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At least 883 records · Page 49
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Highly Basic Clusters in the Herpes Simplex Virus 1 Nuclear Egress Complex Drive Membrane Budding by Inducing Lipid Ordering

During replication of herpesviruses, capsids escape from the nucleus into the cytoplasm by budding at the inner nuclear membrane. This unusual process is mediated by the viral nuclear egress complex (NEC) that deforms the membrane around the capsid by oligomerizing into a hexagonal, membrane-bound scaffold. Here, we found that highly basic membrane-proximal regions (MPRs) of the NEC alter lipid order by inserting into the lipid headgroups and promote negative Gaussian curvature. We also find that the electrostatic interactions between the MPRs and the membranes are essential for membrane deformation. One of the MPRs is phosphorylated by a viral kinase during infection, and the corresponding phosphomimicking mutations block capsid nuclear egress. We show that the same phosphomimicking mutations disrupt the NEC-membrane interactions and inhibit NEC-mediated budding in vitro, providing a biophysical explanation for the in vivo phenomenon. Our data suggest that the NEC generates negative membrane curvature by both lipid ordering and protein scaffolding and that phosphorylation acts as an off switch that inhibits the membrane-budding activity of the NEC to prevent capsid-less budding.

membrane curvature↗
DOE OSTI2022

Changes in global land use and CO 2 emissions from us bioethanol production: what drives differences in estimates between corn and cellulosic ethanol?

Land use change (LUC) CO 2 emissions associated with bioenergy production depend on the amount of land required to produce bioenergy crops, the carbon stored in such crops (including in the leaves, stalk, roots and soil), and the carbon emitted when another land cover is directly or indirectly displaced as a result. In this study, we use a global integrated assessment model [the Global Change Analysis Model (GCAM)] to explore the differences in estimates of LUC CO 2 emissions for two crops (corn and switchgrass) used to produce ethanol in the United States under alternative assumptions about natural lands protection. Varying the latter assumptions for corn ethanol results in net LUC CO 2 emissions between 7 and 41 gCO 2 per MJ of ethanol, whereas varying the same assumptions for switchgrass ethanol results in net emissions between -26 and 14 gCO 2 per MJ of ethanol. The low-end estimate for each occurs when natural lands are assumed to be fully protected everywhere, which leads to significant cropland intensification. The high-end estimate for each occurs when natural lands are assumed to be unprotected everywhere, leading to greater cropland expansion and associated conversion of unmanaged forest and pasture. Results from this study could be used to inform scenarios of future energy system change or life cycle assessment of biofuels for which LUC emissions would be an input.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Record-Breaking Atmospheric River Drives April 2024 Extreme Precipitation in the United Arab Emirates and the Surrounding Gulf Region

In mid-April 2024, the United Arab Emirates (UAE) and the surrounding Gulf region experienced unprecedented rainfall and catastrophic flooding, causing widespread damage, loss of life, and significant economic costs. During the 3-day period from 15 to 17 April, rainfall in the UAE exceeded 100 mm in the hardest-hit areas, with more than 170% of the typical annual precipitation recorded in just 72 h. The event was associated with exceptionally strong integrated water vapor transport (IVT), driven by a persistent low pressure system and a focused corridor of moisture transport. This environment, combined with favorable dynamical and convective conditions, triggered intense thunderstorms and widespread flooding. This article examines the role of an atmospheric river (AR) in the April 2024 extreme precipitation event, emphasizing the contribution of extreme IVT to preconditioning and amplifying the heavy rainfall. While this event has previously been described primarily in terms of a mesoscale convective system (MCS) and potential vorticity (PV) streamers, here we document and illustrate its close relationship to a record-breaking moisture transport corridor. This AR-based perspective highlights how large-scale moisture-transport frameworks can complement synoptic and mesoscale analyses in understanding extreme rainfall in arid and semiarid regions such as the UAE and the Gulf. The event serves as a stark example of the vulnerabilities faced by arid regions, where atmospheric conditions conducive to extreme flooding may become more frequent in the future.

