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At least 667 records · Page 37
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Isotope analysis reveals dietary overlap among sympatric canids

Abstract When colonizing new regions, invading species might compete strongly with phylogenetically related species native to the regions they are colonizing, eventually leading to coexistence or displacement. In the southeast of the United States, recently established coyotes (Canis latrans) compete with red fox (Vulpes vulpes) and gray fox (Urocyon cinereoargenteus), although it remains unclear if competition is leading to resource partitioning or displacement by species. Using nitrogen and carbon stable isotopes, we tested the hypothesis that coyotes compete with foxes for food resources, with canids partitioning those resources to mitigate competition. We compared diets of canids in the southeast to those in the Plains region of the United States, a region where all three species historically have coexisted. We analyzed 217 hair samples from both regions pre-1960, prior to coyote colonization of the southeast, and post-2000, after coyotes were ubiquitous there, to assess differences in diet among species for both regions (southeast versus Plains and time periods, pre- versus postcolonization by coyotes). Modeling revealed significant dietary overlap among historical and contemporary populations in the southeast. Historically, all species partitioned resources in the Plains. Contemporarily, red fox and coyotes co-occurring in the Plains overlapped in diet; however, gray fox diet did not overlap with those of red fox and coyotes. Absence of partitioning in diet among co-occurring canids in the southeast indicates that interspecific competition could be strong in the region. Competition among canid populations in the southeast could lead to further resource partitioning among species that promotes coexistence or competitive exclusion of smaller fox species where coyote populations are abundant.

Zoology↗
DOE OSTI2023

Constraining properties of asymmetric dark matter candidates from gravitational-wave observations

The accumulation of certain types of dark matter particles in neutron star cores due to accretion over long timescales can lead to the formation of a mini black hole. In this scenario, the neutron star is destabilized and implodes to form a black hole without significantly increasing its mass. When this process occurs in neutron stars in coalescing binaries, one or both stars might be converted to a black hole before they merge. Thus, in the mass range of ~1–2M ⊙ , the Universe might contain three distinct populations of compact binaries: one containing only neutron stars, the second population of only black holes, and a third, mixed population consisting of a neutron star and a black hole. However, it is unlikely to have a mixed population as the various timescales allow for both neutron stars to remain or collapse within a short timescale. In this paper, we explore the capability of future gravitational-wave detector networks, including upgrades of Advanced LIGO and Virgo, and new facilities such as the Cosmic Explorer and Einstein Telescope (XG network), to discriminate between different populations by measuring the effective tidal deformability of the binary, which is zero for binary black holes but nonzero for binary neutron stars. Furthermore, we show that observing the relative abundances of the different populations can be used to infer the timescale for neutron stars to implode into black holes, and in turn, provide constraints on the particle nature of dark matter. Furthermore, the XG network will infer the implosion timescale to within an accuracy of 0.01 Gyr at 90% credible interval and determine the dark matter mass and interaction cross section to within a factor of 2 GeV and 10 cm –2 , respectively.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2020

Relative reproductive phenology and synchrony affect neonate survival in a nonprecocial ungulate

Abstract Degree of reproductive synchronization in prey is hypothesized as a predator defense strategy reducing prey risk via predator satiation or predator avoidance. Species with precocial young, especially those exposed to specialist predators, should be highly synchronous to satiate predators (predator satiation hypothesis), while prey with nonprecocial (i.e. altricial) young, especially those exposed to generalist predators, should become relatively asynchronous to avoid predator detection (predator avoidance hypothesis). The white‐tailed deer Odocoileus virginianus in North America is an example of a nonprecocial ungulate that uses the hider strategy early in life; its primary predator (coyote; Canis latrans ) is a generalist, making white‐tailed deer a good model species to test the predator avoidance hypothesis. We used birth dates and known fates of white‐tailed deer neonates ( n = 1,032) across nine study sites varying in relative synchrony and predator assemblages to test the predator avoidance hypothesis. We predicted that relative birthing asynchrony of the population would increase relative survival at the population level; therefore, at the individual scale, neonate birth date nearer to mean birthing date in a respective population would not influence individual survival. Coyotes were responsible for the majority of predation events, and survival of those neonates increased the closer the individual was born to peak birthing season in each respective population. Also, at the population level, reproductive asynchronization negatively affected survival. Contrary to the predator avoidance hypothesis, our data indicate patterns in neonate survival for white‐tailed deer better support the predator satiation hypothesis at the individual and population level. Additionally, coyotes may present a selective force great enough to shift reproductive synchrony such that predator satiation may become a feasible defense strategy for neonates at local spatial scales. Our results indicate that synchronizing reproduction may still be the most effective strategy to reduce individual predation risk from generalist predators, particularly when the window of heightened resource availability to the prey is narrow. A free Plain Language Summary can be found within the Supporting Information of this article.

