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At least 1,153 records · Page 64
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

The Dark Energy Spectroscopic Instrument: one-dimensional power spectrum from first Ly α forest samples with Fast Fourier Transform

ABSTRACT We present the one-dimensional Ly α forest power spectrum measurement using the first data provided by the Dark Energy Spectroscopic Instrument (DESI). The data sample comprises 26 330 quasar spectra, at redshift z > 2.1, contained in the DESI Early Data Release and the first 2 months of the main survey. We employ a Fast Fourier Transform (FFT) estimator and compare the resulting power spectrum to an alternative likelihood-based method in a companion paper. We investigate methodological and instrumental contaminants associated with the new DESI instrument, applying techniques similar to previous Sloan Digital Sky Survey (SDSS) measurements. We use synthetic data based on lognormal approximation to validate and correct our measurement. We compare our resulting power spectrum with previous SDSS and high-resolution measurements. With relatively small number statistics, we successfully perform the FFT measurement, which is already competitive in terms of the scale range. At the end of the DESI survey, we expect a five times larger Ly α forest sample than SDSS, providing an unprecedented precise one-dimensional power spectrum measurement.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

The Lyman-α forest catalogue from the Dark Energy Spectroscopic Instrument Early Data Release

We present and validate the catalogue of Lyman-α forest fluctuations for 3D analyses using the Early Data Release (EDR) from the Dark Energy Spectroscopic Instrument (DESI) survey. We used 88 511 quasars collected from DESI Survey Validation (SV) data and the first two months of the main survey (M2). We present several improvements to the method used to extract the Lyman-α absorption fluctuations performed in previous analyses from the Sloan Digital Sky Survey (SDSS). In particular, we modify the weighting scheme and show that it can improve the precision of the correlation function measurement by more than 20 percent. This catalogue can be downloaded from https://data.desi.lbl.gov/public/edr/vac/edr/lya/fuji/v0.3, and it will be used in the near future for the first DESI measurements of the 3D correlations in the Lyman-α forest.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

TOI-2374 b and TOI-3071 b: two metal-rich sub-Saturns well within the Neptunian desert

ABSTRACT We report the discovery of two transiting planets detected by the Transiting Exoplanet Survey Satellite (TESS), TOI-2374 b and TOI-3071 b, orbiting a K5V and an F8V star, respectively, with periods of 4.31 and 1.27 d, respectively. We confirm and characterize these two planets with a variety of ground-based and follow-up observations, including photometry, precise radial velocity monitoring and high-resolution imaging. The planetary and orbital parameters were derived from a joint analysis of the radial velocities and photometric data. We found that the two planets have masses of (57 ± 4) M⊕ or (0.18 ± 0.01) MJ, and (68 ± 4) M⊕ or (0.21 ± 0.01) MJ, respectively, and they have radii of (6.8 ± 0.3) R⊕ or (0.61 ± 0.03) RJ and (7.2 ± 0.5) R⊕ or (0.64 ± 0.05) RJ, respectively. These parameters correspond to sub-Saturns within the Neptunian desert, both planets being hot and highly irradiated, with Teq ≈ 745 K and Teq ≈ 1812 K, respectively, assuming a Bond albedo of 0.5. TOI-3071 b has the hottest equilibrium temperature of all known planets with masses between 10 and 300 M⊕ and radii less than 1.5 RJ. By applying gas giant evolution models we found that both planets, especially TOI-3071 b, are very metal-rich. This challenges standard formation models which generally predict lower heavy-element masses for planets with similar characteristics. We studied the evolution of the planets’ atmospheres under photoevaporation and concluded that both are stable against evaporation due to their large masses and likely high metallicities in their gaseous envelopes.

Hacker, Alejandro (ORCID:0009000994520181)↗
DOE OSTI2024

Broad absorption line quasars in the Dark Energy Spectroscopic Instrument Early Data Release

Broad absorption line (BAL) quasars are characterized by gas clouds that absorb flux at the wavelength of common quasar spectral features, although blueshifted by velocities that can exceed $0.1c$. BAL features are interesting as signatures of significant feedback, yet they can also compromise cosmological studies with quasars by distorting the shape of the most prominent quasar emission lines, impacting redshift accuracy and measurements of the matter density distribution traced by the Lyman $\alpha$ forest. We present a catalogue of BAL quasars discovered in the Dark Energy Spectroscopic Instrument (DESI) survey Early Data Release, which were observed as part of DESI Survey Validation, as well as the first two months of the main survey. We describe our method to automatically identify BAL quasars in DESI data, the quantities we measure for each BAL, and investigate the completeness and purity of this method with mock DESI observations. We mask the wavelengths of the BAL features and re-evaluate each BAL quasar redshift, finding new redshifts which are $243\, {\rm km}\, {\rm s}^{-1}$ smaller on average for the BAL quasar sample. These new, more accurate redshifts are important to obtain the best measurements of quasar clustering, especially at small scales. Finally, we present some spectra of rarer classes of BALs that illustrate the potential of DESI data to identify such populations for further study.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

