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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 991 records · Page 55
All sourcesNASA NTRSDOE OSTI
DOE OSTI2012

Contribution of Partial Charge Interactions and Base Stacking to the Efficiency of Primer Extension at and beyond Abasic Sites in DNA

During DNA synthesis, base stacking and Watson-Crick (WC) hydrogen bonding increase the stability of nascent base pairs when they are in a ternary complex. To evaluate the contribution of base stacking to the incorporation efficiency of dNTPs when a DNA polymerase encounters an abasic site, we varied the penultimate base pairs (PBs) adjacent to the abasic site using all 16 possible combinations. We then determined pre-steady-state kinetic parameters with an RB69 DNA polymerase variant and solved nine structures of the corresponding ternary complexes. The efficiency of incorporation for incoming dNTPs opposite an abasic site varied between 2- and 210-fold depending on the identity of the PB. We propose that the A rule can be extended to encompass the fact that DNA polymerase can bypass dA/abasic sites more efficiently than other dN/abasic sites. Crystal structures of the ternary complexes show that the surface of the incoming base was stacked against the PB's interface and that the kinetic parameters for dNMP incorporation were consistent with specific features of base stacking, such as surface area and partial charge-charge interactions between the incoming base and the PB. Without a templating nucleotide residue, an incoming dNTP has no base with which it can hydrogen bond and cannot be desolvated, so that these surrounding water molecules become ordered and remain on the PB's surface in the ternary complex. When these water molecules are on top of a hydrophobic patch on the PB, they destabilize the ternary complex, and the incorporation efficiency of incoming dNTPs is reduced.

08 HYDROGEN↗
DOE OSTI2026

Advancing Protein Display on Bacterial Spores through an Extensive Survey of Coat Components

The profound stability of bacterial spores makes them a promising platform for biotechnological applications like biocatalysis, bioremediation, drug delivery, etc. However, though the Bacillus subtilis spore is composed of >40 types of proteins, only ∼12 have been explored as fusion carriers for protein display. Here, we assessed the suitability of 33 spore proteins (SPs) as enzyme display carriers by direct allele tagging at native genomic loci. Of the 33 SPs investigated, 26 formed functional fusions with β-glucuronidase (GUS)─a ∼272 kDa homotetramer. This almost triples the number of SPs assessed for enzyme display and doubles the number of functional fusions documented in the literature. We quantitatively assessed 1) SP promoter activation dynamics, 2) GUS activity on spores, 3) surface availability, and 4) protection from thermal and proteolytic degradation. Multicopy expression and pairwise coexpression of the most promising SP-GUS fusions highlighted the complexity of spore structure/assembly and the difficulty in predicting compatibility between different SP fusions. We also assessed the suitability of engineered spores to degrade PET (polyethylene terephthalate) films and found that surface-exposed SPs were most effective. Beyond the broad survey, a key outcome of our work was the identification of SscA (small spore coat assembly protein A) as an effective spore display carrier. SscA supported enzyme activity at least 4-fold higher than any other SP, including the well-established anchor, CotY. We attribute this to its promoter, which demonstrated early and sustained activation relative to other SPs and its small size (∼3 kDa), which likely minimally interferes with enzyme folding, oligomerization, and activity. Labeling and genetic studies, its hydrophobic nature, and low surface availability suggest that SscA assembles within the inner spore coat, which makes it stabilizing and suitable for many biocatalytic applications. Overall, this work serves as a knowledge base to advance the biotechnological utility of B. subtilis spores.

