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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 829 records · Page 46
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Comparing multi-source urban flood indicators: satellite, simulation, and citizen-reported data

Urban flooding arises from complex mechanisms, making it challenging to capture accurately with a single detection method. This study evaluates three complementary approaches to detect flooding across three Chicago neighborhoods: (i) Sentinel-1 synthetic aperture radar (SAR), offering weather-independent, high-resolution (10 m) imagery of surface inundation; (ii) the storm water management model (SWMM), simulating combined sewer overflow and drainage performance; and (iii) citizen-generated 311 service requests, capturing observed flooding impacts. By analyzing six storms ranging from severe to mild, we examine how each source uniquely contributes to identifying urban flood events. SAR imagery effectively identifies standing water but can miss brief flooding due to satellite revisit constraints. SWMM provides detailed insights into system-wide drainage behavior yet may underestimate localized street-level flooding. Meanwhile, 311 calls reflect real-world flooding impacts but are vulnerable to underreporting. Statistical overlap analysis highlights chronic flood hotspots repeatedly identified across multiple detection methods, indicating persistent infrastructure and topographic vulnerabilities. Temporal analysis further reveals that while SWMM flooding aligns closely with rainfall peaks, 311 calls typically precede or persist beyond these peaks. Our findings emphasize the value of using satellite observations, hydrological modeling, and resident-reported data in a complementary manner to better interpret patterns in flood timing, severity, and spatial distribution—providing insights that can inform targeted infrastructure improvements and contribute to urban flood resilience planning.

311↗
DOE OSTI2025

Comparative Performance Evaluation of Large Language Models for Extracting Molecular Interactions and Pathway Knowledge

Understanding the interactions and regulatory relationships among biomolecules is essential for deciphering complex biological systems and elucidating the mechanisms behind diverse biological functions. Traditionally, the collection of such molecular interaction data has relied on expert curation, a process that is both time-consuming and labor-intensive. To address these limitations, this study explores the use of large language models (LLMs) to automate the genome-scale extraction of molecular interaction knowledge. Here, we evaluate the performance of various LLMs on key biological tasks, including the identification of protein-protein interactions, detection of genes associated with pathways influenced by low-dose radiation, and inference of gene regulatory relationships. Our findings demonstrate that larger LLMs tend to perform better, particularly in extracting intricate gene and protein interactions. Despite their strengths, these models face challenges in recognizing functionally diverse gene groups and highly correlated regulatory relationships. Through a comprehensive analysis using established molecular interaction and pathway databases, we show that LLMs possess the potential to identify relevant biomolecules and predict their interactions, offering valuable insights and marking a significant step toward AI-driven biological knowledge discovery.

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗
DOE OSTI2022

Effects of short-interval reburns in the boreal forest on soil bacterial communities compared to long-interval reburns

Abstract Increasing fire frequency in some biomes is leading to fires burning in close succession, triggering rapid vegetation change and altering soil properties. We studied the effects of short-interval (SI) reburns on soil bacterial communities of the boreal forest of northwestern Canada using paired sites (n = 44). Both sites in each pair had burned in a recent fire; one site had burned within the previous 20 years before the recent fire (SI reburn) and the other had not. Paired sites were closely matched in prefire ecosite characteristics, prefire tree species composition, and stand structure. We hypothesized that there would be a significant effect of short vs. long fire-free intervals on community composition and that richness would not be consistently different between paired sites. We found that Blastococcus sp. was consistently enriched in SI reburns, indicating its role as a strongly ‘pyrophilous’ bacterium. Caballeronia sordidicola was consistently depleted in SI reburns. The depletion of this endophytic diazotroph raises questions about whether this is contributing to—or merely reflects—poor conifer seedling recolonization post-fire at SI reburns. While SI reburns had no significant effect on richness, dissimilarity between short- and long-interval pairs was significantly correlated with difference in soil pH, and there were small significant changes in overall community composition.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Comparative chemical genomic profiling across plant-based hydrolysate toxins reveals widespread antagonism in fitness contributions

Abstract The budding yeast Saccharomyces cerevisiae has been used extensively in fermentative industrial processes, including biofuel production from sustainable plant-based hydrolysates. Myriad toxins and stressors found in hydrolysates inhibit microbial metabolism and product formation. Overcoming these stresses requires mitigation strategies that include strain engineering. To identify shared and divergent mechanisms of toxicity and to implicate gene targets for genetic engineering, we used a chemical genomic approach to study fitness effects across a library of S. cerevisiae deletion mutants cultured anaerobically in dozens of individual compounds found in different types of hydrolysates. Relationships in chemical genomic profiles identified classes of toxins that provoked similar cellular responses, spanning inhibitor relationships that were not expected from chemical classification. Our results also revealed widespread antagonistic effects across inhibitors, such that the same gene deletions were beneficial for surviving some toxins but detrimental for others. This work presents a rich dataset relating gene function to chemical compounds, which both expands our understanding of plant-based hydrolysates and provides a useful resource to identify engineering targets.

