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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 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Island influences on plant functional traits and trait–trait associations across species‐ and community‐scales

The island rule predicts gigantism or dwarfism in body size of island species relative to their mainland counterparts. However, whether other functional traits shift and whether trait–trait associations on islands differ between species and community levels remains unclear. We measured 13 carbon- and water-related functional traits in 37 shared tree species across 35 eastern Chinese islands and 66 nearby mainland plots. We examined species-level trait value shifts and associations under the island rule and compared trait associations between species and communities. Most size-related, wood-anatomical, and hydraulic traits shifted on islands, with large values decreasing and small values increasing; yet, their associations remained stable, aligning with the global trait spectrum and trait–trait coevolution. This stability, despite trait value shifts, suggests evolutionary integration of functional strategies. By contrast, island community-scale trait associations diverged from shared species-level patterns and sometimes reversed, such as positive relationships between wood density and resource-acquisitive traits. Community-level trait associations were stronger on islands, likely reflecting constrained environmental filtering and migration limitation. These contrasting patterns suggest that dominant species can restructure trait associations at the community level, with implications for ecosystem functioning and carbon storage, thereby advancing understanding of plant trait strategies in island systems.

Archipelagos↗
DOE OSTI2026

Recurrent acquisition of nuclease-protease pairs in antiviral immunity

Antiviral immune systems diversify by integrating new genes into existing pathways, creating new mechanisms of viral resistance. We identified genes encoding a predicted nuclease paired with a trypsin-like protease repeatedly acquired by multiple, otherwise unrelated antiviral immune systems in bacteria. Cell-based and biochemical assays revealed that the nuclease is a proenzyme that cleaves DNA only after activation by its partner protease. Two distinct immune systems, Hachiman and AVAST (antiviral adenosine triphosphatase/nucleoside triphosphatase of the STAND superfamily, Avs), use the same mechanism of proteolytic activation despite their independent evolutionary origins. Examination of nuclease-protease inheritance patterns identified caspase-nuclease (canu) genomic loci that confer antiviral defense in a pathway reminiscent of eukaryotic caspase activation. These results uncover the coordinated activities of pronucleases and their activating proteases within different immune systems and show how coevolution enables defense system innovation.

Tuck, Owen T↗
DOE OSTI2022

Marmot V2

MARMOT is a robust numerical tool for mesoscale modeling of fuel performance developed under the NEAMS Fuels technical area to predict the coevolution of microstructure and properties in fuel and cladding materials. MARMOT accomplishes this using the phase field method coupled with finite strain mechanics and heat conduction. MARMOT is based on the open source Multiphysics Object-Oriented Simulation Environment (MOOSE) and solves the coupled partial differential equations defining the physics using the finite element method. MARMOT is being developed in order to facilitate the development of improved materials models for fuel performance, but it is also being developed as a powerful tool in and of itself for the simulation of mesoscale fuel performance.

Aagesen, LarryK.↗
DOE OSTI2025

JGI-Trichoderma v1.0

There is a series of Python and bash scripts to parse genomics datasets used to evaluate the coevolution of gene families and the feature importance of gene families using an SVM classifier. - Cover analysis: takes a list of single-copy genes in a set of genomes, aligns and builds the gene trees to determine if two gene families have a signature of covariation with one another. It parses the files to run phykit cover script described here: https://jlsteenwyk.com/PhyKIT/usage/index.html - SVM-classifier: This Python script is an SVM-based genomic classifier designed for biological data analysis. It combines machine learning with feature selection to identify important genomic markers and classify biological samples. Core Functionality: The script uses Support Vector Machines from scikit-learn to classify genomic data, incorporating SelectKBest for automated feature selection and leave-one-out cross-validation for performance assessment. It operates in multiple modes: feature ranking, optimal combination discovery, and sample prediction. Primary Applications: Genomic sample classification and biomarker discovery Feature importance analysis in high-dimensional biological datasets Prediction of sample categories based on genomic profiles Research applications requiring robust classification of biological data Key Advantages: High-dimensional handling: SVMs excel with genomic data's typical high feature-to-sample ratios Integrated feature selection: Reduces noise and computational overhead while identifying key markers Probability estimation: Provides confidence scores essential for biological interpretation Validation robustness: Leave-one-out cross-validation ensures reliable performance metrics Operational flexibility: Multiple analysis modes support different research phases from exploration to prediction

