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At least 343 records · Page 19
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Range wide genetic differentiation in the bull kelp Nereocystis luetkeana with a seascape genetic focus on the Salish Sea

Introduction: In temperate regions, one of the most critical determinants of present range-wide genetic diversity was the Pleistocene climate oscillations, the most recent one created by the last glacial maximum (LGM). This study aimed to describe N. luetkeana genetic structure across its entire range (Alaska to California) and test different models of population connectivity within the Salish Sea. This region was colonized after the LGM and has been under increased disturbance in recent decades. Methods: We utilized microsatellite markers to study N. luetkeana genetic diversity at 53 sites across its range. Using higher sampling density in the Salish Sea, we employed a seascape genetics approach and tested isolation by hydrodynamic transport and environment models. Results: At the species distribution scale, we found four main groups of genetic co-ancestry, Alaska; Washington with Vancouver Island’s outer coast and Juan de Fuca Strait; Washington’s inner Salish Sea; and Oregon with California. The highest allelic richness (AR) levels were found in California, near the trailing range edge, although AR was also high in Alaska. The inner Salish Sea region had the poorest diversity across the species distribution. Nevertheless, a pattern of isolation by hydrodynamic transport and environment was supported in this region. Discussion: The levels of allelic, private allele richness and genetic differentiation suggest that during the LGM, bull kelp had both northern and southern glacial refugia in the Prince of Wales Island-Haida Gwaii region and Central California, respectively. Genetic diversity in Northern California sites seems resilient to recent disturbances, whereas the low levels of genetic diversity in the inner Salish Sea are concerning.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Genome-Wide Transcription Factor DNA Binding Sites and Gene Regulatory Networks in Clostridium thermocellum

Clostridium thermocellum is a thermophilic bacterium recognized for its natural ability to effectively deconstruct cellulosic biomass. While there is a large body of studies on the genetic engineering of this bacterium and its physiology to-date, there is limited knowledge in the transcriptional regulation in this organism and thermophilic bacteria in general. The study herein is the first report of a large-scale application of DNA-affinity purification sequencing (DAP-seq) to transcription factors (TFs) from a bacterium. We applied DAP-seq to > 90 TFs in C. thermocellum and detected genome-wide binding sites for 11 of them. We then compiled and aligned DNA binding sequences from these TFs to deduce the primary DNA-binding sequence motifs for each TF. These binding motifs are further validated with electrophoretic mobility shift assay (EMSA) and are used to identify individual TFs’ regulatory targets in C. thermocellum . Our results led to the discovery of novel, uncharacterized TFs as well as homologues of previously studied TFs including RexA-, LexA-, and LacI-type TFs. We then used these data to reconstruct gene regulatory networks for the 11 TFs individually, which resulted in a global network encompassing the TFs with some interconnections. As gene regulation governs and constrains how bacteria behave, our findings shed light on the roles of TFs delineated by their regulons, and potentially provides a means to enable rational, advanced genetic engineering of C. thermocellum and other organisms alike toward a desired phenotype.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

In-vivo neuronal dysfunction by Aβ and tau overlaps with brain-wide inflammatory mechanisms in Alzheimer’s disease

