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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Topological network analysis of patient similarity for precision management of acute blood pressure in spinal cord injury

Background: Predicting neurological recovery after spinal cord injury (SCI) is challenging. Using topological data analysis, we have previously shown that mean arterial pressure (MAP) during SCI surgery predicts long-term functional recovery in rodent models, motivating the present multicenter study in patients. Methods: Intra-operative monitoring records and neurological outcome data were extracted (n = 118 patients). We built a similarity network of patients from a low-dimensional space embedded using a non-linear algorithm, Isomap, and ensured topological extraction using persistent homology metrics. Confirmatory analysis was conducted through regression methods. Results: Network analysis suggested that time outside of an optimum MAP range (hypotension or hypertension) during surgery was associated with lower likelihood of neurological recovery at hospital discharge. Logistic and LASSO (least absolute shrinkage and selection operator) regression confirmed these findings, revealing an optimal MAP range of 76–[104-117] mmHg associated with neurological recovery. Conclusions: We show that deviation from this optimal MAP range during SCI surgery predicts lower probability of neurological recovery and suggest new targets for therapeutic intervention. Funding: NIH/NINDS: R01NS088475 (ARF); R01NS122888 (ARF); UH3NS106899 (ARF); Department of Veterans Affairs: 1I01RX002245 (ARF), I01RX002787 (ARF); Wings for Life Foundation (ATE, ARF); Craig H. Neilsen Foundation (ARF); and DOD: SC150198 (MSB); SC190233 (MSB); DOE: DE-AC02-05CH11231 (DM).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Publication and Impact of Preprints Included in the First 100 Editions of the CDC COVID-19 Science Update: Content Analysis

Preprints are publicly available manuscripts posted to various servers that have not been peer reviewed. Although preprints have existed since 1961, they have gained increased popularity during the COVID-19 pandemic due to the need for immediate, relevant information. The aim of this study is to evaluate the publication rate and impact of preprints included in the Centers for Disease Control and Prevention (CDC) COVID-19 Science Update and assess the performance of the COVID-19 Science Update team in selecting impactful preprints. All preprints in the first 100 editions (April 1, 2020, to July 30, 2021) of the Science Update were included in the study. Preprints that were not published were categorized as “unpublished preprints.” Preprints that were subsequently published exist in 2 versions (in a peer-reviewed journal and on the original preprint server), which were analyzed separately and referred to as “peer-reviewed preprint” and “original preprint,” respectively. Time to publish was the time interval between the date on which a preprint was first posted and the date on which it was first available as a peer-reviewed article. Impact was quantified by Altmetric Attention Score and citation count for all available manuscripts on August 6, 2021. Preprints were analyzed by publication status, publication rate, preprint server, and time to publication. Of the 275 preprints included in the CDC COVID-19 Science Update during the study period, most came from three servers: medRxiv (n=201, 73.1%), bioRxiv (n=41, 14.9%), and SSRN (n=25, 9.1%), with 8 (2.9%) coming from other sources. Additionally, 152 (55.3%) were eventually published. The median time to publish was 2.3 (IQR 1.4-3.7). When preprints posted in the last 2.3 months were excluded (to account for the time to publish), the publication rate was 67.8%. Moreover, 76 journals published at least one preprint from the CDC COVID-19 Science Update, and 18 journals published at least three. The median Altmetric Attention Score for unpublished preprints (n=123, 44.7%) was 146 (IQR 22-552) with a median citation count of 2 (IQR 0-8); for original preprints (n=152, 55.2%), these values were 212 (IQR 22-1164) and 14 (IQR 2-40), respectively; for peer-review preprints, these values were 265 (IQR 29-1896) and 19 (IQR 3-101), respectively. Prior studies of COVID-19 preprints found publication rates between 5.4% and 21.1%. Preprints included in the CDC COVID-19 Science Update were published at a higher rate than overall COVID-19 preprints, and those that were ultimately published were published within months and received higher attention scores than unpublished preprints. These findings indicate that the Science Update process for selecting preprints had a high fidelity in terms of their likelihood to be published and their impact. The incorporation of high-quality preprints into the CDC COVID-19 Science Update improves this activity’s capacity to inform meaningful public health decision-making.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Genome-Wide Discovery of G-Quadruplexes in Wheat: Distribution and Putative Functional Roles