Stecca Steindorff, Andrei [Lawrence Berkeley Natio↗
DOE OSTI2021

Identification and characterization of proteins of unknown function (PUFs) in Clostridium thermocellum DSM 1313 strains as potential genetic engineering targets

Abstract Background Mass spectrometry-based proteomics can identify and quantify thousands of proteins from individual microbial species, but a significant percentage of these proteins are unannotated and hence classified as proteins of unknown function (PUFs). Due to the difficulty in extracting meaningful metabolic information, PUFs are often overlooked or discarded during data analysis, even though they might be critically important in functional activities, in particular for metabolic engineering research. Results We optimized and employed a pipeline integrating various “guilt-by-association” (GBA) metrics, including differential expression and co-expression analyses of high-throughput mass spectrometry proteome data and phylogenetic coevolution analysis, and sequence homology-based approaches to determine putative functions for PUFs in Clostridium thermocellum . Our various analyses provided putative functional information for over 95% of the PUFs detected by mass spectrometry in a wild-type and/or an engineered strain of C. thermocellum . In particular, we validated a predicted acyltransferase PUF (WP_003519433.1) with functional activity towards 2-phenylethyl alcohol, consistent with our GBA and sequence homology-based predictions. Conclusions This work demonstrates the value of leveraging sequence homology-based annotations with empirical evidence based on the concept of GBA to broadly predict putative functions for PUFs, opening avenues to further interrogation via targeted experiments.

09 BIOMASS FUELS↗
DOE OSTI2023

The gut microbiome mediates adaptation to scarce food in Coleoptera

Beetles are ubiquitous cave invertebrates worldwide that adapted to scarce subterranean resources when they colonized caves. Here, we investigated the potential role of gut microbiota in the adaptation of beetles to caves from different climatic regions of the Carpathians. The beetles’ microbiota was host-specific, reflecting phylogenetic and nutritional adaptation. The microbial community structure further resolved conspecific beetles by caves suggesting microbiota-host coevolution and influences by local environmental factors. The detritivore species hosted a variety of bacteria known to decompose and ferment organic matter, suggesting turnover and host cooperative digestion of the sedimentary microbiota and allochthonous-derived nutrients. The cave Carabidae, with strong mandibula, adapted to predation and scavenging of animal and plant remains, had distinct microbiota dominated by symbiotic lineages Spiroplasma or Wolbachia. All beetles had relatively high levels of fermentative Carnobacterium and Vagococcus involved in lipid accumulation and a reduction of metabolic activity, and both features characterize adaptation to caves.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Targeting tRNA-synthetase interactions towards novel therapeutic discovery against eukaryotic pathogens

The development of chemotherapies against eukaryotic pathogens is especially challenging because of both the evolutionary conservation of drug targets between host and parasite, and the evolution of strain-dependent drug resistance. There is a strong need for new nontoxic drugs with broad-spectrum activity against trypanosome parasites such as Leishmania and Trypanosoma. A relatively untested approach is to target macromolecular interactions in parasites rather than small molecular interactions, under the hypothesis that the features specifying macromolecular interactions diverge more rapidly through coevolution. We computed tRNA Class-Informative Features in humans and independently in eight distinct clades of trypanosomes, identifying parasite-specific informative features, including base pairs and base mis-pairs, that are broadly conserved over approximately 250 million years of trypanosome evolution. Validating these observations, we demonstrated biochemically that tRNA:aminoacyl-tRNA synthetase (aaRS) interactions are a promising target for anti-trypanosomal drug discovery. From a marine natural products extract library, we identified several fractions with inhibitory activity toward Leishmania major alanyl-tRNA synthetase (AlaRS) but no activity against the human homolog. These marine natural products extracts showed cross-reactivity towards Trypanosoma cruzi AlaRS indicating the broad-spectrum potential of our network predictions. We also identified Leishmania major threonyl-tRNA synthetase (ThrRS) inhibitors from the same library. We discuss why chemotherapies targeting multiple aaRSs should be less prone to the evolution of resistance than monotherapeutic or synergistic combination chemotherapies targeting only one aaRS.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Host Dark Matter Halos of SDSS Red and Blue Quasars: No Significant Difference in Large-scale Environment