Michel, Eric S.↗
DOE OSTI2024

Body size and early marine conditions drive changes in Chinook salmon productivity across northern latitude ecosystems

Disentangling the influences of climate change from other stressors affecting the population dynamics of aquatic species is particularly pressing for northern latitude ecosystems, where climate‐driven warming is occurring faster than the global average. Chinook salmon (Oncorhynchus tshawytscha) in the Yukon‐Kuskokwim (YK) region occupy the northern extent of their species' range and are experiencing prolonged declines in abundance resulting in fisheries closures and impacts to the well‐being of Indigenous people and local communities. These declines have been associated with physical (e.g., temperature, streamflow) and biological (e.g., body size, competition) conditions, but uncertainty remains about the relative influence of these drivers on productivity across populations and how salmon–environment relationships vary across watersheds. To fill these knowledge gaps, we estimated the effects of marine and freshwater environmental indicators, body size, and indices of competition, on the productivity (adult returns‐per‐spawner) of 26 Chinook salmon populations in the YK region using a Bayesian hierarchical stock‐recruitment model. Across most populations, productivity declined with smaller spawner body size and sea surface temperatures that were colder in the winter and warmer in the summer during the first year at sea. Decreased productivity was also associated with above average fall maximum daily streamflow, increased sea ice cover prior to juvenile outmigration, and abundance of marine competitors, but the strength of these effects varied among populations. Maximum daily stream temperature during spawning migration had a nonlinear relationship with productivity, with reduced productivity in years when temperatures exceeded thresholds in main stem rivers. These results demonstrate for the first time that well‐documented declines in body size of YK Chinook salmon were associated with declining population productivity, while taking climate into account.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Nonparallel transcriptional divergence during parallel adaptation

Abstract How underlying mechanisms bias evolution toward predictable outcomes remains an area of active debate. In this study, we leveraged phenotypic plasticity and parallel adaptation across independent lineages of Trinidadian guppies ( Poecilia reticulata ) to assess the predictability of gene expression evolution during parallel adaptation. Trinidadian guppies have repeatedly and independently adapted to high‐ and low‐predation environments in the wild. We combined this natural experiment with a laboratory breeding design to attribute transcriptional variation to the genetic influences of population of origin and developmental plasticity in response to rearing with or without predators. We observed substantial gene expression plasticity, as well as the evolution of expression plasticity itself, across populations. Genes exhibiting expression plasticity within populations were more likely to also differ in expression between populations, with the direction of population differences more likely to be opposite those of plasticity. While we found more overlap than expected by chance in genes differentially expressed between high‐ and low‐predation populations from distinct evolutionary lineages, the majority of differentially expressed genes were not shared between lineages. Our data suggest alternative transcriptional configurations associated with shared phenotypes, highlighting a role for transcriptional flexibility in the parallel phenotypic evolution of a species known for rapid adaptation.

