A comprehensive transcriptome analysis has been performed on protein-coding RNAs of Strongylocentrotus purpuratus, including 10 different embryonic stages, six feeding larval and metamorphosed ...juvenile stages, and six adult tissues. In this study, we pooled the transcriptomes from all of these sources and focused on the insights they provide for gene structure in the genome of this recently sequenced model system. The genome had initially been annotated by use of computational gene model prediction algorithms. A large fraction of these predicted genes were recovered in the transcriptome when the reads were mapped to the genome and appropriately filtered and analyzed. However, in a manually curated subset, we discovered that more than half the computational gene model predictions were imperfect, containing errors such as missing exons, prediction of nonexistent exons, erroneous intron/exon boundaries, fusion of adjacent genes, and prediction of multiple genes from single genes. The transcriptome data have been used to provide a systematic upgrade of the gene model predictions throughout the genome, very greatly improving the research usability of the genomic sequence. We have constructed new public databases that incorporate information from the transcriptome analyses. The transcript-based gene model data were used to define average structural parameters for S. purpuratus protein-coding genes. In addition, we constructed a custom sea urchin gene ontology, and assigned about 7000 different annotated transcripts to 24 functional classes. Strong correlations became evident between given functional ontology classes and structural properties, including gene size, exon number, and exon and intron size.
The Gaia-ESO Survey: Calibration strategy Pancino, E.; Lardo, C.; Altavilla, G. ...
Astronomy and astrophysics (Berlin),
02/2017, Letnik:
598
Journal Article, Web Resource
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The Gaia-ESO survey (GES) is now in its fifth and last year of observations and has produced tens of thousands of high-quality spectra of stars in all Milky Way components. This paper presents the ...strategy behind the selection of astrophysical calibration targets, ensuring that all GES results on radial velocities, atmospheric parameters, and chemical abundance ratios will be both internally consistent and easily comparable with other literature results, especially from other large spectroscopic surveys and from Gaia. The calibration of GES is particularly delicate because of (i) the large space of parameters covered by its targets, ranging from dwarfs to giants, from O to M stars; these targets have a large wide of metallicities and also include fast rotators, emission line objects, and stars affected by veiling; (ii) the variety of observing setups, with different wavelength ranges and resolution; and (iii) the choice of analyzing the data with many different state-of-the-art methods, each stronger in a different region of the parameter space, which ensures a better understanding of systematic uncertainties. An overview of the GES calibration and homogenization strategy is also given, along with some examples of the usage and results of calibrators in GES iDR4, which is the fourth internal GES data release and will form the basis of the next GES public data release. The agreement between GES iDR4 recommended values and reference values for the calibrating objects are very satisfactory. The average offsets and spreads are generally compatible with the GES measurement errors, which in iDR4 data already meet the requirements set by the main GES scientific goals.
Abstract
We present a family of self-consistent axisymmetric rotating globular cluster models which are fitted to spectroscopic data for NGC 362, NGC 1851, NGC 2808, NGC 4372, NGC 5927 and NGC 6752 ...to provide constraints on their physical and kinematic properties, including their rotation signals. They are constructed by flattening Modified Plummer profiles, which have the same asymptotic behaviour as classical Plummer models, but can provide better fits to young clusters due to a slower turnover in the density profile. The models are in dynamical equilibrium as they depend solely on the action variables. We employ a fully Bayesian scheme to investigate the uncertainty in our model parameters (including mass-to-light ratios and inclination angles) and evaluate the Bayesian evidence ratio for rotating to non-rotating models. We find convincing levels of rotation only in NGC 2808. In the other clusters, there is just a hint of rotation (in particular, NGC 4372 and NGC 5927), as the data quality does not allow us to draw strong conclusions. Where rotation is present, we find that it is confined to the central regions, within radii of R ≤ 2r
h
. As part of this work, we have developed a novel q-Gaussian basis expansion of the line-of-sight velocity distributions, from which general models can be constructed via interpolation on the basis coefficients.
G-protein-coupled receptors (GPCRs) transduce signals from extracellular transmitters to the inside of the cell by activating G proteins. Mutation and overexpression of these receptors have revealed ...that they can reach their active state even in the absence of agonist, as a result of a natural shift in the equilibrium between their inactive and active conformations. Such agonist-independent (constitutive) activity has been observed for the glutamate GPCRs (the metabotropic glutamate receptors mGluR1a and mGluR5) when they are overexpressed in heterologous cells. Here we show that in neurons, the constitutive activity of these receptors is controlled by Homer proteins, which bind directly to the receptors' carboxy-terminal intracellular domains. Disruption of this interaction by mutagenesis or antisense strategies, or expression of endogenous Homer1a (H1a), induces constitutive activity in mGluR1a or mGluR5. Our results show that these glutamate GPCRs can be directly activated by intracellular proteins as well as by agonists.
