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At least 253 records · Page 14
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Single-molecule epitranscriptomic analysis of full-length HIV-1 RNAs reveals functional roles of site-specific m6As

Abstract Although the significance of chemical modifications on RNA is acknowledged, the evolutionary benefits and specific roles in human immunodeficiency virus (HIV-1) replication remain elusive. Most studies have provided only population-averaged values of modifications for fragmented RNAs at low resolution and have relied on indirect analyses of phenotypic effects by perturbing host effectors. Here we analysed chemical modifications on HIV-1 RNAs at the full-length, single RNA level and nucleotide resolution using direct RNA sequencing methods. Our data reveal an unexpectedly simple HIV-1 modification landscape, highlighting three predominant N 6 -methyladenosine (m 6 A) modifications near the 3′ end. More densely installed in spliced viral messenger RNAs than in genomic RNAs, these m 6 As play a crucial role in maintaining normal levels of HIV-1 RNA splicing and translation. HIV-1 generates diverse RNA subspecies with distinct m 6 A ensembles, and maintaining multiple of these m 6 As on its RNAs provides additional stability and resilience to HIV-1 replication, suggesting an unexplored viral RNA-level evolutionary strategy.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Impact of crowding on the diversity of expanding populations

Crowding effects critically impact the self-organization of densely packed cellular assemblies, such as biofilms, solid tumors, and developing tissues. When cells grow and divide, they push each other apart, remodeling the structure and extent of the population’s range. Recent work has shown that crowding has a strong impact on the strength of natural selection. However, the impact of crowding on neutral processes, which controls the fate of new variants as long as they are rare, remains unclear. Here, we quantify the genetic diversity of expanding microbial colonies and uncover signatures of crowding in the site frequency spectrum. By combining Luria–Delbrück fluctuation tests, lineage tracing in a novel microfluidic incubator, cell-based simulations, and theoretical modeling, we find that the majority of mutations arise behind the expanding frontier, giving rise to clones that are mechanically “pushed out” of the growing region by the proliferating cells in front. These excluded-volume interactions result in a clone-size distribution that solely depends on where the mutation first arose relative to the front and is characterized by a simple power law for low-frequency clones. Our model predicts that the distribution depends on a single parameter—the characteristic growth layer thickness—and hence allows estimation of the mutation rate in a variety of crowded cellular populations. Combined with previous studies on high-frequency mutations, our finding provides a unified picture of the genetic diversity in expanding populations over the whole frequency range and suggests a practical method to assess growth dynamics by sequencing populations across spatial scales.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Nanodomain Formation and Temperature-Dependent Diffusion in Deep Eutectic Solvents Revealed by Single-Molecule Tracking

Deep eutectic solvents (DESs) are typically regarded as homogeneous liquids; however, recent work shows that many exhibit nanoscale structural heterogeneity. Most studies attribute these nanoscale features to short-range chemical interactions. It is still unclear whether a long-range physical mechanism also plays a role. Here, in this study, we examined the nanoscale structure in two hydrophobic DESs, 1:3 tetrabutylammonium bromide: l-menthol (DES-butyl) and 1:3 tetraoctylammonium bromide: l-menthol (DES-octyl). The notation 1:3 represents the molar ratio of the hydrogen bond acceptors to hydrogen bond donors used in the synthesis of the DESs. Single-molecule tracking (SMT) coupled with maximum entropy method (MEM) analysis was used to measure the number of diffusion populations of a dilute concentration of an added fluorescent probe. The presence of more than one population of diffusion coefficients indicates the existence of multiple local environments for the fluorescent probe (i.e., nanoscale structures in the DES). DES-butyl showed a relatively narrow diffusion coefficient distribution centered at 0.55 μm 2 /s, whereas DES-octyl displayed two distinct diffusing populations at 20 °C, with diffusion coefficients of 0.12 μm 2 /s and 0.53 μm 2 /s for the slow and fast populations, respectively. As DES-octyl was heated, the slow-diffusing population steadily diminished and disappeared above ∼30 °C, indicating that the nanodomains present at lower temperatures collapse as the liquid becomes more thermodynamically mixed. This temperature-dependent homogenization is consistent with a physical mechanism of nanostructure formation, for example, liquid–liquid phase separation (LLPS), wherein the structure is not driven solely by specific chemical interactions. The SMT-MEM results suggest that a long-range physical mechanism is the most plausible origin of the measured nanoscale structure in DES-octyl.