The molecular mechanisms underlying neuronal dysfunction in Alzheimer’s disease (AD) remain uncharacterized. Here, we identify genes, molecular pathways and cellular components associated with whole-brain dysregulation caused by amyloid-beta (Aβ) and tau deposits in the living human brain. We obtained in-vivo resting-state functional MRI (rs-fMRI), Aβ- and tau-PET for 47 cognitively unimpaired and 16 AD participants from the Translational Biomarkers in Aging and Dementia cohort. Adverse neuronal activity impacts by Aβ and tau were quantified with personalized dynamical models by fitting pathology-mediated computational signals to the participant’s real rs-fMRIs. Then, we detected robust brain-wide associations between the spatial profiles of Aβ-tau impacts and gene expression in the neurotypical transcriptome (Allen Human Brain Atlas). Within the obtained distinctive signature of in-vivo neuronal dysfunction, several genes have prominent roles in microglial activation and in interactions with Aβ and tau. Moreover, cellular vulnerability estimations revealed strong association of microglial expression patterns with Aβ and tau’s synergistic impact on neuronal activity (q < 0.001). These results further support the central role of the immune system and neuroinflammatory pathways in AD pathogenesis. Neuronal dysregulation by AD pathologies also associated with neurotypical synaptic and developmental processes. In addition, we identified drug candidates from the vast LINCS library to halt or reduce the observed Aβ-tau effects on neuronal activity. Top-ranked pharmacological interventions target inflammatory, cancer and cardiovascular pathways, including specific medications undergoing clinical evaluation in AD. Our findings, based on the examination of molecular-pathological-functional interactions in humans, may accelerate the process of bringing effective therapies into clinical practice.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Elemental profiling and genome-wide association studies reveal genomic variants modulating ionomic composition in Populus trichocarpa leaves

The ionome represents elemental composition in plant tissues and can be an indicator of nutrient status as well as overall plant performance. Thus, identifying genetic determinants governing elemental uptake and storage is an important goal for breeding and engineering biomass feedstocks with improved performance. In this study, we coupled high-throughput ionome characterization of leaf tissues with high-resolution genome-wide association studies (GWAS) to uncover genetic loci that modulate ionomic composition in leaves of poplar ( Populus trichocarpa ). Significant agreement was observed across the three ionomic profiling platforms tested: inductively coupled plasma-mass spectrometry (ICP-MS), neutron activation analysis (NAA) and laser-induced breakdown spectroscopy (LIBS). Relative quantification of 20 elements using ICP-MS across a population of 584 genotypes, revealed larger variation in micro-nutrients and trace elements content than for macro-nutrients across genotypes. The GWAS performed using a set of high-density (>8.2 million) single nucleotide polymorphisms, identified over 600 loci significantly associated with variations in these mineral elements, pointing to numerous uncharacterized candidate genes. A significant enrichment for genes related to ion homeostasis and transport was observed, including several members of the cation-proton antiporters (CPA) family and MATE efflux transporters, previously reported to be critical for plant growth and fitness in other species. Our results also included a polymorphic copy of the high-affinity molybdenum transporter MOT1 found directly associated to molybdenum content. For the first time in a perennial plant, our results provide evidence of genetic control of mineral content in a model tree species.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

A Free-floating or Wide-orbit Planet in the Microlensing Event OGLE-2019-BLG-0551

High-cadence observations of the Galactic bulge by the microlensing surveys led to the discovery of a handful of extremely short-timescale microlensing events that can be attributed to free-floating or wide-orbit planets. Here, we report the discovery of another strong free-floating planet candidate, which was found from the analysis of the gravitational microlensing event OGLE-2019-BLG-0551. The light curve of the event is characterized by a very short duration (≲3 days) and a very small amplitude (≲0.1 mag). From modeling of the light curve, we find that the Einstein timescale, t{sub E}=0.381±0.017 day, is much shorter, and the angular Einstein radius, θ{sub E}=4.35±0.34 μas, is much smaller than those of typical lensing events produced by stellar-mass lenses (t{sub E}∼20 days, θ{sub E}∼0.3 mas), indicating that the lens is very likely to be a planetary-mass object. We conduct an extensive search for possible signatures of a companion star in the light curve of the event, finding no significant evidence for the putative host star. For the first time, we also demonstrate that the angular Einstein radius of the lens does not depend on blending in the low-magnification events with strong finite source effects.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

A Wide and Deep Exploration of Radio Galaxies with Subaru HSC (WERGS). III. Discovery of a z = 4.72 Radio Galaxy with the Lyman Break Technique

