BAT3 Guides Misfolded Glycoproteins Out of the Endoplasmic Reticulum

Secretory and membrane proteins that fail to acquire their native conformation within the lumen of the Endoplasmic Reticulum (ER) are usually targeted for ubiquitin-dependent degradation by the proteasome. How partially folded polypeptides are kept from aggregation once ejected from the ER into the cytosol is not known. We show that BAT3, a cytosolic chaperone, is recruited to the site of dislocation through its interaction with Derlin2. Furthermore, we observe cytoplasmic BAT3 in a complex with a polypeptide that originates in the ER as a glycoprotein, an interaction that depends on the cytosolic disposition of both, visualized even in the absence of proteasomal inhibition. Cells depleted of BAT3 fail to degrade an established dislocation substrate. We thus implicate a cytosolic chaperone as an active participant in the dislocation of ER glycoproteins.United States. National Institutes of HealthBoehringer Ingelheim Fond

The SDSS-IV extended Baryon Oscillation Spectroscopic Survey : Luminous Red Galaxy Target Selection

We describe the algorithm used to select the Luminous Red Galaxy (LRG) sample for the extended Baryon Oscillation Spectroscopic Survey (eBOSS) of the Sloan Digital Sky Survey IV (SDSS-IV) using photometric data from both the SDSS and the Wide-Field Infrared Survey Explorer (WISE). LRG targets are required to meet a set of color selection criteria and have z-band and i-band MODEL magnitudes z <19.95 and 19.9 <i < 21.8, respectively. Our algorithm selects roughly 50 LRG targets per square degree, the great majority of which lie in the redshift range 0.6 <z <1.0 (median redshift 0.71). We demonstrate that our methods are highly effective at eliminating stellar contamination and lower-redshift galaxies. We perform a number of tests using spectroscopic data from SDSS-III/BOSS to determine the redshift reliability of our target selection and its ability to meet the science requirements of eBOSS. The SDSS spectra are of high enough signal-to-noise ratio that at least 89% of the target sample yields secure redshift measurements. We also present tests of the uniformity and homogeneity of the sample, demonstrating that it should be clean enough for studies of the large-scale structure of the universe at higher redshifts than SDSS-III/BOSS LRGs reached.Publisher PDFPeer reviewe

The Sloan Digital Sky Survey Quasar catalog : fourteenth data release

We present the data release 14 Quasar catalog (DR14Q) from the extended Baryon Oscillation Spectroscopic Survey (eBOSS) of the Sloan Digital Sky Survey IV (SDSS-IV). This catalog includes all SDSS-IV/eBOSS objects that were spectroscopically targeted as quasar candidates and that are confirmed as quasars via a new automated procedure combined with a partial visual inspection of spectra, have luminosities Mi [z = 2] < −20.5 (in a Λ CDM cosmology with H0 = 70 km s−1 Mpc−1, ΩM =0.3, and ΩΛ = 0.7), and either display at least one emission line with a full width at half maximum larger than 500 km s−1 or, if not, have interesting/complex absorption features. The catalog also includes previously spectroscopically-confirmed quasars from SDSS-I, II, and III. The catalog contains 526 356 quasars (144 046 are new discoveries since the beginning of SDSS-IV) detected over 9376 deg2 (2044 deg2 having new spectroscopic data available) with robust identification and redshift measured by a combination of principal component eigenspectra. The catalog is estimated to have about 0.5% contamination. Redshifts are provided for the Mg II emission line. The catalog identifies 21 877 broad absorption line quasars and lists 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. 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, covering the wavelength region 3610–10 140 Å at a spectral resolution in the range 1300 < R < 2500, can be retrieved from the SDSS Science Archiver Server.Publisher PDFPeer reviewe

The clustering of the SDSS-IV extended Baryon Oscillation Spectroscopic Survey DR14 quasar sample : measurement of the growth rate of structure from the anisotropic correlation function between redshift 0.8 and 2.2

