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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 181 records · Page 10
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Sequence-based generative AI design of versatile tryptophan synthases

Enzymes are powerful and sustainable catalysts, but their widespread application is limited by the difficulty of identifying functional starting points for optimization, creating a major bottleneck in early- stage biocatalyst discovery. Designing libraries of such starting enzymes remains particularly challenging. Here, we use the GenSLM protein language model to generate novel β-subunit of tryptophan synthase (TrpB) enzymes that express in Escherichia coli and are both stable and catalytically active. Many generated TrpBs also display significant substrate promiscuity, outperforming their natural counterparts on non-native substrates. Some even surpass laboratory-evolved TrpBs. Comparison of the most-active and most-promiscuous generated TrpB to its closest natural homolog confirms that the enhanced versatility is absent from the natural enzyme, highlighting the creative potential of generative models. These results demonstrate that the generated TrpBs not only preserve natural structure and function but also acquire non-natural properties, establishing generative models as powerful tools for biocatalyst discovery and engineering.

biocatalysis↗
DOE OSTI2026

BiG-SCAPE 2.0 and BiG-SLiCE 2.0: scalable, accurate and interactive sequence clustering of metabolic gene clusters

Microbial metabolic gene clusters encode the biosynthesis or catabolism of metabolites that facilitate ecological specialization, mediate microbiome interactions and constitute a major source of medicines and crop protection agents. Here, we present BiG-SCAPE and BiG-SLiCE 2.0, next-generation methods that facilitate scalable, accurate and interactive gene cluster analyses. BiG-SCAPE 2.0 updates its classification, alignment methods, and visualizations, enabling more accurate analysis, up to 8x faster runtimes and halved memory requirements. BiG-SLiCE 2.0 updates its distance metric, pHMM database, and classification logic, resulting in increased sensitivity nearing that of BiG-SCAPE. Analysis of 260,630 biosynthetic gene clusters from publicly available genomes reveals that both tools generate concurring estimates of gene cluster diversity, thus providing significantly extended methodological support for recent evidence indicating that the vast majority of natural product diversity remains unexplored. Together, these updates will facilitate global genome mining efforts for natural product discovery and microbiome analyses scalable with current data sizes.

Draisma, Arjan [Wageningen University & Research (↗
DOE OSTI2025

An evaporite sequence from ancient brine recorded in Bennu samples

Evaporation or freezing of water-rich fluids with dilute concentrations of dissolved salts can produce brines, as observed in closed basins on Earth and detected by remote sensing on icy bodies in the outer Solar System. The mineralogical evolution of these brines is well understood in regard to terrestrial environments, but poorly constrained for extraterrestrial systems owing to a lack of direct sampling. Here we report the occurrence of salt minerals in samples of the asteroid (101955) Bennu returned by the OSIRIS-REx mission. These include sodium-bearing phosphates and sodium-rich carbonates, sulfates, chlorides and fluorides formed during evaporation of a late-stage brine that existed early in the history of Bennu’s parent body. Discovery of diverse salts would not be possible without mission sample return and careful curation and storage, because these decompose with prolonged exposure to Earth’s atmosphere. Similar brines probably still occur in the interior of icy bodies Ceres and Enceladus, as indicated by spectra or measurement of sodium carbonate on the surface or in plumes.

58 GEOSCIENCES↗
DOE OSTI2024

Unveiling the microbial realm with VEBA 2.0: a modular bioinformatics suite for end-to-end genome-resolved prokaryotic, (micro)eukaryotic and viral multi-omics from either short- or long-read sequencing

Abstract The microbiome is a complex community of microorganisms, encompassing prokaryotic (bacterial and archaeal), eukaryotic, and viral entities. This microbial ensemble plays a pivotal role in influencing the health and productivity of diverse ecosystems while shaping the web of life. However, many software suites developed to study microbiomes analyze only the prokaryotic community and provide limited to no support for viruses and microeukaryotes. Previously, we introduced the Viral Eukaryotic Bacterial Archaeal (VEBA) open-source software suite to address this critical gap in microbiome research by extending genome-resolved analysis beyond prokaryotes to encompass the understudied realms of eukaryotes and viruses. Here we present VEBA 2.0 with key updates including a comprehensive clustered microeukaryotic protein database, rapid genome/protein-level clustering, bioprospecting, non-coding/organelle gene modeling, genome-resolved taxonomic/pathway profiling, long-read support, and containerization. We demonstrate VEBA’s versatile application through the analysis of diverse case studies including marine water, Siberian permafrost, and white-tailed deer lung tissues with the latter showcasing how to identify integrated viruses. VEBA represents a crucial advancement in microbiome research, offering a powerful and accessible software suite that bridges the gap between genomics and biotechnological solutions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Structure and sequence evolution in the pennycress ( Thlaspi arvense ) pangenome