Fischer, Eva K.↗
DOE OSTI2020

Conscientious vaccination exemptions in kindergarten to eighth-grade children across Texas schools from 2012 to 2018: A regression analysis

Background: As conscientious vaccination exemption (CVE) percentages rise across the United States, so does the risk and occurrence of outbreaks of vaccine-preventable diseases such as measles. In the state of Texas, the median CVE percentage across school systems more than doubled between 2012 and 2018. During this period, the proportion of schools surpassing a CVE percentage of 3% rose from 2% to 6% for public schools, 20% to 26% for private schools, and 17% to 22% for charter schools. The aim of this study was to investigate this phenomenon at a fine scale. Methods and findings: Here, we use beta regression models to study the socioeconomic and geographic drivers of CVE trends in Texas. Using annual counts of CVEs at the school system level from the 2012–2013 to the 2017–2018 school year, we identified county-level predictors of median CVE percentage among public, private, and charter schools, the proportion of schools below a high-risk threshold for vaccination coverage, and five-year trends in CVEs. Since the 2012–2013 school year, CVE percentages have increased in 41 out of 46 counties in the top 10 metropolitan areas of Texas. We find that 77.6% of the variation in CVE percentages across metropolitan counties is explained by median income, the proportion of the population that holds a bachelor's degree, the proportion of the population that self-reports as ethnically white, the proportion of the population that is English speaking, and the proportion of the population that is under the age of five years old. Across the 10 top metropolitan areas in Texas, counties vary considerably in the proportion of school systems reporting CVE percentages above 3%. Sixty-six percent of that variation is explained by the proportion of the population that holds a bachelor’s degree and the proportion of the population affiliated with a religious congregation. Three of the largest metropolitan areas—Austin, Dallas–Fort Worth, and Houston—are potential vaccination exemption "hotspots," with over 13% of local school systems above this risk threshold. The major limitations of this study are inconsistent school-system-level CVE reporting during the study period and a lack of geographic and socioeconomic data for individual private schools. Conclusions: In this study, we have identified high-risk communities that are typically obscured in county-level risk assessments and found that public schools, like private schools, are exhibiting predictable increases in vaccination exemption percentages. As public health agencies confront the reemerging threat of measles and other vaccine-preventable diseases, findings such as ours can guide targeted interventions and surveillance within schools, cities, counties, and sociodemographic subgroups.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Preliminary Design of a New Pulsed-Neutron Die--Away Experiments with Absorbers (IER-552 CED-1)

This report presents the preliminary design (CED-1) of IER-552, pulsed-neutron die-away (PNDA) experiments with absorbers, to be conducted by Lawrence Livermore National Laboratory (LLNL). The goal of the PNDA experiments with absorbing materials is to produce high-quality, low-cost integral benchmarks that can be used to validate cross sections that are high priority nuclear data for the Department of Energy’s Nuclear Criticality Safety Program (NCSP). PNDA experiments can be used to generate nuclear data validation benchmarks quickly and cheaply, as they do not require fissile material or a nuclear facility to conduct them. The original PNDA experiments were set up at LLNL under IER-501. Extending the PNDA experiments to include absorbing materials leverages existing facilities and resources at LLNL to validate cross sections, with a basic experiment design that uses a neutron generator to impinge a short, mono-energetic neutron pulse on a poisoned, moderating target sample. The neutron pulse lasts 100 µs, after which the neutron population in the sample reaches thermal equilibrium and later spatial equilibrium. In this fully equilibrized state, the neutron population has a characteristic decay-time eigenvalue. The eigenvalue can be used as an integral parameter to validate nuclear data involved with neutron scattering and absorption. Two observables can be measured: the neutron population and the population of secondary γ-rays produced by inelastic and capture reactions. This report explores the feasibility of both approaches. For γ-ray measurements, this allows for direct measurement of reactions of interest for validation. During the neutron burst time, inelastic (prompt) γ-rays dominate, and these data can be isolated for validation of neutron inelastic scattering data. After the pulse ends, neutron capture (delayed) γ-rays dominate and are produced by many reaction channels as neutrons slow down to thermal energies. Two sets of γ-ray spectra (inelastic, capture) can be produced for validation. Additionally, the time-dependent decay of the capture γ-ray population when the neutron population is thermalized and in its fundamental mode can be used for validation. Two experiments can be imagined where pulsed neutrons are used to validate the nuclear data of absorbing materials. The first integrates well into the existing PNDA testbed at LLNL. The absorber material would be introduced into a moderating target and the same neutron generator, neutron detectors, electronics, and shielding box used for IER-501 would be employed. From the same experimental setup, many absorbing materials can be validated by simply changing the neutron poison in the moderator. The only significant modification would be the introduction of a γ-ray detector. Such an experiment would primarily serve to validate nuclear data in the thermal energy range. The second kind of experiment would validate the fast and epithermal energy range. It would involve pulsing neutron into a bare assembly of the absorber material and measuring the die-away of neutrons. The fast leakage of such an assembly requires nanosecond neutron-generator pulse widths and fast detectors/electronics that could measure ~200 ns die-away curves. This kind of experiment would ideally be performed at a cyclotron, like that available at Lawrence Berkeley National Laboratory.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

