Atdmc1 or mutants that are unable to make DSBs like Atspo11-1. We found that in Arabidopsis thaliana at least four proteins are necessary for driving meiotic DSB repair via the homologous chromosomes. These include the previously characterised DMC1 and the Hop1-related ASY1 proteins, but also the meiotic specific cyclin SDS as well as the Hop2 Arabidopsis homologue AHP2. Analysing the mutants defective in DSB formation, we identified the previously characterised AtSPO11-1, AtSPO11-2, and AtPRD1 as well as two new genes, AtPRD2 and AtPRD3. Our data thus increase the number of proteins necessary for DSB formation in Arabidopsis thaliana to five. Unlike SPO11 and (to a minor extent) PRD1, these two new proteins are poorly conserved among species, suggesting that the DSB formation mechanism, but not its regulation, is conserved among eukaryotes

The Baryon Oscillation Spectroscopic Survey of SDSS-III

The Baryon Oscillation Spectroscopic Survey (BOSS) is designed to measure the scale of baryon acoustic oscillations (BAO) in the clustering of matter over a larger volume than the combined efforts of all previous spectroscopic surveys of large-scale structure. BOSS uses 1.5 million luminous galaxies as faint as i = 19.9 over 10,000 deg(2) to measure BAO to redshifts z < 0.7. Observations of neutral hydrogen in the Ly alpha forest in more than 150,000 quasar spectra (g < 22) will constrain BAO over the redshift range 2.15 < z < 3.5. Early results from BOSS include the first detection of the large-scale three-dimensional clustering of the Ly alpha forest and a strong detection from the Data Release 9 data set of the BAO in the clustering of massive galaxies at an effective redshift z = 0.57. We project that BOSS will yield measurements of the angular diameter distance d(A) to an accuracy of 1.0% at redshifts z = 0.3 and z = 0.57 and measurements of H(z) to 1.8% and 1.7% at the same redshifts. Forecasts for Ly alpha forest constraints predict a measurement of an overall dilation factor that scales the highly degenerate D-A(z) and H-1(z) parameters to an accuracy of 1.9% at z similar to 2.5 when the survey is complete. Here, we provide an overview of the selection of spectroscopic targets, planning of observations, and analysis of data and data quality of BOSS