Opare-Addo, Jemima [Ames Laboratory (AMES), Ames, ↗
DOE OSTI2020

Spectroscopic Probe Molecule Selection Using Quantum Theory, First-Principles Calculations, and Machine Learning

Probe molecule vibrational spectra have a long history of being used to characterize materials including metals, oxides, metal-organic frameworks, and even human proteins. Furthermore, recent advances in machine learning have enabled computationally generated spectra to aid in detailed characterization of complex surfaces with probe molecules. Despite widespread use of probe molecules, the science of probe molecule selection is underdeveloped. Here, we develop physical concepts, including orbital interaction energy and the energy overlap integral, to explain and predict the ability of probe molecules to discriminate structural descriptors. We resolve the crystal orbital overlap population (COOP) to specific molecular orbitals and quantify their bonding character, which directly influences vibrational frequencies. Using only a single adsorbate calculation from density function theory (DFT), we compute the interaction energy of individual adsorbate molecular orbitals with adsorption site atomic orbitals across many different sites. Combining the molecular orbital resolved COOP and changes in orbital interaction energy enables probe molecule selection for improved discrimination of various sites. We demonstrate these concepts by comparing the predicted effectiveness of carbon monoxide (CO), nitric oxide (NO), and ethylene (C 2 H 4 ) to probe Pt adsorption sites. Finally, using a previously developed machine learning framework, we show that models trained on hundreds of thousand C 2 H 4 spectra, computed from DFT, which regress surface binding-type and generalized coordination number (GCN), outperform those trained using CO and NO spectra. Lastly, a python package, pDOS_overlap, for implementing the electron density based analysis on any combination of adsorbates and materials, is also made available.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2026

Optical cycling on thorium monoxide for an improved test of fundamental symmetries

Optical cycling refers to repeated excitation and spontaneous emission on an electronic transition in an atom or molecule. Optical cycling in molecules can enable a wide range of quantum control and readout techniques, but unfortunately it has only been demonstrated on a small class of alkalilike or alkaline-earth-like molecules. Thorium monoxide (ThO), a molecule used in one of the most precise permanent electron electric dipole moment (eEDM) searches (ACME†) [Andreev et al., Nature (London) 562, 355 (2018)], does not fall into this category. In this work, we demonstrate the first optical cycling on this nonconventional class over a range of experimental parameter space, including laser intensity, polarization switching rate, and interaction time. We show that both the 𝐽 = 1 and 𝐽 = 2 rotational levels of ThO molecule are capable of cycling an average of 11(2) photons with a single laser, at scattering rates of 1.9⁢(6) × 10 6 and 2.3⁢(7) × 10 6 s −1 , respectively, before population is lost to other vibronic levels. We outline a scheme to apply this demonstrated optical cycling in an ACME-style eEDM measurement, improving the detection efficiency by over fourfold compared to noncycling fluorescence detection. This would lead to over a twofold enhancement in the statistical sensitivity of the eEDM search. This optical-cycling scheme can be further extended to scatter ∼100 photons, which would enable a wider range of quantum control and sensing using ThO molecules.

Atomic & molecular processes in external fields↗
DOE OSTI2021

Genetic and behavioral adaptation of Candida parapsilosis to the microbiome of hospitalized infants revealed by in situ genomics, transcriptomics, and proteomics

Background Candida parapsilosis is a common cause of invasive candidiasis, especially in newborn infants, and infections have been increasing over the past two decades. C. parapsilosis has been primarily studied in pure culture, leaving gaps in understanding of its function in a microbiome context. Results. Here, we compare five unique C. parapsilosis genomes assembled from premature infant fecal samples, three of which are newly reconstructed, and analyze their genome structure, population diversity, and in situ activity relative to reference strains in pure culture. All five genomes contain hotspots of single nucleotide variants, some of which are shared by strains from multiple hospitals. A subset of environmental and hospital-derived genomes share variants within these hotspots suggesting derivation of that region from a common ancestor. Four of the newly reconstructed C. parapsilosis genomes have 4 to 16 copies of the gene RTA3, which encodes a lipid translocase and is implicated in antifungal resistance, potentially indicating adaptation to hospital antifungal use. Time course metatranscriptomics and metaproteomics on fecal samples from a premature infant with a C. parapsilosis blood infection revealed highly variable in situ expression patterns that are distinct from those of similar strains in pure cultures. For example, biofilm formation genes were relatively less expressed in situ, whereas genes linked to oxygen utilization were more highly expressed, indicative of growth in a relatively aerobic environment. In gut microbiome samples, C. parapsilosis co-existed with Enterococcus faecalis that shifted in relative abundance over time, accompanied by changes in bacterial and fungal gene expression and proteome composition. Conclusions The results reveal potentially medically relevant differences in Candida function in gut vs. laboratory environments, and constrain evolutionary processes that could contribute to hospital strain persistence and transfer into premature infant microbiomes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

