Molecular basis for glycan recognition and reaction priming of eukaryotic oligosaccharyltransferase.

Oligosaccharyltransferase (OST) is the central enzyme of N-linked protein glycosylation. It catalyzes the transfer of a pre-assembled glycan, GlcNAc2Man9Glc3, from a dolichyl-pyrophosphate donor to acceptor sites in secretory proteins in the lumen of the endoplasmic reticulum. Precise recognition of the fully assembled glycan by OST is essential for the subsequent quality control steps of glycoprotein biosynthesis. However, the molecular basis of the OST-donor glycan interaction is unknown. Here we present cryo-EM structures of S. cerevisiae OST in distinct functional states. Our findings reveal that the terminal glucoses (Glc3) of a chemo-enzymatically generated donor glycan analog bind to a pocket formed by the non-catalytic subunits WBP1 and OST2. We further find that binding either donor or acceptor substrate leads to distinct primed states of OST, where subsequent binding of the other substrate triggers conformational changes required for catalysis. This alternate priming allows OST to efficiently process closely spaced N-glycosylation sites

Gaia Focused Product Release: A catalogue of sources around quasars to search for strongly lensed quasars

Context. Strongly lensed quasars are fundamental sources for cosmology. The Gaia space mission covers the entire sky with the unprecedented resolution of $0.18$" in the optical, making it an ideal instrument to search for gravitational lenses down to the limiting magnitude of 21. Nevertheless, the previous Gaia Data Releases are known to be incomplete for small angular separations such as those expected for most lenses. Aims. We present the Data Processing and Analysis Consortium GravLens pipeline, which was built to analyse all Gaia detections around quasars and to cluster them into sources, thus producing a catalogue of secondary sources around each quasar. We analysed the resulting catalogue to produce scores that indicate source configurations that are compatible with strongly lensed quasars. Methods. GravLens uses the DBSCAN unsupervised clustering algorithm to detect sources around quasars. The resulting catalogue of multiplets is then analysed with several methods to identify potential gravitational lenses. We developed and applied an outlier scoring method, a comparison between the average BP and RP spectra of the components, and we also used an extremely randomised tree algorithm. These methods produce scores to identify the most probable configurations and to establish a list of lens candidates. Results. We analysed the environment of 3 760 032 quasars. A total of 4 760 920 sources, including the quasars, were found within 6" of the quasar positions. This list is given in the Gaia archive. In 87\% of cases, the quasar remains a single source, and in 501 385 cases neighbouring sources were detected. We propose a list of 381 lensed candidates, of which we identified 49 as the most promising. Beyond these candidates, the associate tables in this Focused Product Release allow the entire community to explore the unique Gaia data for strong lensing studies further.Comment: 35 pages, 60 figures, accepted for publication by Astronomy and Astrophysic

Gaia Focused Product Release: Radial velocity time series of long-period variables

The third Gaia Data Release (DR3) provided photometric time series of more than 2 million long-period variable (LPV) candidates. Anticipating the publication of full radial-velocity (RV) in DR4, this Focused Product Release (FPR) provides RV time series for a selection of LPVs with high-quality observations. We describe the production and content of the Gaia catalog of LPV RV time series, and the methods used to compute variability parameters published in the Gaia FPR. Starting from the DR3 LPVs catalog, we applied filters to construct a sample of sources with high-quality RV measurements. We modeled their RV and photometric time series to derive their periods and amplitudes, and further refined the sample by requiring compatibility between the RV period and at least one of the $G$, $G_{\rm BP}$, or $G_{\rm RP}$ photometric periods. The catalog includes RV time series and variability parameters for 9\,614 sources in the magnitude range $6\lesssim G/{\rm mag}\lesssim 14$, including a flagged top-quality subsample of 6\,093 stars whose RV periods are fully compatible with the values derived from the $G$, $G_{\rm BP}$, and $G_{\rm RP}$ photometric time series. The RV time series contain a mean of 24 measurements per source taken unevenly over a duration of about three years. We identify the great most sources (88%) as genuine LPVs, with about half of them showing a pulsation period and the other half displaying a long secondary period. The remaining 12% consists of candidate ellipsoidal binaries. Quality checks against RVs available in the literature show excellent agreement. We provide illustrative examples and cautionary remarks. The publication of RV time series for almost 10\,000 LPVs constitutes, by far, the largest such database available to date in the literature. The availability of simultaneous photometric measurements gives a unique added value to the Gaia catalog (abridged)Comment: 36 pages, 38 figure

