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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 1,549 records · Page 86
All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

Soil and water conservation using the socioeconomics, sustainability concerns, and policy preference for residual biomass harvest

While woody bioenergy opens up a new market opportunity for residual biomass, overharvesting of residual biomass can adversely affect soil health, water quality, timber health and stand productivity, among others. As such, it is important to understand the proportion of residual biomass forestland owners are willing to leave unharvested for soil nutrient and other environmental benefit purposes, their sustainability concerns, and policy preferences. Toward this end, we conducted a mail survey on 900 randomly selected forestland owners in Virginia and used ordinal logistic regression, cluster analyses, and Cochran-Armitage trend tests to analyze the data. Our analyses of the 121 most complete responses suggest that factors such as ownership tenure, mode of land acquisition, size of forestland, and forestland own- ership objectives, among other factors, affect decisions regarding the proportion of residual biomass forestland owners choose to leave unharvested. Analyses of landowners’ sustainability concerns indicate a clustering pattern, where concerns about sufficiency of best management practices and the potential implications of harvest decision on soil and water quality are among the statistical representatives of their respective clusters. Respondents likely to engage in harvest practices that do not leave any residual biomass on the ground have a preference for policies that help cover management cost. Decision makers administering or considering such policy proposals should be aware of the inadvertent effect such cost sharing arrange- ments can have in encouraging unsustainable practices.These results also hint at the potential need for combining such cost sharing arrangements with extension and outreach programs. Lastly, by accounting for landowners’ concerns and preferences, this study complements previous studies that primarily adopt engineering based approaches and solutions.

bioenergy↗
DOE OSTI2021

Model Reduction for Steady Hypersonic Aerodynamics via Conservative Manifold Least-Squares Petrov–Galerkin Projection

High-speed aerospace engineering applications rely heavily on computational fluid dynamics (CFD) models for design and analysis. This reliance on CFD models necessitates performing accurate and reliable uncertainty quantification (UQ) of the CFD models, which can be very expensive for hypersonic flows. Additionally, UQ approaches are many-query problems requiring many runs with a wide range of input parameters. One way to enable computationally expensive models to be used in such many-query problems is to employ projection-based reduced-order models (ROMs) in lieu of the (high-fidelity) full-order model (FOM). In particular, the least-squares Petrov–Galerkin (LSPG) ROM (equipped with hyper-reduction) has demonstrated the ability to significantly reduce simulation costs while retaining high levels of accuracy on a range of problems, including subsonic CFD applications. This allows LSPG ROM simulations to replace the FOM simulations in UQ studies, making UQ tractable even for large-scale CFD models. This work presents the first application of LSPG to a hypersonic CFD application, the Hypersonic International Flight Research Experimentation 1 (HIFiRE-1) in a three-dimensional, turbulent Mach 7.1 flow. This paper shows the ability of the ROM to significantly reduce computational costs while maintaining high levels of accuracy in computed quantities of interest.

42 ENGINEERING↗
DOE OSTI2026

Genome collection processing for “Conserved upper thermal limits and small safety margins in soil copiotrophic bacteria”

We extracted the genomic DNA of 400 randomly selected isolates using a Quick-DNA Microprep Kit (Zymo Research D3020) according to the manufacturer’s protocol. We then submitted the extracted gDNA samples for short-read Illumina sequencing (200 Mbp) at SeqCoast Genomics (Portsmouth, NH, USA). After preprocessing the sequences using Trimmommatic (Bolger et al. 2014), we assembled the genomes using SPADES (Bankevich et al. 2012) and checked the quality of each assembly using QUAST (Gurevich et al. 2013). We processed the genome assemblies using a KBase (v1.4.0) pipeline (Allen et al. 2017; Arkin et al. 2018). Briefly, we used DRAM (v0.1.2) with default settings to annotate the genome assemblies. We then evaluated genome quality and possible contamination levels using CheckM (v1.0.18) (Parks et al. 2015) and retained genomes with completeness above 98% and contamination below 5% (n = 354), following the authors' guidelines. We then obtained taxonomic assignments for all remaining isolates using the Genome Taxonomy Database tool GTDB-Tk (v2.3.2, database version r214) (Chaumeil et al. 2019). We constructed a phylogenetic tree using the tool SpeciesTree (v2.2.0). We then trimmed the tree (using Trim SpeciesTree to GenomeSet- v1.4.0), retaining only tips within our collection with measured thermal performance.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Dataset_for_Conserved_macromolecular_architecture_of_Poplar_secondary_cell_walls_revealed_by_ssNMR_and_atomistic_modeling

