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All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Genome assembly PYCC 8100

The yeast Torulaspora delbrueckii is gaining importance for biotechnology due to its ability to increase wine sensorial complexity and for enhancing pre-frozen bread dough leavening. However, little is known about its population structure, and variation in gene content, or possible domestication routes have not been investigated. Here, we address these issues and update the circumscription of T. delbrueckii, which is composed of five major clades. Among the three European clades, a lineage associated with the wild arboreal niche is sister to the two other lineages that are linked with anthropic environments, one to wine fermentations and the other one to diverse sources including dairy products and bread dough (Mix- Anthropic clade). Using 62 genomes we identified 5629 genes in the pangenome of T. delbrueckii and 270 genes in the cloud genome. A pangenome tree analysis showed that wine strains have a genome composition were more similar to European wild arboreal strains than to those of the Mix Anthropic clade, in contradiction with the phylogenetic analysis. An association of gene content and ecology gave further support to the hypothesis that the Mix - Anthropic clade has the most specialized genome content and indicated that some of the exclusive genes were implicated in galactose and maltose utilization. More detailed analyses traced the acquisition of a cluster of GAL genes in strains associated with dairy products and the expansion and functional diversification of MAL genes in strains isolated from bread dough. Contrary to S. cerevisiae, domestication in T. delbrueckii is not primed by alcoholic fermentation and appears to be a recent event.

Sampaio, Jose P.↗
NASA NTRS2010

Whistler Waves Driven by Anisotropic Strahl Velocity Distributions: Cluster Observations

Observed properties of the strahl using high resolution 3D electron velocity distribution data obtained from the Cluster/PEACE experiment are used to investigate its linear stability. An automated method to isolate the strahl is used to allow its moments to be computed independent of the solar wind core+halo. Results show that the strahl can have a high temperature anisotropy (T(perpindicular)/T(parallell) approximately > 2). This anisotropy is shown to be an important free energy source for the excitation of high frequency whistler waves. The analysis suggests that the resultant whistler waves are strong enough to regulate the electron velocity distributions in the solar wind through pitch-angle scattering

Vinas, A.F.↗
NASA NTRS1986

Self-regulated cooling flows in elliptical galaxies and in cluster cores - Is exclusively low mass star formation really necessary?

A self-consistent treatment of the heating by supernovae associated with star formation in a spherically symmetric cooling flow in a cluster core or elliptical galaxy is presented. An initial stellar mass function similar to that in the solar neighborhood is adopted. Inferred star-formation rates, within the cooling region - typically the inner 100 kpc around dominant galaxies at the centers of cooling flows in XD clusters - are reduced by about a factor of 2, relative to rates inferred when the heat input from star formation is ignored. Truncated initial mass functions (IMFs) are also considered, in which massive star formation is suppressed in accordance with previous treatments, and colors are predicted for star formation in cooling flows associated with central dominant elliptical galaxies and with isolated elliptical galaxies surrounded by gaseous coronae. The low inferred cooling-flow rates around isolated elliptical galaxies are found to be insensitive to the upper mass cutoff in the IMF, provided that the upper mass cutoff exceeds 2 M solar mass. Comparison with observed colors favors a cutoff in the IMF above 1 M solar mass in at least two well-studied cluster cooling flows, but a normal IMF cannot be excluded definitively. Models for NGC 1275 support a young (less than about 3 Gyr) cooling flow. As for the isolated elliptical galaxies, the spread in colors is consistent with a normal IMF. A definitive test of the IMF arising via star formation in cooling flows requires either UV spectral data or supernova searches in the cooling-flow-centered galaxies.

