Positional variations among heterogeneous nucleosome maps give dynamical information on chromatin

Although nucleosome remodeling is essential to transcriptional regulation in eukaryotes, little is known about its genome-wide behavior. Since a number of nucleosome positioning maps in vivo have been recently determined, we examined if their comparisons might be used for obtaining a genome-wide profile of nucleosome remodeling. Using seven yeast maps, the local variability of nucleosomes, measured by the entropy, was significantly higher in a set of reported unstable nucleosomes. The binding sites of four transcription factors, known as the remodeling factors, were distinctively high both in entropy and linker ratio, whereas those of Yhp1, their potential inhibitor, showed the lowest values in both of them. Taken together, our map shows the general information of nucleosome dynamics reasonably well. The “nucleosome dynamics” map provides the new significant correlation with the degree of expression variety instead of their intensity. Furthermore, the associations with gene function and histone modification were also discussed here

5-HT1A receptor blockade reverses GABAA receptor α3 subunit-mediated anxiolytic effects on stress-induced hyperthermia

Stress-related disorders are associated with dysfunction of both serotonergic and GABAergic pathways, and clinically effective anxiolytics act via both neurotransmitter systems. As there is evidence that the GABA(A) and the serotonin receptor system interact, a serotonergic component in the anxiolytic actions of benzodiazepines could be present. The main aim of the present study was to investigate whether the anxiolytic effects of (non-)selective alpha subunit GABA(A) receptor agonists could be reversed with 5-HT1A receptor blockade using the stress-induced hyperthermia (SIH) paradigm. The 5-HT1A receptor antagonist WAY-100635 (0.1-1 mg/kg) reversed the SIH-reducing effects of the non-alpha-subunit selective GABA(A) receptor agonist diazepam (1-4 mg/kg) and the GABA(A) receptor alpha(3)-subunit selective agonist TP003 (1 mg/kg), whereas WAY-100635 alone was without effect on the SIH response or basal body temperature. At the same time, co-administration of WAY-100635 with diazepam or TP003 reduced basal body temperature. WAY-100635 did not affect the SIH response when combined with the preferential alpha(1)-subunit GABA(A) receptor agonist zolpidem (10 mg/kg), although zolpidem markedly reduced basal body temperature. The present study suggests an interaction between GABA(A) receptor alpha-subunits and 5-HT1A receptor activation in the SIH response. Specifically, our data indicate that benzodiazepines affect serotonergic signaling via GABA(A) receptor alpha(3)-subunits. Further understanding of the interactions between the GABA(A) and serotonin system in reaction to stress may be valuable in the search for novel anxiolytic drugs

Dark Energy Survey Year 1 results: the effect of intracluster light on photometric redshifts for weak gravitational lensing

We study the effect of diffuse intracluster light on the critical surface mass density estimated from photometric redshifts of lensing source galaxies, and the resulting bias in a weak lensing measurement of galaxy cluster mass. Under conservative assumptions, we find the bias to be negligible for imaging surveys like the Dark Energy Survey with a recommended scale cut of ≥200kpc distance from cluster centres. For significantly deeper lensing source galaxy catalogues from present and future surveys like the Large Synoptic Survey Telescope program, more conservative scale and source magnitude cuts or a correction of the effect may be necessary to achieve percent level lensing measurement accuracy, especially at the massive end of the cluster population

The chromatin remodelling enzymes SNF2H and SNF2L position nucleosomes adjacent to CTCF and other transcription

Within the genomes of metazoans, nucleosomes are highly organised adjacent to the binding sites for a subset of transcription factors. Here we have sought to investigate which chromatin remodelling enzymes are responsible for this. We find that the ATP-dependent chromatin remodelling enzyme SNF2H plays a major role organising arrays of nucleosomes adjacent to the binding sites for the architectural transcription factor CTCF sites and acts to promote CTCF binding. At many other factor binding sites SNF2H and the related enzyme SNF2L contribute to nucleosome organisation. The action of SNF2H at CTCF sites is functionally important as depletion of CTCF or SNF2H affects transcription of a common group of genes. This suggests that chromatin remodelling ATPase's most closely related to the Drosophila ISWI protein contribute to the function of many human gene regulatory elements