Bacillus subtilis↗
DOE OSTI2019

Random Force Perturbations: A New Extension of the Cell Perturbation Method for Turbulence Generation in Multiscale Atmospheric Boundary Layer Simulations

Coupling between mesoscale and large eddy simulation (LES) is critically important for many atmospheric model applications, from predictions of wind energy to fire propagation. The grid-nesting technique enables bridging between vastly different scales without incurring prohibitive computational costs. Yet, the transition from coarser to finer resolutions often requires a large number of grid points from inflow boundaries for the development of fine-scale turbulence features in the LES domain. Recently, the cell perturbation method (CPM) was developed to reduce the turbulence development region with high computational efficiency. Herein, we explore a new method based on the CPM that uses force perturbations in both the horizontal and vertical directions (Force Cell Perturbation Method) instead of the potential temperature perturbations in the original CPM, as an attempt to further explore the performance of the random perturbation techniques. This method is tested for a neutral and a convective atmospheric boundary layer under idealized conditions. Overall, similar performance is found between the optimal configurations of the CPM and the Force Cell Perturbation Method pointing to the robustness of this family of perturbation methods in accelerating turbulence generation in nested domains. Vertical force perturbations performed better than horizontal force perturbations for both atmospheric stability conditions. The CPM performed best under convective stability conditions. The combination of the force and potential temperature perturbations is found to provide no additional performance improvement over the stand-alone application of the individual methods.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

On an Extensive Late Hydrologic Event in Gale Crater as Indicated by Water‐Rich Fracture Halos

Abstract We analyze spatially pervasive, light‐toned “halos” associated with fractures in a sedimentary unit (Stimson) of Gale crater, Mars, and report a similar network of halos discovered in a separate geologic group (Bradbury). Through a dedicated active neutron measurement campaign, we provide independent confirmation of the water‐rich nature of these features. Together with mineralogical and geochemical data, these features are consistent with abundant hydrated amorphous silica (opal‐A). We suggest that the mineral and amorphous assemblages are indicative of formation under low‐temperature and predominantly low‐pH conditions (passive silica enrichment) with minor contribution of silica (active silica enrichment) from adjacent units. We show that there is significant amorphous silica in the array of sedimentary rocks in Gale crater, allowing them to play a role in an active silica enrichment phase of halo formation. We suggest that the involved alteration event was short lived and our finding of vast halo networks in a distant, older unit implies a more vast network of hydrologic subsurface conduits than previously known. This relatively recent subsurface hydrologic system was present long after the transition from a warm and wet to a cold and dry Martian environment, extending the habitability conditions on Mars to an epoch that is generally considered not favorable for life on the surface. Finally, our bulk H quantification of these features, which ranges from ∼3–6 wt% H 2 O‐equivalent‐H, suggests that the amorphous material in halos hosts ample supplies of readily released water, making them a considerable resource at the otherwise dry Martian equator.

Gabriel, Travis S. J.↗
DOE OSTI2023

Extension of Large Fire Emissions From Summer to Autumn and Its Drivers in the Western US

Abstract Burned areas in the western US have increased ten‐fold since 1980s, which are attributable to multiple factors, including increasing heat, changing precipitation patterns, and extended drought. To better understand how these factors contribute to large fire emissions (gridded monthly fire emissions >95th percentile of all the fire emissions in the western US; 0.009 Gg/month), we build a machine learning model to predict fire emissions (PM 2.5 ) over the western US at 0.25° resolution, interpreted using explainable artificial intelligence (XAI). From the predictor contributions derived from XAI, we conduct k‐means clustering analysis to identify four clusters of predictor variables representing different drivers of large fire emissions. The four clusters feature the contributions of fuel load (Cluster 1) and different levels of dryness (Cluster 2–4), controlled by fuel moisture, drought condition, and fire‐favorable large‐scale meteorological patterns featuring high temperature, high pressure, and low relative humidity. In the past two decades, large fire emissions peak in summer. However, large fire emissions increased significantly in September and October in 2010–2020 relative to 2000–2009, extending the peak large fire emissions from summer to autumn. The larger enhancements of large fire emissions during autumn compared to summer are contributed by decreased fuel moisture, along with more frequent concurrent fire‐favorable large‐scale meteorological patterns and drought. These results highlight fuel drying as a common driver supported by multiple drivers, such as warmer temperature and more frequent synoptic patterns favorable for fires, in increasing the autumn risk of large fire emissions across the western US.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Extensive Secondary Cratering From the InSight Sol 1034a Impact Event