Optimal 1D Ly α forest power spectrum estimation – III. DESI early data

ABSTRACT The 1D power spectrum P1D of the Ly α forest provides important information about cosmological and astrophysical parameters, including constraints on warm dark matter models, the sum of the masses of the three neutrino species, and the thermal state of the intergalactic medium. We present the first measurement of P1D with the quadratic maximum likelihood estimator (QMLE) from the Dark Energy Spectroscopic Instrument (DESI) survey early data sample. This early sample of 54 600 quasars is already comparable in size to the largest previous studies, and we conduct a thorough investigation of numerous instrumental and analysis systematic errors to evaluate their impact on DESI data with QMLE. We demonstrate the excellent performance of the spectroscopic pipeline noise estimation and the impressive accuracy of the spectrograph resolution matrix with 2D image simulations of raw DESI images that we processed with the DESI spectroscopic pipeline. We also study metal line contamination and noise calibration systematics with quasar spectra on the red side of the Ly α emission line. In a companion paper, we present a similar analysis based on the Fast Fourier Transform estimate of the power spectrum. We conclude with a comparison of these two approaches and discuss the key sources of systematic error that we need to address with the upcoming DESI Year 1 analysis.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

Project Dinos I: A joint lensing–dynamics constraint on the deviation from the power law in the mass profile of massive ellipticals

The mass distribution in massive elliptical galaxies encodes their evolutionary history, thus providing an avenue to constrain the baryonic astrophysics in their evolution. The power-law assumption for the radial mass profile in ellipticals has been sufficient to describe several observables to the noise level, including strong lensing and stellar dynamics. In this paper, we quantitatively constrained any deviation, or the lack thereof, from the power-law mass profile in massive ellipticals through joint lensing–dynamics analysis of a large statistical sample with 77 galaxy–galaxy lens systems. We performed an improved and uniform lens modelling of these systems from archival Hubble Space Telescope imaging using the automated lens modelling pipeline dolphin. We combined the lens model posteriors with the stellar dynamics to constrain the deviation from the power law after accounting for the line-of-sight lensing effects, a first for analyses on galaxy–galaxy lenses. We find that the Sloan Lens ACS Survey lens galaxies with a mean redshift of 0.2 are consistent with the power-law profile within 1.1σ (2.8σ) and the Strong Lensing Legacy Survey lens galaxies with a mean redshift of 0.6 are consistent within 0.8σ (2.1σ), for a spatially constant (Osipkov–Merritt) stellar anisotropy profile. We adopted the spatially constant anisotropy profile as our baseline choice based on previous dynamical observables of local ellipticals. However, spatially resolved stellar kinematics of lens galaxies are necessary to differentiate between the two anisotropy models. Future studies will use our lens models to constrain the mass distribution individually in the dark matter and baryonic components.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

Mechanistic insights from structure of Mycobacterium smegmatis topoisomerase I with ssDNA bound to both N- and C-terminal domains

Abstract Type IA topoisomerases interact with G-strand and T-strand ssDNA to regulate DNA topology. However, simultaneous binding of two ssDNA segments to a type IA topoisomerase has not been observed previously. We report here the crystal structure of a type IA topoisomerase with ssDNA segments bound in opposite polarity to the N- and C-terminal domains. Titration of small ssDNA oligonucleotides to Mycobacterium smegmatis topoisomerase I with progressive C-terminal deletions showed that the C-terminal region has higher affinity for ssDNA than the N-terminal active site. This allows the C-terminal domains to capture one strand of underwound negatively supercoiled DNA substrate first and position the N-terminal domains to bind and cleave the opposite strand in the relaxation reaction. Efficiency of negative supercoiling relaxation increases with the number of domains that bind ssDNA primarily with conserved aromatic residues and possibly with assistance from polar/basic residues. A comparison of bacterial topoisomerase I structures showed that a conserved transesterification unit (N-terminal toroid structure) for cutting and rejoining of a ssDNA strand can be combined with two different types of C-terminal ssDNA binding domains to form diverse bacterial topoisomerase I enzymes that are highly efficient in their physiological role of preventing excess negative supercoiling in the genome.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