Gaia Focused Product Release: Asteroid orbital solution: Properties and assessment

Context. We report the exploitation of a sample of Solar System observations based on data from the third Gaia Data Release (Gaia DR3) of nearly 157 000 asteroids. It extends the epoch astrometric solution over the time coverage planned for the Gaia DR4, which is not expected before the end of 2025. This data set covers more than one full orbital period for the vast majority of these asteroids. The orbital solutions are derived from the Gaia data alone over a relatively short arc compared to the observation history of many of these asteroids. Aims. The work aims to produce orbital elements for a large set of asteroids based on 66 months of accurate astrometry provided by Gaia and to assess the accuracy of these orbital solutions with a comparison to the best available orbits derived from independent observations. A second validation is performed with accurate occultation timings. Methods. We processed the raw astrometric measurements of Gaia to obtain astrometric positions of moving objects with 1D sub-mas accuracy at the bright end. For each asteroid that we matched to the data, an orbit fitting was attempted in the form of the best fit of the initial conditions at the median epoch. The force model included Newtonian and relativistic accelerations to derive the observation equations, which were solved with a linear least-squares fit. Results. Orbits are provided in the form of state vectors in the International Celestial Reference Frame for 156 764 asteroids, including near-Earth objects, main-belt asteroids, and Trojans. For the asteroids with the best observations, the (formal) relative uncertainty σa/a is better than 10−10. Results are compared to orbits available from the Jet Propulsion Laboratory and MPC. Their orbits are based on much longer data arcs, but from positions of lower quality. The relative differences in semi-major axes have a mean of 5 × 10−10 and a scatter of 5 × 10−9

Gaia Focused Product Release: Sources from Service Interface Function image analysis

Context. Gaia’s readout window strategy is challenged by very dense fields in the sky. Therefore, in addition to standard Gaia observations, full Sky Mapper (SM) images were recorded for nine selected regions in the sky. A new software pipeline exploits these Service Interface Function (SIF) images of crowded fields (CFs), making use of the availability of the full two-dimensional (2D) information. This new pipeline produced half a million additional Gaia sources in the region of the omega Centauri (ω Cen) cluster, which are published with this Focused Product Release. We discuss the dedicated SIF CF data reduction pipeline, validate its data products, and introduce their Gaia archive table. Aims. Our aim is to improve the completeness of the Gaia source inventory in a very dense region in the sky, ω Cen. Methods. An adapted version of Gaia’s Source Detection and Image Parameter Determination software located sources in the 2D SIF CF images. These source detections were clustered and assigned to new SIF CF or existing Gaia sources by Gaia s cross-match software. For the new sources, astrometry was calculated using the Astrometric Global Iterative Solution software, and photometry was obtained in the Gaia DR3 reference system. We validated the results by comparing them to the public Gaia DR3 catalogue and external Hubble Space Telescope data. Results. With this Focused Product Release, 526 587 new sources have been added to the Gaia catalogue in ω Cen. Apart from positions and brightnesses, the additional catalogue contains parallaxes and proper motions, but no meaningful colour information. While SIF CF source parameters generally have a lower precision than nominal Gaia sources, in the cluster centre they increase the depth of the combined catalogue by three magnitudes and improve the source density by a factor of ten. Conclusions. This first SIF CF data publication already adds great value to the Gaia catalogue. It demonstrates what to expect for the fourth Gaia catalogue, which will contain additional sources for all nine SIF CF regions

Gaia Focused Product Release: Spatial distribution of two diffuse interstellar bands