Celotno besedilo
Dostopno za:
DOBA, IJS, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Aims. We present the first extensive spectroscopic study of the global population in star clusters Trumpler 16, Trumpler 14, and Collinder 232 in the Carina nebula, using data from the Gaia-ESO ...Survey, down to solar-mass stars. Methods. In addition to the standard homogeneous survey data reduction, a special processing was applied here because of the bright nebulosity surrounding Carina stars. Results. We find about 400 good candidate members ranging from OB types down to slightly subsolar masses. About 100 heavily reddened early-type Carina members found here were previously unrecognized or poorly classified, including two candidate O stars and several candidate Herbig Ae/Be stars. Their large brightness makes them useful tracers of the obscured Carina population. The spectroscopically derived temperatures for nearly 300 low-mass members enables the inference of individual extinction values and the study of the relative placement of stars along the line of sight. Conclusions. We find a complex spatial structure with definite clustering of low-mass members around the most massive stars and spatially variable extinction. By combining the new data with existing X-ray data, we obtain a more complete picture of the three-dimensional spatial structure of the Carina clusters and of their connection to bright and dark nebulosity and UV sources. The identification of tens of background giants also enables us to determine the total optical depth of the Carina nebula along many sightlines. We are also able to put constraints on the star formation history of the region with Trumpler 14 stars found to be systematically younger than stars in other subclusters. We find a large percentage of fast-rotating stars among Carina solar-mass members, which provide new constraints on the rotational evolution of pre-main-sequence stars in this mass range.
We present the first results of the EMBLA survey (Extremely Metal-poor BuLge stars with AAOmega), aimed at finding metal-poor stars in the Milky Way bulge, where the oldest stars should now ...preferentially reside. EMBLA utilizes SkyMapper photometry to pre-select metal-poor candidates, which are subsequently confirmed using AAOmega spectroscopy. We describe the discovery and analysis of four bulge giants with −2.72 ≤ Fe/H ≤ −2.48, the lowest metallicity bulge stars studied with high-resolution spectroscopy to date. Using FLAMES/UVES spectra through the Gaia-ESO Survey we have derived abundances of twelve elements. Given the uncertainties, we find a chemical similarity between these bulge stars and halo stars of the same metallicity, although the abundance scatter may be larger, with some of the stars showing unusual α/Fe ratios.
Aims. Observational studies of the Milky Way bulge are providing increasing evidence of its complex chemo-dynamical patterns and morphology. Our intent is to use the iDR1 Gaia-ESO Survey (GES) data ...set to provide new constraints on the metallicity and kinematic trends of the Galactic bulge, exploring the viability of the currently proposed formation scenarios. Methods. We analyzed the stellar parameters and radial velocities of ~1200 stars in five bulge fields wich are located in the region −10°<l< 7° and −10°<b< −4°. We use VISTA Variables in the Via Lactea (VVV) photometry to verify the internal consistency of the atmospheric parameters recommended by the consortium. As a by-product, we obtained reddening values using a semi-empirical Teff-color calibration. We constructed the metallicity distribution functions and combined them with photometric and radial velocity data to analyze the properties of the stellar populations in the observed fields. Results. From a Gaussian decomposition of the metallicity distribution functions, we unveil a clear bimodality in all fields, with the relative size of components depending of the specific position on the sky. In agreement with some previous studies, we find a mild gradient along the minor axis (−0.05 dex/deg between b = −6° and b = −10°) that arises from the varying proportion of metal-rich and metal-poor components. The number of metal-rich stars fades in favor of the metal-poor stars with increasing b. The K-magnitude distribution of the metal-rich population splits into two peaks for two of the analyzed fields that intersects the near and far branches of the X-shaped bulge structure. In addition, two lateral fields at (l,b) = (7, −9) and (l,b) = (−10, −8) present contrasting characteristics. In the former, the metallicity distribution is dominated by metal-rich stars, while in the latter it presents a mix of a metal-poor population and and a metal-intermediate one, of nearly equal sizes. Finally, we find systematic differences in the velocity dispersion between the metal-rich and the metal-poor components of each field. Conclusions. The iDR1 bulge data show chemo-dynamical distributions that are consistent with varying proportions of stars belonging to (i) a metal-rich boxy/peanut X-shaped component, with bar-like kinematics; and (ii) a metal-poor more extended rotating structure with a higher velocity dispersion that dominates far from the Galactic plane. These first GES data already allow studying the detailed spatial dependence of the Galactic bulge populations, thanks to the analysis of individual fields with relatively high statistics.