We report a discovery of a z = 4.72 radio galaxy, HSC J083913.17+011308.1, using the Lyman break technique with the Hyper Suprime-Cam Subaru Strategic Survey (HSC-SSP) catalog for Very Large Array Faint Images of the Radio Sky at Twenty centimeter radio sources. The number of known high-z radio galaxies (HzRGs) at z > 3 is quite small to constrain the evolution of HzRGs so far. The deep and wide-area optical survey by HSC-SSP enables us to apply the Lyman break technique to a large search for HzRGs. For an HzRG candidate among pre-selected r-band dropouts with a radio detection, a follow-up optical spectroscopy with the Gemini Multi-Object Spectrographs (GMOS)/Gemini has been performed. The obtained spectrum presents a clear Lyα emission line redshifted to z = 4.72. The spectral energy distribution fitting analysis with the rest-frame UV and optical photometries suggests the massive nature of this HzRG with logM{sub ∗}/M{sub ⊙}=11.4. The small equivalent width of Lyα and the moderately red UV colors indicate its dusty host galaxy, implying a chemically evolved and dusty system. The radio spectral index does not meet a criterion for an ultra-steep spectrum, α{sub 1400}{sup 325} of −1.1 and α{sub 1400}{sup 150} of −0.9, demonstrating that the HSC-SSP survey compensates for a subpopulation of HzRGs that are missed in surveys focusing on an ultra-steep spectral index.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

Two-epoch Orbit Estimation for Wide Binaries Resolved in Hipparcos and Gaia

The Hipparcos catalog and its Double and Multiple System Annex (DMSA) lists 4099 components with individual proper motions and coordinates on the epoch 1991.25. Many of these long-period binary stars are also present in Gaia Data Release 2 (DR2). Using the available relative positions and proper motions separated by 24.25 yr, the equations of relative orbital motion can be solved for the two epoch eccentric anomalies, orbital period, and eccentricity. This method employs elimination of the linear Thiele–Innes unknowns and nonlinear optimization of the remaining condition equations. The quality of these solutions is compromised by the insufficient condition and modest precision of the Hipparcos astrometric data, as revealed by Monte Carlo simulations with artificially perturbed data points. The presence of multiple systems and optical pairs can also perturb the results. Limited experiments with artificial data indicate that useful estimates can be obtained with a 25 yr epoch difference for wide binaries with orbital periods up to ~500 yr. The prospects of this method dramatically improve with the proposed next-generation space astrometry missions such as Gaia-NIR and Theia, especially when additional conditions are included from astrometric or spectroscopic measurements. An ancillary catalog of cross-identification and astrometric information for 1295 double-star pairs cross-matched in Gaia DR2 and Hipparcos is also published.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

Statistics of Wide Pre-main-sequence Binaries in the Orion OB1 Association

Statistics of low-mass pre-main-sequence binaries in the Orion OB1 association with separations ranging from 0."6 to 20" (220 to 7400 au at 370 pc) are studied using images from the VISTA Orion mini survey and astrometry from Gaia. The input sample based on the CVSO catalog contains 1137 stars of K and M spectral types (masses between 0.3 and 0.9 M ⊙ ), 1021 of which are considered to be association members. There are 135 physical binary companions to these stars with mass ratios above ~0.13. The average companion fraction is 0.09 ± 0.01 over 1.2 decades in separation, slightly less than, but still consistent with, the field. We found a difference between the Ori OB1a and OB1b groups, the latter being richer in binaries by a factor of 1.6 ± 0.3. No overall dependence of the wide-binary frequency on the observed underlying stellar density is found, although in the Ori OB1a off-cloud population, these binaries seem to avoid dense clusters. The multiplicity rates in Ori OB1 and in sparse regions like Taurus differ significantly, hinting that binaries in the field may originate from a mixture of diverse populations.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Host Star Metallicity of Directly Imaged Wide-orbit Planets: Implications for Planet Formation