This dataset contains solid-state 13C NMR data and atomistic molecular dynamics simulation files supporting the study of nanoscale secondary cell wall architecture across 13 genetically diverse Populus trichocarpa genotypes grown under uniform greenhouse conditions in 13C-enriched CO2 atmospheres (~89% 13C enrichment).The dataset contains two collections of solid-state 13C NMR data. (1) 200 MHz data (Bruker Avance III HD, 4 mm HX probe, 10 kHz MAS): raw Bruker TopSpin experiment folders and DMFIT-exported ascii spectra for selective and non-selective 1D 13C-13C spin diffusion experiments (3000 ms mixing) used to quantify inter-polymer spatial proximities, and short-mixing (1 ms) reference spectra used for polymeric abundance quantification by spectral deconvolution. (2) 600 MHz data (Bruker Avance III, 1.6 mm PhoenixNMR HXY probe, 30 kHz MAS): raw Bruker TopSpin experiment folders containing 2D CORD, 2D CP-INADEQUATE, and 13C/1H relaxation (T1, T1rho) experiments for all 13 genotypes, with processed Excel workbooks per experiment type. Molecular dynamics simulation code, coordinate files, and analysis scripts (NAMD/CHARMM/Python) for six atomistic cell wall models are included. Summarized ssNMR data are compiled into a single excel file and subjected to statistical analysis. Multivariate analysis code (PCA, Pearson correlation) and summary data are provided as excel worksheets and Jupyter notebooks (Python 3).

09 BIOMASS FUELS↗
DOE OSTI2015

Genomic analysis of six new Geobacillus strains reveals highly conserved carbohydrate degradation architectures and strategies

In this work we report the whole genome sequences of six new Geobacillus xylanolytic strains along with the genomic analysis of their capability to degrade carbohydrates. The six sequenced Geobacillus strains described here have a range of GC contents from 43.9% to 52.5% and clade with named Geobacillus species throughout the entire genus. We have identified a ~200 kb unique super-cluster in all six strains, containing five to eight distinct carbohydrate degradation clusters in a single genomic region, a feature not seen in other genera. The Geobacillus strains rely on a small number of secreted enzymes located within distinct clusters for carbohydrate utilization, in contrast to most biomass-degrading organisms which contain numerous secreted enzymes located randomly throughout the genomes. All six strains are able to utilize fructose, arabinose, xylose, mannitol, gluconate, xylan, and α-1,6-glucosides. The gene clusters for utilization of these seven substrates have identical organization and the individual proteins have a high percent identity to their homologs. The strains show significant differences in their ability to utilize inositol, sucrose, lactose, α-mannosides, α-1,4-glucosides and arabinan.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Campylobacter jejuni Demonstrates Conserved Proteomic and Transcriptomic Responses When Co-cultured With Human INT 407 and Caco-2 Epithelial Cells