Silk, J.↗
NASA NTRS1999

Formation and Levitation of Unconfined Droplet Clusters

Combustion experiments using arrays of droplets seek to provide a link between single droplet combustion phenomena and the behavior of complex spray combustion systems. Both single droplet and droplet array studies have been conducted in microgravity to better isolate the droplet interaction phenomena and eliminate or reduce the confounding effects of buoyancy-induced convection. In most experiments involving droplet arrays, the droplets are supported on fibers to keep them stationary and close together before the combustion event. The presence of the fiber, however, disturbs the combustion process by introducing a source of heat transfer and asymmetry into the configuration. As the number of drops in a droplet array increases, supporting the drops on fibers becomes less practical because of the cumulative effect of the fibers on the combustion process. The overall objective of this research is to study the combustion of well-characterized drop clusters in a microgravity environment. Direct experimental observations and measurements of the combustion of droplet clusters would fill a large gap in our current understanding of droplet and spray combustion and provide unique experimental data for the verification and improvement of spray combustion models. This paper describes current work on the design and performance of an apparatus to generate and stabilize droplet clusters using acoustic and electrostatic forces.

Liu, S.↗
DOE OSTI2025

New approaches to secondary metabolite discovery from anaerobic gut microbes

The animal gut microbiome is a complex system of diverse, predominantly anaerobic microbiota with secondary metabolite potential. These metabolites likely play roles in shaping microbial community membership and influencing animal host health. As such, novel secondary metabolites from gut microbes hold significant biotechnological and therapeutic interest. Despite their potential, gut microbes are largely untapped for secondary metabolites, with gut fungi and obligate anaerobes being particularly under-explored. To advance understanding of these metabolites, culture-based and (meta)genome-based approaches are essential. Culture-based approaches enable isolation, cultivation, and direct study of gut microbes, and (meta)genome-based approaches utilize in silico tools to mine biosynthetic gene clusters (BGCs) from microbes that have not yet been successfully cultured. In this mini-review, we highlight recent innovations in this area, including anaerobic biofoundries like ExFAB, the NSF BioFoundry for Extreme & Exceptional Fungi, Archaea, and Bacteria. These facilities enable high-throughput workflows to study oxygen-sensitive microbes and biosynthetic machinery. Such recent advances promise to improve our understanding of the gut microbiome and its secondary metabolism.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1989

Formation of large-scale structure from cosmic strings and massive neutrinos

Numerical simulations of large-scale structure formation from cosmic strings and massive neutrinos are described. The linear power spectrum in this model resembles the cold-dark-matter power spectrum. Galaxy formation begins early, and the final distribution consists of isolated density peaks embedded in a smooth background, leading to a natural bias in the distribution of luminous matter. The distribution of clustered matter has a filamentary appearance with large voids.

Scherrer, Robert J.↗
DOE OSTI2024

CO 2 hydrogenation over rhodium cluster catalyst nucleated within a manganese oxide framework

Rhodium-based manganese oxide frameworks were explored as a prototype for carbon dioxide reactive capture and conversion. Three-dimensional frameworks of MnOx were utilized as support structures to isolate Rh metal centers. V, Na, and Zn were introduced as counterions to stabilize the structure and for their beneficial effect as promoters. Here, with this multicomponent catalyst, Rh active centers with MnOxs and varied counterions, we were able to selectively tune the catalytic performance of the material via the choice of counterion and structure of the host material. With cryptomelane-type tunnel manganese oxides octahedral molecular sieve (OMS2), we found that Rh-V-OMS2 was highly stable even after 48 hours on stream with a reaction rate of around 1.5x10 -4 mol CO 2 /g Rh /s, surpassing the net reactivity of other initially more active combinations. Furthermore, during CO 2 hydrogenation, in situ XAFS showed that single Rh atoms nucleated into nanoparticles/ sub-nanometer clusters with a coordination number of 5.5 or less. Our finding of the correlation between the reaction rate and particle size offers the potential for enhanced control over the reaction rate by tuning particle size. Our activity study with control experiments demonstrates that the activities of the catalysts are proved due to the unique metal support interaction offered by the Rh-X-MnO.