DeepZipper. II. Searching for Lensed Supernovae in Dark Energy Survey Data with Deep Learning

Gravitationally lensed supernovae (LSNe) are important probes of cosmic expansion, but they remain rare and difficult to find. Current cosmic surveys likely contain 5-10 LSNe in total while next-generation experiments are expected to contain several hundred to a few thousand of these systems. We search for these systems in observed Dark Energy Survey (DES) five year SN fields—10 3 sq. deg. regions of sky imaged in the griz bands approximately every six nights over five years. To perform the search, we utilize the DeepZipper approach: a multi-branch deep learning architecture trained on image-level simulations of LSNe that simultaneously learns spatial and temporal relationships from time series of images. We find that our method obtains an LSN recall of 61.13% and a false-positive rate of 0.02% on the DES SN field data. DeepZipper selected 2245 candidates from a magnitude-limited (m i < 22.5) catalog of 3,459,186 systems. We employ human visual inspection to review systems selected by the network and find three candidate LSNe in the DES SN fields

Dark Energy Survey Year 1 results: validation of weak lensing cluster member contamination estimates from P(z) decomposition

Weak lensing source galaxy catalogues used in estimating the masses of galaxy clusters can be heavily contaminated by cluster members, prohibiting accurate mass calibration. In this study, we test the performance of an estimator for the extent of cluster member contamination based on decomposing the photometric redshift P(z) of source galaxies into contaminating and background components. We perform a full scale mock analysis on a simulated sky survey approximately mirroring the observational properties of the Dark Energy Survey Year One observations (DES Y1), and find excellent agreement between the true number profile of contaminating cluster member galaxies in the simulation and the estimated one. We further apply the method to estimate the cluster member contamination for the DES Y1 redMaPPer cluster mass calibration analysis, and compare the results to an alternative approach based on the angular correlation of weak lensing source galaxies. We find indications that the correlation based estimates are biased by the selection of the weak lensing sources in the cluster vicinity, which does not strongly impact the P(z) decomposition method. Collectively, these benchmarks demonstrate the strength of the P(z) decomposition method in alleviating membership contamination and enabling highly accurate cluster weak lensing studies without broad exclusion of source galaxies, thereby improving the total constraining power of cluster mass calibration via weak lensing

Novel phages of healthy skin metaviromes from South Africa

Recent skin metagenomic studies have investigated the harbored viral diversity and its possible influence on healthy skin microbial populations, and tried to establish global patterns of skin-phage evolution. However, the detail associated with the phages that potentially play a role in skin health has not been investigated. While skin metagenome and -metavirome studies have indicated that the skin virome is highly site specific and shows marked interpersonal variation, they have not assessed the presence/absence of individual phages. Here, we took a semi-culture independent approach (metaviromic) to better understand the composition of phage communities on skin from South African study participants. Our data set adds over 130 new phage species of the skin to existing databases. We demonstrated that identical phages were present on different individuals and in different body sites, and we conducted a detailed analysis of the structural organization of these phages. We further found that a bacteriophage related to the Staphylococcus capitis phage Stb20 may be a common skin commensal virus potentially regulating its host and its activities on the ski

Candidate periodically variable quasars from the Dark Energy Survey and the Sloan Digital Sky Survey

