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At least 1,045 records · Page 58
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Defining Lipidomic Responses to Coronavirus Infection

Highly pathogenic human coronavirus infection can cause a severe atypical, rapid onset pneumonia with a mortality rate of up to 10% for severe acute respiratory syndrome coronavirus 1 (SARS-CoV 1), 35% for Middle East respiratory syndrome coronavirus (MERS-CoV), or 1% for severe acute respiratory syndrome coronavirus 2 (SARS-CoV 2 causative agent of COVID 19). While medical countermeasures successfully controlled the worldwide SARS-CoV epidemic, the MERS-CoV epidemic is still ongoing and continues to be a concern for travelers in the Middle East and the multi-year SARS-CoV 2 pandemic underscore the importance of defining biomarkers that are diagnostic and/or predictive of severe disease outcomes for respiratory viruses. Systems biology approaches provide global snapshots of infection induced changes in host cells/tissues and provide extremely rich datasets for understanding host pathogen interactions. Metabolites, especially lipids, are critical for viral replication but less is understood about infection induced changes to lipids due to limits in lipid species detection and identification. To characterize how individual lipid species and proteins with lipid associated functions contribute to highly pathogenic human coronavirus replication and disease severity, existing datasets were probed to determine cell type specific lipid responses to MERS-CoV infection and verification studies were performed to determine if modification of the host lipid signature (by inhibiting enzymatic functions that produce specific lipid species) can perturb CoV replication in human lung cells. MERS-CoV infects human lung epithelial, endothelial and fibroblast cells. All three cell types were infected with MERS-CoV and samples collected to analyze lipids, proteins, metabolites, and transcripts from 12 to 48 hours post infection. Time matched mock-infected cells were collected in parallel for each cell type. Following sample and statistical analysis, functional enrichment and bioinformatic analysis was performed to identify differentially expressed lipids and proteins. Two lipid species were found to be significantly upregulated following MERS-CoV infection, ceramides, and triacylglycerol both of which are indicative of cells undergoing apoptotic cell death. In contrast, sphingomyelins (lipid molecules that can serve as a precursor for one pathway for ceramide synthesis) had significantly decreased expression in MERS-CoV infected cells. An inhibitor of acid sphingomyelinase (that converts sphingomyelin to ceramides and phosphorylcholine) reduced MERS-CoV replication suggesting that production of ceramides is key for successful viral replication and transmission. Acyl-CoA-synthetase 3 (ACSL3), the only protein whose function is lipid associated and had increased differential expression in our dataset, regulates the synthesis of triacylglycerol (increased expression). Inhibitors that directly block ACSL3 (Triacsin C) but not steps later in the triacylglycerol synthesis pathway (Etomoxir) inhibit MERS-CoV replication suggesting that triacylglycerol production and/or ACSL3 activity is also key for viral replication. ACSL3 expression is also upregulated in lung cancer cells and is predicted to promote continued cell viability which would also enhance viral replication. The differentially expressed lipid and lipid-associated protein species identified in our studies suggest that MERS-CoV infection is activating cellular death pathways to limit the number of cells that become infected but also stimulating the production of lipid-associated enzymes that can prolong host cell viability and the amount of time progeny virions can be produced and released. As the inhibitors that worked against MERS-CoV infection were also efficacious against SARS-CoV 2 infection, countermeasures that target these host pathways may provide novel ways to block highly pathogenic human coronavirus infection and/or prevent severe disease outcomes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

The Influence of Soil Properties on Sea-Breeze Circulations in the Southeast U.S.