Directly imaged planets (DIPs) are self-luminous companions of pre-main-sequence and young main-sequence stars. They reside in wider orbits (∼tens to thousands of astronomical units) and generally are more massive compared to the close-in (≲10 au) planets. Determining the host star properties of these outstretched planetary systems is important to understand and discern various planet formation and evolution scenarios. We present the stellar parameters and metallicity ([Fe/H]) for a subsample of 18 stars known to host planets discovered by the direct imaging technique. We retrieved the high-resolution spectra for these stars from public archives and used the synthetic spectral fitting technique and Bayesian analysis to determine the stellar properties in a uniform and consistent way. For eight sources, the metallicities are reported for the first time, while the results are consistent with the previous estimates for the other sources. Our analysis shows that metallicities of stars hosting DIPs are close to solar with a mean [Fe/H] = −0.04 ± 0.27 dex. The large scatter in metallicity suggests that a metal-rich environment may not be necessary to form massive planets at large orbital distances. We also find that the planet mass–host star metallicity relation for the directly imaged massive planets in wide orbits is very similar to that found for the well-studied population of short-period (≲1 yr) super-Jupiters and brown dwarfs around main-sequence stars.

36 MATERIALS SCIENCE↗
DOE OSTI2021

A New Method for Aerosol Measurement Using Wide-field Photometry

We present a new method to measure the vertical aerosol optical depth (VAOD) during clear nights using a wide-field imager—a CCD camera with a photographic lens on an equatorial mount. A series of 30 s exposures taken at different altitudes above the horizon can be used to measure the VAOD with a precision better than 0.008 optical depths within a few minutes. Such a measurement does not produce any light and is thus suitable for use at sites where other astronomical instruments are located. The precision of the VAOD measurement depends on the laboratory calibration of spectral properties of the system and of the response of the camera electronics to varying illumination levels, as well as careful considerations of the details of stellar photometry and modeling of the dependence of the measured stellar flux, the star color, and the position within the field of view. The results obtained with robotic setups at the future sites of the Cerenkov Telescope Array show good internal consistency and agreement with simultaneous measurements from a Sun/Moon photometer located at the same sites.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2023

A Wide View of the Galactic Globular Cluster NGC 2808: Red Giant and Horizontal Branch Star Spatial Distributions

Wide-field and deep DECam multiband photometry, combined with HST data for the core of the Galactic globular cluster NGC 2808, allowed us to study the distribution of various stellar subpopulations and stars in different evolutionary phases out to the cluster tidal radius. We used the C ugi = (u - g) - (g - i) index to identify three chemically distinct subpopulations along the red giant branch and compared their spatial distributions. The most light-element-enriched subpopulation (P3) is more centrally concentrated; however, it shows a more extended distribution in the external regions of the cluster compared to the primordial (P1) and intermediate (P2) composition populations. Furthermore, the P3 subpopulation centroid is off-center relative to those of the P1 and P2 groups. We also analyzed the spatial distribution of horizontal branch stars and found that the relative fraction of red horizontal branch stars increases for radial distances larger than ≈1$^{'}_{.}$5, while that of the blue and hotter stars decreases. These new observations, combined with literature spectroscopic measurements, suggest that the red horizontal branch stars are the progeny of all the stellar subpopulations in NGC 2808, i.e., primordial and light-element enhanced, while the blue stars are possibly the result of a combination of the "hot-flasher" and the "helium-enhanced" scenarios. A similar distribution of different red giant branch subpopulations and horizontal branch stars was also found for the most massive Galactic globular cluster, ω Cen, based on combined DECam and HST data, which suggests that the two may share a similar origin.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Wide Dust Gaps in Protoplanetary Disks Induced by Eccentric Planets: A Mass-eccentricity Degeneracy