G-quadruplexes are nucleic acid secondary structures formed by a stack of square planar G-quartets. G-quadruplexes were implicated in many biological functions including telomere maintenance, replication, transcription, and translation, in many species including humans and plants. For wheat, however, though it is one of the world’s most important staple food, no G-quadruplex studies have been reported to date. Here, we computationally identify putative G4 structures (G4s) in wheat genome for the first time and compare its distribution across the genome against five other genomes (human, maize, Arabidopsis, rice, and sorghum). We identified close to 1 million G4 motifs with a density of 76 G4s/Mb across the whole genome and 93 G4s/Mb over genic regions. Remarkably, G4s were enriched around three regions, two located on the antisense and one on the sense strand at the following positions: 1) the transcription start site (TSS) (antisense), 2) the first coding domain sequence (CDS) (antisense), and 3) the start codon (sense). Functional enrichment analysis revealed that the gene models containing G4 motifs within these peaks were associated with specific gene ontology (GO) terms, such as developmental process, localization, and cellular component organization or biogenesis. We investigated genes encoding MADS-box transcription factors and showed examples of G4 motifs within critical regulatory regions in the VRN-1 genes in wheat. Furthermore, comparison with other plants showed that monocots share a similar distribution of G4s, but Arabidopsis shows a unique G4 distribution. Our study shows for the first time the prevalence and possible functional roles of G4s in wheat.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Zymogen and activated protein C have similar structural architecture

Activated protein C is a trypsin-like protease with anticoagulant and cytoprotective properties that is generated by thrombin from the zymogen precursor protein C in a reaction greatly accelerated by the cofactor thrombomodulin. The molecular details of this activation remain elusive due to the lack of structural information. We now fill this gap by providing information on the overall structural organization of these proteins using single molecule Förster resonance energy transfer and small angle X-ray scattering. Under physiological conditions, both zymogen and protease adopt a conformation with all domains vertically aligned along an axis 76 Å long and maximal particle size of 120 Å. This conformation is stabilized by binding of Ca 2+ to the Gla domain and is affected minimally by interaction with thrombin. Hence, the zymogen protein C likely interacts with the thrombin-thrombomodulin complex through a rigid body association that produces a protease with essentially the same structural architecture. This scenario stands in contrast to an analogous reaction in the coagulation cascade where conversion of the zymogen prothrombin to the protease meizothrombin by the prothrombinase complex is linked to a large conformational transition of the entire protein. The presence of rigid EGF domains in protein C as opposed to kringles in prothrombin likely accounts for the different conformational plasticity of the two zymogens. The new structural features reported here for protein C have general relevance to vitamin K-dependent clotting factors containing EGF domains, such as factors VII, IX, and X.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Two DOT1 enzymes cooperatively mediate efficient ubiquitin-independent histone H3 lysine 76 tri-methylation in kinetoplastids

In higher eukaryotes, a single DOT1 histone H3 lysine 79 (H3K79) methyltransferase processively produces H3K79me2/me3 through histone H2B mono-ubiquitin interaction, while the kinetoplastid Trypanosoma brucei di-methyltransferase DOT1A and tri-methyltransferase DOT1B efficiently methylate the homologous H3K76 without H2B mono-ubiquitination. Based on structural and biochemical analyses of DOT1A, we identify key residues in the methyltransferase motifs VI and X for efficient ubiquitin-independent H3K76 methylation in kinetoplastids. Substitution of a basic to an acidic residue within motif VI (Gx 6 K ) is essential to stabilize the DOT1A enzyme-substrate complex, while substitution of the motif X sequence VYGE by CAKS renders a rigid active-site loop flexible, implying a distinct mechanism of substrate recognition. We further reveal distinct methylation kinetics and substrate preferences of DOT1A (H3K76me0) and DOT1B (DOT1A products H3K76me1/me2) in vitro, determined by a Ser and Ala residue within motif IV, respectively, enabling DOT1A and DOT1B to mediate efficient H3K76 tri-methylation non-processively but cooperatively, and suggesting why kinetoplastids have evolved two DOT1 enzymes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Diverse signatures of convergent evolution in cactus-associated yeasts