10 SYNTHETIC FUELS↗
DOE OSTI2020

The Architecture of Metabolism Maximizes Biosynthetic Diversity in the Largest Class of Fungi

Abstract Ecological diversity in fungi is largely defined by metabolic traits, including the ability to produce secondary or “specialized” metabolites (SMs) that mediate interactions with other organisms. Fungal SM pathways are frequently encoded in biosynthetic gene clusters (BGCs), which facilitate the identification and characterization of metabolic pathways. Variation in BGC composition reflects the diversity of their SM products. Recent studies have documented surprising diversity of BGC repertoires among isolates of the same fungal species, yet little is known about how this population-level variation is inherited across macroevolutionary timescales. Here, we applied a novel linkage-based algorithm to reveal previously unexplored dimensions of diversity in BGC composition, distribution, and repertoire across 101 species of Dothideomycetes, which are considered the most phylogenetically diverse class of fungi and known to produce many SMs. We predicted both complementary and overlapping sets of clustered genes compared with existing methods and identified novel gene pairs that associate with known secondary metabolite genes. We found that variation among sets of BGCs in individual genomes is due to nonoverlapping BGC combinations and that several BGCs have biased ecological distributions, consistent with niche-specific selection. We observed that total BGC diversity scales linearly with increasing repertoire size, suggesting that secondary metabolites have little structural redundancy in individual fungi. We project that there is substantial unsampled BGC diversity across specific families of Dothideomycetes, which will provide a roadmap for future sampling efforts. Our approach and findings lend new insight into how BGC diversity is generated and maintained across an entire fungal taxonomic class.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Distinguishing Leptothrix and Sphaerotilus genera by an integrated genomic-phenotypic analysis supported by new Leptothrix genomes

The Sphaerotilus-Leptothrix group of bacteria includes one of the first described microorganisms, Leptothrix ochracea, an uncultured type strain, plus isolates of Leptothrix and Sphaerotilus. This group is unified by the ability to form sheaths and oxidize metals, although L. ochracea exhibits obvious ecological, morphological, and functional differences from the rest of Sphaerotilus-Leptothrix. Recently, there have been calls to combine the group into one genus, Sphaerotilus; however, these studies lacked adequate genomic representation of L. ochracea. Here, we present a comprehensive comparative genomic analysis of the Sphaerotilus-Leptothrix group, including expanded representation of L. ochracea, a closely related novel species, Leptothrix toolikensis, and two new isolates (Leptothrix mechoopdaensis). Analysis of 38 genomes resolves three phylogenetic and functional groups: the ochracea-type Leptothrix (Group 1), the mobilis-type Leptothrix (Group 2), and Sphaerotilus (Group 3). Group 1 genomes form a separate genus based on average nucleotide identity and alignment fraction. The genomes clearly diverge from the rest of Sphaerotilus-Leptothrix in phylogeny, size, and metabolic potential. Group 1 genomes are much smaller (2.59–3.04 Mb) than those of Groups 2 (4.55–6.06 Mb) and 3 (3.94–5.07 Mb), while encoding more metal oxidases and fewer carbohydrate-active enzymes. Group 2 clusters with Group 3 phylogenetically and is similar in organic carbon metabolisms but maintains more metal oxidation genes. Group 2 members lack homogeneity in phenotype and genotype, suggesting that additional isolates and genomes are needed for confident classification. However, Group 1 genomes (L. ochracea and L. toolikensis) show clear divergence, precluding their inclusion in Sphaerotilus and supporting the retention of the genus Leptothrix.