MLL1 is regulated by KSHV LANA and is important for virus latency

Abstract Mixed lineage leukemia 1 (MLL1) is a histone methyltransferase. Kaposi's sarcoma-associated herpesvirus (KSHV) is a leading cause of malignancy in AIDS. KSHV latently infects tumor cells and its genome is decorated with epigenetic marks. Here, we show that KSHV latency-associated nuclear antigen (LANA) recruits MLL1 to viral DNA where it establishes H3K4me3 modifications at the extensive KSHV terminal repeat elements during primary infection. LANA interacts with MLL1 complex members, including WDR5, integrates into the MLL1 complex, and regulates MLL1 activity. We describe the 1.5-Å crystal structure of N-terminal LANA peptide complexed with MLL1 complex member WDR5, which reveals a potential regulatory mechanism. Disruption of MLL1 expression rendered KSHV latency establishment highly deficient. This deficiency was rescued by MLL1 but not by catalytically inactive MLL1. Therefore, MLL1 is LANA regulable and exerts a central role in virus infection. These results suggest broad potential for MLL1 regulation, including by non-host factors.

Tan, Min↗
DOE OSTI2021

Structural basis of chromatin regulation by histone variant H2A.Z

Abstract The importance of histone variant H2A.Z in transcription regulation has been well established, yet its mechanism-of-action remains enigmatic. Conflicting evidence exists in support of both an activating and a repressive role of H2A.Z in transcription. Here we report cryo-electron microscopy (cryo-EM) structures of nucleosomes and chromatin fibers containing H2A.Z and those containing canonical H2A. The structures show that H2A.Z incorporation results in substantial structural changes in both nucleosome and chromatin fiber. While H2A.Z increases the mobility of DNA terminus in nucleosomes, it simultaneously enables nucleosome arrays to form a more regular and condensed chromatin fiber. We also demonstrated that H2A.Z’s ability to enhance nucleosomal DNA mobility is largely attributed to its characteristic shorter C-terminus. Our study provides the structural basis for H2A.Z-mediated chromatin regulation, showing that the increase flexibility of the DNA termini in H2A.Z nucleosomes is central to its dual-functions in chromatin regulation and in transcription.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Introducing the Bacterial and Viral Bioinformatics Resource Center (BV-BRC): a resource combining PATRIC, IRD and ViPR

The National Institute of Allergy and Infectious Diseases (NIAID) established the Bioinformatics Resource Center (BRC) program to assist researchers with analyzing the growing body of genome sequence and other omics-related data. In this report, we describe the merger of the PAThosystems Resource Integration Center (PATRIC), the Influenza Research Database (IRD) and the Virus Pathogen Database and Analysis Resource (ViPR) BRCs to form the Bacterial and Viral Bioinformatics Resource Center (BV-BRC) https://www.bv-brc.org/. The combined BV-BRC leverages the functionality of the bacterial and viral resources to provide a unified data model, enhanced web-based visualization and analysis tools, bioinformatics services, and a powerful suite of command line tools that benefit the bacterial and viral research communities.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

The interaction between transport-segment DNA and topoisomerase IA—crystal structure of MtbTOP1 in complex with both G- and T-segments

Abstract Each catalytic cycle of type IA topoisomerases has been proposed to comprise multistep reactions. The capture of the transport-segment DNA (T-segment) into the central cavity of the N-terminal toroidal structure is an important action, which is preceded by transient gate-segment (G-segment) cleavage and succeeded by G-segment religation for the relaxation of negatively supercoiled DNA and decatenation of DNA. The T-segment passage in and out of the central cavity requires significant domain–domain rearrangements, including the movement of D3 relative to D1 and D4 for the opening and closing of the gate towards the central cavity. Here we report a direct observation of the interaction of a duplex DNA in the central cavity of a type IA topoisomerase and its associated domain–domain conformational changes in a crystal structure of a Mycobacterium tuberculosis topoisomerase I complex that also has a bound G-segment. The duplex DNA within the central cavity illustrates the non-sequence-specific interplay between the T-segment DNA and the enzyme. The rich structural information revealed from the novel topoisomerase–DNA complex, in combination with targeted mutagenesis studies, provides new insights into the mechanism of the topoisomerase IA catalytic cycle.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Kaposi's sarcoma herpesvirus exploits the DNA damage response to circularize its genome