We present the clustering measurements of quasars in configuration space based on the Data Release 14 (DR14) of the Sloan Digital Sky Survey IV extended Baryon Oscillation Spectroscopic Survey. This dataset includes 148,659 quasars spread over the redshift range 0.8 ≤ z ≤ 2.2 and spanning 2112.9 square degrees. We use the Convolution Lagrangian Perturbation Theory (CLPT) approach with a Gaussian Streaming (GS) model for the redshift space distortions of the correlation function and demonstrate its applicability for dark matter halos hosting eBOSS quasartracers. At the effective redshift zeff = 1.52, we measure the linear growth rate of structure fσ8(zeff)= 0.426 ± 0.077, the expansion rate H(zeff) = 159^{+12}_{-13} (r_s^fid/rs)km.s-1.Mpc-1, and the angular diameterdistance DA(zeff)=1850^{+90}_{-115} (rs/r_s^fid) Mpc, where rs is the sound horizon at the end of the baryon drag epoch and r_s^fid is its value in the fiducial cosmology. The quoted errors include both systematic and statistical contributions. The results on the evolution of distances are consistent with the predictions of flat Λ-Cold Dark Matter (Λ-CDM) cosmology with Planck parameters, and the measurement of fσ8 extends the validity of General Relativity (GR) to higher redshifts (z > 1). This paper is released with companion papers using the same sample. The results on the cosmological parameters of the studies are found to be in very good agreement, providing clear evidence of the complementarity and of the robustness of the first full-shape clustering measurements with the eBOSS DR14 quasar sample.PostprintPeer reviewe

Enzymatic Blockade of the Ubiquitin-Proteasome Pathway

Ubiquitin-dependent processes control much of cellular physiology. We show that expression of a highly active, Epstein-Barr virus-derived deubiquitylating enzyme (EBV-DUB) blocks proteasomal degradation of cytosolic and ER-derived proteins by preemptive removal of ubiquitin from proteasome substrates, a treatment less toxic than the use of proteasome inhibitors. Recognition of misfolded proteins in the ER lumen, their dislocation to the cytosol, and degradation are usually tightly coupled but can be uncoupled by the EBV-DUB: a misfolded glycoprotein that originates in the ER accumulates in association with cytosolic chaperones as a deglycosylated intermediate. Our data underscore the necessity of a DUB activity for completion of the dislocation reaction and provide a new means of inhibition of proteasomal proteolysis with reduced cytotoxicity.National Institutes of Health (U.S.)EMBO (long term Fellowship 2008-379)Boehringer Ingelheim Fond

Technology-assisted dietary assessment

Dietary intake provides valuable insights for mounting intervention programs for prevention of disease. With growing concern for adolescent obesity, the need to accurately measure diet becomes imperative. Assessment among adolescents is problematic as this group has irregular eating patterns and have less enthusiasm for recording food intake. Preliminary studies among adolescents suggest that innovative use of technology may improve the accuracy of diet information from young people. In this paper, we propose a novel food record method using a mobile device that will provide an accurate account of daily food and nutrient intake among adolescents. Our approach includes the use of image analysis tools for identification and quantification of food consumption. Images obtained before and after food is consumed can be used to estimate the diet of an individual. In this paper we describe our initial results and indicate the potential of the proposed system

Comparison of methods for evaluating the suitability of Vertisols for Gossypium hirsutum (Bt cotton) in two contrasting agro-ecological regions

This is the author accepted manuscript. The final version is available from Taylor and Francis (Routledge) via the DOI in this record.Cotton (Gossypium sp.) is a major crop grown under rainfed conditions in Vertisols and associated soils in semi-arid tropical (SAT) regions of Peninsular India. In recent years, cotton productivity has declined due to various biophysical factors including pest and diseases, seasonal water stress soil degradation and poor crop management practices. In this study, we compare two methods for evaluating the suitability of Vertisols for cotton in contrasting two agro-ecological regions viz., sub-humid moist (SHM) region and semi-arid dry(SAD) were characterized. Twelve cotton growing Vertisols (seven from SHM and five from SAD) were evaluated for their suitability for cotton cultivation using soil quality index (SQI) and modified Sys-FAO method. SQIs were calculated using the weighted additive index from transformed scores of selected indicators by principal component analysis. For Sys-FAO method both biophysical and soil characteristics were considered for suitability evaluation. We found that the soils of SHM region were moderately suitable for cotton cultivation with soil moisture as the major limiting factor, whereas the soils of SAD region are marginally suitable due to high exchangeable sodium percentage and poor hydraulic conductivity. From this, it may be concluded that the weighted SQI has better agreement with the cotton yield

The Fourteenth Data Release of the Sloan Digital Sky Survey: First Spectroscopic Data from the extended Baryon Oscillation Spectroscopic Survey and from the second phase of the Apache Point Observatory Galactic Evolution Experiment