Many distantly related organisms have convergently evolved traits and lifestyles that enable them to live in similar ecological environments. However, the extent of phenotypic convergence evolving through the same or distinct genetic trajectories remains an open question. Here, we leverage a comprehensive dataset of genomic and phenotypic data from 1,049 yeast species in the subphylum Saccharomycotina (Kingdom Fungi, Phylum Ascomycota) to explore signatures of convergent evolution in cactophilic yeasts, ecological specialists associated with cacti. We inferred that the ecological association of yeasts with cacti arose independently approximately 17 times. Using a machine learning–based approach, we further found that cactophily can be predicted with 76% accuracy from both functional genomic and phenotypic data. The most informative feature for predicting cactophily was thermotolerance, which we found to be likely associated with altered evolutionary rates of genes impacting the cell envelope in several cactophilic lineages. We also identified horizontal gene transfer and duplication events of plant cell wall–degrading enzymes in distantly related cactophilic clades, suggesting that putatively adaptive traits evolved independently through disparate molecular mechanisms. Notably, we found that multiple cactophilic species and their close relatives have been reported as emerging human opportunistic pathogens, suggesting that the cactophilic lifestyle—and perhaps more generally lifestyles favoring thermotolerance—might preadapt yeasts to cause human disease. This work underscores the potential of a multifaceted approach involving high-throughput genomic and phenotypic data to shed light onto ecological adaptation and highlights how convergent evolution to wild environments could facilitate the transition to human pathogenicity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Xylan-cellulose core structure of oat water-extractable β-glucan macromolecule: Insight into interactions and organization of the cell wall complex

Water-extractable β-glucan with high molar mass (HM) determines health benefits of oat food. Oat β-glucan was extracted by a standardized in vitro digestion method and co-existing water-extractable polysaccharide (WEP) fraction and its HM-arabinoxylan (HM-AX) subfraction were isolated to identify their highly acid-resistant subunit and investigate molecular interactions between constituent polymers. The WEP and HM-AX samples consisted of arabinoxylans (AXs) (74 and 76 %, respectively), however, cellulose constituted the secondary component (6.6 and 12.8 %, respectively). Multi-detection HPSEC along with specific enzymatic hydrolysis of AXs revealed the presence of the HM-xylan domain (16 and 34 %, respectively) built of numerous single- and multi-component populations with random coil and rod-like conformations, which were embedded in a xylan matrix with spherical conformation and controlled the macromolecular shape. Unlike single-component populations, the multi-component ones were resistant to hydrolytic action of AX-hydrolyzing enzymes and represented the subunits that anchor matrix polysaccharides onto cellulose surface. These results indicate that water-extractable β-glucan macromolecule comprises as integral element a cellulose core with two linking populations, HM-xylan and low molar mass glucomannan, which are surrounded by a feruloylated AX-arabinan-arabinogalactan composite and next laminated by β-glucan matrix. Here, the stiff cellulose-xylan backbone is the basis of HM β-glucan organization, controlled by its cellulose-like segments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Drizzle, Turbulence, and Density Currents Below Post Cold Frontal Open Cellular Marine Stratocumulus Clouds

Nine cases of postcold frontal marine stratocumulus clouds exhibiting open cellular mesoscale organization are analyzed to characterize the drizzle, turbulence, and density currents below them. Data collected by the vertically pointing Doppler cloud radar and multiple lidars part of the Atmospheric Radiation Measurement (ARM) Eastern North Atlantic (ENA) site are used in these analyses. A total of 251 drizzle shafts passed over the site with 76 shafts sampled for more than 15 min by the vertically pointing instruments. On average the drizzle shafts were ~18 km wide with below-cloud drizzle water path of ~40 g m −2 , cloud base rain rate of 7.78 mm day −1 , and cloud base drizzle modal diameter of 393 μm. The widths of the drizzle shafts did not exhibit any relationship with the cloud base rain rate, below-cloud drizzle water path, and the total water removed from the cloud. The downdrafts in the lowest 500 m within the drizzle cells strengthened with increasing cloud base rain rates, while the updrafts within drizzle cells did not exhibit this behavior. On average, the surface air density, pressure, water vapor mixing ratio, and wind speed along the background wind during the drizzle shaft were higher by 1.88 g m −3 , 8.60 Pa, 0.24 g kg −1 , and 1.22 m s −1 , respectively, from their background values. On the other hand, the surface air temperature was lower by 0.43 K during the drizzle shaft than its background value. The coincident measurements highlight the drizzle-turbulence-surface coupling in these cloud systems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Genomic Signatures of a Major Adaptive Event in the Pathogenic Fungus Melampsora larici-populina

