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All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Hanseniaspora smithiae sp. nov., a Novel Apiculate Yeast Species From Patagonian Forests That Lacks the Typical Genomic Domestication Signatures for Fermentative Environments

During a survey of Nothofagus trees and their parasitic fungi in Andean Patagonia (Argentina), genetically distinct strains of Hanseniaspora were obtained from the sugar-containing stromata of parasitic Cyttaria spp. Phylogenetic analyses based on the single-gene sequences (encoding rRNA and actin) or on conserved, single-copy, orthologous genes from genome sequence assemblies revealed that these strains represent a new species closely related to Hanseniaspora valbyensis. Additionally, delimitation of this novel species was supported by genetic distance calculations using overall genome relatedness indices (OGRI) between the novel taxon and its closest relatives. To better understand the mode of speciation in Hanseniaspora , we examined genes that were retained or lost in the novel species in comparison to its closest relatives. These analyses show that, during diversification, this novel species and its closest relatives, H. valbyensis and Hanseniaspora jakobsenii , lost mitochondrial and other genes involved in the generation of precursor metabolites and energy, which could explain their slower growth and higher ethanol yields under aerobic conditions. Similarly, Hanseniaspora mollemarum lost the ability to sporulate, along with genes that are involved in meiosis and mating. Based on these findings, a formal description of the novel yeast species Hanseniaspora smithiae sp. nov. is proposed, with CRUB 1602 H as the holotype.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Determining the biogeochemical transformations of organic matter composition in rivers using molecular signatures

Inland waters are hotspots for biogeochemical activity, but the environmental and biological factors that govern the transformation of organic matter (OM) flowing through them are still poorly constrained. Here we evaluate data from a crowdsourced sampling campaign led by the Worldwide Hydrobiogeochemistry Observation Network for Dynamic River Systems (WHONDRS) consortium to investigate broad continental-scale trends in OM composition compared to localized events that influence biogeochemical transformations. Samples from two different OM compartments, sediments and surface water, were collected from 97 streams throughout the Northern Hemisphere and analyzed to identify differences in biogeochemical processes involved in OM transformations. By using dimensional reduction techniques, we identified that putative biogeochemical transformations and microbial respiration rates vary across sediment and surface water along river continua independent of latitude (18°N–68°N). In contrast, we reveal small- and large-scale patterns in OM composition related to local (sediment vs. water column) and reach (stream order, latitude) characteristics. These patterns lay the foundation to modeling the linkage between ecological processes and biogeochemical signals. We further showed how spatial, physical, and biogeochemical factors influence the reactivity of the two OM pools in local reaches yet find emergent broad-scale patterns between OM concentrations and stream order. OM processing will likely change as hydrologic flow regimes shift and vertical mixing occurs on different spatial and temporal scales. As our planet continues to warm and the timing and magnitude of surface and subsurface flows shift, understanding changes in OM cycling across hydrologic systems is critical, given the unknown broad-scale responses and consequences for riverine OM.

rivers↗
DOE OSTI2025

Phenotypically anchored transcriptomics across diverse agrichemicals reveals conserved pathways and unique gene expression signatures in zebrafish

Agrichemicals such as herbicides, fungicides, insecticides, and biocides are widely used in agriculture, yet some are associated with adverse effects in humans and the environment. While many of these chemicals have been extensively studied in vitro and are included in the EPA’s ToxCast program, comprehensive in vivo comparisons using RNA sequencing across structurally diverse agrichemicals, in a single screening platform, are lacking. In this study, we examined structurally diverse agrichemicals found in the U.S. Environmental Protection Agency’s (EPA) Toxcast Phase I and II library by statically exposing early life stage zebrafish at 6 h post fertilization (hpf) until 120 hpf at concentrations ranging from 0.25 to 100 µM. Morphological outcomes were assessed at 120 hpf across 10 endpoints, including yolk sac edema, craniofacial malformations, and axis abnormalities. Chemicals that produced robust concentration-response relationships were selected for transcriptomic profiling. For transcriptomic analysis, zebrafish were statically exposed to each chemical and sampled at 48 hpf, prior to the onset of morphological effects observed at 120 hpf. Differential expression analysis identified between 0 and 4,538 differentially expressed genes (DEGs) per chemical, with no clear correlation to morphological severity. Both DEG and co-expression network analyses revealed chemical-specific expression patterns that converged on shared biological pathways, including neurodevelopment and cytoskeletal organization. Key regulatory genes such as mylpfa and krt4 were identified within co-expression modules, suggesting their potential role in conserved toxicity mechanisms. Semantic similarity analysis of enriched gene ontology (GO) terms, when compared to existing datasets, highlighted gaps in the annotation of neurodevelopmental processes, indicating that some in vivo effects may not be fully captured by current curated resources. The results provide new insights into the modes of action of diverse agrichemicals and establish a framework for understanding how agrichemical structure relates to biological function in a vertebrate model.