HSQC spectra of lignin isolated from poplar roots

Here we present a curated dataset of two-dimensional heteronuclear single quantum coherence (HSQC) nuclear magnetic resonance (NMR) spectra of lignin isolated from roots of a greenhouse grown natural population of an energy crop poplar (Populus trichocarpa). Dormant cuttings of field-grown poplar were grown in 6-liter pots in a peat-based media containing bark, perlite, vermiculite, dolomite lime and a wetting agent in an environmentally controlled greenhouse. Temperatures were between 21 and 23 °C, with supplemental lighting to support a 16-h day length using 1000-watt high-pressure sodium lights in greenhouse. Once established, all plants were cut-back, allowed to regrow and harvested at the same time following an eight-month long growth period. Plants were harvested and the belowground roots were washed off soils, blotted, dried in an oven at 70 °C for 3 days, and Wiley milled (mesh size 20). The roots were Soxhlet-extracted with toluene/ethanol for 24 h to remove extractives. The extracted roots were ball-milled in a Retsch PM100 planetary ball mill using a porcelain jar with ceramic balls at 600 rpm for 2 h (in 5 min on and 5 min off cycles to avoid excessive sample heating). The ball-milled materials were then subjected to enzymatic hydrolysis for 48 h followed by centrifugation and washing with deionized water. The solid residue was extracted twice with 96% (v/v) 1,4-dioxane/water mixture at room temperature overnight. The extracts were combined, rotary evaporated, and freeze-dried to recover lignin. The dry lignin samples were dissolved in deuterated dimethyl sulfoxide (d6) and transferred into a 5 mm tube. 13C–1H HSQC experiments were performed in a Bruker Avance III HD 500 MHz NMR spectrometer operating at a frequency of 125.12 MHz for the 13C nucleus using a standard Bruker pulse sequence on a Prodigy platform cryoprobe. The NMR spectra were acquired under the following acquisition conditions: 220 ppm spectral width in F1 (13C) dimension with 256 data points and 12 ppm spectral width in F2 (1H) dimension with 1024 data points, a 90° pulse, a one bond C–H coupling constant of 145 Hz, a 1.0 s pulse delay, and 64 scans. Spectra were processed using the Bruker TopSpin software. Additional meta data is embedded in the raw spectra figures.

HSQC, lignin, poplar, roots, CBI↗
DOE OSTI2023

Dimming the Lights: 2D Simulations of Deflagrations of Hybrid C/O/Ne White Dwarfs Using FLASH

The dimmest and most numerous outlier of the Type Ia supernova population, the Type Iax event, is increasingly being found in the results of observational campaigns. There is currently no single accepted model to describe these events. This 2D study explores the viability of modeling Type Iax events as a hybrid C/O/Ne white dwarf progenitor undergoing a deflagration using the multiphysics software FLASH. This hybrid was created using the stellar evolution code MESA, and its C-depleted core and mixed structure have demonstrated lower yields than traditional C/O progenitors in previous deflagration-to-detonation studies. To generate a sample, 30 “realizations” of this simulation were performed, the only difference being the shape of the initial match head used to start the deflagration. Consistent with earlier work, these realizations produce the familiar hot dense bound remnant surrounded by sparse ejecta. Our results indicate that the majority of the star remains unburned (∼70%) and bound (>90%). Our realizations produce total ejecta yields on the order of 10 −2 –10 −1 M ☉ , ejected 56 Ni yields on the order of 10 −4 –10 −2 M ☉ , and ejecta kinetic energies on the order of 10 48 –10 49 erg. Compared to yields inferred from recent observations of the dimmest Type Iax events—SN 2007qd, SN 2008ha, SN 2010ae, SN 2019gsc, SN 2019muj, SN 2020kyg, and SN 2021fcg—our simulation produces comparable 56 Ni yields but too-small total yields and kinetic energies. Reignition of the remnant is also seen in some realizations.