The recent availability of genome-wide sequencing techniques has allowed systematic screening for molecular signatures of adaptation, including in nonmodel organisms. Host–pathogen interactions constitute good models due to the strong selective pressures that they entail. We focused on an adaptive event which affected the poplar rust fungus Melampsora larici-populina when it overcame a resistance gene borne by its host, cultivated poplar. Based on 76 virulent and avirulent isolates framing narrowly the estimated date of the adaptive event, we examined the molecular signatures of selection. Using an array of genome scan methods based on different features of nucleotide diversity, we detected a single locus exhibiting a consistent pattern suggestive of a selective sweep in virulent individuals (excess of differentiation between virulent and avirulent samples, linkage disequilibrium, genotype–phenotype statistical association, and long-range haplotypes). Our study pinpoints a single gene and further a single amino acid replacement which may have allowed the adaptive event. Although our samples are nearly contemporary to the selective sweep, it does not seem to have affected genome diversity further than the immediate vicinity of the causal locus, which can be explained by a soft selective sweep (where selection acts on standing variation) and by the impact of recombination in mitigating the impact of selection. Therefore, it seems that properties of the life cycle of M. larici-populina, which entails both high genetic diversity and outbreeding, has facilitated its adaptation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Synergistic cellulase–xylanase formulations for enhanced dewatering and fiber bonding toward energy-efficient and sustainable paper and packaging production

A mechanistic understanding of the synergistic effects of enzymes on cellulosic fibers dewatering and fiber bonding is essential for advancing energy-efficiency and lightweight production of paper and packaging materials. This study investigates the impact of varying cellulase and xylanase formulations on equilibrium moisture content (EMC) after pressing and tensile strength of cellulosic fiber webs using a factorial experimental design. Nine custom enzyme formulations were evaluated at controlled dosages ranging from ∼20 to 76 FPU/mL cellulase and ∼500–1130 IU/mL xylanase. Response surface modeling revealed a significant synergy, particularly at 20–40 FPU/mL cellulase combined with ≥ 1000 IU/mL xylanase. Under these conditions, EMC decreased by up to 3.6% compared with the untreated refined control, while tensile index gains of up to 16% were statistically significant for optimized blends (p < 0.05). The interaction between cellulase and xylanase was also significant for the tensile response (p = 0.010). Protein efficiency analysis showed that optimized formulations containing 30–40% less protein outperformed the commercial benchmark. The nonlinear synergy between cellulase and xylanase is attributed to their complementary substrate specificities. Endoglucanase- and β‑glucosidase‑rich cellulases hydrolyze internal β‑1,4‑glycosidic bonds in amorphous cellulose, loosening fiber walls and increasing flexibility, while xylanases target hemicellulose, primarily xylan-rich domains, enhancing porosity and improve cellulase accessibility. Tailoring enzyme formulations at low loadings overcomes traditional trade-offs between strength and dewatering, enabling cost-effective, energy-efficient, low-carbon solutions for sustainable packaging and hygiene products.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

VirION2: a short- and long-read sequencing and informatics workflow to study the genomic diversity of viruses in nature

Microbes play fundamental roles in shaping natural ecosystem properties and functions, but do so under constraints imposed by their viral predators. However, studying viruses in nature can be challenging due to low biomass and the lack of universal gene markers. Though metagenomic short-read sequencing has greatly improved our virus ecology toolkit—and revealed many critical ecosystem roles for viruses—microdiverse populations and fine-scale genomic traits are missed. Some of these microdiverse populations are abundant and the missed regions may be of interest for identifying selection pressures that underpin evolutionary constraints associated with hosts and environments. Though long-read sequencing promises complete virus genomes on single reads, it currently suffers from high DNA requirements and sequencing errors that limit accurate gene prediction. Here we introduce VirION2, an integrated short- and long-read metagenomic wet-lab and informatics pipeline that updates our previous method (VirION) to further enhance the utility of long-read viral metagenomics. Using a viral mock community, we first optimized laboratory protocols (polymerase choice, DNA shearing size, PCR cycling) to enable 76% longer reads (now median length of 6,965 bp) from 100-fold less input DNA (now 1 nanogram). Using a virome from a natural seawater sample, we compared viromes generated with VirION2 against other library preparation options (unamplified, original VirION, and short-read), and optimized downstream informatics for improved long-read error correction and assembly. VirION2 assemblies combined with short-read based data (‘enhanced’ viromes), provided significant improvements over VirION libraries in the recovery of longer and more complete viral genomes, and our optimized error-correction strategy using long- and short-read data achieved 99.97% accuracy. In the seawater virome, VirION2 assemblies captured 5,161 viral populations (including all of the virus populations observed in the other assemblies), 30% of which were uniquely assembled through inclusion of long-reads, and 22% of the top 10% most abundant virus populations derived from assembly of long-reads. Viral populations unique to VirION2 assemblies had significantly higher microdiversity means, which may explain why short-read virome approaches failed to capture them. These findings suggest the VirION2 sample prep and workflow can help researchers better investigate the virosphere, even from challenging low-biomass samples. Our new protocols are available to the research community on protocols.io as a ‘living document’ to facilitate dissemination of updates to keep pace with the rapid evolution of long-read sequencing technology.