agrichemical↗
DOE OSTI2023

Validation of a Proteomic Signature of Lung Cancer Risk from Bronchial Specimens of Risk-Stratified Individuals

A major challenge in lung cancer prevention and cure hinges on identifying the at-risk population that ultimately develops lung cancer. Previously, we reported proteomic alterations in the cytologically normal bronchial epithelial cells collected from the bronchial brushings of individuals at risk for lung cancer. The purpose of this study is to validate, in an independent cohort, a selected list of 55 candidate proteins associated with risk for lung cancer with sensitive targeted proteomics using selected reaction monitoring (SRM). Bronchial brushings collected from individuals at low and high risk for developing lung cancer as well as patients with lung cancer, from both a subset of the original cohort (batch 1: n = 10 per group) and an independent cohort of 149 individuals (batch 2: low risk (n = 32), high risk (n = 34), and lung cancer (n = 83)), were analyzed using multiplexed SRM assays. ALDH3A1 and AKR1B10 were found to be consistently overexpressed in the high-risk group in both batch 1 and batch 2 brushing specimens as well as in the biopsies of batch 1. Validation of highly discriminatory proteins and metabolic enzymes by SRM in a larger independent cohort supported their use to identify patients at high risk for developing lung cancer.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

X-ray Fluorescence Microscopy to Develop Elemental Classifiers and Investigate Elemental Signatures in BALB/c Mouse Intestine a Week after Exposure to 8 Gy of Gamma Rays

Iron redistribution in the intestine after total body irradiation is an established phenomenon. However, in the literature, there are no reports about the use of X-ray fluorescence microscopy or equivalent techniques to generate semi-quantitative 2D maps of iron in sectioned intestine samples from irradiated mice. In this work, we used X-ray fluorescence microscopy (XFM) to map the elemental content of iron as well as phosphorus, sulfur, calcium, copper and zinc in tissue sections of the small intestine from eight-week-old BALB/c male mice that developed gastrointestinal acute radiation syndrome (GI-ARS) in response to exposure to 8 Gray of gamma rays. Seven days after irradiation, we found that the majority of the iron is localized as hot spots in the intercellular regions of the area surrounding crypts and stretching between the outer perimeter of the intestine and the surface cell layer of villi. In addition, this study represents our current efforts to develop elemental cell classifiers that could be used for the automated generation of regions of interest for analyses of X-ray fluorescence maps. Once developed, such a tool will be instrumental for studies of effects of radiation and other toxicants on the elemental content in cells and tissues. While XFM studies cannot be conducted on living organisms, it is possible to envision future scenarios where XFM imaging of single cells sloughed from the human (or rodent) intestine could be used to follow up on the progression of GI-ARS.

X-ray fluorescence microscopy↗
DOE OSTI2023

Plutonium Signatures in Molten-Salt Reactor Off-Gas Tank and Safeguards Considerations

Fluid-fueled molten-salt reactors (MSRs) are actively being developed by several companies, with plans to deploy them internationally. The current IAEA inspection tools are largely incompatible with the unique design features of liquid fuel MSRs (e.g., the complex fuel chemistry, circulating fuel inventory, bulk accountancy, and high radiation environment). For these reasons, safeguards for MSRs are seen as challenging and require the development of new techniques. This paper proposes one such technique through the observation of the reactor’s off-gas. Any reactor design using low-enriched uranium will build up plutonium as the fuel undergoes burnup. Plutonium has different fission product yields than uranium. Therefore, a shift in fission product production is expected with fuel evolution. The passive removal of certain gaseous fission products to the off-gas tank of an MSR provides a valuable opportunity for analysis without significant modifications to the design of the system. Uniquely, due to the gaseous nature of the isotopes, beta particle emissions are available for observation. The ratios of these fission product isotopes can, thus, be traced back to the relative amount and types of fissile isotopes in the core. This proposed technique represents an effective safeguards tool for bulk accountancy which, while avoiding being onerous, could be used in concert with other techniques to meet the IAEA’s timeliness goals for the detection of a diversion.