Sea-breeze circulations (SBCs) are common weather phenomena at and near coastal regions. They form because of a thermal gradient between the land surface at the coast and the sea surface. In a mid-day regime, a “thermal low” generated at the warm coast will lead to rising air motion, creating a wind shift coming from the sea near the surface displacing the coastal air. A “return flow” moving back towards the sea is generated by upper-level divergence because of the rising motion from the thermal low. SBCs propagate and serve as a method of urban pollutant dispersion in the Los Angeles region of California and are constrained to the coast due to the topography of surrounding mountains serving as a boundary for further inland propagation. Within the northeast U.S. SBCs are seen in the warm season but tend to remain coastally bound due to Coriolis distortion over long distances. Within the southeast U.S. (SEUS), the paradigmatic example of SBCs occurs over the Florida peninsula, where thunderstorms form on a nearly daily occurrence due to the convergence of SBCs from the east and west sides of the peninsula. However, there are further examples of sea-breezes in the SEUS that warrant study. Within the region bordering the SEUS and the Mid-Atlantic, just east of the southern Appalachian Mountains, warm-season SBCs form at the coast of Georgia and the Carolinas. Relatively flat topography ~150-200km inland allows for mostly unimpeded inland SBC propagation. Through visual analysis, Viner et al. catalogued several SBCs that propagated as far inland as the Central Savannah River Area surrounding Augusta, Georgia. Wermter et al. found that while the land-sea thermal gradient at the coast can influence coastal SBC genesis, the inland-coastal thermal gradient over the land is the primary influencer on the speed and depth of inland propagation of SBCs in this region. Additionally, soil moisture itself is a known correlative factor to sea-breeze formation, as it influences the soil temperature and the thermal gradient needed for SBC genesis and inland penetration. Physick determined that higher latent heat fluxes associated with wetter soil dampen the land-sea thermal gradient and suppress the formation of a SBC. Physick determined that higher latent heat fluxes associated with wetter soil dampen the land-sea thermal gradient and suppress the formation of a SBC. Conversely, drier soil enhances the thermal gradient and promotes SBC formation. However, while there is an inverse relationship between soil moisture and SBCs, higher soil moisture can actually promote more convective rainfall following a SBC if it does not significantly impact the thermal gradient. While the relationship between soil moisture and SBC formation has been conceptually explored and modeled numerically, there is a research gap in observed connections. The Soil Moisture Active Passive (SMAP) satellite mission has been operational since 2015 and has been used to create high-resolution re-analytical Level 4 (L4) datasets of soil moisture and soil temperature at different soil depths: the surface (0-5cm) and rootzone (0-1m). The surface soil temperature effectively acts as the “skin temperature” of the surface at these levels, and a spatial map of the land-sea as well as the coastal-inland thermal gradients can be represented. SMAP data are also assimilated in some atmospheric models such at the High Resolution Rapid Refresh (HRRR) mesoscale model. We propose leveraging the use of SMAP products to fill in spatial gaps left by weather and mesonet stations within the SEUS region, as well as assessing the effectiveness of utilizing SMAP products towards SBC forecasting in both deterministic and machine learning (ML) models.

58 GEOSCIENCES↗
DOE OSTI2023

Performance Assessment Maintenance Plan for the Active Low-Level Burial Ground Trenches 31, 34, and 94 at the Hanford Site

This report documents the maintenance plan for the Hanford Site 200 West Area Active Low-Level Burial Ground Trenches 31 and 34 and 200 East Area Active Trench 94 performance assessment (PA). The PA maintenance plan is one of several supporting documents that are compendiums to the active trenches (Trenches 31, 34, and 94) PA as required in DOE O 435.1, Radioactive Waste Management . The PA is documented in DOE/RL-2021-26, Performance Assessment of Active Trenches in 200 East and West Low-Level Burial Grounds at the Hanford Site . This plan follows the requirements and outline specified in the applicable U.S. Department of Energy (DOE) standard used for developing documents supporting DOE-STD-5002-2017, Disposal Authorization Statement and Tank Closure Documentation . This maintenance plan summarizes the following major activities DOE plans to conduct to maintain the Trenches 31, 34, and 94 PA: Monitoring; Research and development; Planned reviews and analyses; Revisions of Trenches 31, 34, and 94 PA. The planned research and development activities relate to evaluating the key assumptions, including evaluating conceptual model assumptions and parameter value assumptions used in the PA. The planned research and development activities include those that are designed to track the release mechanisms for Category 1, Category 3, and uranium billet waste sources, as well as continued characterization and related modeling of the natural environment in the Central Plateau of the Hanford Site. In addition, the planned research and development activities include focused testing and evaluation of engineered and natural materials to reduce the uncertainty in the conceptual models and parameter values used in the PA. All key and secondary issues identified during the review of the PA by the Low-Level Waste Disposal Facility Federal Review Group have been resolved prior to finalization of the PA. There are no outstanding issues.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2023

Performance Assessment Closure Plan for the Active Low-Level Burial Ground Trenches 31, 34, and 94 at the Hanford Site