The Critical Need for Innovations in Instruments and Techniques to Enable In-Situ Cold Ion and Cold Electron Measurements within the Magnetosphere

Relatively few studies have focused on the cold plasma populations of the magnetosphere due to difficulties associated with obtaining measurements. The cold particle populations are defined here as those with total energy approximately <100 eV which is an energy range for which measurements are difficult (regardless of species), but which often make up the bulk of the plasma density. These populations have known and suspected impacts on the structure and dynamics of the magnetosphere. Unfortunately, the lack of accurate measurements of the cold ion and cold electron populations through the magnetosphere makes closure of these science questions extremely difficult if not impossible. In a complex system of interconnected parts like the Earth’s magnetosphere, a lack of understanding of one part of the system (the cold electron and ion populations) is disabling. Hence, until cold electron and cold ion measurements are obtained robustly with every mission, the magnetospheric plasma environment cannot be completely understood. This will require innovations in plasma spectrometers and associated techniques required to obtain high-fidelity in-situ measurements of the cold ion and cold electron populations in the magnetosphere. This paper seeks to review the instruments and techniques that have been used to date and present possible options for future missions.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2023

Genetics and Genomics of Pathogen Resistance in Switchgrass (Final Report)

This project was funded by DOE under Grant no. DE-SC0016108. Originally approved for the 2016-2019 period, two no-cost extensions were solicited and approved, which prolonged the lifespan through July 2021. This final report informs on the results obtained so far from the research implemented. The research hinged on integrating genomics (genomic selection, RNAseq, virus-plant interactions) with classical genetics (conventional breeding) to incorporate durable resistance to fungal (rust) and viral (mosaic) diseases in switchgrass (Panicum virgatum) populations being bred for bioenergy. Higher biomass yield, higher quality (low lignin content), and durable disease resistance are key features to make lignocellulosic switchgrass feedstocks economically competitive and sustainable. Genomic selection is being applied on three generations of a switchgrass population derived from crossing two ecotypes (Kanlow as lowland female and Summer as upland male) with differential performance in terms of biomass yield and quality, disease resistance, and winter survivability. Target populations were screened for rust and mosaic in field and/or lab and phenotyped for biomass yield and quality traits. Genetic analyses were applied across generations to capture the joint inheritance of the targeted traits and predict breeding values for parents and progeny with greater accuracy. Parental and a panel of different switchgrass populations were genotyped with the DArTseq technology to develop SNP (0, 1, 2) and in-silico (presence/absence) DArT markers. Rust inoculations techniques were developed and applied successfully on switchgrass. The original populations (Kanlow and Summer) were sequenced with RNAseq to capture the gene expression profiles across sequential time-points and appraise the basis of greater resistance in the Kanlow vs the Summer ecotype. Constructs of PMV and sPMV mosaic virus were assembled and tested first on proso millet to find the best protocol to use later on switchgrass. Results from the preliminary analyses indicate that 1) ample additive genetic variation is available for selection and improving this inter-ecotypic population for yield, quality, and disease traits, 2) significant gains are to be expected with the genetic correlations being favorable between yield and lignin content and between yield and disease ratings, 3) substantial differences exist in the genetic regions controlling rust resistance in the two ecotypes, 4) co-infection with PMV isolates from Nebraska and its satellite from Kansas elicit severe mosaic symptoms, and 5) two different genetic systems are responsible for imparting resistance to rust and virus in switchgrass.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Microbiome Variation Across Two Hemlock Species With Hemlock Woolly Adelgid Infestation