Hydrodynamical simulations↗
DOE OSTI2022

Large-Scale Simulation of Regional Demand Flexibility Implementation and Customer Economic Impact

The Distribution System Operator with Transactive (DSO+T) study conducted a large-scale simulation of over 60,000 customers in a region the size of Texas to demonstrate the effective coordination of distributed energy resources (DERs) in commercial and residential buildings. The integrated simulation included both the bulk (wholesale generation and transmission) and distribution systems. The DERs (including batteries, electric vehicles, air conditioning, and water heaters) participated in a transactive energy retail market that was integrated into an existing competitive wholesale market. The engineering and economic performance of the resulting demand flexibility was evaluated over annual simulations for both moderate and high renewable generation scenarios. A detailed parametric cost model was developed to enable detailed economic analysis of key stakeholders. In addition, fixed and dynamic customer tariffs were designed and applied to the customer population. This allowed the impact on annual customer bills to be analyzed for various building types (residential versus commercial; single- versus multi-family). This paper presents results showing the relative flexibility of batteries, electric vehicles, and building loads throughout the year and under different renewable scenarios. This feeds a detailed breakdown of the impact this flexibility has on the operating costs of the grid and the resulting net economic benefit. Finally, the study showed that practically all customer classes (including non-participating customers) save money under the proposed demand flexibility scheme. The study found overall net annual economic savings of $3.3-5.0B for a region the size of Texas equating to average customer bill savings of 10-16%.

Reeve, Hayden M.↗
DOE OSTI2021

Acceleration of Oxygen Ions in Dipolarization Events: 1. CPS Distributions

Abstract Using an MHD simulation of near tail reconnection associated with a flow burst and the collapse (dipolarization) of the inner tail in combination with test particle tracing we study the acceleration and flux increases of energetic oxygen ions (O + ). The characteristic orbits, distributions, and acceleration mechanisms are governed by the dimensionless parameter σ = ω ci t n , where ω ci is the ion gyro frequency and t n a characteristic Alfvén time of the MHD simulation. For σ < 1, central plasma sheet (CPS) populations after the passage of the dipolarization front are found to resemble half‐shells in velocity space oriented toward dusk. They originate from within the CPS and are energized typically by a single encounter of the region of enhanced cross‐tail electric field associated with the flow burst. For larger σ values ( σ > 1) the O + distributions resemble more closely those of protons, consisting of two counter‐streaming field‐aligned beams and an, albeit more tenuous and irregular, ring population perpendicular to the magnetic field. The existence of the beams, however, depends on suitable earthward moving source populations in the plasma sheet boundary layer or the adjacent lobes. The acceleration to higher energies is found to indicate a charge dependence, consistent with a dominance of more highly charged ions at energies of a few hundred keV. As in earlier simulations, the simulated fluxes show large anisotropies and nongyrotropic effects, phase bunching, and spatially and temporally localized beams.

Birn, J.↗
DOE OSTI2021

Adaptive Phenotypic Plasticity Stabilizes Evolution in Fluctuating Environments

Fluctuating environmental conditions are ubiquitous in natural systems, and populations have evolved various strategies to cope with such fluctuations. The particular mechanisms that evolve profoundly influence subsequent evolutionary dynamics. One such mechanism is phenotypic plasticity, which is the ability of a single genotype to produce alternate phenotypes in an environmentally dependent context. Here, we use digital organisms (self-replicating computer programs) to investigate how adaptive phenotypic plasticity alters evolutionary dynamics and influences evolutionary outcomes in cyclically changing environments. Specifically, we examined the evolutionary histories of both plastic populations and non-plastic populations to ask: (1) Does adaptive plasticity promote or constrain evolutionary change? (2) Are plastic populations better able to evolve and then maintain novel traits? And (3), how does adaptive plasticity affect the potential for maladaptive alleles to accumulate in evolving genomes? We find that populations with adaptive phenotypic plasticity undergo less evolutionary change than non-plastic populations, which must rely on genetic variation from de novo mutations to continuously readapt to environmental fluctuations. Indeed, the non-plastic populations undergo more frequent selective sweeps and accumulate many more genetic changes. We find that the repeated selective sweeps in non-plastic populations drive the loss of beneficial traits and accumulation of maladaptive alleles, whereas phenotypic plasticity can stabilize populations against environmental fluctuations. This stabilization allows plastic populations to more easily retain novel adaptive traits than their non-plastic counterparts. In general, the evolution of adaptive phenotypic plasticity shifted evolutionary dynamics to be more similar to that of populations evolving in a static environment than to non-plastic populations evolving in an identical fluctuating environment. All natural environments subject populations to some form of change; our findings suggest that the stabilizing effect of phenotypic plasticity plays an important role in subsequent adaptive evolution.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