This report documents the closure plan for the active trenches within the Low-Level Burial Grounds of the Hanford Site, namely Trenches 31 and 34 in the 200 West Area and Trench 94 in 200 East Area. This closure plan is developed to meet the requirements of DOE O 435.1, Radioactive Waste Management. It is one of the several technical basis documents, along with the performance assessment (DOE/RL-2021-26, Performance Assessment of Active Trenches in 200 East and West Low-Level Burial Grounds at the Hanford Site), which is required for maintaining the Operating Disposal Authorization Statement as described in DOE-STD-5002-2017, Disposal Authorization Statement and Tank Closure Documentation.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2024

Assessing Impacts of Waves on Hub-Height Winds off the U.S. West Coast Using Lidar Buoys and Coupled Modeling Approaches

Given the importance of offshore wind energy development to the U.S. clean energy targets, it is vital to be able to characterize the wind resource in that environment accurately. Toward that end, two Bureau of Ocean Energy Management buoys equipped with Doppler lidar are being maintained by Pacific Northwest National Laboratory on behalf of the Department of Energy and deployed to regions of potential offshore wind development. In addition to standard meteorological and oceanographic measurements, the buoys document the wind profile between about 40 m and 250 m above the sea surface through Doppler lidar retrievals. After a multiyear deployment of two buoys along the U.S. East Coast, the buoys were redeployed to the U.S. West coast from 2020 – 2022 to locations near the Humboldt and Morro Bay lease areas. The buoys provide nearly continuous, multiyear datasets that can be used to evaluate predictions of hub-height (~100 m) wind speed for standard atmospheric models in the region. In the absence of measurements at the study site, offshore wind developers rely on model-based data to assess site conditions. Potential sources of model error in this environment include under-resolution or misrepresentation of coastal topographically forced flows, marine boundary layer dynamics and the evolution of their associated cloud and turbulence fields, the role of upwelling and other currents on surface heat fluxes into the boundary layer, and the impact of wave fields on surface momentum fluxes and thus the wind speed profile. In particular, most predictive models of wind speed do not predict wave fields at all, relying on parameterizations to represent their effects. In thus study, we focus on evaluating the role of wind / wave interactions on modeled hub-height wind speed and error by using the Coupled Ocean–Atmosphere–Wave–Sediment–Transport Modeling System to capture two-way interactions between an atmospheric model (Weather Research and Forecasting (WRF)) and a wave model (WAVEWATCHIII (WW3)) and compare to both stand-alone WRF and one-way coupled WRF / WW3 configurations. Our approach is similar to that used in Gaudet et al. (2022) to evaluate wind / wave coupling over the U.S. East Coast, but applied to the very different environment of the U.S. West Coast. We show examples for two cases, a cold-season frontal case and a warm-season low-level jet case. We find that wind / wave coupling makes little impact on model error for these cases at the location of the lidar buoys, for which other misrepresentations of model physics seems to be responsible for model-observation discrepancies. However, domain-wide evaluations, which also make use of the National Buoy Data Center network, show that a two-way coupling approach is less prone to systematic errors in the hub-height wind field than the one-way coupled approach. WRF resolution of kilometer-scale or less is needed to properly capture the sharp wind speed gradients that can be found along the coastline, and WW3 simulations driven by the downscaled WRF produce better bulk and spectral wave fields when compared to observations. Implications of the results for wind resource characterization are then discussed.

17 WIND ENERGY↗
DOE OSTI2024

Hydro-EKG: In-Stream Streaming-potential (SP) Electrical Monitoring of the Lifeblood of Watersheds during Disturbance

In order to develop improved methods for characterization and monitoring of hyporheic exchange along stream and river corridors, this project evaluated and compared concentration (C) and discharge (Q) correlations between the dam-managed, intermittent Rio Grande River and the perennial East Fork Poplar Creek in Oak Ridge, Tennessee. Additionally, a multimethod geoelectric survey was implemented between January and March 2022 along a 220-meter long reach of the bedrock-lined East Fork Poplar Creek in Oak Ridge, Tennessee to identify locations of surface-water and groundwater exchange in the bedrock-lined streambed and characterize the subsurface flow paths that convey water between the stream and flood plain.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Investigating spatial variability of aerosol, cloud condensation nuclei, and ice nucleating particles in mountainous terrain