Periodically variable quasars have been suggested as close binary supermassive black holes. We present a systematic search for periodic light curves in 625 spectroscopically confirmed quasars with a median redshift of 1.8 in a 4.6 deg2 overlapping region of the Dark Energy Survey Supernova (DES-SN) fields and the Sloan Digital Sky Survey Stripe 82 (SDSS-S82). Our sample has a unique 20-yr long multicolour (griz) light curve enabled by combining DES-SN Y6 observations with archival SDSS-S82 data. The deep imaging allows us to search for periodic light curves in less luminous quasars (down to r ∼23.5 mag) powered by less massive black holes (with masses ≳ 108.5M⊙) at high redshift for the first time. We find five candidates with significant (at >99.74 per cent single-frequency significance in at least two bands with a global p-value of ∼7 × 10−4–3 × 10−3 accounting for the look-elsewhere effect) periodicity with observed periods of ∼3–5 yr (i.e. 1–2 yr in rest frame) having ∼4–6 cycles spanned by the observations. If all five candidates are periodically variable quasars, this translates into a detection rate of ∼0.8+0.5−0.3 per cent or ∼1.1+0.7−0.5 quasar per deg2. Our detection rate is 4–80 times larger than those found by previous searches using shallower surveys over larger areas. This discrepancy is likely caused by differences in the quasar populations probed and the survey data qualities. We discuss implications on the future direct detection of low-frequency gravitational waves. Continued photometric monitoring will further assess the robustness and characteristics of these candidate periodic quasars to determine their physical origins

Dark Energy Survey Year 1 results: validation of weak lensing cluster member contamination estimates from P(z) decomposition

Weak lensing source galaxy catalogues used in estimating the masses of galaxy clusters can be heavily contaminated by cluster members, prohibiting accurate mass calibration. In this study, we test the performance of an estimator for the extent of cluster member contamination based on decomposing the photometric redshift P(z) of source galaxies into contaminating and background components. We perform a full scale mock analysis on a simulated sky survey approximately mirroring the observational properties of the Dark Energy Survey Year One observations (DES Y1), and find excellent agreement between the true number profile of contaminating cluster member galaxies in the simulation and the estimated one. We further apply the method to estimate the cluster member contamination for the DES Y1 redMaPPer cluster mass calibration analysis, and compare the results to an alternative approach based on the angular correlation of weak lensing source galaxies. We find indications that the correlation based estimates are biased by the selection of the weak lensing sources in the cluster vicinity, which does not strongly impact the P(z) decomposition method. Collectively, these benchmarks demonstrate the strength of the P(z) decomposition method in alleviating membership contamination and enabling highly accurate cluster weak lensing studies without broad exclusion of source galaxies, thereby improving the total constraining power of cluster mass calibration via weak lensing

Consistency of cosmic shear analyses in harmonic and real space

Recent cosmic shear studies have reported discrepancies of up to 1σ on the parameter S8=σ8Ωm/0.3‾‾‾‾‾‾‾√S8=σ8Ωm/0.3 between the analysis of shear power spectra and two-point correlation functions, derived from the same shear catalogues. It is not a priori clear whether the measured discrepancies are consistent with statistical fluctuations. In this paper, we investigate this issue in the context of the forthcoming analyses from the third year data of the Dark Energy Survey (DES Y3). We analyse DES Y3 mock catalogues from Gaussian simulations with a fast and accurate importance sampling pipeline. We show that the methodology for determining matching scale cuts in harmonic and real space is the key factor that contributes to the scatter between constraints derived from the two statistics. We compare the published scales cuts of the KiDS, Subaru-HSC, and DES surveys, and find that the correlation coefficients of posterior means range from over 80 per cent for our proposed cuts, down to 10 per cent for cuts used in the literature. We then study the interaction between scale cuts and systematic uncertainties arising from multiple sources: non-linear power spectrum, baryonic feedback, intrinsic alignments, uncertainties in the point spread function, and redshift distributions. We find that, given DES Y3 characteristics and proposed cuts, these uncertainties affect the two statistics similarly; the differential biases are below a third of the statistical uncertainty, with the largest biases arising from intrinsic alignment and baryonic feedback. While this work is aimed at DES Y3, the tools developed can be applied to Stage-IV surveys where statistical errors will be much smaller