Abstract To establish lifelong, latent infection, herpesviruses circularize their linear, double-stranded, DNA genomes through an unknown mechanism. Kaposi's sarcoma (KS) herpesvirus (KSHV), a gamma herpesvirus, is tightly linked with KS, primary effusion lymphoma, and multicentric Castleman's disease. KSHV persists in latently infected cells as a multi-copy, extrachromosomal episome. Here, we show the KSHV genome rapidly circularizes following infection, and viral protein expression is unnecessary for this process. The DNA damage response (DDR) kinases, ATM and DNA-PKcs, each exert roles, and absence of both severely compromises circularization and latency. These deficiencies were rescued by expression of ATM and DNA-PKcs, but not catalytically inactive mutants. In contrast, γH2AX did not function in KSHV circularization. The linear viral genomic ends resemble a DNA double strand break, and non-homologous DNA end joining (NHEJ) and homologous recombination (HR) reporters indicate both NHEJ and HR contribute to KSHV circularization. Last, we show, similar to KSHV, ATM and DNA-PKcs have roles in circularization of the alpha herpesvirus, herpes simplex virus-1 (HSV-1), while γH2AX does not. Therefore, the DDR mediates KSHV and HSV-1 circularization. This strategy may serve as a general herpesvirus mechanism to initiate latency, and its disruption may provide new opportunities for prevention of herpesvirus disease.

Li, Shijun↗
DOE OSTI2024

CRISPR-COPIES: an in silico platform for discovery of neutral integration sites for CRISPR/Cas-facilitated gene integration

Abstract The CRISPR/Cas system has emerged as a powerful tool for genome editing in metabolic engineering and human gene therapy. However, locating the optimal site on the chromosome to integrate heterologous genes using the CRISPR/Cas system remains an open question. Selecting a suitable site for gene integration involves considering multiple complex criteria, including factors related to CRISPR/Cas-mediated integration, genetic stability, and gene expression. Consequently, identifying such sites on specific or different chromosomal locations typically requires extensive characterization efforts. To address these challenges, we have developed CRISPR-COPIES, a COmputational Pipeline for the Identification of CRISPR/Cas-facilitated intEgration Sites. This tool leverages ScaNN, a state-of-the-art model on the embedding-based nearest neighbor search for fast and accurate off-target search, and can identify genome-wide intergenic sites for most bacterial and fungal genomes within minutes. As a proof of concept, we utilized CRISPR-COPIES to characterize neutral integration sites in three diverse species: Saccharomyces cerevisiae, Cupriavidus necator, and HEK293T cells. In addition, we developed a user-friendly web interface for CRISPR-COPIES (https://biofoundry.web.illinois.edu/copies/). We anticipate that CRISPR-COPIES will serve as a valuable tool for targeted DNA integration and aid in the characterization of synthetic biology toolkits, enable rapid strain construction to produce valuable biochemicals, and support human gene and cell therapy applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Unveiling the microbial realm with VEBA 2.0: a modular bioinformatics suite for end-to-end genome-resolved prokaryotic, (micro)eukaryotic and viral multi-omics from either short- or long-read sequencing

Abstract The microbiome is a complex community of microorganisms, encompassing prokaryotic (bacterial and archaeal), eukaryotic, and viral entities. This microbial ensemble plays a pivotal role in influencing the health and productivity of diverse ecosystems while shaping the web of life. However, many software suites developed to study microbiomes analyze only the prokaryotic community and provide limited to no support for viruses and microeukaryotes. Previously, we introduced the Viral Eukaryotic Bacterial Archaeal (VEBA) open-source software suite to address this critical gap in microbiome research by extending genome-resolved analysis beyond prokaryotes to encompass the understudied realms of eukaryotes and viruses. Here we present VEBA 2.0 with key updates including a comprehensive clustered microeukaryotic protein database, rapid genome/protein-level clustering, bioprospecting, non-coding/organelle gene modeling, genome-resolved taxonomic/pathway profiling, long-read support, and containerization. We demonstrate VEBA’s versatile application through the analysis of diverse case studies including marine water, Siberian permafrost, and white-tailed deer lung tissues with the latter showcasing how to identify integrated viruses. VEBA represents a crucial advancement in microbiome research, offering a powerful and accessible software suite that bridges the gap between genomics and biotechnological solutions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

An unexpected hydratase synthesizes the green light-absorbing pigment fucoxanthin