Major foodborne bacterial pathogens, such as Campylobacter jejuni , have devised complex strategies to establish and foster intestinal infections. For more than two decades, researchers have used immortalized cell lines derived from human intestinal tissue to dissect C. jejuni -host cell interactions. Known from these studies is that C. jejuni virulence is multifactorial, requiring a coordinated response to produce virulence factors that facilitate host cell interactions. This study was initiated to identify C. jejuni proteins that contribute to adaptation to the host cell environment and cellular invasion. We demonstrated that C. jejuni responds to INT 407 and Caco-2 cells in a similar fashion at the cellular and molecular levels. Active protein synthesis was found to be required for C. jejuni to maximally invade these host cells. Proteomic and transcriptomic approaches were then used to define the protein and gene expression profiles of C. jejuni co-cultured with cells. By focusing on those genes showing increased expression by C. jejuni when co-cultured with epithelial cells, we discovered that C. jejuni quickly adapts to co-culture with epithelial cells by synthesizing gene products that enable it to acquire specific amino acids for growth, scavenge for inorganic molecules including iron, resist reactive oxygen/nitrogen species, and promote host cell interactions. Based on these findings, we selected a subset of the genes involved in chemotaxis and the regulation of flagellar assembly and generated C. jejuni deletion mutants for phenotypic analysis. Binding and internalization assays revealed significant differences in the interaction of C. jejuni chemotaxis and flagellar regulatory mutants. The identification of genes involved in C. jejuni adaptation to culture with host cells provides new insights into the infection process.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Genomics, Exometabolomics, and Metabolic Probing Reveal Conserved Proteolytic Metabolism of Thermoflexus hugenholtzii and Three Candidate Species From China and Japan

Thermoflexus hugenholtzii JAD2 T , the only cultured representative of the Chloroflexota order Thermoflexales, is abundant in Great Boiling Spring (GBS), NV, United States, and close relatives inhabit geothermal systems globally. However, no defined medium exists for T. hugenholtzii JAD2 T and no single carbon source is known to support its growth, leaving key knowledge gaps in its metabolism and nutritional needs. Here, we report comparative genomic analysis of the draft genome of T. hugenholtzii JAD2 T and eight closely related metagenome-assembled genomes (MAGs) from geothermal sites in China, Japan, and the United States, representing “Candidatus Thermoflexus japonica,” “Candidatus Thermoflexus tengchongensis,” and “Candidatus Thermoflexus sinensis.” Genomics was integrated with targeted exometabolomics and 13 C metabolic probing of T. hugenholtzii. The Thermoflexus genomes each code for complete central carbon metabolic pathways and an unusually high abundance and diversity of peptidases, particularly Metallo- and Serine peptidase families, along with ABC transporters for peptides and some amino acids. The T. hugenholtzii JAD2 T exometabolome provided evidence of extracellular proteolytic activity based on the accumulation of free amino acids. However, several neutral and polar amino acids appear not to be utilized, based on their accumulation in the medium and the lack of annotated transporters. Adenine and adenosine were scavenged, and thymine and nicotinic acid were released, suggesting interdependency with other organisms in situ. Metabolic probing of T. hugenholtzii JAD2 T using 13 C-labeled compounds provided evidence of oxidation of glucose, pyruvate, cysteine, and citrate, and functioning glycolytic, tricarboxylic acid (TCA), and oxidative pentose-phosphate pathways (PPPs). However, differential use of position-specific 13 C-labeled compounds showed that glycolysis and the TCA cycle were uncoupled. Thus, despite the high abundance of Thermoflexus in sediments of some geothermal systems, they appear to be highly focused on chemoorganotrophy, particularly protein degradation, and may interact extensively with other microorganisms in situ.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Green microalga Chromochloris zofingiensis conserves substrate uptake pattern but changes their metabolic uses across trophic transition

The terrestrial green alga Chromochloris zofingiensis is an emerging model species with potential applications including production of triacylglycerol or astaxanthin. How C. zofingiensis interacts with the diverse substrates during trophic transitions is unknown. To characterize its substrate utilization and secretion dynamics, we cultivated the alga in a soil-based defined medium in transition between conditions with and without glucose supplementation. Then, we examined its exometabolite and endometabolite profiles. This analysis revealed that regardless of trophic modes, C. zofingiensis preferentially uptakes exogenous lysine, arginine, and purines, while secreting orotic acid. Here, we obtained metabolomic evidences that C. zofingiensis may use arginine for putrescine synthesis when in transition to heterotrophy, and for the TCA cycle during transition to photoautotrophy. We also report that glucose and fructose most effectively inhibited photosynthesis among thirteen different sugars. The utilized or secreted metabolites identified in this study provide important information to improve C. zofingiensis cultivation, and to expand its potential industrial and pharmaceutical applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Two major chromosome evolution events with unrivaled conserved gene content in pomegranate