Massoud, Elias [ORNL] (ORCID:0000000217725361)↗
DOE OSTI2025

Forest Breeze–Cold Pool Interactions Drive Convective Organization over Heterogeneous Vegetation

Heterogeneous landscapes can influence the development of convection through the generation of thermally driven mesoscale circulations. To assess the impacts of these circulations and their interaction with sea breezes, we simulated convection in an idealized coastal environment using the Regional Atmospheric Modeling System (RAMS). We compared simulations with striped patterns of surface vegetation to those of uniform vegetation to identify the importance of vegetation heterogeneity in impacting convective development. Under dry soil conditions representative of those during the Tracking Aerosol Convection Interactions Experiment (TRACER) and Experiment of Sea Breeze Convection, Aerosols, Precipitation, and Environment (ESCAPE) campaigns in June 2022, we found that these vegetation-induced circulations, referred to in the literature as “forest breezes,” are more important than the sea breeze in determining the location of convection initiation. Convection and precipitation are also found to be favored over forests and suppressed over pasture and suburban landscapes as a result of greater surface sensible heat flux over the forest. Our findings also indicate that forest breezes are important for initiating convection along the boundaries of the forest, but that cold pools may play a key role in propagating the forest breezes toward the center of the forest stripe. In our simulations, the collisions of these breezes in the center of the forest stripe lead to uplift and strong convection there; however, a different width of the forest stripe would alter when the forest breezes collide or whether they collide at all. The presence of these cold pools may therefore impact the “ideal stripe width,” the width of each vegetation stripe which maximizes domain-wide precipitation.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2019

What Drives Upper-Ocean Temperature Variability in Coupled Climate Models and Observations?

Abstract A key question in climate modeling is to what extent sea surface temperature and upper-ocean heat content are driven passively by air–sea heat fluxes, as opposed to forcing by ocean dynamics. This paper investigates the question using a climate model at different resolutions, and observations, for monthly variability. At the grid scale in a high-resolution climate model with resolved mesoscale ocean eddies, ocean dynamics (i.e., ocean heat flux convergence) dominates upper 50 m heat content variability over most of the globe. For deeper depths of integration to 400 m, the heat content variability at the grid scale is almost totally controlled by ocean heat flux convergence. However, a strong dependence on spatial scale is found—for the upper 50 m of ocean, after smoothing the data to around 7°, air–sea heat fluxes, augmented by Ekman heat transports, dominate. For deeper depths of integration to 400 m, the transition scale becomes larger and is above 10° in western boundary currents. Comparison of climate model results with observations show that the small-scale influence of ocean intrinsic variability is well captured by the high-resolution model but is missing from a comparable model with parameterized ocean-eddy effects. In the deep tropics, ocean dynamics dominates in all cases and all scales. In the subtropical gyres at large scales, air–sea heat fluxes play the biggest role. In the midlatitudes, at large scales >10°, atmosphere-driven air–sea heat fluxes and Ekman heat transport variability are the dominant processes except in the western boundary currents for the 400 m heat content.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

The Relative Importance of Forced and Unforced Temperature Patterns in Driving the Time Variation of Low-Cloud Feedback

Abstract Atmospheric models forced with observed sea surface temperatures (SSTs) suggest a trend toward a more-stabilizing cloud feedback in recent decades, partly due to the surface cooling trend in the eastern Pacific (EP) and the warming trend in the western Pacific (WP). Here, we show model evidence that the low-cloud feedback has contributions from both forced and unforced feedback components and that its time variation arises in large part through changes in the relative importance of the two over time, rather than through variations in forced or unforced feedbacks themselves. Initial-condition large ensembles (LEs) suggest that the SST patterns are dominated by unforced variations for 30-yr windows ending prior to the 1980s. In general, unforced SSTs are representative of an ENSO-like pattern, which corresponds to weak low-level stability in the tropics and less-stabilizing low-cloud feedback. Since the 1980s, the forced signals have become stronger, outweighing the unforced signals for the 30-yr windows ending after the 2010s. Forced SSTs are characterized by relatively uniform warming with an enhancement in the WP, corresponding to a more-stabilizing low-cloud feedback in most cases. The time-evolving SST pattern due to this increasing importance of forced signals is the dominant contributor to the recent stabilizing shift of low-cloud feedback in the LEs. Using single-forcing LEs, we further find that if only greenhouse gases evolve with time, the transition to the domination of forced signals occurs 10–20 years earlier compared to the LEs with full forcings, which can be understood through the compensating effect between aerosols and greenhouse gases.