The ASR-supported Surface Atmosphere Integrated field Laboratory (SAIL) in the East River Watershed (ERW) of the Upper Colorado River Basin in southwestern Colorado ran from fall 2021 to spring 2023. Two monitoring sites were deployed in the East River Watershed as part of SAIL. The two sites were the Aerosol Observation System (AOS) located on Crested Butte Ski Mountain, and the ARM Mobile Facility (AMF-2), located at the Rocky Mountain Biological Laboratory in Gothic, Colorado. To gain a more comprehensive understanding of aerosols in complex, mountainous terrain, Handix Scientific deployed SAIL-Net, a distributed network of six measurement nodes spanning the domain of the SAIL research area from October 2021 to July 2023. Each node measured aerosol particles between 140 nm and 3.4 μm in diameter using a small particle counter (POPS, (Gao et al., 2016)), CNN using a miniature CCN counter (CloudPuck), and INP using the Time-Resolved Aerosol Filter Sampler (TRAPS, Creamean et al. (2018)). Our approach was similar to other studies that aimed to better characterize and understand aerosols and gas-phase pollutants using networks of lower-cost sensors (Caubel et al., 2019; Kelly et al., 2021; Asher et al., 2022). Such studies have identified neighborhood-level variations in pollutant concentrations (Schneider et al., 2017; Popoola et al., 2018; Caubel et al., 2019). Small-scale variations such as this are poorly represented in models and poorly measured by a single monitoring system (Caubel et al., 2019). Previous work has shown the representation error (the ability of measurements to represent a larger area) increases with complex orography, leading to decreases in model accuracy (Schutgens et al., 2017). The overall goal of SAIL-Net was to improve our understanding of the variability of aerosol in ERW, thus increasing our knowledge of aerosol-cloud interactions in this region and informing the usefulness of distributed networks of measurements for future studies.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Phased Construction Completion Report for Decontamination Laundry Demolition at the Oak Ridge National Laboratory

This Phased Construction Completion Report (PCCR) documents completion of demolition, waste disposition, and slab stabilization activities of Building 2523 (Decontamination Laundry) for the Oak Ridge National Laboratory (ORNL). The Decontamination Laundry is located directly north of the intersection of White Oak Avenue and the 2519 Access Road. This demolition scope included the removal of the above-grade structures and facility components associated with Building 2523. This scope included the removal of Building 2523 (and all remaining contents inside), Trailer 2523A (and all remaining contents inside), an above-grade wastewater tank, and a wooden access porch connecting Buildings 2523 and Trailer 2523A. On the north side of Building 2523, above-grade portions of selected remaining foundations/stairs were removed from former Building 2517 to make room to stage waste containers. Building 2621 is west of the Laundry Building and Buildings 2547 and 2649 are to the east, while Building 2525 is to the north. Building 2523 is located within Bethel Valley Exposure Unit (EU) 3. The total area of the EU is approximately 39 acres. The area within EU 3 is bounded by First Street on the west, Central Avenue on the north, Third Street on the east and south. The slab of Building 2523 has been stabilized with a cap of flowable fill concrete and asphalt to contain residual radiological contamination and to provide surface suitable for vehicle parking. No below-grade demolition actions were performed during this task.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2025

Results and lessons learned from accelerating radio frequency modeling using machine learning [slides]

The “advanced tokamak” reactor concept is a leading candidate for a steady state fusion pilot plant. An advanced tokamak (AT) sustains a majority of the required plasma current with effects resulting from maintenance of the peaked pressure at the device center. This current is augmented by auxiliary current drive sources. These auxiliary actuators may consist of neutral particle beams and/or radio frequency (RF) systems such as lower hybrid current drive (LHCD) and high harmonic fast wave (HHFW) current drive using radio and microwaves from antennas. The primary focus of this work is to develop models of RF current profile control suitable for use in integrated modeling frameworks and for real-time control in experiments. Direct physics models of RF current drive can be computationally intensive. In order to achieve predictive times appropriate for the thousands of calls needed in real-time control of experiments and for use in integrated models, we will apply modern machine learning (ML) techniques to accelerate these models and interpolate their results. To generate the fast and accurate models for use in control level algorithms and integrated modeling we need to replace present models with high dimensional interpolation of their results. We will perform additional simulations across a broader parameter range for EAST and other tokamaks in different physics regimes (Alcator C-Mod, DIII-D, WEST, CFETR, ARC, ITER) and combine them into a larger database for training and testing of the ML models. Further testing of the control level models with experimental current profile data from EAST and C-Mod tokamaks will provide additional confirmation of the control level model before integration in a tokamak control system or integrated modeling suite. ML will be used to optimize the selection of training data consisting of RF current driven at different values of density profile, temperature profile, plasma current, and wavenumber. ML will also be used to facilitate classification of current drive from these input data. The output of this effort will be a validated classifier capable of determining the current drive profiles for HHFW CD and LHCD on a mille-second timescale. This will provide a breakthrough capability enabling real-time control of RF driven current profiles in experiments including ITER ICRF and use integrated modeling frameworks requiring thousands of current profile calculations in discharge simulations.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2025

