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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 OSTI2025

Unique trajectory of gene family evolution from genomic analysis of nearly all known species in an ancient yeast lineage

Gene gains and losses are a major driver of genome evolution; their precise characterization can provide insights into the origin and diversification of major lineages. Here, we examined gene family evolution of 1154 genomes from nearly all known species in the medically and technologically important yeast subphylum Saccharomycotina. We found that yeast gene family evolution differs from that of plants, animals, and filamentous ascomycetes, and is characterized by smaller overall gene numbers yet larger gene family sizes for a given gene number. Faster-evolving lineages (FELs) in yeasts experienced significantly higher rates of gene losses—commensurate with a narrowing of metabolic niche breadth—but higher speciation rates than their slower-evolving sister lineages (SELs). Gene families most often lost are those involved in mRNA splicing, carbohydrate metabolism, and cell division and are likely associated with intron loss, metabolic breadth, and non-canonical cell cycle processes. Our results highlight the significant role of gene family contractions in the evolution of yeast metabolism, genome function, and speciation, and suggest that gene family evolutionary trajectories have differed markedly across major eukaryotic lineages.

Comparative Genomics↗
DOE OSTI2023

Structure of the Wnt–Frizzled–LRP6 initiation complex reveals the basis for coreceptor discrimination

Wnt morphogens are critical for embryonic development and tissue regeneration. Canonical Wnts form ternary receptor complexes composed of tissue-specific Frizzled (Fzd) receptors together with the shared LRP5/6 coreceptors to initiate β-catenin signaling. The cryo-EM structure of a ternary initiation complex of an affinity-matured XWnt8–Frizzled8–LRP6 complex elucidates the basis of coreceptor discrimination by canonical Wnts by means of their N termini and linker domains that engage the LRP6 E1E2 domain funnels. Chimeric Wnts bearing modular linker “grafts” were able to transfer LRP6 domain specificity between different Wnts and enable non-canonical Wnt5a to signal through the canonical pathway. Synthetic peptides comprising the linker domain serve as Wnt-specific antagonists. The structure of the ternary complex provides a topological blueprint for the orientation and proximity of Frizzled and LRP6 within the Wnt cell surface signalosome.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Structure of saguaro cactus virus 3′ translational enhancer mimics 5′ cap for eIF4E binding

The genomes of several plant viruses contain RNA structures at their 3' ends called cap-independent translation enhancers (CITEs) that bind the host protein factors such as mRNA 5' cap-binding protein eIF4E for promoting cap-independent genome translation. However, the structural basis of such 5' cap-binding protein recognition by the uncapped RNA remains largely unknown. Here, we have determined the crystal structure of a 3' CITE, panicum mosaic virus-like translation enhancer (PTE) from the saguaro cactus virus (SCV), using a Fab crystallization chaperone. The PTE RNA folds into a three-way junction architecture with a pseudoknot between the purine-rich R domain and pyrimidine-rich Y domain, which organizes the overall structure to protrude out a specific guanine nucleotide, G18, from the R domain that comprises a major interaction site for the eIF4E binding. The superimposable crystal structures of the wild-type, G18A, G18C, and G18U mutants suggest that the PTE scaffold is preorganized with the flipped-out G18 ready to dock into the eIF4E 5' cap-binding pocket. The binding studies with wheat and human eIF4Es using gel electrophoresis and isothermal titration calorimetry, and molecular docking computation for the PTE–eIF4E complex demonstrated that the PTE structure essentially mimics the mRNA 5' cap for eIF4E binding. Such 5' cap mimicry by the uncapped and structured viral RNA highlights how viruses can exploit RNA structures to mimic the host protein-binding partners and bypass the canonical mechanisms for their genome translation, providing opportunities for a better understanding of virus-host interactions and non-canonical translation mechanisms found in many pathogenic RNA viruses.

3' cap-independent translation enhancers↗
DOE OSTI2024

Present and future of $\mathcal{C}$osmo $\mathcal{L}$attice

We discuss the present state and planned updates of Cosmo Lattice, a cutting-edge code for lattice simulations of non-linear dynamics of scalar-gauge field theories in an expanding background. We first review the current capabilities of the code, including the simulation of interacting singlet scalars and of Abelian and non-Abelian scalar-gauge theories. We also comment on new features recently implemented, such as the simulation of gravitational waves from scalar and gauge fields. Secondly, we discuss new extensions of Cosmo Lattice that we plan to release publicly. We comment on new physics modules, which include axion-gauge interactions $\phi F\tilde{F}$, non-minimal gravitational couplings $\phi ^2R$, creation and evolution of cosmic-defect networks, and magnetohydrodynamics. Finally, we also discuss new technical features, including evolvers for non-canonical interactions, arbitrary initial conditions, simulations in 2+1 dimensions, and higher-accuracy spatial derivatives.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2025

Engineering of xylose metabolic pathways in Rhodotorula toruloides for sustainable biomanufacturing