The observed optical colors of quasars are generally interpreted in one of two frameworks: unified models that attribute the color to the random orientation of the accretion disk along the line of sight, and evolutionary models that invoke connections between quasar systems and their environments. We test these schemas by probing the dark matter halo environments of optically selected quasars as a function of g – i optical color by measuring the two-point correlation functions of ~0.34 million eBOSS quasars as well as the gravitational deflection of cosmic microwave background photons around ~0.66 million XDQSO photometric quasar candidates. We do not detect a trend of halo bias with optical color through either analysis, finding that optically selected quasars at 0.8 < z < 2.2 occupy halos of characteristic mass M h ~ 3 × 10 12 h –1 M ⊙ regardless of their color. This result implies that a quasar's large-scale halo environment is not strongly connected to its observed optical color. We also confirm the findings of fundamental differences in the radio properties of red and blue quasars by stacking 1.4 GHz FIRST images at their positions, suggesting the observed differences cannot be attributed to orientation. Instead, the differences between red and blue quasars likely arise on nuclear-galactic scales, perhaps owing to reddening by a nuclear dusty wind. Finally, we show that optically selected quasars' halo environments are also independent of their r – W2 optical–infrared colors, while previous work has suggested that mid-infrared-selected obscured quasars occupy more massive halos. We discuss the implications of this result for models of quasar and galaxy coevolution.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

DESI Survey Validation Data in the COSMOS/Hyper Suprime-Cam Field: Cool Gas Trace Main-sequence Star-forming Galaxies at the Cosmic Noon

We present the first result in exploring the gaseous halo and galaxy correlation using the Dark Energy Spectroscopic Instrument survey validation data in the Cosmic Evolution Survey (COSMOS) and Hyper Suprime-Cam field. We obtain multiphase gaseous halo properties in the circumgalactic medium by using 115 quasar spectra (signal-to-noise ratio > 3). We detect Mg ii absorption at redshift 0.6 < z < 2.5, C iv absorption at 1.6 < z < 3.6, and H i absorption associated with the Mg ii and C iv. By crossmatching the COSMOS2020 catalog, we identify the Mg ii and C iv host galaxies in 10 quasar fields at 0.9< z < 3.1. We find that within the impact parameter of 250 kpc, a tight correlation is seen between the strong Mg ii equivalent width and the host galaxy star formation rate. The covering fraction f c of the strong Mg ii selected galaxies, which is the ratio of the absorbing galaxy in a certain galaxy population, shows significant evolution in the main-sequence galaxies and marginal evolution in all the galaxy populations within 250 kpc at 0.9 < z < 2.2. The f c increase in the main-sequence galaxies likely suggests the coevolution of strong Mg ii absorbing gas and the main-sequence galaxies at the cosmic noon. Furthermore, Mg ii and C iv absorbing gas is detected out of the galaxy virial radius, tentatively indicating the feedback produced by the star formation and/or the environmental effects.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Hard X-Ray to Radio Multiwavelength SED Analysis of Local U/LIRGs in the GOALS Sample with a Self-consistent AGN Model including a Polar-dust Component