Evaluation of Hanford 200 West Area Tank Farms (241-S/241-SX-/241-U tank farms) Physical Properties Data for Use in Development of West Area Tank Treatment (WATT) Processing

With the recent acceptance of West Area Tank Treatment disposition alternative for 200 West Area tanks at the Hanford Site by the State of Washington and the U.S. Department of Energy, a review was initiated to identify the physical properties data available in the literature for the Hanford 241-S, 241-SX, and 241-U tank farms. The literature reviewed indicated that there is a relatively small set of useful data on physical properties of 200 West Area tanks, and the data that do exist are biased around a narrow range of tank samples. Much of the testing between the 1990s and mid-2010s was intended to support either enhanced sludge washing or feed delivery to the Pretreatment Facility at the Hanford Waste Treatment and Immobilization Plant. As such, some physical properties of 200 West Area samples were measured under conditions that are no longer relevant. Because of the distinctly different nature of many past processes at the 200 West Area compared to the 200 East Area, insight from waste testing in the 200 East Area waste should be used with caution, as there may be significantly different qualities in the physical properties data between these two areas (both in situ and as measured in laboratory analyses). Based on this assessment, there is a need to collect additional physical property data to support planning for 200 West Area retrievals.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2026

Volume Change from Solidification Correlation for Hanford Tank Waste.

The U.S. Department of Energy (DOE), Hanford Field Office’s primary mission is to safely and effectively treat Hanford’s tank waste and deliver environmental remediation. Mixed radioactive waste is stored in the underground tanks at the Hanford Site. It was recently estimated that retrieval of the waste in the 200 West Area underground tanks in the SY, S, SX, and U Tank Farms will result in about 41 million gallons of mixed low-level waste (MLLW) (RPP-RPT-65147, Rev. 1). The current plan is to retrieve at least 22 S, SX, and U Farm tanks and pretreat1 to produce pretreated tank waste (PTW) which will be further treated (including solidification /immobilization) for Resource Conservation and Recovery Act (RCRA) Land Disposal Restriction (LDR) organics and inorganics before being transferred to an offsite out-of-state facility for disposal (RPP-PLAN-66135, Rev. 2). In addition, solidified PTW from the 200 East Area may also be transferred to an offsite out-of-state facility for disposal to ensure availability of critical Double-Shell Tank space, meet retrieval obligations, and optimize 200 East Area operations.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2026

ESnet Watershed Field Science Data Backhaul Campaign Report

ESnet’s Watershed Field Science Data Backhaul Campaign is intended to improve the ability to gather data from sensors deployed across the East River and Trail Creek watersheds, with a special focus on the Snodgrass distributed sensor area, the Pumphouse instruments with co-located U.S. Department of Energy (DOE) Atmospheric Radiation Measurement (ARM) User Facility Surface Atmosphere Integrated Field Laboratory (SAIL) tethered balloon setup, and the former ARM SAIL campaign’s second ARM Mobile Facility (AMF2) site by the Watershed Function Science Focus Area (WFSFA) program. This program is not funded by ARM, but collaborates with ARM as part of the SAIL campaign, collocated with the WFSFA field sites in Colorado’s East River Watershed.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Best Practices for Resilience Hub Development and Management

The Carbon League and its community partners in East St. Louis, Illinois, have identified five facilities to serve as resilience hubs. These hubs are intended to support the local community through a range of services and resources during blue-sky (everyday), gray-sky (pre-event), and black-sky (emergency) conditions. Transforming these facilities into fully functional resilience hubs requires a broad operational improvement and programmatic planning roadmap. This memo outlines best practices to guide the development of these resilience hubs in East St. Louis, including recommendations for infrastructure services; safety and physical protection; community services; operational protocols; and a phased implementation strategy aligned with realistic funding and capacity constraints. Infrastructure recommendations include strengthening electric power, communications, water, sanitation, and transportation/logistics capabilities, all of which are essential for hubs that may serve as cooling and warming centers, distribution points, and information hubs during emergencies. Safety recommendations focus on accessibility, emergency action planning, indoor air quality, and secure storage of critical equipment. A phased roadmap provides guidance from immediate, low-cost readiness actions to long-term optimization and community integration. Performance metrics and maintenance protocols ensure continuous improvement and operational readiness. This guidance draws on best practices that can be used to support the development of resilient, community-centered hubs capable of enhancing public safety, health, and well-being during everyday operations and emergencies alike.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2021