Diffuse interstellar bands (DIBs) are absorption features seen in optical and infrared spectra of stars and extragalactic objects that are probably caused by large and complex molecules in the galactic interstellar medium (ISM). Here we investigate the Galactic distribution and properties of two DIBs identified in almost six million stellar spectra collected by the Gaia Radial Velocity Spectrometer. These measurements constitute a part of the Gaia Focused Product Release to be made public between the Gaia DR3 and DR4 data releases. In order to isolate the DIB signal from the stellar features in each individual spectrum, we identified a set of 160 000 spectra at high Galactic latitudes (|b| ⩾ 65°) covering a range of stellar parameters which we consider to be the DIB-free reference sample. Matching each target spectrum to its closest reference spectra in stellar parameter space allowed us to remove the stellar spectrum empirically, without reference to stellar models, leaving a set of six million ISM spectra. Using the star’s parallax and sky coordinates, we then allocated each ISM spectrum to a voxel (VOlume piXEL) on a contiguous three-dimensional grid with an angular size of 1.8° (level 5 HEALPix) and 29 unequally sized distance bins. Identifying the two DIBs at 862.1 nm (λ862.1) and 864.8 nm (λ864.8) in the stacked spectra, we modelled their shapes and report the depth, central wavelength, width, and equivalent width (EW) for each, along with confidence bounds on these measurements. We then explored the properties and distributions of these quantities and compared them with similar measurements from other surveys. Our main results are as follows: (1) the strength and spatial distribution of the DIB λ862.1 are very consistent with what was found in Gaia DR3, but for this work we attained a higher signal-to-noise ratio in the stacked spectra to larger distances, which allowed us to trace DIBs in the outer spiral arm and beyond the Scutum–Centaurus spiral arm; (2) we produced an all-sky map below ±65° of Galactic latitude to ~4000 pc of both DIB features and their correlations; (3) we detected the signals of DIB λ862.1 inside the Local Bubble (≲200 pc); and (4) there is a reasonable correlation with the dust reddening found from stellar absorption and EWs of both DIBs with a correlation coefficient of 0.90 for λ862.1 and 0.77 for λ864.8

Gaia Focused Product Release: Radial velocity time series of long-period variables

Context. The third Gaia Data Release (DR3) provided photometric time series of more than 2 million long-period variable (LPV) candidates. Anticipating the publication of full radial-velocity data planned with Data Release 4, this Focused Product Release (FPR) provides radial-velocity time series for a selection of LPV candidates with high-quality observations. Aims. We describe the production and content of the Gaia catalog of LPV radial-velocity time series, and the methods used to compute the variability parameters published as part of the Gaia FPR. Methods. Starting from the DR3 catalog of LPV candidates, we applied several filters to construct a sample of sources with high-quality radial-velocity measurements. We modeled their radial-velocity and photometric time series to derive their periods and amplitudes, and further refined the sample by requiring compatibility between the radial-velocity period and at least one of the G, GBP, or GRP photometric periods. Results. The catalog includes radial-velocity time series and variability parameters for 9614 sources in the magnitude range 6 ≲ G/mag ≲ 14, including a flagged top-quality subsample of 6093 stars whose radial-velocity periods are fully compatible with the values derived from the G, GBP, and GRP photometric time series. The radial-velocity time series contain a mean of 24 measurements per source taken unevenly over a duration of about three years. We identify the great majority of the sources (88%) as genuine LPV candidates, with about half of them showing a pulsation period and the other half displaying a long secondary period. The remaining 12% of the catalog consists of candidate ellipsoidal binaries. Quality checks against radial velocities available in the literature show excellent agreement. We provide some illustrative examples and cautionary remarks. Conclusions. The publication of radial-velocity time series for almost ten thousand LPV candidates constitutes, by far, the largest such database available to date in the literature. The availability of simultaneous photometric measurements gives a unique added value to the Gaia catalog

AssistConf: a Grid configuration tool for the ASSIST parallel programming environment

This paper presents AssistConf, a graphical user interface designed to configure an ASSIST program and to run it on a Grid platform. ASSIST (A Software development System based upon Integrated Skeleton Technology) is a new programming environment for the development of parallel and distributed high-performance applications. The main goals of ASSIST are allowing high-level programmability and software productivity for complex multidisciplinary applications, and performance portability across different platforms, including homogenous parallel machines and cluster/Beowulf systems, heterogeneous clusters, and computational Grids. AssistConf is used to configure the ASSIST program and establish a mapping between the program modules and the most suitable machines in the Grid candidate to execute them. It simplifies the creation of the XML ASSIST configuration file, giving users the machines to be used for execution. Finally, the configuration program over the Grid

ASSIST demo: a high level, high performance, portable, structured parallel programming environment at work

This work summarizes the possibilities offered by parallel programming environment ASSIST by outlining some of the features that will be demonstrated at the conference demo session. We'll substantially show how this environment can be deployed on a Linux workstation network/cluster, how applications can be compiled and run using ASSIST and eventually, we'll discuss some ASSIST scalability and performance features. We'll also outline how the ASSIST environment can be used to target GRID architectures