Pain in infants is undertreated and poorly understood, representing a major clinical problem. In part, this is due to our inability to objectively measure pain in nonverbal populations. We present ...and validate an electroencephalography-based measure of infant nociceptive brain activity that is evoked by acute noxious stimulation and is sensitive to analgesic modulation. This measure should be valuable both for mechanistic investigations and for testing analgesic efficacy in the infant population.
Context. The Gaia-ESO Survey (GES) is a large spectroscopic survey that provides a unique opportunity to study the distribution of spectroscopic multiple systems among different populations of the ...Galaxy. Aims. Our aim is to detect binarity/multiplicity for stars targeted by the GES from the analysis of the cross-correlation functions (CCFs) of the GES spectra with spectral templates. Methods. We developed a method based on the computation of the CCF successive derivatives to detect multiple peaks and determine their radial velocities, even when the peaks are strongly blended. The parameters of the detection of extrema (doe) code have been optimized for each GES GIRAFFE and UVES setup to maximize detection. The doe code therefore allows to automatically detect multiple line spectroscopic binaries (SBn, n ≥ 2). Results. We apply this method on the fourth GES internal data release and detect 354 SBn candidates (342 SB2, 11 SB3, and even one SB4), including only nine SBs known in the literature. This implies that about 98% of these SBn candidates are new because of their faint visual magnitude that can reach V = 19. Visual inspection of the SBn candidate spectra reveals that the most probable candidates have indeed a composite spectrum. Among the SB2 candidates, an orbital solution could be computed for two previously unknown binaries: CNAME 06404608+0949173 (known as V642 Mon) in NGC 2264 and CNAME 19013257-0027338 in Berkeley 81 (Be 81). A detailed analysis of the unique SB4 (four peaks in the CCF) reveals that CNAME 08414659-5303449 (HD 74438) in the open cluster IC 2391 is a physically bound stellar quadruple system. The SB candidates belonging to stellar clusters are reviewed in detail to discard false detections. We suggest that atmospheric parameters should not be used for these system components; SB-specific pipelines should be used instead. Conclusions. Our implementation of an automatic detection of spectroscopic binaries within the GES has allowed the efficient discovery of many new multiple systems. With the detection of the SB1 candidates that will be the subject of a forthcoming paper, the study of the statistical and physical properties of the spectroscopic multiple systems will soon be possible for the entire GES sample.
Characterizing large genomic variants is essential to expanding the research and clinical applications of genome sequencing. While multiple data types and methods are available to detect these ...structural variants (SVs), they remain less characterized than smaller variants because of SV diversity, complexity, and size. These challenges are exacerbated by the experimental and computational demands of SV analysis. Here, we characterize the SV content of a personal genome with Parliament, a publicly available consensus SV-calling infrastructure that merges multiple data types and SV detection methods.
We demonstrate Parliament's efficacy via integrated analyses of data from whole-genome array comparative genomic hybridization, short-read next-generation sequencing, long-read (Pacific BioSciences RSII), long-insert (Illumina Nextera), and whole-genome architecture (BioNano Irys) data from the personal genome of a single subject (HS1011). From this genome, Parliament identified 31,007 genomic loci between 100 bp and 1 Mbp that are inconsistent with the hg19 reference assembly. Of these loci, 9,777 are supported as putative SVs by hybrid local assembly, long-read PacBio data, or multi-source heuristics. These SVs span 59 Mbp of the reference genome (1.8%) and include 3,801 events identified only with long-read data. The HS1011 data and complete Parliament infrastructure, including a BAM-to-SV workflow, are available on the cloud-based service DNAnexus.
HS1011 SV analysis reveals the limits and advantages of multiple sequencing technologies, specifically the impact of long-read SV discovery. With the full Parliament infrastructure, the HS1011 data constitute a public resource for novel SV discovery, software calibration, and personal genome structural variation analysis.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
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