Mitochondrial Genomes of the United States Distribution of Gray Fox (Urocyon cinereoargenteus) Reveal a Major Phylogeographic Break at the Great Plains Suture Zone

We examined phylogeographic structure in gray fox (Urocyon cinereoargenteus) across the United States to identify the location of secondary contact zone(s) between eastern and western lineages and investigate the possibility of additional cryptic intraspecific divergences. We generated and analyzed complete mitochondrial genome sequence data from 75 samples and partial control region mitochondrial DNA sequences from 378 samples to investigate levels of genetic diversity and structure through population- and individual-based analyses including estimates of divergence (FST and SAMOVA), median joining networks, and phylogenies. We used complete mitochondrial genomes to infer phylogenetic relationships and date divergence times of major lineages of Urocyon in the United States. Despite broad-scale sampling, we did not recover additional major lineages of Urocyon within the United States, but identified a deep east-west split (~0.8 million years) with secondary contact at the Great Plains Suture Zone and confirmed the Channel Island fox (Urocyon littoralis) is nested within U. cinereoargenteus. Genetic diversity declined at northern latitudes in the eastern United States, a pattern concordant with post-glacial recolonization and range expansion. Beyond the east-west divergence, morphologically-based subspecies did not form monophyletic groups, though unique haplotypes were often geographically limited. Gray foxes in the United States displayed a deep, cryptic divergence suggesting taxonomic revision is needed. Secondary contact at a common phylogeographic break, the Great Plains Suture Zone, where environmental variables show a sharp cline, suggests ongoing evolutionary processes may reinforce this divergence. Follow-up study with nuclear markers should investigate whether hybridization is occurring along the suture zone and characterize contemporary population structure to help identify conservation units. Comparative work on other wide-ranging carnivores in the region should test whether similar evolutionary patterns and processes are occurring.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

A chromosome-level genome assembly of the Chinese cork oak (Quercus variabilis)

Quercus variabilis (Fagaceae) is an ecologically and economically important deciduous broadleaved tree species native to and widespread in East Asia. It is a valuable woody species and an indicator of local forest health, and occupies a dominant position in forest ecosystems in East Asia. However, genomic resources from Q. variabilis are still lacking. Here, we present a high-quality Q. variabilis genome generated by PacBio HiFi and Hi-C sequencing. The assembled genome size is 787 Mb, with a contig N50 of 26.04 Mb and scaffold N50 of 64.86 Mb, comprising 12 pseudo-chromosomes. The repetitive sequences constitute 67.6% of the genome, of which the majority are long terminal repeats, accounting for 46.62% of the genome. We used ab initio , RNA sequence-based and homology-based predictions to identify protein-coding genes. A total of 32,466 protein-coding genes were identified, of which 95.11% could be functionally annotated. Evolutionary analysis showed that Q. variabilis was more closely related to Q. suber than to Q. lobata or Q. robur. We found no evidence for species-specific whole genome duplications in Quercus after the species had diverged. This study provides the first genome assembly and the first gene annotation data for Q. variabilis. These resources will inform the design of further breeding strategies, and will be valuable in the study of genome editing and comparative genomics in oak species.

Han, Biao↗
DOE OSTI2023

Population Subdivision in the Gopher Frog (Rana capito) across the Fragmented Longleaf Pine-Wiregrass Savanna of the Southeastern USA