Abstract The ketocarotenoid fucoxanthin and its derivatives can absorb blue–green light enriched in marine environments. Fucoxanthin is widely adopted by phytoplankton species as a main light-harvesting pigment, in contrast to land plants that primarily employ chlorophylls. Despite its supreme abundance in the oceans, the last steps of fucoxanthin biosynthesis have remained elusive. Here, we identified the carotenoid isomerase-like protein CRTISO5 as the diatom fucoxanthin synthase that is related to the carotenoid cis–trans isomerase CRTISO from land plants but harbors unexpected enzymatic activity. A crtiso5 knockout mutant in the model diatom Phaeodactylum tricornutum completely lacked fucoxanthin and accumulated the acetylenic carotenoid phaneroxanthin. Recombinant CRTISO5 converted phaneroxanthin into fucoxanthin in vitro by hydrating its carbon–carbon triple bond, instead of functioning as an isomerase. Molecular docking and mutational analyses revealed residues essential for this activity. Furthermore, a photophysiological characterization of the crtiso5 mutant revealed a major structural and functional role of fucoxanthin in photosynthetic pigment–protein complexes of diatoms. As CRTISO5 hydrates an internal alkyne physiologically, the enzyme has unique potential for biocatalytic applications. The discovery of CRTISO5 illustrates how neofunctionalization leads to major diversification events in evolution of photosynthetic mechanisms and the prominent brown coloration of most marine photosynthetic eukaryotes.

Biochemistry & Molecular Biology↗
DOE OSTI2026

Exploration of Neutron-Rich Isotopes around N = 50 via the In-Flight Fission of a 345 MeV/Nucleon 238 U Beam

A search for new neutron-rich isotopes beyond $Z=28$ and $N=50$ was performed using a 345 MeV/nucleon $^{238}$U beam at RI Beam Factory in RIKEN Nishina Center. The BigRIPS separator and state-of-the-art radiation detectors were used to efficiently separate and identify the produced nuclei. For the first time, we have observed and determined the production cross sections for eight neutron-rich isotopes $^{72}$Cr, $^{74,75}$Mn, $^{77}$Fe, $^{79,80}$Co, $^{85}$Cu, and $^{90}$Ga. This study broadens our understanding of nuclear existence and paves the way for investigating the properties of neutron-rich medium-mass nuclei.

Shimizu, Yohei [RIKEN, Saitama (Japan); et al.]↗
DOE OSTI2022

Optimizing the Internal Cell Structure of the Radon Monitor Based on Electrostatic Collection Method

Abstract As Rn-222 decays, an alpha particle is emitted and the residual polonium nucleus recoils in the opposite direction. At the end of the recoil path, 88% of the polonium atoms have a positive charge and 12% are neutral. The electric potential distribution in the 60 ml hemispherical internal cell of the radon monitor based on electrostatic collection is studied for reducing the combined probability of the positively charged Po-218 and the OH− produced by the ionization of water vapour in the air. The COMSOL software is used to simulate the electric potential distribution in the internal cell of the radon monitor based on the electrostatic collection method at 27°C, a pressure of 0.1 Mpa. For improving the collection efficiency of Po-218 ions, the average collection time along vertical and oblique lines is calculated when the upper surface of the internal cell is plastic, uncharged metal and charged metal, respectively. Assuming that the gas in the internal cell is uniformly distributed, the results show that if the upper surface of the hemispherical internal cell is plastic or uncharged metal, the electric potential formed in the internal cell is more uniform, and it is beneficial to reduce the total collection time of the positively charged Po-218 ions, thereby improving collection efficiency. The simulation results can be used as an effective reference for optimizing the design of the internal cell structure of the radon monitor based on electrostatic collection method.

Fan, Zhongkai (ORCID:0000000181247459)↗
DOE OSTI2021

Pandemic drugs at pandemic speed: infrastructure for accelerating COVID-19 drug discovery with hybrid machine learning- and physics-based simulations on high-performance computers

The race to meet the challenges of the global pandemic has served as a reminder that the existing drug discovery process is expensive, inefficient and slow. There is a major bottleneck screening the vast number of potential small molecules to shortlist lead compounds for antiviral drug development. New opportunities to accelerate drug discovery lie at the interface between machine learning methods, in this case, developed for linear accelerators, and physics-based methods. The two in silico methods, each have their own advantages and limitations which, interestingly, complement each other. Here, we present an innovative infrastructural development that combines both approaches to accelerate drug discovery. The scale of the potential resulting workflow is such that it is dependent on supercomputing to achieve extremely high throughput. We have demonstrated the viability of this workflow for the study of inhibitors for four COVID-19 target proteins and our ability to perform the required large-scale calculations to identify lead antiviral compounds through repurposing on a variety of supercomputers.

97 MATHEMATICS AND COMPUTING↗