58 GEOSCIENCES↗
DOE OSTI2020

Small and mighty: adaptation of superphylum Patescibacteria to groundwater environment drives their genome simplicity

The newly defined superphylum Patescibacteria such as Parcubacteria (OD1) and Microgenomates (OP11) has been found to be prevalent in groundwater, sediment, lake, and other aquifer environments. Recently increasing attention has been paid to this diverse superphylum including > 20 candidate phyla (a large part of the candidate phylum radiation, CPR) because it refreshed our view of the tree of life. However, adaptive traits contributing to its prevalence are still not well known. Results Here, we investigated the genomic features and metabolic pathways of Patescibacteria in groundwater through genome-resolved metagenomics analysis of >600 Gbp sequence data. We observed that, while the members of Patescibacteria have reduced genomes (~ 1 Mbp) exclusively, functions essential to growth and reproduction such as genetic information processing were retained. Surprisingly, they have sharply reduced redundant and nonessential functions, including specific metabolic activities and stress response systems. The Patescibacteria have ultra-small cells and simplified membrane structures, including flagellar assembly, transporters, and two-component systems. Despite the lack of CRISPR viral defense, the bacteria may evade predation through deletion of common membrane phage receptors and other alternative strategies, which may explain the low representation of prophage proteins in their genomes and lack of CRISPR. By establishing the linkages between bacterial features and the groundwater environmental conditions, our results provide important insights into the functions and evolution of this CPR group.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Host genetic variation drives the differentiation in the ecological role of the native Miscanthus root-associated microbiome

Microbiome recruitment is influenced by plant host, but how host plant impacts the assembly, functions, and interactions of perennial plant root microbiomes is poorly understood. Here we examined prokaryotic and fungal communities between rhizosphere soils and the root endophytic compartment in two native Miscanthus species (Miscanthus sinensis and Miscanthus floridulus) of Taiwan and further explored the roles of host plant on root-associated microbiomes. Our results suggest that host plant genetic variation, edaphic factors, and site had effects on the root endophytic and rhizosphere soil microbial community compositions in both Miscanthus sinensis and Miscanthus floridulus, with a greater effect of plant genetic variation observed for the root endophytic communities. Host plant genetic variation also exerted a stronger effect on core prokaryotic communities than on non-core prokaryotic communities in each microhabitat of two Miscanthus species. From rhizosphere soils to root endophytes, prokaryotic co-occurrence network stability increased, but fungal co-occurrence network stability decreased. Furthermore, we found root endophytic microbial communities in two Miscanthus species were more strongly driven by deterministic processes rather than stochastic processes. Root-enriched prokaryotic OTUs belong to Gammaproteobacteria, Alphaproteobacteria, Betaproteobacteria, Sphingobacteriia, and [Saprospirae] both in two Miscanthus species, while prokaryotic taxa enriched in the rhizosphere soil are widely distributed among different phyla. We provide empirical evidence that host genetic variation plays important roles in root-associated microbiome in Miscanthus. The results of this study have implications for future bioenergy crop management by providing baseline data to inform translational research to harness the plant microbiome to sustainably increase agriculture productivity.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Identification of mechanisms driving heterogeneous void growth in ductile aluminum

Void growth plays a central role in ductile fracture, yet the specific mechanisms that control this remain obscure. Classical models, such as those proposed by Rice and Tracey in 1969, are able to capture average rates of void growth, but cannot capture the heterogeneity of individual void growth. Building on recent work, the present study employs laboratory-based diffraction contrast tomography and in-situ x-ray computed tomography to investigate the effect of grain structure and other microstructural factors on void growth in an Al-2219 alloy. Crystal plasticity finite element (CP-FE) modeling is used alongside experimental data to evaluate the contributions of local mechanical states, grain orientation, grain size, and neighboring microstructural features. No strong linear relationships are found with any of the considered descriptors and void growth rate. Potential complex nonlinear relationships are explored with the use of a random forest regression model, which identifies initial void volume, void aspect ratio, local normal stress state, local shear stress state, and local equivalent plastic strain (EQPS) as features that most improve void growth rate predictions. The combination of these analyses suggests that these features should be prioritized to improve models of void growth.