Pomegranate has a unique evolutionary history given that different cultivars have eight or nine bivalent chromosomes with possible crossability between the two classes. Therefore, it is important to study chromosome evolution in pomegranate to understand the dynamics of its population. Here, we de novo assembled the Azerbaijani cultivar “Azerbaijan guloyshasi” (AG2017; 2n = 16) and re-sequenced six cultivars to track the evolution of pomegranate and to compare it with previously published de novo assembled and re-sequenced cultivars. High synteny was observed between AG2017, Bhagawa (2n = 16), Tunisia (2n = 16), and Dabenzi (2n = 18), but these four cultivars diverged from the cultivar Taishanhong (2n = 18) with several rearrangements indicating the presence of two major chromosome evolution events. Major presence/absence variations were not observed as >99% of the five genomes aligned across the cultivars, while >99% of the pan-genic content was represented by Tunisia and Taishanhong only. We also revisited the divergence between soft- and hard-seeded cultivars with less structured population genomic data, compared to previous studies, to refine the selected genomic regions and detect global migration routes for pomegranate. We reported a unique admixture between soft- and hard-seeded cultivars that can be exploited to improve the diversity, quality, and adaptability of local pomegranate varieties around the world. Our study adds body knowledge to understanding the evolution of the pomegranate genome and its implications for the population structure of global pomegranate diversity, as well as planning breeding programs aiming to develop improved cultivars.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Temporal Resource Continuity Increases Predator Abundance in a Metapopulation Model: Insights for Conservation and Biocontrol

The amount of habitat in a landscape is an important metric for evaluating the effects of land cover on biodiversity, yet it fails to capture complex temporal dimensions of resource availability that could be consequential for species population dynamics. Here, we use a spatially-explicit predator–prey metapopulation model to test the effect of different spatiotemporal resource patterns on insect predators and their prey. We examined population responses in model landscapes that varied in both the amount and temporal variability of basal vegetation. Further, we examined cases where prey comprised either a single generalist species or two specialist species that use different resources available either early or late in the growing season. We found that predators and generalist prey benefitted from lower temporal variance of basal resources, which increased landscape-scale abundances. However, increasing the amount of basal resources also increased the variability of generalist prey populations. Specialist prey, on the other hand, did not benefit from less temporally variable basal resources, as they were restricted by habitat type, while also suffering greater predation. Predators achieved greater prey suppression in landscapes with less temporally variable resources, but the overall effects on prey abundance depended on prey habitat specialization. Our simulations demonstrate the joint importance of both the amount and temporal variability of resources for understanding how landscape heterogeneity influences biodiversity and ecosystem services such as the biological control of agricultural pests.

Spiesman, Brian↗
DOE OSTI2022

Unveiling the Occupational Exposure to Microbial Contamination in Conservation–Restoration Settings

Assuring a proper environment for the fulfillment of professional activities is one of the Sustainable Development Goals and is contemplated in the One Health approach assumed by the World Health Organization. This particular study is applied to an often neglected sector of our society—the conservators/restorers—despite the many health issues reported by these professionals. Three different specialties (textiles, paintings and wood sculpture) and locations were selected for evaluation by placement of electrostatic dust cloths. After treatment of the samples, bacterial and fungal contamination were assessed, as well as mycotoxin determination, the presence of azole-resistant strains and cytotoxicity of the microorganisms encountered. Bacteria were only present in one of medias used and showed relatively low numbers. The highest level of contamination by fungi was identified in one of the textiles settings. The textile area also showed the highest variability for fungi. Aspergillus sp. are one indicator of possible environmental issues, and A. sections Fumigati and Circumdati were particularly relevant in two of the settings and identified in all of them. No mycotoxins were detected and the large majority of the fungi identified were non-cytotoxic. Overall, these can be considered low-contaminated environments but attention should be given to the Aspergillus sp. contamination. Additional studies are needed not only to make these results more robust, but also to test if the environmental sampling alone is the best approach in a setting where there is very little movement and dust displacement and where professionals are in very close proximity to the artefacts being treated, which may suggest the existence of a micro-atmosphere worth evaluating and comparing to the obtained results.