09 BIOMASS FUELS↗
DOE OSTI2021

Comparative genome analyses suggest a hemibiotrophic lifestyle and virulence differences for the beech bark disease fungal pathogens Neonectria faginata and Neonectria coccinea

Abstract Neonectria faginata and Neonectria coccinea are the causal agents of the insect-fungus disease complex known as beech bark disease (BBD), known to cause mortality in beech forest stands in North America and Europe. These fungal species have been the focus of extensive ecological and disease management studies, yet less progress has been made toward generating genomic resources for both micro- and macro-evolutionary studies. Here, we report a 42.1 and 42.7 mb highly contiguous genome assemblies of N. faginata and N. coccinea, respectively, obtained using Illumina technology. These species share similar gene number counts (12,941 and 12,991) and percentages of predicted genes with assigned functional categories (64 and 65%). Approximately 32% of the predicted proteomes of both species are homologous to proteins involved in pathogenicity, yet N. coccinea shows a higher number of predicted mitogen-activated protein kinase genes, virulence determinants possibly contributing to differences in disease severity between N. faginata and N. coccinea. A wide range of genes encoding for carbohydrate-active enzymes capable of degradation of complex plant polysaccharides and a small number of predicted secretory effector proteins, secondary metabolite biosynthesis clusters and cytochrome oxidase P450 genes were also found. This arsenal of enzymes and effectors correlates with, and reflects, the hemibiotrophic lifestyle of these two fungal pathogens. Phylogenomic analysis and timetree estimations indicated that the N. faginata and N. coccinea species divergence may have occurred at ∼4.1 million years ago. Differences were also observed in the annotated mitochondrial genomes as they were found to be 81.7 kb (N. faginata) and 43.2 kb (N. coccinea) in size. The mitochondrial DNA expansion observed in N. faginata is attributed to the invasion of introns into diverse intra- and intergenic locations. These first draft genomes of N. faginata and N. coccinea serve as valuable tools to increase our understanding of basic genetics, evolutionary mechanisms and molecular physiology of these two nectriaceous plant pathogenic species.

Salgado-Salazar, Catalina↗
DOE OSTI2021

Comparative phylogenetics of repetitive elements in a diverse order of flowering plants (Brassicales)

Genome sizes of plants have long piqued the interest of researchers due to the vast differences among organisms. However, the mechanisms that drive size differences have yet to be fully understood. Two important contributing factors to genome size are expansions of repetitive elements, such as transposable elements (TEs), and whole-genome duplications (WGD). Although studies have found correlations between genome size and both TE abundance and polyploidy, these studies typically test for these patterns within a genus or species. The plant order Brassicales provides an excellent system to further test if genome size evolution patterns are consistent across larger time scales, as there are numerous WGDs. This order is also home to one of the smallest plant genomes, Arabidopsis thaliana—chosen as the model plant system for this reason—as well as to species with very large genomes. With new methods that allow for TE characterization from low-coverage genome shotgun data and 71 taxa across the Brassicales, we confirm the correlation between genome size and TE content, however, we are unable to reconstruct phylogenetic relationships and do not detect any shift in TE abundance associated with WGD.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Comparative transcriptomics provides insights into molecular mechanisms of zinc tolerance in the ectomycorrhizal fungus Suillus luteus

Zinc (Zn) is a major soil contaminant and high Zn levels can disrupt growth, survival, and reproduction of fungi. Some fungal species evolved Zn tolerance through cell processes mitigating Zn toxicity, although the genes and detailed mechanisms underlying mycorrhizal fungal Zn tolerance remain unexplored. To fill this gap in knowledge, we investigated the gene expression of Zn tolerance in the ectomycorrhizal fungus Suillus luteus. We found that Zn tolerance in this species is mainly a constitutive trait that can also be environmentally dependent. Zinc tolerance in S. luteus is associated with differences in the expression of genes involved in metal exclusion and immobilization, as well as recognition and mitigation of metal-induced oxidative stress. Differentially expressed genes were predicted to be involved in transmembrane transport, metal chelation, oxidoreductase activity, and signal transduction. Some of these genes were previously reported as candidates for S. luteus Zn tolerance, while others are reported here for the first time. Our results contribute to understanding the mechanisms of fungal metal tolerance and pave the way for further research on the role of fungal metal tolerance in mycorrhizal associations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Viral niche-partitioning: comparative genomics of giant viruses across environmental gradients in a high Arctic freshwater-saltwater lake