Leptothrix↗
DOE OSTI2023

Zinc Speciation and Propane Dehydrogenation in Zn/H-ZSM-5 Catalysts

Zn/H-ZSM-5 catalysts have been frequently investigated for propane dehydrogenation (PDH); however, the active site remains unresolved due to the complexity of the system. We employed in situ FTIR spectroscopy and a kinetics method to correlate the Zn speciation and PDH activity in Zn/H-ZSM-5 with two Si/Al ratios (15 and 39) and a range of Zn/Al ratios (0–1.7). Incremental additions of zinc show that Zn 2+ sites are preferentially formed on H-ZSM-5 over a fraction of paired Al sites followed by [Zn-O-Zn] 2+ and [ZnOH] + sites and then ZnO x clusters. The [Zn-OH] + and [Zn-O-Zn] 2+ sites in H-ZSM-5 are more active and selective than isolated Zn 2+ for PDH. [Zn-OH] + species sublimate over time on stream, leading to catalyst deactivation, while [Zn-O-Zn] 2+ species are stable even after high-temperature reduction (750 °C for 60 min). Three distinct Zn sites ([Zn-O-Zn] 2+ , Zn 2+ , and [ZnOH] + ) show a similar propane reaction order (close to 1) and H 2 reaction order (close to 0). Combined with the lack of Zn hydride when propane flows over the catalyst at 550 °C, it is concluded that propane adsorption and dissociation is a rate-determining step and H 2 desorption is fast. This work indicates that the preparation of H-ZSM-5 with abundant Al pairs may be a strategy to form stable and selective Zn/H-ZSM-5 catalysts for propane dehydrogenation. Furthermore, it is also highlighted that examining the effect of both metal/Al ratios and Al distribution of the zeolite is crucial in identifying the metal cations in metal–zeolite systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

First-principles insights into chromium-induced oxide phases in NiO

The high-temperature oxidation of Ni–Cr alloys leads to complex oxide scales comprising Ni(Cr)O solid solutions, NiCr 2 O 4 spinel, and Cr 2 O 3 corundum within the NiO matrix. Understanding the atomic-scale mechanisms of Cr segregation and precipitate formation is crucial for enhancing oxidation resistance. Here, we employ density functional theory calculations to investigate Cr behavior on NiO(100), (110), and (111) surfaces and in the bulk. Our results reveal that isolated Cr atoms preferentially segregate to the surfaces, stabilizing Ni(Cr)O solid solutions via strong Cr–O bonding, whereas Cr pairs and clusters favor subsurface migration and bulk aggregation, promoting nucleation of NiCr 2 O 4 and Cr 2 O 3 phases. These findings elucidate a size-dependent segregation mechanism linking Cr coordination environments to oxide phase evolution. This atomic-scale insight informs strategies to tailor oxide microstructures and enhance the high-temperature oxidation resistance of Ni–Cr alloys.

Chromium Segregation↗
DOE OSTI2023

Genome Sequence of Mycobacteriophage Bassalto

Bassalto is a newly isolated phage of Mycobacterium smegmatis mc 2 155 from the campus grounds of Norfolk State University in Norfolk, VA. Bassalto belongs to the cluster B and subcluster B3 mycobacteriophages, based on the nucleotide composition and comparison to known mycobacteriophages.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

FY 2026 Midyear Report: Seismic Monitoring of Underground Vibration Sources Using Distributed Acoustic Sensing and Seismometers

Safeguards-relevant temporal changes in underground facilities can be observed using geophysical monitoring techniques. Seismic waves, in particular, provide valuable insights into subsurface activities and can serve as an important tool for detecting anomalous events that may indicate containment breaches at geological repositories. This midyear report summarizes ongoing efforts to automatically and rapidly detect and locate anomalous vibration signals that could be indicative of potential containment breaches. Previous work during FY25 focused on compiling continuous seismic datasets from two underground sites and developing a database of continuous waveforms and ground-truth event data derived from multiple sensing modalities. Building on this foundation, we are adapting anomaly detection and geolocation algorithms to explore methods for monitoring underground activities using two relatively low-maintenance sensing technologies: a dense surface geophone array deployed at the Pleasant Gap mine in Pennsylvania, and a three-dimensional fiber-optic cable array for distributed acoustic sensing (DAS) installed in the subsurface at the Sanford Underground Research Facility (SURF) in South Dakota. This report summarizes work conducted during the first two quarters of FY26, during which we refined a dynamic power spectral density (PSD)-based detector, applied it independently to each geophone station, and then combined the per‑station detections with density-based spatial clustering of applications with noise (DBSCAN) to cluster events and produce spatial maps over a nine‑day interval. In addition, we outline plans for a field trial at the Waste Isolation Pilot Plant (WIPP) in New Mexico to compare traditional seismic monitoring approaches with DAS techniques and to evaluate the benefits of combined data analysis. Activities during the past two quarters have included the preparation and submission of a Field Test Plan to WIPP for approval, as well as submission to headquarters for review and feedback.