Abstract Impact cratering is one of the fundamental processes throughout the history of the Solar System. The formation of new impact craters on planetary bodies has been observed with repeat images from orbiting satellites. However, the time gap between images is often large enough to preclude detailed analysis of smaller‐scale features such as secondary impact craters, which are often removed or buried over a short time period. Here we use a seismic event detected on Mars by the NASA InSight mission to investigate secondary cratering at a new impact crater. We strengthen the case that the seismic event that occurred on Sol 1034 (S1034a) is the result of a new impact cratering event. Using the exact timing of this event from InSight, we investigated the resulting new impact crater in orbital image data. The S1034a impact crater is approximately 9 m in diameter but is responsible for over 900 secondary impact events in the form of low albedo spots that are located at distances of up to almost 7 km from the primary crater. We suggest that the low albedo spots formed from relatively low energy ejecta, with individual ejecta block velocities less than 200 m s −1 . We estimate that the low albedo spots, the main evidence of secondary impact processes at this new impact event, fade within 200–300 days after formation.

Grindrod, P. M. [Natural History Museum London UK]↗
DOE OSTI2016

Sequencing wild and cultivated cassava and related species reveals extensive interspecific hybridization and genetic diversity

Cassava (Manihot esculenta) provides calories and nutrition for more than half a billion people. It was domesticated by native Amazonian peoples through cultivation of the wild progenitor M. esculenta ssp. flabellifolia and is now grown in tropical regions worldwide. Here we provide a high-quality genome assembly for cassava with improved contiguity, linkage, and completeness; almost 97% of genes are anchored to chromosomes. We find that paleotetraploidy in cassava is shared with the related rubber tree Hevea, providing a resource for comparative studies. We also sequence a global collection of 58 Manihot accessions, including cultivated and wild cassava accessions and related species such as Ceará or India rubber (M. glaziovii), and genotype 268 African cassava varieties. We find widespread interspecific admixture, and detect the genetic signature of past cassava breeding programs. As a clonally propagated crop, cassava is especially vulnerable to pathogens and abiotic stresses. This genomic resource will inform future genome-enabled breeding efforts to improve this staple crop.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure

While prokaryotic pan-genomes have been shown to contain many more genes than any individual organism, the prevalence and functional significance of differentially present genes in eukaryotes remains poorly understood. Whole-genome de novo assembly and annotation of 54 lines of the grass Brachypodium distachyon yield a pan-genome containing nearly twice the number of genes found in any individual genome. Genes present in all lines are enriched for essential biological functions, while genes present in only some lines are enriched for conditionally beneficial functions (e.g., defense and development), display faster evolutionary rates, lie closer to transposable elements and are less likely to be syntenic with orthologous genes in other grasses. Our data suggest that differentially present genes contribute substantially to phenotypic variation within a eukaryote species, these genes have a major influence in population genetics, and transposable elements play a key role in pan-genome evolution.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Swift and extensive Omicron outbreak in China after sudden exit from ‘zero-COVID’ policy

In late 2022, China transitioned from a strict ‘zero-COVID’ policy to rapidly abandoning nearly all interventions and data reporting. This raised great concern about the presumably-rapid but unreported spread of the SARS-CoV-2 Omicron variant in a very large population of very low pre-existing immunity. By modeling a combination of case count and survey data, we show that Omicron spread extremely rapidly, at a rate of 0.42/day (95% credibility interval: [0.35, 0.51]/day), translating to an epidemic doubling time of 1.6 days ([1.6, 2.0] days) after the full exit from zero-COVID on Dec. 7, 2022. Consequently, we estimate that the vast majority of the population (97% [95%, 99%], sensitivity analysis lower limit of 90%) was infected during December, with the nation-wide epidemic peaking on Dec. 23. Overall, our results highlight the extremely high transmissibility of the variant and the importance of proper design of intervention exit strategies to avoid large infection waves.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Extensive 3D mapping of dislocation structures in bulk aluminum