Diffraction contrast tomography (DCT)↗
DOE OSTI2025

Data for "Constitutive Down-Regulation of Liguleless Alleles in Sorghum Drives Increased Productivity and Water Use Efficiency"

Plant architecture influences the microenvironment throughout the canopy layer. Plants with a more erect leaf architecture allow for an increase in planting densities and allow more light to reach lower canopy leaves. This is predicted to increase crop carbon assimilation. Frictional resistance to wind reduces air movement in the lower canopy, resulting in higher humidity. By increasing the proportion of canopy photosynthesis in the more humid lower canopy, gains in the efficiency of water use might be expected, although this may be slightly offset by the more open erectophile form canopy. An anatomical feature in members of the Poaceae family that impacts leaf angle is the articulated junction of the sheath and blade, which also bares the ligule and auricles. Mutants, which lack ligules and auricles, show no articulation at this junction, resulting in leaves that are near vertical. In maize, these phenotypes termed liguleless result from null mutations of genes: ZmLG1 (Zm00001eb67740) and ZmLG2 (Zm00001eb147220). In sorghum, SbiRTx430.06G264300 (SbLG1) and SbiRTx430.03G392300 (SbLG2) are annotated as the respective maize homologues. A hair-pin element designed to down-regulate both SbLG1 and SbLG2 was introduced into the grain sorghum genotype RTx430. Derived transgenic events harbouring the hair-pin failed to develop ligules and displayed reduced leaf angles to the vertical, but less vertical than in null mutations. Under field settings, plots sown with these sorghum events having an erect architecture phenotype displayed an increase in photosynthesis in lower canopy levels, which led to increases in above-ground biomass and seed yield, without an increase in water use.

Genome Engineering↗
DOE OSTI2024

Scalable stable comb-to-tone integrated RF photonic drive for superconducting qubits

The recent advent of quantum computing has the potential to overhaul security, communications, and scientific modeling. Superconducting qubits are a leading platform that is advancing noise-tolerant intermediate-scale quantum processors. The implementation requires scaling to large numbers of superconducting qubits, circuit depths, and gate speeds, wherein high-purity RF signal generation and effective cabling transport are desirable. Fiber photonic-enhanced RF signal generation has demonstrated the principle of addressing both signal generation and transport requirements, supporting intermediate qubit numbers and robust packaging efforts; however, fiber-based approaches to RF signal distribution are often bounded by their phase instability. Here, we present a silicon photonic integrated circuit-based version of a photonic-enhanced RF signal generator that demonstrates the requisite stability, as well as a path towards the necessary signal fidelity.

47 OTHER INSTRUMENTATION↗
DOE OSTI2022

Cbp1, a fungal virulence factor under positive selection, forms an effector complex that drives macrophage lysis

Intracellular pathogens secrete effectors to manipulate their host cells. Histoplasma capsulatum (Hc) is a fungal intracellular pathogen of humans that grows in a yeast form in the host. Hc yeasts are phagocytosed by macrophages, where fungal intracellular replication precedes macrophage lysis. The most abundant virulence factor secreted by Hc yeast cells is Calcium Binding Protein 1 (Cbp1), which is absolutely required for macrophage lysis. Here we take an evolutionary, structural, and cell biological approach to understand Cbp1 function. We find that Cbp1 is present only in the genomes of closely related dimorphic fungal species of the Ajellomycetaceae family that lead primarily intracellular lifestyles in their mammalian hosts (Histoplasma, Paracoccidioides, and Emergomyces), but not conserved in the extracellular fungal pathogen Blastomyces dermatitidis. We observe a high rate of fixation of non-synonymous substitutions in the Cbp1 coding sequences, indicating that Cbp1 is under positive selection. We determine the de novo structures of Hc H88 Cbp1 and the Paracoccidioides americana (Pb03) Cbp1, revealing a novel “binocular” fold consisting of a helical dimer arrangement wherein two helices from each monomer contribute to a four-helix bundle. In contrast to Pb03 Cbp1, we show that Emergomyces Cbp1 orthologs are unable to stimulate macrophage lysis when expressed in the Hc cbp1 mutant. Consistent with this result, we find that wild-type Emergomyces africanus yeast are able to grow within primary macrophages but are incapable of lysing them. Finally, we use subcellular fractionation of infected macrophages and indirect immunofluorescence to show that Cbp1 localizes to the macrophage cytosol during Hc infection, making this the first instance of a phagosomal human fungal pathogen directing an effector into the cytosol of the host cell. We additionally show that Cbp1 forms a complex with Yps-3, another known Hc virulence factor that accesses the cytosol. Taken together, these data imply that Cbp1 is a fungal virulence factor under positive selection that localizes to the cytosol to trigger host cell lysis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Phylogenomic Analyses of Non-Dikarya Fungi Supports Horizontal Gene Transfer Driving Diversification of Secondary Metabolism in the Amphibian Gastrointestinal Symbiont, Basidiobolus