58 GEOSCIENCES↗
DOE OSTI2021

Bioinformatic and Mechanistic Analysis of the Palmerolide PKS-NRPS Biosynthetic Pathway From the Microbiome of an Antarctic Ascidian

Complex interactions exist between microbiomes and their hosts. Increasingly, defensive metabolites that have been attributed to host biosynthetic capability are now being recognized as products of host-associated microbes. These unique metabolites often have bioactivity targets in human disease and can be purposed as pharmaceuticals. Polyketides are a complex family of natural products that often serve as defensive metabolites for competitive or pro-survival purposes for the producing organism, while demonstrating bioactivity in human diseases as cholesterol lowering agents, anti-infectives, and anti-tumor agents. Marine invertebrates and microbes are a rich source of polyketides. Palmerolide A, a polyketide isolated from the Antarctic ascidian Synoicum adareanum, is a vacuolar-ATPase inhibitor with potent bioactivity against melanoma cell lines. The biosynthetic gene clusters (BGCs) responsible for production of secondary metabolites are encoded in the genomes of the producers as discrete genomic elements. A candidate palmerolide BGC was identified from a S. adareanum microbiome-metagenome based on a high degree of congruence with a chemical structure-based retrobiosynthetic prediction. Protein family homology analysis, conserved domain searches, active site and motif identification were used to identify and propose the function of the ~75 kbp trans-acyltransferase (AT) polyketide synthase-non-ribosomal synthase (PKS-NRPS) domains responsible for the stepwise synthesis of palmerolide A. Though PKS systems often act in a predictable co-linear sequence, this BGC includes multiple trans-acting enzymatic domains, a non-canonical condensation termination domain, a bacterial luciferase-like monooxygenase (LLM), and is found in multiple copies within the metagenome-assembled genome (MAG). Detailed inspection of the five highly similar pal BGC copies suggests the potential for biosynthesis of other members of the palmerolide chemical family. This is the first delineation of a biosynthetic gene cluster from an Antarctic microbial species, recently proposed as Candidatus Synoicihabitans palmerolidicus. These findings have relevance for fundamental knowledge of PKS combinatorial biosynthesis and could enhance drug development efforts of palmerolide A through heterologous gene expression.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Physiology of Highly Radioresistant Escherichia coli After Experimental Evolution for 100 Cycles of Selection

Ionizing radiation (IR) is lethal to most organisms at high doses, damaging every cellular macromolecule via induction of reactive oxygen species (ROS). Utilizing experimental evolution and continuing previous work, we have generated the most IR-resistant Escherichia coli populations developed to date. After 100 cycles of selection, the dose required to kill 99% the four replicate populations (IR9-100, IR10-100, IR11-100, and IR12-100) has increased from 750 Gy to approximately 3,000 Gy. Fitness trade-offs, specialization, and clonal interference are evident. Long-lived competing sub-populations are present in three of the four lineages. In IR9, one lineage accumulates the heme precursor, porphyrin, leading to generation of yellow-brown colonies. Major genomic alterations are present. IR9 and IR10 exhibit major deletions and/or duplications proximal to the chromosome replication terminus. Contributions to IR resistance have expanded beyond the alterations in DNA repair systems documented previously. Variants of proteins involved in ATP synthesis (AtpA), iron-sulfur cluster biogenesis (SufD) and cadaverine synthesis (CadA) each contribute to IR resistance in IR9-100. Major genomic and physiological changes are emerging. An isolate from IR10 exhibits protein protection from ROS similar to the extremely radiation resistant bacterium Deinococcus radiodurans, without evident changes in cellular metal homeostasis. Selection is continuing with no limit to IR resistance in evidence as our E. coli populations approach levels of IR resistance typical of D. radiodurans.