A robust method of nuclei isolation for single-cell RNA sequencing of solid tissues from the plant genus Populus

Single-cell transcriptome analysis has been extensively applied in humans and animal models to uncover gene expression heterogeneity between the different cell types of a tissue or an organ. It demonstrated its capability to discover key regulatory elements that determine cell fate during developmental programs. Single-cell analysis requires the isolation and labeling of the messenger RNA (mRNA) derived from each cell. These challenges were primarily addressed in mammals by developing microfluidic-based approaches. For plant species whose cells contain cell walls, these approaches have generally required the generation of isolated protoplasts. Many plant tissues’ secondary cell wall hinders enzymatic digestion required for individual protoplast isolation, resulting in an unequal representation of cell types in a protoplast population. This limitation is especially critical for cell types located in the inner layers of a tissue or the inner tissues of an organ. Consequently, single-cell RNA sequencing (scRNA-seq) studies using microfluidic approaches in plants have mainly been restricted to Arabidopsis roots, for which well-established procedures of protoplast isolation are available. Here we present a simple alternative approach to generating high-quality protoplasts from plant tissue by characterizing the mRNA extracted from individual nuclei instead of whole cells. We developed the protocol using two different plant materials with varying cellular complexity levels and cell wall structure, Populus shoot apices, and more lignified stems. Using the 10× Genomics Chromium technology, we show that this procedure results in intact mRNA isolation and limited leakage, with a broad representation of individual cell transcriptomes.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Low power implementation of high frequency SiPM readout for Cherenkov and scintillation detectors in TOF-PET

State-of-the-art (SoA) electronic readout for silicon photomultiplier (SiPM)-based scintillation detectors that demonstrate experimental limits in achievable coincidence time resolution (CTR) leverage low noise, high frequency signal processing to facilitate a single photon time response that is near the limit of the SiPMs architecture. This readout strategy can optimally exploit fast luminescence and prompt photon populations, and promising measurements show detector concepts employing this readout can greatly advance PET detector CTR, relative to SoA in clinical systems. However, the technique employs power hungry components which make the electronics chain impractical for channel-dense time-of-flight (TOF)-PET detectors. We have developed and tested a low noise and high frequency readout circuit which is performant at low power and consists of discrete elements with small footprints, making it feasible for integration into TOF-PET detector prototypes. A 3 × 3 mm 2 Broadcom SiPM with this readout chain exhibited sub-100 ps single photon time resolution at 10 mW of power consumption, with a relatively minor performance degradation to 120 ± 2 ps FWHM at 5 mW. CTR measurements with 3 × 3 × 20 mm 3 LYSO and fast LGSO scintillators demonstrated 127 ± 3 ps and 113 ± 2 ps FWHM at optimal power operation and 133 ± 2 ps and 121 ± 3 ps CTR at 5 mW. BGO crystals 3 × 3 × 20 mm 3 in size show 271 ± 5 ps FWHM CTR (1174 ± 14 ps full-width-at-tenth-maximum (FWTM)) at optimal power dissipation and 289 ± 8 ps (1296 ± 33 ps FWTM) at 5 mW. The compact and low power readout topology that achieves this performance thereby offers a platform to greatly advance PET system CTR and also opportunities to provide high performance TOF-PET at reduced material cost.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2022

Developing the S 32 ( p , d ) S * 31 ( p ) ( γ ) reaction to probe the P 30 ( p , γ ) S 31 reaction rate in classical novae