The hemlock woolly adelgid ( Adelges tsugae , HWA), an invasive insect, is devastating native hemlock populations in eastern North America, and management outcomes have so far had limited success. While many plant microbiomes influence and even support plant immune responses to insect herbivory, relatively little is known about the hemlock microbiome and its interactions with pathogens or herbivores such as HWA. Using 16S rRNA and ITS gene amplicon sequencing, we characterized the needle, branch, root, and rhizosphere microbiome of two hemlock species, Tsuga canadensis and T. sieboldii , that displayed low and high levels of HWA populations. We found that both archaeal/bacterial and fungal needle communities, as well as the archaeal/bacterial branch and root communities, varied in composition in both hemlock species relative to HWA population levels. While host species and plant-associated habitats explained a greater proportion of the variance in the microbiome than did HWA population level, high HWA populations were associated with enrichment of 100 likely fungal pathogen sequence variants across the four plant-associated habitats (e.g., needle, branch, root, rhizosphere) compared to trees with lower HWA populations. This work contributes to a growing body of literature linking plant pathogens and pests with the changes in the associated plant microbiome and host health. Furthermore, this work demonstrates the need to further investigate plant microbiome effects across multiple plant tissues to understand their influences on host health.

16S rRNA↗
DOE OSTI2023

A review of instrument techniques to measure magnetospheric cold electrons and ions

A review of the instruments and techniques to directly measure the full distributions of the cold-ion and cold-electron populations in the magnetosphere is presented. Relatively few studies have focused on the cold plasma populations of the magnetosphere due to difficulties associated with obtaining measurements. The cold particle populations are defined here as those with total energy approximately <100 eV which is an energy range for which measurements are difficult (regardless of species), but which often make up the bulk of the plasma density. These populations have known and suspected impacts on the structure and dynamics of the magnetosphere but to date have not yet been measured adequately. The lack of accurate measurements cold ion and electron populations through the magnetosphere makes closure of these science questions extremely difficult if not impossible. Reaching closure will require innovations in plasma spectrometers and associated techniques required to obtain high-fidelity measurements of the cold ion and electron populations in the magnetosphere. This paper seeks to review the instruments and techniques that have been used to date and present possible options for future missions.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Utility of Physiologically Based Pharmacokinetic Modeling to Investigate the Impact of Physiological Changes of Pregnancy and Cancer on Oncology Drug Pharmacokinetics

The treatment of cancer during pregnancy remains challenging with knowledge gaps in drug dosage, safety, and efficacy due to the under-representation of this population in clinical trials. Our aim was to investigate physiological changes reported in both pregnancy and cancer populations into a PBPK modeling framework that allows for a more accurate estimation of PK changes in pregnant patients with cancer. Methods: Paclitaxel and docetaxel were selected to validate a population model using clinical data from pregnant patients with cancer. The validated population model was subsequently used to predict the PK of acalabrutinib in pregnant patients with cancer. Results: The Simcyp pregnancy population model reasonably predicted the PK of docetaxel in pregnant patients with cancer, while a modified model that included a 2.5-fold increase in CYP2C8 abundance, consistent with the increased expression during pregnancy, was needed to reasonably predict the PK of paclitaxel in pregnant patients with cancer. Changes in protein binding levels of patients with cancer had a minimal impact on the predicted clearance of paclitaxel and docetaxel. PBPK modeling predicted approximately 60% lower AUC and Cmax for acalabrutinib in pregnant versus non-pregnant patients with cancer. Conclusions: Our results suggest that PBPK modeling is a promising approach to investigate the effects of pregnancy and cancer on the PK of oncology drugs and potentially inform dosing for pregnant patients with cancer. Further evaluation and refinement of the population model are needed for pregnant patients with cancer with additional compounds and clinical PK data.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