The tidal perturbation of embedded protoplanets on their natal disks has been widely attributed to be the cause of gap-ring structures in submillimeter images of protoplanetary disks around T Tauri stars. Numerical simulations of this process have been used to propose scaling of characteristic dust-gap width/gap-ring distance with respect to planet mass. Applying such scaling to analyze observed gap samples yields a continuous mass distribution for a rich population of hypothetical planets in the range of several Earth to Jupiter masses. In contrast, the conventional core-accretion scenario of planet formation predicts a bimodal mass function due to (1) the onset of runaway gas accretion above ~20 Earth masses and (2) suppression of accretion induced by gap opening. Here, we examine the dust disk response to the tidal perturbation of eccentric planets as a possible resolution of this paradox. Based on simulated gas and dust distributions, we show the gap-ring separation of Neptune-mass planets with small eccentricities might become comparable to that induced by Saturn-mass planets on circular orbits. Furthermore, this degeneracy may obliterate the discrepancy between the theoretical bimodal mass distribution and the observed continuous gap width distribution. Despite damping due to planet–disk interaction, modest eccentricity may be sustained either in the outer regions of relatively thick disks or through resonant excitation among multiple super Earths. Moreover, the ring-like dust distribution induced by planets with small eccentricities is axisymmetric even in low viscosity environments, consistent with the paucity of vortices in Atacama Large Millimeter/submillimeter Array images.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Kilonova Detectability with Wide-field Instruments

Abstract Kilonovae are ultraviolet, optical, and infrared transients powered by the radioactive decay of heavy elements following a neutron star merger. Joint observations of kilonovae and gravitational waves can offer key constraints on the source of Galactic r -process enrichment, among other astrophysical topics. However, robust constraints on heavy element production require rapid kilonova detection (within ∼1 day of merger) as well as multiwavelength observations across multiple epochs. In this study, we quantify the ability of 13 wide-field-of-view instruments to detect kilonovae, leveraging a large grid of over 900 radiative transfer simulations with 54 viewing angles per simulation. We consider both current and upcoming instruments, collectively spanning the full kilonova spectrum. The Roman Space Telescope has the highest redshift reach of any instrument in the study, observing kilonovae out to z ∼ 1 within the first day post-merger. We demonstrate that BlackGEM, DECam, GOTO, the Vera C. Rubin Observatory’s LSST, ULTRASAT, VISTA, and WINTER can observe some kilonovae out to z ∼ 0.1 (∼475 Mpc), while DDOTI, MeerLICHT, PRIME, Swift/UVOT, and ZTF are confined to more nearby observations. Furthermore, we provide a framework to infer kilonova ejecta properties following nondetections and explore variation in detectability with these ejecta parameters.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

The DECam MAGIC Survey: A Wide-field Photometric Metallicity Study of the Sculptor Dwarf Spheroidal Galaxy

The metallicity distribution function (MDF) and internal chemical variations of a galaxy are fundamental to understand its formation and assembly history. In this work, we analyze photometric metallicities for 3883 stars over 7 half-light radii (rh) in the Sculptor (Scl) dwarf spheroidal (dSph) galaxy, using new narrowband imaging data from the Mapping the Ancient Galaxy in CaHK (MAGIC) survey conducted with the Dark Energy Camera (DECam) at the 4 m Blanco Telescope. This work demonstrates the scientific potential of MAGIC using the Scl dSph galaxy, one of the most well-studied satellites of the Milky Way. Our sample ranges from [Fe/H] ≈ –4.0 to [Fe/H] ≈ –0.6, includes six new extremely metal-poor candidates ([Fe/H] ≤ –3.0), and is almost 3 times larger than the largest spectroscopic metallicity data set in the Scl dSph. Our spatially unbiased sample of metallicities provides a more accurate representation of the MDF, revealing a more metal-rich peak than observed in the most recent spectroscopic sample. It also reveals a break in the metallicity gradient, with a strong change in the slope: from −3.26 ± 0.18 dex deg −1 for stars inside ∼1 rh to −0.55 ± 0.26 dex deg −1 for the outer part of the Scl dSph. Our study demonstrates that combining photometric metallicity analysis with the wide field of view of DECam offers an efficient and unbiased approach for studying the stellar populations of dwarf galaxies in the Local Group.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

Selection of high-redshift Lyman-Break Galaxies from broadband and wide photometric surveys