Viegas, Carla (ORCID:0000000215456479)↗
DOE OSTI2022

Comparative Penicillium spp. Transcriptomics: Conserved Pathways and Processes Revealed in Ungerminated Conidia and during Postharvest Apple Fruit Decay

Blue mold, caused by Penicillium spp., is an impactful postharvest disease resulting in significant economic losses due to reduced pome fruit quality and mycotoxin contamination. Using two Penicillium species with different levels of aggressiveness, transcriptomics were implemented in order to identify genes expressed during apple fruit decay and loci expressed in ungerminated conidia. Total RNA was isolated from ungerminated conidia and decayed apple fruit infected with P. expansum R19 or P. polonicum RS1. There were 2442 differentially expressed genes (DEGs) between the R19 and RS1 in apple. Comparisons within species between apple and conidia revealed 4404 DEGs for R19 and 2935 for RS1, respectively. Gene ontology (GO) analysis revealed differential regulation in fungal transport and metabolism genes during decay, suggesting a flux in nutrient acquisition and detoxification strategies. In R19, the oxidoreductase GO category comprised 20% of all DEG groups in apple verses conidia. Ungerminated conidia from both species showed DEGs encoding the glyoxylate shunt and beta-oxidation, specifying the earliest metabolic requirements for germination. This is the first study to identify pre-loaded transcripts in conidia from blue mold fungi, reveal unique genes between species expressed during apple decay, and show the expression dynamics of known fungal virulence factors. These findings will enable development of targeted approaches for blue mold abatement strategies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Targeting a Conserved Lysine in the Hydrophobic Pocket of HIV-1 gp41 Improves Small Molecule Antiviral Activity

Human Immunodeficiency virus (HIV-1) fusion is mediated by glycoprotein-41, a protein that has not been widely exploited as a drug target. Small molecules directed at the gp41 ectodomain have proved to be poorly drug-like, having moderate efficacy, high hydrophobicity and/or high molecular weight. We recently investigated conversion of a fairly potent hydrophobic inhibitor into a covalent binder, by modifying it to react with a lysine residue on the protein. We demonstrated a 10-fold improvement in antiviral efficacy. Here, we continue this study, utilizing instead molecules with better inherent drug-like properties. Molecules possessing low to no antiviral activity as equilibrium binders were converted into µM inhibitors upon addition of an electrophilic warhead in the form of a sulfotetrafluorophenyl (STP) activated ester. We confirmed specificity for gp41 and for entry. The small size of the inhibitors described here offers an opportunity to expand their reach into neighboring pockets while retaining drug-likeness. STP esterification of equilibrium binders is a promising avenue to explore for inhibiting HIV-1 entry. Many gp41 targeting molecules studied over the years possess carboxylic acid groups which can be easily converted into the corresponding STP ester. It may be worth the effort to evaluate a library of such inhibitors as a way forward to small molecule inhibition of fusion of HIV and possibly other enveloped viruses.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

Food, Fracking, and Freshwater: The Potential for Markets and Cross-Sectoral Investments to Enable Water Conservation

Hydraulic fracturing—the injection of pressurized fluid, often water, to increase recovery of oil or gas—has become increasingly popular in combination with horizontal drilling. Hydraulic fracturing improves production from a well, but requires a significant amount of water to do so and could put pressure on existing water resources, especially in water-stressed areas. To supply water needs, some water rights holders sell or lease their water resources to oil and gas producers in an informal water market. These transactions enable the opportunity for cross-sectoral investments, by which the energy sector either directly or indirectly provides the capital for water efficiency improvements in the agricultural sector as a mechanism to increase water availability for other purposes, including oil and gas production. In this analysis, we employ an original water and cost model to evaluate the water market in Texas and the potential for cross-sectoral collaboration on water efficiency improvements through a case study of the Lower Rio Grande Valley in Texas. We find that, if irrigation efficiency management practices were fully implemented, between 420 and 800 million m3 of water could be spared per year over a ten year period, potentially enabling freshwater use in oil and gas production for up to 26,000 wells, while maintaining agricultural productivity and possibly improving water flows to the ecosystem.

Cook, Margaret↗