A Search for L4 Earth Trojan Asteroids Using a Novel Track-before-detect Multiepoch Pipeline

We report Earth Trojan asteroids are an important but elusive population that co-orbit with Earth at the L4 and L5 Lagrange points. There is only one known, but a large population is theoretically stable and could provide insight into our solar system’s past and present, as well as planetary defense. In this paper, we present the results of an Earth Trojan survey that uses a novel shift-and-stack detection method on 2 nights of data from the Dark Energy Camera. We find no new Earth Trojan asteroids. We calculate an upper limit on the population that is consistent with previous searches despite much less sky coverage. Additionally, we elaborate on previous upper-limit calculations using current asteroid population statistics and an extensive asteroid simulation to provide the most up-to-date population constraints. We find an L4 Earth Trojan population of N ET < 1 for H = 13.93, N ET < 10 for H = 16, and N ET < 938 for H = 22.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

Disentangling the Black Hole Mass Spectrum with Photometric Microlensing Surveys

Abstract From the formation mechanisms of stars and compact objects to nuclear physics, modern astronomy frequently leverages surveys to understand populations of objects to answer fundamental questions. The population of dark and isolated compact objects in the Galaxy contains critical information related to many of these topics, but is only practically accessible via gravitational microlensing. However, photometric microlensing observables are degenerate for different types of lenses, and one can seldom classify an event as involving either a compact object or stellar lens on its own. To address this difficulty, we apply a Bayesian framework that treats lens type probabilistically and jointly with a lens population model. This method allows lens population characteristics to be inferred despite intrinsic uncertainty in the lens class of any single event. We investigate this method’s effectiveness on a simulated ground-based photometric survey in the context of characterizing a hypothetical population of primordial black holes (PBHs) with an average mass of 30 M ⊙ . On simulated data, our method outperforms current black hole (BH) lens identification pipelines and characterizes different subpopulations of lenses while jointly constraining the PBH contribution to dark matter to ≈25%. Key to robust inference, our method can marginalize over population model uncertainty. We find the lower mass cutoff for stellar origin BHs, a key observable in understanding the BH mass gap, particularly difficult to infer in our simulations. This work lays the foundation for cutting-edge PBH abundance constraints to be extracted from current photometric microlensing surveys.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

A Perspective on the Milky Way Bulge Bar as Seen from the Neutron-capture Elements Cerium and Neodymium with APOGEE

Abstract This study probes the chemical abundances of the neutron-capture elements cerium and neodymium in the inner Milky Way from an analysis of a sample of ∼2000 stars in the Galactic bulge bar spatially contained within ∣X Gal ∣ < 5 kpc, ∣Y Gal ∣ < 3.5 kpc, and ∣Z Gal ∣ < 1 kpc, and spanning metallicities between −2.0 ≲ [Fe/H] ≲ +0.5. We classify the sample stars into low- or high-[Mg/Fe] populations and find that, in general, values of [Ce/Fe] and [Nd/Fe] increase as the metallicity decreases for the low- and high-[Mg/Fe] populations. Ce abundances show a more complex variation across the metallicity range of our bulge-bar sample when compared to Nd, with ther-process dominating the production of neutron-capture elements in the high-[Mg/Fe] population ([Ce/Nd] < 0.0). We find a spatial chemical dependence of Ce and Nd abundances for our sample of bulge-bar stars, with low- and high-[Mg/Fe] populations displaying a distinct abundance distribution. In the region close to the center of the MW, the low-[Mg/Fe] population is dominated by stars with low [Ce/Fe], [Ce/Mg], [Nd/Mg], [Nd/Fe], and [Ce/Nd] ratios. The low [Ce/Nd] ratio indicates a significant contribution in this central region fromr-process yields for the low-[Mg/Fe] population. The chemical pattern of the most metal-poor stars in our sample suggests an early chemical enrichment of the bulge dominated by yields from core-collapse supernovae andr-process astrophysical sites, such as magnetorotational supernovae.