Background: The 30 P(p,γ) 31 S reaction rate is one of the largest remaining sources of uncertainty in the final abundances of nuclei created in a classical nova involving a ONe white dwarf. The reaction rate directly influences silicon isotopic ratios, which are used as identifiers of presolar grains with nova origins. Additionally, the uncertainty in the 30 P(p,γ) 31 S reaction rate has been found to limit the use of nova nuclear thermometers based on observations of elemental ratios in nova ejecta. Purpose: Reduce uncertainties in the nuclear data for proton-unbound states in 31 S, which act as resonances for the 30 P(p,γ) 31 S reaction at classical nova temperatures, and develop a technique for high efficiency, high-resolution reaction-decay coincidence measurements. Methods: Here, the 32 S(p,d) 31 S reaction was used to populate the states of interest in 31 S. The experiment was performed at the Texas A&M Cyclotron Institute using the LLNL Hyperion array for the detection of charged particles and γ rays. A downstream silicon telescope was used to select reaction deuterons, and a single upstream silicon detector was used to measure protons emitted in the decay of unbound 31 S levels. Results: Several states in 31 S above the proton separation energy were observed to have been populated. Decay protons from the resonant states in 31 S were identified as events in the upstream silicon detectors that came in coincidence with deuterons in the downstream telescope. Protons emitted from these states were measured and branching ratios extracted. Conclusions: While no new reaction rate is derived, spin-parity assignments for several higher-lying proton unbound states have been confirmed. Measured p 0 branching ratios for these levels have been compared to previous measurements with good agreement, and in some cases provided a reduction in uncertainty. The previously identified T = 3/2 state may have been incorrectly assigned a large p 0 branching ratio in a previous measurement. The technique of measuring reaction-decay coincidences with a particle-gamma setup appears promising.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2020

Population genomic response to geographic gradients by widespread and endemic fishes of the Arabian Peninsula

Genetic structure within marine species may be driven by local adaptation to their environment, or alternatively by historical processes, such as geographic isolation. The gulfs and seas bordering the Arabian Peninsula offer an ideal setting to examine connectivity patterns in coral reef fishes with respect to environmental gradients and vicariance. The Red Sea is characterized by a unique marine fauna, historical periods of desiccation and isolation, as well as environmental gradients in salinity, temperature, and primary productivity that vary both by latitude and by season. The adjacent Arabian Sea is characterized by a sharper environmental gradient, ranging from extensive coral cover and warm temperatures in the southwest, to sparse coral cover, cooler temperatures, and seasonal upwelling in the northeast. Reef fish, however, are not confined to these seas, with some Red Sea fishes extending varying distances into the northern Arabian Sea, while their pelagic larvae are presumably capable of much greater dispersal. These species must therefore cope with a diversity of conditions that invoke the possibility of steep clines in natural selection. Here, we test for genetic structure in two widespread reef fish species (a butterflyfish and surgeonfish) and eight range-restricted butterflyfishes across the Red Sea and Arabian Sea using genome-wide single nucleotide polymorphisms. We performed multiple matrix regression with randomization analyses on genetic distances for all species, as well as reconstructed scenarios for population subdivision in the species with signatures of isolation. We found that (a) widespread species displayed more genetic subdivision than regional endemics and (b) this genetic structure was not correlated with contemporary environmental parameters but instead may reflect historical events. We propose that the endemic species may be adapted to a diversity of local conditions, but the widespread species are instead subject to ecological filtering where different combinations of genotypes persist under divergent ecological regimes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Follow-up of Young Stars Identified with BANYAN Σ: New Low-mass Members of Nearby Moving Groups

The characterization of moving groups offers a powerful means to identify large populations of young stars. In this paper, we present a sample of follow-up observations for 56 systems that have previously been proposed as members of young stellar associations through the application of the BANYAN Σ kinematic classification tool. Our measurements, which probe seven different associations, provide a sample of 39 stellar systems that either are confirmed or appear consistent with being young members of their respective associations. Nineteen of these are single M dwarfs. This sample expands our knowledge of Upper Centaurus Lupus, Coma Berenices, and AB Doradus Major to cooler temperatures and also significantly increases the known population of the Carina-Near association. The young systems present excellent targets for future planet searches and would also be valuable for studies of star formation and evolution. Additionally, we find two stellar systems that show indications of being rare instances of late-stage circumstellar accretion. Lastly, our follow-up measurements serve as a test of BANYAN Σ, finding an overall contamination rate that is consistent with previous findings (29% for systems with RV measurements, 37% without).