The fourth generation of the Sloan Digital Sky Survey (SDSS-IV) has been in operation since July 2014. This paper describes the second data release from this phase, and the fourteenth from SDSS overall (making this, Data Release Fourteen or DR14). This release makes public data taken by SDSS-IV in its first two years of operation (July 2014-2016). Like all previous SDSS releases, DR14 is cumulative, including the most recent reductions and calibrations of all data taken by SDSS since the first phase began operations in 2000. New in DR14 is the first public release of data from the extended Baryon Oscillation Spectroscopic Survey (eBOSS); the first data from the second phase of the Apache Point Observatory (APO) Galactic Evolution Experiment (APOGEE-2), including stellar parameter estimates from an innovative data driven machine learning algorithm known as "The Cannon"; and almost twice as many data cubes from the Mapping Nearby Galaxies at APO (MaNGA) survey as were in the previous release (N = 2812 in total). This paper describes the location and format of the publicly available data from SDSS-IV surveys. We provide references to the important technical papers describing how these data have been taken (both targeting and observation details) and processed for scientific use. The SDSS website (www.sdss.org) has been updated for this release, and provides links to data downloads, as well as tutorials and examples of data use. SDSS-IV is planning to continue to collect astronomical data until 2020, and will be followed by SDSS-V.Comment: SDSS-IV collaboration alphabetical author data release paper. DR14 happened on 31st July 2017. 19 pages, 5 figures. Accepted by ApJS on 28th Nov 2017 (this is the "post-print" and "post-proofs" version; minor corrections only from v1, and most of errors found in proofs corrected

Application of the rainbow trout derived intestinal cell line (RTgutGC) for ecotoxicological studies: molecular and cellular responses following exposure to copper.

There is an acknowledged need for in vitro fish intestinal model to help understand dietary exposure to chemicals in the aquatic environment. The presence and use of such models is however largely restrictive due to technical difficulties in the culturing of enterocytes in general and the availability of appropriate established cell lines in particular. In this study, the rainbow trout (Oncorhynchus mykiss) intestinal derived cell line (RTgutGC) was used as a surrogate for the "gut sac" method. To facilitate comparison, RTgutGC cells were grown as monolayers (double-seeded) on permeable Transwell supports leading to a two-compartment intestinal model consisting of polarised epithelium. This two-compartment model divides the system into an upper apical (lumen) and a lower basolateral (portal blood) compartment. In our studies, these cells stained weakly for mucosubstances, expressed the tight junction protein ZO-1 in addition to E-cadherin and revealed the presence of polarised epithelium in addition to microvilli protrusions. The cells also revealed a comparable transepithelial electrical resistance (TEER) to the in vivo situation. Importantly, the cell line tolerated apical saline (1:1 ratio) thus mimicking the intact organ to allow assessment of uptake of compounds across the intestine. Following an exposure over 72 h, our study demonstrated that the RTgutGC cell line under sub-lethal concentrations of copper sulphate (Cu) and modified saline solutions demonstrated uptake of the metal with saturation levels comparable to short term ex situ gut sac preparations. Gene expression analysis revealed no significant influence of pH or time on mRNA expression levels of key stress related genes (i.e. CYP3A, GST, mtA, Pgp and SOD) in the Transwell model. However, significant positive correlations were found between all genes investigated suggesting a co-operative relationship amongst the genes studied. When the outlined characteristics of the cell line are combined with the division of compartments, the RTgutGC double seeded model represents a potential animal replacement model for ecotoxicological studies. Overall, this model could be used to study the effects and predict aquatic gastrointestinal permeability of metals and other environmentally relevant contaminants in a cost effective and high throughput manner

SDSS-IV eBOSS emission-line galaxy pilot survey

The Sloan Digital Sky Survey IV extended Baryonic Oscillation Spectroscopic Survey (SDSS-IV/eBOSS) will observe 195 000 emission-line galaxies (ELGs) to measure the baryonic acoustic oscillation (BAO) standard ruler at redshift 0.9. To test different ELG selection algorithms, 9000 spectra were observed with the SDSS spectrograph as a pilot survey based on data from several imaging surveys. First, using visual inspection and redshift quality flags, we show that the automated spectroscopic redshifts assigned by the pipeline meet the quality requirements for a reliable BAO measurement. We also show the correlations between sky emission, signal-to-noise ratio in the emission lines, and redshift error. Then we provide a detailed description of each target selection algorithm we tested and compare them with the requirements of the eBOSS experiment. As a result, we provide reliable redshift distributions for the different target selection schemes we tested. Finally, we determine an target selection algorithms that is best suited to be applied on DECam photometry because they fulfill the eBOSS survey efficiency requirements