Eukaryotic genomes harbor many forms of variation, including nucleotide diversity and structural polymorphisms, which experience natural selection and contribute to genome evolution and biodiversity. Harnessing this variation for agriculture hinges on our ability to detect, quantify, catalog, and deploy genetic diversity. Here, we explore seven complete genomes of the emerging biofuel crop pennycress ( Thlaspi arvense ) drawn from across the species' current genetic diversity to catalog variation in genome structure and content. Across this new pangenome resource, we find contrasting evolutionary modes in different genomic zones. Gene-poor, repeat-rich pericentromeric regions experience frequent rearrangements, including repeated centromere repositioning. By contrast, conserved gene-dense chromosome arms maintain large-scale synteny across accessions even in fast-evolving NOD-like receptor immune genes, where microsynteny breaks down across species, but gene cluster positioning macrosynteny is maintained. Our findings highlight that multiple elements of the genome experience dynamic evolution that conserves functional content on the chromosome scale but allows repositioning and presence–absence variation on a local scale. This diversity is invisible to classical reference-based strategies and highlights the strength and utility of pangenomic resources. These results provide a valuable case study of rapid genomic structural evolution within a species and powerful resources for crop development in an emerging biofuel crop.

Thlaspi arvense↗
DOE OSTI2026

Draft Genome Sequences of 14 Bacterial Isolates from the Rhizosphere of Bioenergy Sorghum

We report the draft genomes of a collection of 15 bacteria, isolated from the rhizosphere soil of bioenergy sorghum (Sorghum bicolor (L.) Moench). These isolates belong to the genera, Acidovorax, Nocardioides, Agrobacterium, Peribacillus, Caulobacter, Cupriavidus, Pseudomonas, Rhizobium, Sphingomonas, Priestia, Dyadobacter, Roseomonas, Ideonella, and Bacillus.

Black, Grace S.↗
DOE OSTI2024

Complete genome sequence of Rhodococcus qingshengii phage Perlina

ABSTRACT Rhodococcus phage Perlina is a novel phage isolated on Rhodococcus qingshengii S10. Perlina encodes 112 open reading frames with typical phage structural genes identified and 3 tRNAs (tRNA-Ile, tRNA-Met, and tRNA-Asn). Few close relatives can be identified at the nucleotide level, suggesting a new phage species.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Anomaly Detection On Network Traffic Using A Sequence Model Approach

The code ingests Zeek logs derived from network packet captures, applies a DBSCAN model, Gower distance to build a feature set as input into a transformer model that will output anomaly scores and provides the option to set a threshold as to what’s considered an anomaly.

Quach, Anna [Idaho National Laboratory (INL), Idah↗
DOE OSTI2025

Factors That Influence Variability in Stress-Drop Measurements Using Spectral Decomposition and Spectral-Ratio Methods for the 2019 Ridgecrest Earthquake Sequence

Stress drop is a fundamental parameter related to earthquake source physics, but is hard to measure accurately. To better understand how different factors influence stress-drop measurements, we compare two different methods using the Ridgecrest stress-drop validation data set: spectral decomposition (SD) and spectral ratio (SR), each with different processing options. Here, we also examine the influence of spectral complexity on source parameter measurement. Applying the SD method, we find that frequency bandwidth and time-window length could influence spectral magnitude calibration, while depth-dependent attenuation is important to correctly map stress-drop variations. For the SR method, we find that the selected source model has limited influence on the measurements; however, the Boatwright model tends to produce smaller standard deviation and larger magnitude dependence than the Brune model. Variance reduction threshold, frequency bandwidth, and time-window length, if chosen within an appropriate parameter range, have limited influence on source parameter measurement. For both methods, wave type, attenuation correction, and spectral complexity strongly influence the result. The scale factor that quantifies the magnitude dependence of stress drop show large variations with different processing options, and earthquakes with complex source spectra deviating from the Brune-type source models tend to have larger scale factor than earthquakes without complexity. Based on these detailed comparisons, we make a few specific suggestions for data processing workflows that could help future studies of source parameters and interpretations.

58 GEOSCIENCES↗
DOE OSTI2024

Discovery of 15 A-F Main Sequence Pulsating Star Candidates

Delta Scuti stars, spanning spectral types A to F with masses between 1.5 and 2.5 solar masses, exhibit a complex mix of radial and non-radial pressure modes. This study focuses on 15 Delta Scuti, Gamma Doradus, and Hybrid candidate stars using TESS satellite photometry data with a time series of exposures ranging from 20 to 600 seconds across different sky regions. Employing the prewhitening technique via fast Fourier transforms, significant frequencies are extracted from light curves. Three approximation methods are used to estimate critical stellar parameters such as density, radius, and mass. This research also verifies the variability of these stars, which are currently not classified as variable in databases like SIMBAD.

79 ASTRONOMY AND ASTROPHYSICS↗