We conduct hard X-ray to radio multiwavelength spectral energy distribution (SED) decomposition for 57 local luminous and ultraluminous infrared galaxies observed with the Nuclear Spectroscopic Telescope Array and/or Swift/Burst Alert Telescope in the GOALS sample. We modify the latest SED-fitting code X-CIGALE by implementing the infrared (IR) CLUMPY model, allowing us to conduct the multiwavelength study with the X-ray torus model XCLUMPY self-consistently. Adopting the torus parameters obtained by the X-ray fitting, we estimate the properties of the host galaxies, active galactic nucleus (AGN) tori, and polar dust. The star formation rates (SFRs) become larger with merger stage and most of them are above the main sequence. The SFRs are correlated with radio luminosity, indicating starburst emission is dominant in the radio band. Although polar-dust extinction is much smaller than torus extinction, the UV-to-IR (mainly IR) polar dust luminosities are ~2 times larger than the torus ones. The polar-dust temperature decreases while the physical size, estimated by the temperature and dust sublimation radius, increases with AGN luminosity from a few tens of parsec (early mergers) to kiloparsec scales (late mergers), where the polar dust likely comes from expanding (i.e., evolving) dusty outflows. A comparison between the SFRs and intrinsic AGN luminosities suggests that starbursts occur first and AGNs arise later, and overall their growth rates follow the simultaneous coevolution local galaxy–SMBH mass relation. We confirm the coexistence of intense starbursts, AGNs, and large-scale outflows in late mergers, supporting a standard AGN feedback scenario.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Software: gcamusa_v5.3_im3

GCAM USA version (gcamusa_v5p3_im3) supporting the publication: Khan, Z., Zhao, M., Ahsan, H., Wolfram, P., Vernon, C., Rice, J., Iyer, G., Binsted, M., Snyder, A., Graham, N., Kyle, P., 2023. Coevolution of future water, energy and land systems across the United States in response to national and global socioeconomic, climate, and energy policy drivers. (In progress) Earths Future, DOI: XXX with further details available at the meta-repository: https://immm-sfa.github.io/khan-etal_2023_im3gcamusa

Climate Change↗
DOE OSTI2023

Output Data: gcam_usa_v5p3_im3

Output databases and tables supporting the publication: Khan, Z., Zhao, M., Ahsan, H., Wolfram, P., Vernon, C., Rice, J., Iyer, G., Binsted, M., Snyder, A., Graham, N., Kyle, P., 2023. Coevolution of future water, energy and land systems across the United States in response to national and global socioeconomic, climate, and energy policy drivers. (In progress) Earths Future, DOI: XXX with further details available at the meta-repository: https://immm-sfa.github.io/khan-etal_2023_im3gcamusa Folder: gcam_usa_im3_outputs (GCAM USA v 5.3 used for IM3 experiment Output Databases): database_rcp45cooler_ssp3.tar.gz database_rcp45cooler_ssp5.tar.gz database_rcp45hotter_ssp5.tar.gz database_rcp45hotter_ssp5.tar.gz database_rcp85cooler_ssp3.tar.gz database_rcp85cooler_ssp5.tar.gz database_rcp85hotter_ssp5.tar.gz database_rcp85hotter_ssp5.tar.gz Folder: gcam_usa_im3_gcamextractor_outputs (gcamextractor post-processing of the GCAM databases for specific downstream models ): dataGCAM_cerf.tar.gz (For CERF Model) dataGCAM_demeter.tar.gz (For Demeter model) dataGCAM_go.tar.gz (For GO model) gcamDataTable.tar.gz (All IM3 scenarios)

Climate Change↗
DOE OSTI2024

Activation of polycystin-1 signaling by binding of stalk-derived peptide agonists