Research into secondary metabolism (SM) production by fungi has resulted in the discovery of diverse, biologically active compounds with significant medicinal applications. The fungi rich in SM production are taxonomically concentrated in the subkingdom Dikarya, which comprises the phyla Ascomycota and Basidiomycota. Here, we explore the potential for SM production in Mucoromycota and Zoopagomycota, two phyla of nonflagellated fungi that are not members of Dikarya, by predicting and identifying core genes and gene clusters involved in SM. The majority of non-Dikarya have few genes and gene clusters involved in SM production except for the amphibian gut symbionts in the genus Basidiobolus. Basidiobolus genomes exhibit an enrichment of SM genes involved in siderophore, surfactin-like, and terpene cyclase production, all these with evidence of constitutive gene expression. Gene expression and chemical assays also confirm that Basidiobolus has significant siderophore activity. Finally, the expansion of SMs in Basidiobolus are partially due to horizontal gene transfer from bacteria, likely as a consequence of its ecology as an amphibian gut endosymbiont.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

ReachNow EV Driving Data From Seattle, WA, Portland, OR, and New York, NY

ReachNow provided Idaho National Laboratory (INL) with a dataset describing approximately 49,000 trips taken by customers and employees in approximately 100 BMW i3 EVs operating in ReachNow's free-floating car-sharing fleets in Seattle, WA, Portland, OR, and New York, NY between May 2016 and February 2017. Data fields include vehicle rental period start and end timestamps, the location where vehicles were parked at the start and end of rental periods, and distance driven during rental periods. A field categorizing the user during each rental period is also included. This field makes it possible to identify when vehicles were rented by customers and when vehicles were driven by fleet management team employees to reposition, charge, or service the vehicles.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2026

ReachNow EV Driving Data From Seattle, WA, Portland, OR, and New York, NY

ReachNow provided Idaho National Laboratory (INL) with a dataset describing approximately 49,000 trips taken by customers and employees in approximately 100 BMW i3 EVs operating in ReachNow's free-floating car-sharing fleets in Seattle, WA, Portland, OR, and New York, NY between May 2016 and February 2017. Data fields include vehicle rental period start and end timestamps, the location where vehicles were parked at the start and end of rental periods, and distance driven during rental periods. A field categorizing the user during each rental period is also included. This field makes it possible to identify when vehicles were rented by customers and when vehicles were driven by fleet management team employees to reposition, charge, or service the vehicles.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2025

Data for Machado-Silva et al. (2024), "Short-Term Groundwater Level Fluctuations Drive Subsurface Redox Variability"

This dataset contains the analytical data reported in Machado-Silva et al. (2024) as part of the COMPASS-FME project, which seeks to advance a scalable, predictive understanding of the fundamental biogeochemical processes, ecological structure, and ecosystem dynamics that distinguish coastal terrestrial-aquatic interfaces from the purely terrestrial or aquatic systems to which they are coupled. The dataset consists of water quality parameters as well as redox potential, water content, and electrical conductivity. These data were collected in 2022 in Crane Creek (CRC), Portage River (PTR), and Old Woman Creek (OWC). Each of these sites included uplands (UP), transitions (TR), wetland-transition edge (WTE), and wetland (W) zones. The sites represent replicates of the Lake Erie terrestrial-aquatic interface under fluctuating water levels and are located in well-preserved areas with natural or restored marsh and forest cover.This dataset consists of a single data file (Machado_Silva_et_al_2024_EST_data.csv) that is in comma-separated value (CSV) format. No special software is required to read it.This dataset uses the ESS-DIVE Hydrologic Monitoring Reporting Format 1.0.

54 ENVIRONMENTAL SCIENCES↗