Dunkle, Nicholas (ORCID:000000027323011X)↗
DOE OSTI2023

Revisiting Experimental Signatures of the Ponderomotive Force

The classical theory of single-electron dynamics in focused laser pulses is the foundation of both the relativistic ponderomotive force (RPF), which underlies models of laser-collective-plasma dynamics, and the discovery of novel strong-field radiation dynamics. Despite this bedrock importance, consensus eludes the community as to whether acceleration of single electrons in vacuum has been observed in experimental conditions. We analyze an early experiment on the RPF with respect to several features that were neglected in modeling and that can restore consistency between theory predictions and experimental data. The right or wrong pulse profile function, laser parameters, or initial electron distribution can each make or break the agreement between predictions and data. The laser phase at which the electron’s interaction with the pulse begins has a large effect, explaining why much larger energies are achieved by electrons liberated in the focal region by photoionization from high-Z atoms and by electrons ejected from a plasma mirror. Finally, we compute the difference in a typical electron spectrum arising from fluctuating focal spot size in state-of-the-art ultra-relativistic laser facilities. Our results emphasize the importance of thoroughly characterizing laser parameters in order to achieve quantitatively accurate predictions and the precision required for discovery science.

Hegelich, Bjorn Manuel↗
DOE OSTI2021

Observational Signatures of Planets in Protoplanetary Disks: Temperature Structures in Spiral Arms

High-resolution imaging of protoplanetary disks has unveiled a rich diversity of spiral structure, some of which may arise from disk-planet interaction. Using 3D hydrodynamics with β cooling to a vertically stratified background, as well as radiative-transfer modeling, we investigate the temperature rise in planet-driven spirals. In rapidly cooling disks, the temperature rise is dominated by a contribution from stellar irradiation, 0.3%–3% inside the planet radius but always < 0.5% outside. When cooling time equals or exceeds dynamical time, however, this is overwhelmed by hydrodynamic PdV work, which introduces a ~10%–20% perturbation within a factor of ~2 from the planet’s orbital radius. We devise an empirical fit of the spiral amplitude Δ(T)=(M{sub p}/M{sub th}){sup c}(f{sub PdV}e{sup -t{sub a}{sub r}{sub m}/t{sub c}}+f{sub rad}) to take into account both effects. Where cooling is slow, we find also that temperature perturbations from buoyancy spirals—a strictly 3D, nonisothermal phenomenon—become nearly as strong as those from Lindblad spirals, which are amenable to 2D and isothermal studies. Our findings may help explain observed thermal features in disks like TW Hydrae and CQ Tauri, and underscore that 3D effects have a qualitatively important effect on disk structure.

42 ENGINEERING↗
DOE OSTI2020

Signatures of Velocity-dependent Dark Matter Self-interactions in Milky Way-mass Halos

In this work, we explore the impact of elastic, anisotropic, velocity-dependent dark matter (DM) self-interactions on the host halo and subhalos of Milky Way (MW)--mass systems. We consider a generic self-interacting dark matter (SIDM) model parameterized by the masses of a light mediator and the DM particle. The ratio of these masses, w, sets the velocity scale above which momentum transfer due to DM self-interactions becomes inefficient. We perform high-resolution zoom-in simulations of an MW-mass halo for values of w that span scenarios in which self-interactions either between the host and its subhalos or only within subhalos efficiently transfer momentum, and we study the effects of self-interactions on the host halo and on the abundance, radial distribution, orbital dynamics, and density profiles of subhalos in each case. The abundance and properties of surviving subhalos are consistent with being determined primarily by subhalo--host halo interactions. In particular, subhalos on radial orbits in models with larger values of the cross section at the host halo velocity scale are more susceptible to tidal disruption owing to mass loss from ram pressure stripping caused by self-interactions with the host. This mechanism suppresses the abundance of surviving subhalos relative to collisionless DM simulations, with stronger suppression for larger values of w. Thus, probes of subhalo abundance around MW-mass hosts can be used to place upper limits on the self-interaction cross section at velocity scales of ~200 km s-1, and combining these measurements with the orbital properties and internal dynamics of subhalos may break degeneracies among velocity-dependent SIDM models.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Photometric Signature of Ultraharmonic Resonances in Barred Galaxies