Polycystin-1 (PC1) is the protein product of thePKD1gene whose mutation causes autosomal dominant Polycystic Kidney Disease (ADPKD). PC1 is an atypical G protein-coupled receptor (GPCR) with an autocatalytic GAIN domain that cleaves PC1 into extracellular N-terminal and membrane-embedded C-terminal (CTF) fragments. Recently, activation of PC1 CTF signaling was shown to be regulated by a stalk tethered agonist (TA), resembling the mechanism observed for adhesion GPCRs. Here, synthetic peptides of the first 9- (p9), 17- (p17), and 21-residues (p21) of the PC1 stalk TA were shown to re-activate signaling by a stalkless CTF mutant in human cell culture assays. Novel Peptide Gaussian accelerated molecular dynamics (Pep-GaMD) simulations elucidated binding conformations of p9, p17, and p21 and revealed multiple specific binding regions to the stalkless CTF. Peptide agonists binding to the TOP domain of PC1 induced close TOP-putative pore loop interactions, a characteristic feature of stalk TA-mediated PC1 CTF activation. Additional sequence coevolution analyses showed the peptide binding regions were consistent with covarying residue pairs identified between the TOP domain and the stalk TA. These insights into the structural dynamic mechanism of PC1 activation by TA peptide agonists provide an in-depth understanding that will facilitate the development of therapeutics targeting PC1 for ADPKD treatment.

Life Sciences & Biomedicine - Other Topics↗
DOE OSTI2023

Adaptations for gas exchange enabled the elongation of lepidopteran proboscises

The extensive biodiversification of butterflies and moths (Lepidoptera) is partly attributed to their unique mouthparts (proboscis [Pr]) that can span in length from less than 1 mm to over 280mm in Darwin's sphinx moths. Lepi-doptera, similar to other insects, are believed to inhale and exhale respiratory gases only through valve-like spi-racles on their thorax and abdomen, making gas exchange through the narrow tracheae (Tr) challenging for the elongated Pr. How Lepidoptera overcome distance effects for gas transport to the Pr is an open question that is important to understanding how the Pr elongated over evolutionary time. Here, we show with scanning electron microscopy and X-ray imaging that distance effects on gas exchange are overcome by previously unreported micropores on the Pr surface and by superhydrophobic Tr that prevent water loss and entry. We find that the density of micropores decreases monotonically along the Pr length with the maxima proportional to the Pr length and that micropore diameters produce a Knudsen number at the boundary between the slip and transition flow regimes. By numerical estimation, we further show that the respiratory gas exchange for the Pr predominantly occurs via diffusion through the micropores. In conclusion, these adaptations are key innovations vital to Pr elongation, which likely facilitated lepidopteran biodiversification and the radiation of angiosperms by coevolutionary processes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

The endosymbiotic box of protective tricks

This month’s Genome Watch underscores how genome and transcriptome sequencing of newly identified endosymbionts helps to connect genetic information to their protective functions.

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 OSTI2025

Local adaptation of both plant and pathogen: an arms‐race compromise in switchgrass rust

In coevolving species, parasites locally adapt to host populations as hosts locally adapt to resist parasites. Parasites often outpace host local adaptation since they have rapid life cycles, but host diversity, the strength of selection, and external environmental influence can result in complex outcomes. To better understand local adaptation in host–parasite systems, we examined locally adapted switchgrass (Panicum virgatum), and its leaf rust pathogen (Puccinia novopanici) across a latitudinal range in North America. We grew switchgrass genotypes in 10 replicated multiyear common gardens, measuring rust severity from natural infection in a ‘host reciprocal transplant’ framework for testing local adaptation. We conducted genome-wide association mapping to identify genetic loci associated with rust severity. Genetically differentiated rust populations were locally adapted to northern and southern switchgrass, despite host local adaptation to environmental conditions in the same regions. Rust resistance was polygenic, and distinct loci were associated with rust severity in the north and south. We narrowed a previously identified large-effect quantitative trait locus for rust severity to a candidate YELLOW STRIPE-LIKE gene and linked numerous other loci to defense-related genes. Overall, our results suggest that both hosts and parasites can be simultaneously locally adapted, especially when parasites impose less selection than other environmental factors.

59 BASIC BIOLOGICAL SCIENCES↗