Radial velocity measurements of B stars in the Scorpius-Centaurus association

We derive single-epoch radial velocities for a sample of 56 B-type stars members of the subgroups Upper Scorpius, Upper Centaurus Lupus and Lower Centaurus Crux of the nearby Sco-Cen OB association. The radial velocity measurements were obtained by means of high-resolution echelle spectra via analysis of individual lines. The internal accuracy obtained in the measurements is estimated to be typically 2-3 km/s, but depends on the projected rotational velocity of the target. Radial velocity measurements taken for 2-3 epochs for the targets HD120307, HD142990 and HD139365 are variable and confirm that they are spectroscopic binaries, as previously identified in the literature. Spectral lines from two stellar components are resolved in the observed spectra of target stars HD133242, HD133955 and HD143018, identifying them as spectroscopic binaries.Comment: accepted for publication in A&

High-throughput isolation and characterization of untagged membrane protein complexes: outer membrane complexes of Desulfovibrio vulgaris.

Cell membranes represent the "front line" of cellular defense and the interface between a cell and its environment. To determine the range of proteins and protein complexes that are present in the cell membranes of a target organism, we have utilized a "tagless" process for the system-wide isolation and identification of native membrane protein complexes. As an initial subject for study, we have chosen the Gram-negative sulfate-reducing bacterium Desulfovibrio vulgaris. With this tagless methodology, we have identified about two-thirds of the outer membrane- associated proteins anticipated. Approximately three-fourths of these appear to form homomeric complexes. Statistical and machine-learning methods used to analyze data compiled over multiple experiments revealed networks of additional protein-protein interactions providing insight into heteromeric contacts made between proteins across this region of the cell. Taken together, these results establish a D. vulgaris outer membrane protein data set that will be essential for the detection and characterization of environment-driven changes in the outer membrane proteome and in the modeling of stress response pathways. The workflow utilized here should be effective for the global characterization of membrane protein complexes in a wide range of organisms

Multi-Wavelength Monitoring of the Changing-Look AGN NGC 2617 during State Changes

Optical and near-infrared photometry, optical spectroscopy, and soft X-ray and UV monitoring of the changing-look active galactic nucleus NGC 2617 show that it continues to have the appearance of a type-1 Seyfert galaxy. An optical light curve for 2010-2017 indicates that the change of type probably occurred between 2010 October and 2012 February and was not related to the brightening in 2013. In 2016 and 2017 NGC 2617 brightened again to a level of activity close to that in 2013 April. However, in 2017 from the end of the March to end of July 2017 it was in very low level and starting to change back to a Seyfert 1.8. We find variations in all passbands and in both the intensities and profiles of the broad Balmer lines. A new displaced emission peak has appeared in Hβ. X-ray variations are well correlated with UV-optical variability and possibly lead by ̃2-3 d. The K band lags the J band by about 21.5 ± 2.5 d and lags the combined B + J bands by ̃25 d. J lags B by about 3 d. This could be because J-band variability arises predominantly from the outer part of the accretion disc, while K-band variability is dominated by thermal re-emission by dust. We propose that spectral-type changes are a result of increasing central luminosity causing sublimation of the innermost dust in the hollow bi-conical outflow. We briefly discuss various other possible reasons that might explain the dramatic changes in NGC 2617.Fil: Oknyansky, V. L.. Sternberg Astronomical Institute; RusiaFil: Gaskell, C. M.. Department of Astronomy and Astrophysics. University of California. Santa Cruz; Estados UnidosFil: Mikailov, K. M.. Shamakhy Astrophysical Observatory, National Academy of Sciences. Pirkuli; AzerbaiyánFil: Lipunov, V. M.. Sternberg Astronomical Institute. M.V.Lomonosov Moscow State University ; RusiaFil: Shatsky, N. I.. Sternberg Astronomical Institute. M.V.Lomonosov Moscow State University; RusiaFil: Tsygankov, S. S.. Tuorla Observatory, Department of Physics and Astronomy. University of Turku.; FinlandiaFil: Gorbovskoy, E. S.. Sternberg Astronomical Institute. M.V.Lomonosov Moscow State University; RusiaFil: Tatarnikov, A. M.. Sternberg Astronomical Institute. M.V.Lomonosov Moscow State University; RusiaFil: Metlov, V. G.. Sternberg Astronomical Institute. M.V.Lomonosov Moscow State University; RusiaFil: Malanchev, K. L.. Sternberg Astronomical Institute. M.V.Lomonosov Moscow State University; RusiaFil: Brotherton, M.B.. University of Wyoming; Estados UnidosFil: Kasper, D.. University of Wyoming; Estados UnidosFil: Du, P.. Institute of High Energy Physics. Chinese Academy of Sciences; ChinaFil: Chen, X.. School of Space Science and Physics. Shandong University; ChinaFil: Burlak, M. A.. Sternberg Astronomical Institute. M.V.Lomonosov Moscow State University; RusiaFil: Buckley, D. A. H.. The South African Astronomical Observatory; SudáfricaFil: Rebolo, R.. Instituto de Astrofisica de Canarias; EspañaFil: Serra-Ricart, M.. Instituto de Astrofisica de Canarias; EspañaFil: Podestá, R.. Universidad Nacional de San Juan; ArgentinaFil: Levato, O. H.. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Juan. Instituto de Ciencias Astronómicas, de la Tierra y del Espacio. Universidad Nacional de San Juan. Instituto de Ciencias Astronómicas, de la Tierra y del Espacio; Argentin