Bars may induce morphological features, such as rings, through their resonances. Previous studies suggested that the presence of "dark gaps," or regions of a galaxy where the difference between the surface brightness along the bar major axis and that along the bar minor axis is maximal, can be attributed to the location of bar corotation. Here, using GALAKOS, a high-resolution N-body simulation of a barred galaxy, we test this photometric method's ability to identify the bar corotation resonance. Contrary to previous work, our results indicate that "dark gaps" are a clear sign of the location of the 4:1 ultraharmonic resonance instead of bar corotation. Measurements of the bar corotation can indirectly be inferred using kinematic information, e.g., by measuring the shape of the rotation curve. We demonstrate our concept on a sample of 578 face-on barred galaxies with both imaging and integral field observations and find that the sample likely consists primarily of fast bars.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

The Signatures of Self-interacting Dark Matter and Subhalo Disruption on Cluster Substructure

The abundance, distribution, and inner structure of satellites of galaxy clusters can be sensitive probes of the properties of dark matter. We run 30 cosmological zoom-in simulations with self-interacting dark matter (SIDM), with a velocity-dependent cross section, to study the properties of subhalos within cluster-mass hosts. We find that the abundance of subhalos that survive in the SIDM simulations are suppressed relative to their cold dark matter (CDM) counterparts. Once the population of disrupted subhalos—which may host orphan galaxies—is taken into account, satellite galaxy populations in CDM and SIDM models can be reconciled. However, even in this case, the inner structures of subhalos are significantly different in the two dark matter models. We study the feasibility of using the weak-lensing signal from the subhalo density profiles to distinguish between the cold and self-interacting dark matter while accounting for the potential contribution of orphan galaxies. We find that the effects of self-interactions on the density profile of subhalos can appear degenerate with subhalo disruption in CDM, when orphans are accounted for. With current error bars from the Subaru Hyper Suprime-Cam Strategic Program, we find that subhalos in the outskirts of clusters (where disruption is less prevalent) can be used to constrain dark matter physics. In the future, the Vera C. Rubin Observatory Legacy Survey of Space and Time will give precise measurements of the weak-lensing profile and can be used to constrain σ $_{T}$/m at the ∼1 cm$^{2}$ g$^{−1}$ level at v ∼ 2000 km s$^{−1}$.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Merger Signatures are Common, but not Universal, in Massive, Recently Quenched Galaxies at z ~ 0.7

We present visual classifications of merger-induced tidal disturbances in 143 M* ~ 10 11 M ⊙ post-starburst galaxies at z ~ 0.7 identified in the $SQuIGG\vec{L}E$ Sample. This sample spectroscopically selects galaxies from the Sloan Digital Sky Survey that have stopped their primary epoch of star formation within the past ~500 Myr. Visual classifications are performed on Hyper Suprime-Cam imaging. We compare to a control sample of mass- and redshift-matched star-forming and quiescent galaxies from the Large Early Galaxy Census and find that post-starburst galaxies are more likely to be classified as disturbed than either category. This corresponds to a factor of $3.6$$^{+2.9}_{-1.3}$ times the disturbance rate of older quiescent galaxies and $2.1$$^{+1.9}_{-.73}$ times the disturbance rate of star-forming galaxies. Assuming tidal features persist for ≲500 Myr, this suggests merging is coincident with quenching in a significant fraction of these post-starbursts. Galaxies with tidal disturbances are younger on average than undisturbed post-starburst galaxies in our sample, suggesting tidal features from a major merger may have faded over time. This may be exacerbated by the fact that, on average, the undisturbed subset is fainter, rendering low-surface-brightness tidal features harder to identify. However, the presence of 10 young (≲150 Myr since quenching) undisturbed galaxies suggests that major mergers are not the only fast physical mechanism that shut down the primary epoch of star formation in massive galaxies at intermediate redshift.

79 ASTRONOMY AND ASTROPHYSICS↗