Giant viruses (GVs; Nucleocytoviricota) impact the biology and ecology of a wide range of eukaryotic hosts, with implications for global biogeochemical cycles. Here, we investigated GV niche separation in highly stratified Lake A at the northern coast of Ellesmere Island, Nunavut, Canada. This lake is composed of a layer of ice-covered freshwater that overlies saltwater derived from the ancient Arctic Ocean, and it therefore provides a broad gradient of environmental conditions and ecological habitats, each with a distinct protist community and rich assemblages of associated GVs. The upper layer (mixolimnion) had measurable light and oxygen, and contained diverse GVs linked to photosynthetic protists, indicating adaptation to surface biotic and abiotic conditions. In contrast, the saline lower layer (monimolimnion), lacking oxygen and light, hosted GVs associated with predicted heterotrophic protists, some of which are known for a predatory lifestyle, and with several viral genes suggesting adaptation to deep-water anaerobic conditions. Our observations underscore the coupling between physical and chemical gradients, microeukaryotes and their associated GVs in Lake A, and provide insight into the potential for GVs to directly and indirectly impact host metabolism. There were similarities between the genetic composition of GVs and the metabolic processes of their potential hosts, implying co-evolution and niche-adaptation within the lake habitats. Notably, we found a greater presence of viral rhodopsins in deeper water layers, suggesting an evolutionary relationship with potential hosts capable of supplementing their energetic needs to thrive in low energy, anoxic conditions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Susceptibility of pESI positive Salmonella to treatment with biocide chemicals approved for use in poultry meat processing as compared to Salmonella without the pESI plasmid

Abstract Salmonella is a common cause of human foodborne illness, which is frequently associated with consumption of contaminated or undercooked poultry meat. Serotype Infantis is among the most common serotypes isolated from poultry meat products globally. Isolates of serotype Infantis carrying the pESI plasmid, the most dominant strain of Infantis, have been shown to exhibit oxidizer tolerance. Therefore, 16 strains of Salmonella with and without pESI carriage were investigated for susceptibility to biocide chemical processing aids approved for use in US poultry meat processing: peracetic acid (PAA), cetylpyridinium chloride (CPC), calcium hypochlorite, and sodium hypochlorite. Strains were exposed for 15 s to simulate spray application and 90 min to simulate application in an immersion chiller. All strains tested were susceptible to all concentrations of PAA, CPC, and sodium hypochlorite when applied for 90 min. When CPC, calcium hypochlorite, and sodium hypochlorite were applied for 15 s to simulate spray time, strains responded similarly to each other. However, strains responded variably to exposure to PAA. The variation was not statistically significant and appears unrelated to pESI carriage. Results highlight the necessity of testing biocide susceptibility in the presence of organic material and in relevant in situ applications.

Biotechnology & Applied Microbiology↗
DOE OSTI2020

PhycoCosm, a comparative algal genomics resource

Abstract Algae are a diverse, polyphyletic group of photosynthetic eukaryotes spanning nearly all eukaryotic lineages of life and collectively responsible for ∼50% of photosynthesis on Earth. Sequenced algal genomes, critical to understanding their complex biology, are growing in number and require efficient tools for analysis. PhycoCosm (https://phycocosm.jgi.doe.gov) is an algal multi-omics portal, developed by the US Department of Energy Joint Genome Institute to support analysis and distribution of algal genome sequences and other ‘omics’ data. PhycoCosm provides integration of genome sequence and annotation for >100 algal genomes with available multi-omics data and interactive web-based tools to enable algal research in bioenergy and the environment, encouraging community engagement and data exchange, and fostering new sequencing projects that will further these research goals.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Na 22 activation level measurements of fused silica rods in the LHC target absorber for neutrals compared to simulations

The Target Absorbers for Neutrals (TANs) are located in a high intensity radiation environment inside the tunnel of the Large Hadron Collider (LHC). TANs are positioned about 140 m downstream from the beam interaction points. Seven 40-cm long fused silica rods with different dopant specifications were irradiated in the TAN by the Beam RAte of Neutrals (BRAN) detector group during p + p data taking from 2016 to 2018 at the LHC. The peak dose delivered to the fused silica rods was 18 MGy. We report measurements of the 22 Na activation of the fused silica rods carried out at the University of Illinois at Urbana-Champaign and Argonne National Laboratory. At the end of the irradiation campaign, the maximum 22 Na activity observed was A = 21 kBq/cm 3 corresponding to a density, ρ = 2.5 x 10 12 /cm 3 , of 22 Na nuclei. FLUKA Monte Carlo simulations have been performed by the CERN FLUKA team to estimate 22 Na activities for the irradiated BRAN rod samples. The simulations reproduce the 22 Na activity profile measured along the rods, with a 35% underestimation of the experimental measurement results.

43 PARTICLE ACCELERATORS↗
DOE OSTI2020

Measurement of diamond nucleation rates from hydrocarbons at conditions comparable to the interiors of icy giant planets

We present measurements of the nucleation rate into a diamond lattice in dynamically compressed polystyrene obtained in a pump-probe experiment using a high-energy laser system and in situ femtosecond x-ray diffraction. Different temperature-pressure conditions that occur in planetary interiors were probed. For a single shock reaching 70 GPa and 3000 K no diamond formation was observed, while with a double shock driving polystyrene to pressures around 150 GPa and temperatures around 5000 K nucleation rates between 10 29 and 10 34 m –3 s –1 were recorded. These nucleation rates do not agree with predictions of the state-of-the-art theoretical models for carbon-hydrogen mixtures by many orders of magnitude. Our data suggest that there is significant diamond formation to be expected inside icy giant planets like Neptune and Uranus.

43 PARTICLE ACCELERATORS↗