Long-reads↗
DOE OSTI2026

The Interactions Between Shading and Organic Fertilizer Application on Dry-farmed Tomato Grown Between Photovoltaic Panels

Agrivoltaic systems are mixed systems of solar photovoltaic (PV) panels and agricultural production, where shade from the panels can result in lower evapotranspiration for crops, which is of particular interest for dryland agriculture. Dry-farmed tomato (Solanum lycopersicum) production in the Willamette Valley of Oregon has lower total yields and higher rates of blossom-end rot (BER) than irrigated tomato production, resulting in reduced marketable yields. To determine how dry-farmed ‘Early Girl’ tomato performed in an agrivoltaics system, a trial was conducted at the Valley Creek Solar Project (Salem, OR, USA) in 2020, using three different amendment treatments and three levels of shading from the panels. Amendment treatments were 0N (receiving no fertilizer), 84N (receiving 84 kg·ha −1 N), and 168N (receiving 168 kg·ha −1 N), applied as processed chicken manure. Plants were estimated to receive an irradiance factor of 30%, 76%, and 89% for full-shade, partial-shade, and full-sun treatments respectively. There was an interaction between amendment treatments and shading treatments in their effects on unblemished yield (yield of fruit without BER or sunscald). The optimum fertilizer application for full-shade and partial-shade rows was 84N, the optimum for full-sun rows was 0N. Fertilizing these rows at these rates resulted in an unblemished yield for the aisle of 11.1 t·ha −1 , which was lower than unblemished yields reported in previous experiments and trials in open fields. However, these results are from a single location and a single year, and other solar sites may behave more similar to open-field conditions. Shading from the panels increased average fruit weight and decreased incidence of BER and sunscald, suggesting that crops were less drought stressed. This resulted in similar unblemished yields for the full-shade and full-sun plots at 84N and 168N. Applying fertilizer resulted in higher total yields, smaller average fruit weight, increased BER incidence, and decreased sunscald incidence. The results suggest a possible synergy between dry-farmed tomato production and agrivoltaics, although several concerns remain, including difficulties managing the vegetation under panels, rules restricting PVs on high-value agricultural soils, and the possibility of soil compaction during PV installation.

14 SOLAR ENERGY↗
DOE OSTI2022

A round-robin approach provides a detailed assessment of biomolecular small-angle scattering data reproducibility and yields consensus curves for benchmarking

Through an expansive international effort that involved data collection on 12 small-angle X-ray scattering (SAXS) and four small-angle neutron scattering (SANS) instruments, 171 SAXS and 76 SANS measurements for five proteins (ribonuclease A, lysozyme, xylanase, urate oxidase and xylose isomerase) were acquired. From these data, the solvent-subtracted protein scattering profiles were shown to be reproducible, with the caveat that an additive constant adjustment was required to account for small errors in solvent subtraction. Further, the major features of the obtained consensus SAXS data over the q measurement range 0–1 Å −1 are consistent with theoretical prediction. The inherently lower statistical precision for SANS limited the reliably measured q -range to <0.5 Å −1 , but within the limits of experimental uncertainties the major features of the consensus SANS data were also consistent with prediction for all five proteins measured in H 2 O and in D 2 O. Thus, a foundation set of consensus SAS profiles has been obtained for benchmarking scattering-profile prediction from atomic coordinates. Additionally, two sets of SAXS data measured at different facilities to q > 2.2 Å −1 showed good mutual agreement, affirming that this region has interpretable features for structural modelling. SAS measurements with inline size-exclusion chromatography (SEC) proved to be generally superior for eliminating sample heterogeneity, but with unavoidable sample dilution during column elution, while batch SAS data collected at higher concentrations and for longer times provided superior statistical precision. Careful merging of data measured using inline SEC and batch modes, or low- and high-concentration data from batch measurements, was successful in eliminating small amounts of aggregate or interparticle interference from the scattering while providing improved statistical precision overall for the benchmarking data set.

59 BASIC BIOLOGICAL SCIENCES↗