An asteroseismic study of the Beta Cephei star Theta Ophiuchi: spectroscopic results

We present the results of a detailed analysis of 121 ground-based high-resolution high S/N spectroscopic measurements spread over 3 years for the Beta Cephei star Theta Ophiuchi. We discovered Theta Oph to be a triple system. In addition to the already known Speckle B5 companion of the B2 primary, we showed the presence of a low-mass spectroscopic companion and we derived an orbital period of 56.71 days with an eccentricity of 0.1670. After removing the orbit we determined two frequencies for the primary in the residual radial velocities: f1 = 7.1160 c/d and f2 = 7.4676 c/d. We also found the presence of f3 = 7.3696 c/d by means of a two dimensional frequency search across the Si III 4567 A profiles. We identified the m-value of the main mode with frequency f1 by taking into account the photometric identifications of the degrees l. By means of the moment method and the amplitude and phase variations across the line profile, we derived (l1,m1) = (2,-1). This result allows us to fix the mode identifications of the whole quintuplet for which three components were detected in photometry. This is of particular use for our forthcoming seismic modelling of the primary. We also determined stellar parameters of the primary by non-local thermodynamic equilibrium hydrogen, helium and silicon line profile fitting and we obtained Teff = 24000 K and log g = 4.1, which is consistent with photometrically determined values.Comment: 8 pages, 6 figure

Cellular gene expression during Hepatitis C virus replication as revealed by Ribosome Profiling

Background: Hepatitis C virus (HCV) infects human liver hepatocytes, often leading to liver cirrhosis and hepatocellular carcinoma (HCC). It is believed that chronic infection alters host gene expression and favors HCC development. In particular, HCV replication in Endoplasmic Reticulum (ER) derived membranes induces chronic ER stress. How HCV replication affects host mRNA translation and transcription at a genome wide level is not yet known. Methods: We used Riboseq (Ribosome Profiling) to analyze transcriptome and translatome changes in the Huh-7.5 hepatocarcinoma cell line replicating HCV for 6 days. Results: Established viral replication does not cause global changes in host gene expression—only around 30 genes are significantly differentially expressed. Upregulated genes are related to ER stress and HCV replication, and several regulated genes are known to be involved in HCC development. Some mRNAs (PPP1R15A/GADD34, DDIT3/CHOP, and TRIB3) may be subject to upstream open reading frame (uORF) mediated translation control. Transcriptional downregulation mainly affects mitochondrial respiratory chain complex core subunit genes. Conclusion: After establishing HCV replication, the lack of global changes in cellular gene expression indicates an adaptation to chronic infection, while the downregulation of mitochondrial respiratory chain genes indicates how a virus may further contribute to cancer cell-like metabolic reprogramming (“Warburg effect”) even in the hepatocellular carcinoma cells used here

FLORA: a novel method to predict protein function from structure in diverse superfamilies

Predicting protein function from structure remains an active area of interest, particularly for the structural genomics initiatives where a substantial number of structures are initially solved with little or no functional characterisation. Although global structure comparison methods can be used to transfer functional annotations, the relationship between fold and function is complex, particularly in functionally diverse superfamilies that have evolved through different secondary structure embellishments to a common structural core. The majority of prediction algorithms employ local templates built on known or predicted functional residues. Here, we present a novel method (FLORA) that automatically generates structural motifs associated with different functional sub-families (FSGs) within functionally diverse domain superfamilies. Templates are created purely on the basis of their specificity for a given FSG, and the method makes no prior prediction of functional sites, nor assumes specific physico-chemical properties of residues. FLORA is able to accurately discriminate between homologous domains with different functions and substantially outperforms (a 2–3 fold increase in coverage at low error rates) popular structure comparison methods and a leading function prediction method. We benchmark FLORA on a large data set of enzyme superfamilies from all three major protein classes (α, β, αβ) and demonstrate the functional relevance of the motifs it identifies. We also provide novel predictions of enzymatic activity for a large number of structures solved by the Protein Structure Initiative. Overall, we show that FLORA is able to effectively detect functionally similar protein domain structures by purely using patterns of structural conservation of all residues

Comparative Structural Analysis of Lipid Binding START Domains

Steroidogenic acute regulatory (StAR) protein related lipid transfer (START) domains are small globular modules that form a cavity where lipids and lipid hormones bind. These domains can transport ligands to facilitate lipid exchange between biological membranes, and they have been postulated to modulate the activity of other domains of the protein in response to ligand binding. More than a dozen human genes encode START domains, and several of them are implicated in a disease.We report crystal structures of the human STARD1, STARD5, STARD13 and STARD14 lipid transfer domains. These represent four of the six functional classes of START domains.Sequence alignments based on these and previously reported crystal structures define the structural determinants of human START domains, both those related to structural framework and those involved in ligand specificity.This article can also be viewed as an enhanced version in which the text of the article is integrated with interactive 3D representations and animated transitions. Please note that a web plugin is required to access this enhanced functionality. Instructions for the installation and use of the web plugin are available in Text S1