Astronomy & Astrophysics↗
DOE OSTI2025

The Dark Matter Content of Milky Way Dwarf Spheroidal Galaxies: Draco, Sextans, and Ursa Minor

The Milky Way Survey of the Dark Energy Spectroscopic Instrument (DESI) has so far observed three classical dwarf spheroidal galaxies (dSphs): Draco, Sextans, and Ursa Minor. Based on the observed line-of-sight velocities and metallicities of their member stars, we apply the axisymmetric Jeans Anisotropic Multi-Gaussian Expansion modeling (JAM) approach to recover their inner dark matter distributions. In particular, both the traditional single-population Jeans model and the multiple population chemodynamical model are adopted. With the chemodynamical model, we divide member stars of each dSph into metal-rich and metal-poor populations. The metal-rich populations are more centrally concentrated and dynamically colder, featuring lower velocity dispersion profiles than the metal-poor populations. We find a diversity of the inner density slopes γ of dark matter halos, with the best constraints by the single-population or chemodynamical models consistent with each other. The inner density slopes are $0.7{1}_{-0.35}^{+0.34}$, $0.2{6}_{-0.12}^{+0.22}$, and $0.3{3}_{-0.16}^{+0.20}$ for Draco, Sextans, and Ursa Minor, respectively. We also present the measured astrophysical J and D factors of the three dSphs. Our results indicate that the study of the dark matter content of dSphs through stellar kinematics is still subject to uncertainties behind both the methodology and the observed data, through comparisons with previous measurements and datasets.

Dark matter↗
DOE OSTI2021

VirION2: a short- and long-read sequencing and informatics workflow to study the genomic diversity of viruses in nature

Microbes play fundamental roles in shaping natural ecosystem properties and functions, but do so under constraints imposed by their viral predators. However, studying viruses in nature can be challenging due to low biomass and the lack of universal gene markers. Though metagenomic short-read sequencing has greatly improved our virus ecology toolkit—and revealed many critical ecosystem roles for viruses—microdiverse populations and fine-scale genomic traits are missed. Some of these microdiverse populations are abundant and the missed regions may be of interest for identifying selection pressures that underpin evolutionary constraints associated with hosts and environments. Though long-read sequencing promises complete virus genomes on single reads, it currently suffers from high DNA requirements and sequencing errors that limit accurate gene prediction. Here we introduce VirION2, an integrated short- and long-read metagenomic wet-lab and informatics pipeline that updates our previous method (VirION) to further enhance the utility of long-read viral metagenomics. Using a viral mock community, we first optimized laboratory protocols (polymerase choice, DNA shearing size, PCR cycling) to enable 76% longer reads (now median length of 6,965 bp) from 100-fold less input DNA (now 1 nanogram). Using a virome from a natural seawater sample, we compared viromes generated with VirION2 against other library preparation options (unamplified, original VirION, and short-read), and optimized downstream informatics for improved long-read error correction and assembly. VirION2 assemblies combined with short-read based data (‘enhanced’ viromes), provided significant improvements over VirION libraries in the recovery of longer and more complete viral genomes, and our optimized error-correction strategy using long- and short-read data achieved 99.97% accuracy. In the seawater virome, VirION2 assemblies captured 5,161 viral populations (including all of the virus populations observed in the other assemblies), 30% of which were uniquely assembled through inclusion of long-reads, and 22% of the top 10% most abundant virus populations derived from assembly of long-reads. Viral populations unique to VirION2 assemblies had significantly higher microdiversity means, which may explain why short-read virome approaches failed to capture them. These findings suggest the VirION2 sample prep and workflow can help researchers better investigate the virosphere, even from challenging low-biomass samples. Our new protocols are available to the research community on protocols.io as a ‘living document’ to facilitate dissemination of updates to keep pace with the rapid evolution of long-read sequencing technology.

Long-reads↗