Abstract Thermomechanical processing such as annealing is one of the main methods to tailor the mechanical properties of materials, however, much is unknown about the reorganization of dislocation structures deep inside macroscopic crystals that give rise to those changes. Here, we demonstrate the self-organization of dislocation structures upon high-temperature annealing in a mm-sized single crystal of aluminum. We map a large embedded 3D volume ( $$100\times 300\times 300$$ 100 × 300 × 300 $$\upmu$$ μ m $$^3$$ 3 ) of dislocation structures using dark field X-ray microscopy (DFXM), a diffraction-based imaging technique. Over the wide field of view, DFXM’s high angular resolution allows us to identify subgrains, separated by dislocation boundaries, which we identify and characterize down to the single-dislocation level using computer-vision methods. We demonstrate how even after long annealing times at high temperatures, the remaining low density of dislocations still pack into well-defined, straight dislocation boundaries (DBs) that lie on specific crystallographic planes. In contrast to conventional grain growth models, our results show that the dihedral angles at the triple junctions are not the predicted 120 $$^{\circ }$$ ∘ , suggesting additional complexities in the boundary stabilization mechanisms. Mapping the local misorientation and lattice strain around these boundaries shows that the observed strain is shear, imparting an average misorientation around the DB of $$\approx$$ ≈ 0.003 to 0.006 $$^{\circ }$$ ∘ .

36 MATERIALS SCIENCE↗
DOE OSTI2022

Extensive urban air pollution footprint evidenced by submicron organic aerosols molecular composition

Transport and transformation of urban air pollutants are among the major factors driving the changes in the atmospheric composition in the downwind rural/remote areas of a megacity. Here, we assess the impacts of urban air pollution in a subtropical forest through characterization of the organic markers in submicron aerosol particles. The aerosol samples were collected and analyzed using TD-PTR-ToF-MS, where 163 ions were detected. The concentration of these extracted ions accounts for 83% of the mass of submicron organic aerosols, which are accordingly characterized by a median formula of C 7 H 10 O 2 . Molecular speciation indicates that urban and biomass burning pollution contributed substantially to the budget of organic aerosols, which were enhanced particularly by the liquid water content and acidity of the aerosols. Our results evidence that the footprint of urban air pollution was extended to its downwind forested areas and caused changes in the concentration and composition of submicron aerosols.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2016

Schizophyllum commune has an extensive and functional alternative splicing repertoire

Recent genome-wide studies have demonstrated that fungi possess the machinery to alternatively splice pre-mRNA. However, there has not been a systematic categorization of the functional impact of alternative splicing in a fungus. We investigate alternative splicing and its functional consequences in the model mushroom forming fungus Schizophyllum commune. Alternative splicing was demonstrated for 2,285 out of 12,988 expressed genes, resulting in 20% additional transcripts. Intron retentions were the most common alternative splicing events, accounting for 33% of all splicing events, and 43% of the events in coding regions. On the other hand, exon skipping events were rare in coding regions (1%) but enriched in UTRs where they accounted for 57% of the events. Specific functional groups, including transcription factors, contained alternatively spliced genes. Alternatively spliced transcripts were regulated differently throughout development in 19% of the 2,285 alternatively spliced genes. Notably, 69% of alternatively spliced genes have predicted alternative functionality by loss or gain of functional domains, or by acquiring alternative subcellular locations. S. commune exhibits more alternative splicing than any other studied fungus. Finally, taken together, alternative splicing increases the complexity of the S. commune proteome considerably and provides it with a rich repertoire of alternative functionality that is exploited dynamically.

59 BASIC BIOLOGICAL SCIENCES↗