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Cumulative effects of piscivorous colonial waterbirds on juvenile salmonids: A multi predator-prey species evaluation

We investigated the cumulative effects of predation by piscivorous colonial waterbirds on the survival of multiple salmonid ( Oncorhynchus spp.) populations listed under the U.S. Endangered Species Act (ESA) and determined what proportion of all sources of fish mortality (1 –survival) were due to birds in the Columbia River basin, USA. Anadromous juvenile salmonids (smolts) were exposed to predation by Caspian terns ( Hydroprogne caspia ), double-crested cormorants ( Nannopterum auritum ), California gulls ( Larus californicus ), and ring-billed gulls ( L . delawarensis ), birds known to consume both live and dead fish. Avian consumption and survival probabilities (proportion of available fish consumed or alive) were estimated for steelhead trout ( O . mykiss ), yearling Chinook salmon ( O . tshawytscha ), sub-yearling Chinook salmon, and sockeye salmon ( O . nerka ) during out-migration from the lower Snake River to the Pacific Ocean during an 11-year study period (2008–2018). Results indicated that probabilities of avian consumption varied greatly across salmonid populations, bird species, colony location, river reach, and year. Cumulative consumption probabilities (consumption by birds from all colonies combined) were consistently the highest for steelhead, with annual estimates ranging from 0.22 (95% credible interval = 0.20–0.26) to 0.51 (0.43–0.60) of available smolts. The cumulative effects of avian consumption were significantly lower for yearling and sub-yearling Chinook salmon, with consumption probabilities ranging annually from 0.04 (0.02–0.07) to 0.10 (0.07–0.15) and from 0.06 (0.3–0.09) to 0.15 (0.10–0.23), respectively. Avian consumption probabilities for sockeye salmon smolts was generally higher than for Chinook salmon smolts, but lower than for steelhead smolts, ranging annually from 0.08 (0.03–0.22) to 0.25 (0.14–0.44). Although annual consumption probabilities for birds from certain colonies were more than 0.20 of available smolts, probabilities from other colonies were less than 0.01 of available smolts, indicating that not all colonies of birds posed a substantial risk to smolt mortality. Consumption probabilities were lowest for small colonies and for colonies located a considerable distance from the Snake and Columbia rivers. Total mortality attributed to avian consumption was relatively small for Chinook salmon (less than 10%) but was the single greatest source of mortality for steelhead (greater than 50%) in all years evaluated. Results suggest that the potential benefits to salmonid populations of managing birds to reduce smolt mortality would vary widely depending on the salmonid population, the species of bird, and the size and location of the breeding colony.

Evans, Allen F.↗
DOE OSTI2024

The Abundance and Sources of Ice Nucleating Particles Within Alaskan Ice Fog

Abstract The Alaskan Layered Pollution and Chemical Analysis (ALPACA) field campaign included deployment of a suite of atmospheric measurements in January–February 2022 with the goal of better understanding atmospheric processes and pollution under cold and dark conditions in Fairbanks, Alaska. We report on measurements of particle composition, particle size, ice nucleating particle (INP) composition, and INP size during an ice fog period (29 January–3 February). During this period, coarse particulate matter (PM 10 ) concentrations increased by 150% in association with a decrease in air temperature, a stronger temperature inversion, and relatively stagnant conditions. Results also show a 18%–78% decrease in INPs during the ice fog period, indicating that particles had activated into the ice fog via nucleation. Peroxide and heat treatments performed on INPs indicated that, on average, the largest contributions to the INP population were heat‐labile (potentially biological, 63%), organic (31%), then inorganic (likely dust, 6%). Measurements of levoglucosan and bulk and single‐particle composition corroborate the presence of dust and aerosols from combustion sources. Heat‐labile and organic INPs decreased during the peak period of the ice fog, indicating those were preferentially activated, while inorganic INPs increased, suggesting they remained as interstitial INPs. In general, INP concentrations were unexpectedly high in Fairbanks compared to other locations in the Arctic during winter. The fact that these INPs likely facilitated ice fog formation in Fairbanks has implications for other high latitude locations subject to the hazards associated with ice fog.

Meteorology & Atmospheric Sciences↗