Delineating genetically distinct population segments of threatened species and quantifying population connectivity are important steps in developing effective conservation and management strategies aimed at preventing extinction. The gopher frog (Rana capito) is a xeric-adapted, pond-breeding species endemic to the Gulf and Atlantic coastal plains of the southeastern United States. This species has experienced extensive habitat loss and fragmentation in the formerly widespread longleaf pine-wiregrass savanna where it lives, resulting in individual abundance declines and population extinctions throughout its range. We used individual-based clustering methods along with Bayesian inference of historical migration based on almost 1500 multilocus microsatellite genotypes to examine genetic structure in this taxon. Clustering analyses identified panhandle and peninsular populations in Florida as distinct genetic clusters separated by the Aucilla River, consistent with the division between the Coastal Plain and peninsular mitochondrial lineages, respectively. Analysis of historical migration indicated an east–west population divergence event followed by immigration to the east. Together, our results indicate that the genetically distinct Coastal Plain and peninsular Florida lineages should be considered separately for conservation and management purposes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

National Prevalence of Caprine Prion Protein Genetic Variability at Codons 146, 211, and 222 in Goat Herds in the United States

Scrapie is a neurodegenerative disease that impacts sheep and goats, characterized by gradual and progressive changes in neurological function. Recent research shows that the scrapie incubation period is significantly influenced by specific variations in amino acids within the prion protein gene (PRNP). The objective of this study was to estimate the national prevalence of caprine PRNP genetic variability at codons 146, 211, and 222 in goat populations across the United States. A total of 3052 blood, ear tissue, and brain tissue samples were collected from goats from 50 states. The participating states were categorized into four Veterinary Service (VS) district regions. The samples underwent DNA extraction, and the PRNP variants corresponding to codons 146, 211, and 222 were amplified and sequenced. The analysis of PRNP variants, when compared to the PRNP reference sequence, revealed seven alleles in twelve genotypes. The homozygous 146NN, 211RR, and 222QQ alleles, which have been linked to an increased risk of scrapie, were found to be the most prevalent among all the goats. The heterozygous 222QK, 211RQ, 146SD, 146ND, and 146NS alleles and the homozygous 222KK, 146SS, and 146DD alleles, known to be associated with reduced scrapie susceptibility and a prolonged incubation period after experimental challenge, were found in 1.098% (222QK), 2.33% (211RQ), 0.58% (146SD), 3.13% (146ND), 20.68% (146NS), 0.005% (222KK), 3.31% (146SS), and 0.67% (146DD) of goats, respectively. The 222QK allele was found most frequently in goats tested from the east (VS District 1, 1.59%) and southwest (VS District 4, 1.08%) regions, whereas the 211RQ allele was found most often in goats tested from the Midwest (VS District 2, 8.03%) and east (VS District 1, 6.53%) regions. The 146NS allele was found most frequently in goats tested from the northwest (VS District 3, 29.02%) and southwest (VS District 4, 20.69%) regions. Our results showed that the prevalence of less susceptible genotypes at PRNP codon 146 may be sufficient to use genetic susceptibility testing in some herds. This may reduce the number of goats removed as part of a herd clean-up plan and may promote the selective breeding goats for less susceptible alleles in high-risk herds at the national level.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Review of TEAMER Awards for WEC-Sim Support: Preprint

Testing Expertise and Access for Marine Energy Research (TEAMER) is a U.S. Department of Energy Water Power Technologies Office sponsored program, overseen by the Pacific Ocean Energy Trust, which aims to advance the state of marine energy technologies. The program connects technology developers with experts at U.S. facilities, including numerical modeling and analysis facilities, like WEC-Sim. The WEC-Sim facility is supported by the WEC-Sim development team at Sandia National Laboratories and the National Renewable Energy Laboratory. WEC-Sim (Wave Energy Converter SIMulator) is an open-source software for simulating wave energy converters. WEC-Sim can model the multi-body dynamics of devices comprised of bodies, joints, power take-off systems, and mooring systems. Since TEAMER's first round of support in 2020, there have been eighteen TEAMER awards focused on numerical model development in WEC-Sim. TEAMER awards for WEC-Sim support have modeled a wide range of wave energy converter archetypes, including point absorbers, attenuators, oscillating water columns, and many other novel architectures. A wide variety of studies have been conducted, leading to important insights for TEAMER partners and software improvements for WECSim. This article highlights several successful WEC-Sim TEAMER awards. The awards described herein include TEAMER recipients Ocean Motion Technologies, AquaHarmonics, iProTech, East Carolina University, Virginia Tech, Maiden Wave Energy, and the University of Massachusetts Dartmouth. The awards of these seven partners contain a wide range of investigations and cover the creation of baseline hydrodynamic models, PTO modeling, geometry optimization in both boundary element methods and WECSim, and model tuning and validation.

industry support↗