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗
NASA NTRS1982

30/20 GHz communications satellite multibeam antenna

A 20 GHz downlink satellite antenna design is described. The aperture simultaneously radiates 18 fixed, 0.3 deg width pencil beams directed at 18 cities distributed over CONUS for Trunking Service. All beams use the same trunk frequency allocation for 18 reuses of the band. The same aperture also radiates six additional 0.3 deg spot beams for Customer Premises Service (CPS) for TDMA beam hopping operation to small terminals anywhere in CONUS. Each CPS beam scans one sector of CONUS and all six beams are frequency reused in a CPS band. Offset dual reflector optics are used with a feed array and multiport beam forming network (BFN). For so many frequency reuses, sidelobes per beam must be 30 to 40 dB down over CONUS. Novel dual reflector optics were devised with shaped surfaces providing low aberrations for all beam positions over CONUS (+ or - 12 BW by + or - 5 BW). Scan loss under 1 dB is calculated with nearly constant sidelobes. For each beam position, a 7-element cluster of feeds is activated in the feed array with coefficients adjusted by the BFN to maintain low sidelobes and thus high beam isolation for frequency reuse.

Scott, W. G.↗
NASA NTRS1990

High-velocity interstellar gas in the lines of sight to the Wolf-Rayet stars HD 97152 and HD 96548

The interstellar medium was studied in the direction to the WR stars HD 96548 and HD 97152, and the results are reported. New observational data on the UV spectra of several field stars near both these WR stars are presented. The high-velocity gas seen in the spectra of these stars suggests that the detected expanding interstellar gas structure consists of two OB cluster supershells. The presence of high-velocity absorption components in one of five field star spectra in the direction of the more isolated WR star HD 96548 suggests that this expanding gas does not originate from the optical ring nebula RCW 58 surrounding HD 96548, as previously believed, but instead indicates the detection of a previously unknown expanding interstellar shell in this line of sight.

Nichols-Bohlin, Joy↗
DOE OSTI2025

Thiohalorhabdus methylotropha sp. nov., an extremely halophilic autotrophic methylotiotroph from hypersaline lakes

So far, there have been no reports of trimethylamine (TMA)-utilizing extremely halophilic microorganisms in hypersaline habitats. Our aerobic enrichments at 4 M total Na + with 5 mM TMA inoculated with surface sediments from hypersaline soda (at pH 9.5) or chloride-sulfate (at pH 7) lakes in southwestern Siberia were successful only for the latter. The initial enrichment included both bacteria and haloarchaea but only the bacterial component was able to grow as a pure culture with TMA. Strain Cl-TMA forms a new-species lineage within the genus Thiohalorhabdus which includes extremely halophilic and obligate lithoautotrophic sulfur-oxidizing gammaproteobacteria. Cl-TMA can grow methyloautotrophically utilizing TMA, dimethylamine (DMA) and methanol (MeOH) as the electron donors or chemolithoautotrophically with thiosulfate. Mixotrophic growth was also observed with the three methyl compounds and thiosulfate. Carbon is assimilated autotrophically via the Calvin-Benson-Basham pathway. Unlike the type species of Thiohalorhabdus, T. denitrificans , Cl-TMA was incapable of anaerobic growth via denitrification. The isolate belongs to extreme halophiles growing between 2.5 and 5 M NaCl with an optimum at 3–3.5 M. Genome analysis identified two gene clusters coding for PQQ-dependent methanol dehydrogenases (MxaFI and XoxF), four homologues of the formaldehyde activating enzymes (Faes), a TMA/DMA oxidation locus, and two cluster of genes encoding an N-methylglutamate dehydrogenase pathway (NMGP) for methylamine oxidation. The first steps of C 1 -subtrate conversions are followed by the tetrahydrofolate (THF)-linked and tetrahydromethanopterin (H4MPT)-linked formaldehyde oxidation pathways and two formate dehydrogenases. All of those signatures of methylotrophy were absent in T. denitrificans . In contrast, genes for two key sulfur oxidation enzymes, thiosulfate dehydrogenase TsdAB and sulfide dehydrogenase FccAB, that are present in the type species are missing in Cl-TMA. Thiosulfate is oxidized to sulfate by a combination of an incomplete Sox cycle and an sHdr system. Strain Cl-TMA T (JCM 35977 = UQM 41915) is proposed to be classified as Thiohalorhabdus methylotrophus sp. nov.

59 BASIC BIOLOGICAL SCIENCES↗