In this paper, we investigate the possibility of selecting high-redshift Lyman-Break Galaxies (LBG) using current and future broadband wide photometric surveys, such as the Ultraviolet Near Infrared Optical Northern Survey (UNIONS) or the Vera C. Rubin Legacy Survey of Space and Time (LSST), using a Random Forest algorithm. This work is conducted in the context of future large-scale structure spectroscopic surveys like DESI-II, the next phase of the Dark Energy Spectroscopic Instrument (DESI), which will start around 2029.We use deep imaging data from the Hyper Suprime Camera (HSC) and the Canada-France-Hawaii Telescope Large Area U-band Deep Survey (CLAUDS) on the COSMOS and XMM-LSS fields. To predict the selection performance of LBGs with image quality similar to UNIONS, we degrade the u,g,r,i and z bands to UNIONS depth.The Random Forest algorithm is trained with the u,g,r,i and z bands to classify LBGs in the 2.5 < z < 3.5 range.We find that fixing a target density budget of 1,100 deg$^{-2}$, the Random Forest approach gives a density of z > 2 targets of 873 deg$^{-2}$, and a density of 493 deg$^{-2}$ of confirmed LBGs after spectroscopic confirmation with DESI. This UNIONS-like selection was tested in a dedicated spectroscopic observation campaign of 1,000 targets with DESI on the COSMOS field, providing a safe spectroscopic sample with a mean redshift of 3. This sample is used to derive forecasts for DESI-II, assuming a sky coverage of 5,000 deg$^{2}$. We predict uncertainties on Alcock-Paczynski parameters α$_{⊥}$ and α$_{∥}$ to be 0.7% and 1% for 2.6 < z < 3.2, resulting in a potential 2% measurement of the dark energy fraction at high redshift. Additionally, we estimate the uncertainty in local non-Gaussianity and predict σ$_{fNL}$ ≈ 7, which would be comparable to the current best precision achieved by Planck. The latter forecast suggests that achieving the precision required to place stringent constraints on inflationary models (σ$_{fNL}$ ≈ 1) using spectroscopic galaxy surveys necessitates the development of a next-generation (Stage V) spectroscopic survey.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

Recorder trace files of 91 built-in tests from three widely-used I/O libraries (Dec 24, 2024)

This dataset contains the Recorder trace files of 91 built-in tests from three widely-used I/O libraries. It was utilized in our IPDPS'25 paper, "VerifyIO: Verifying Adherence to Parallel I/O Consistency Semantics". The dataset can be used to reproduce the results presented in the paper and to conduct additional analyses

Wang, Chen [Lawrence Livermore National Laboratory↗
DOE OSTI2021

Genome-wide Transcription Factor DNA Binding Sites and Gene Regulatory Networks in Clostridium thermocellum

Clostridium thermocellum is a thermophilic bacterium recognized for its natural ability to effectively deconstruct cellulosic biomass. While there is a large body of studies on the genetic engineering of this bacterium and its physiology to-date, there is limited knowledge in the transcriptional regulation in this organism and thermophilic bacteria in general. The study herein is the first report of a high-throughput application of DNA-affinity purification sequencing (DAP-seq) to transcription factors (TFs) from a thermophile. We applied DAP-seq to >90 TFs in C. thermocellum and detected genome-wide binding sites for 11 of them. We then compiled and aligned DNA binding sequences from these TFs to deduce the primary DNA-binding sequence motifs for each TF. These binding motifs are further validated with electrophoretic mobility shift assay (EMSA) and are used to identify individual TFs’ regulatory targets in C. thermocellum. Our results led to the discovery of novel, uncharacterized TFs as well as homologues of previously studied TFs including RexA-, LexA- and LacI-type TFs. We then used these data to reconstruct gene regulatory networks for the 11 TFs individually, which resulted in a global network encompassing the TFs with some interconnections. As gene regulation governs and constrains how bacteria behave, our findings shed light on the roles of TFs delineated by their regulons, and potentially provides a means to enable rational, advanced genetic engineering of C. thermocellum and other organisms alike towards a desired phenotype.

09 BIOMASS FUELS↗