Abstract The oleaginous yeast Rhodotorula toruloides is a promising microbial cell factory for the sustainable production of biofuels and value-added chemicals from renewable carbon sources. Unlike the conventional yeast Saccharomyces cerevisiae, R. toruloides can naturally metabolize xylose, the second most abundant sugar in lignocellulosic hydrolysates. However, its native xylose metabolism is inefficient, characterized by slow xylose uptake and accumulation of D-arabitol. Moreover, despite its phenotype, research on the enzymes involved in xylose metabolism has yet to reach a consensus. Therefore, this review provides a comprehensive analysis of the non-canonical xylose metabolism in R. toruloides, focusing on the properties of key enzymes involved in xylose metabolism. Native xylose reductase and xylitol dehydrogenase exhibit broad substrate promiscuity compared to their counterparts in the xylose-fermenting Scheffersomyces stipitis. Additionally, the absence of xylulokinase expression under xylose-utilizing conditions redirects metabolism toward D-arabitol accumulation. Consequently, D-arabitol dehydrogenases and ribulokinase play essential roles in the xylose metabolism of R. toruloides. These findings highlight the fundamental differences between R. toruloides xylose metabolism and the oxidoreductase pathways observed in other xylose-fermenting yeast, providing insights for metabolic engineering strategies to improve xylose utilization and enhance bioconversion of cellulosic hydrolysates to different bioproducts by R. toruloides.

Biotechnology & Applied Microbiology↗
DOE OSTI2025

BONCAT-Live for isolation and cultivation of active environmental bacteria

In diverse environments, microbes drive a myriad of processes, from geochemical and nutrient cycling to interspecies interactions, including associations with plants and animals. Their physiological state is dynamic and impacted by abiotic and biotic conditions, responding to environmental fluctuations by changes in cellular metabolism, according to their genetic potential. Molecular, cellular, and genomic approaches can identify and measure microbial responses and adaptation to environmental changes in native communities. However, isolating individual microbial cells that respond to specific changes for cultivation has been difficult. To address this, we implemented a novel bacterial isolation approach (BONCAT-Live) by integrating bio-orthogonal non-canonical amino acid tagging (BONCAT) in diverse native communities, with isolation and cultivation of cells responding to specific stimuli, at different time scales. In frozen Arctic permafrost samples, we identified and isolated dormant bacteria that become active after thawing under native or nutrient-enriched conditions. From the Populus tree rhizosphere, we isolated strains that thrive under high concentrations of root exudates that act as defense compounds and nutrients. In the human microbiome, we identified and isolated bacteria that rapidly proliferated when exposed to metabolites provided by the host or other co-occurring microbes. Further characterization of isolated bacterial strains will provide opportunities for in-depth determination of how these microbes adapt to changes in their environments, individually and as part of model communities.

Analytical Methods↗
DOE OSTI2023

H2A.X promotes endosperm-specific DNA methylation in Arabidopsis thaliana

Background: H2A.X is an H2A variant histone in eukaryotes, unique for its ability to respond to DNA damage, initiating the DNA repair pathway. H2A.X replacement within the histone octamer is mediated by the FAcilitates Chromatin Transactions (FACT) complex, a key chromatin remodeler. FACT is required for DEMETER (DME)-mediated DNA demethylation at certain loci in Arabidopsis thaliana female gametophytes during reproduction. Here, we sought to investigate whether H2A.X is involved in DME- and FACT-mediated DNA demethylation during reproduction. Results: H2A.X is encoded by two genes in Arabidopsis genome, HTA3 and HTA5. We generated h2a.x double mutants, which displayed a normal growth profile, whereby flowering time, seed development, and root tip organization, S-phase progression and proliferation were all normal. However, h2a.x mutants were more sensitive to genotoxic stress, consistent with previous reports. H2A.X fused to Green Fluorescent Protein (GFP) under the H2A.X promoter was highly expressed especially in newly developing Arabidopsis tissues, including in male and female gametophytes, where DME is also expressed. We examined DNA methylation in h2a.x developing seeds and seedlings using whole genome bisulfite sequencing, and found that CG DNA methylation is decreased genome-wide in h2a.x mutant endosperm. Hypomethylation was most striking in transposon bodies, and occurred on both parental alleles in the developing endosperm, but not the embryo or seedling. h2a.x-mediated hypomethylated sites overlapped DME targets, but also included other loci, predominately located in heterochromatic transposons and intergenic DNA. Conclusions: Our genome-wide methylation analyses suggest that H2A.X could function in preventing access of the DME demethylase to non-canonical sites. Overall, our data suggest that H2A.X is required to maintain DNA methylation homeostasis in the unique chromatin environment of the Arabidopsis endosperm.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Identifying Hot Spots and Hot Moments of Metabolic Activity in Salt Marsh Sediments through BONCAT-FISH Microscale Mapping (Final Technical Report)

Understanding the biogeography and timing of microbial metabolic activity is a key priority for microbial ecologists. With such knowledge, the cumulative biogeochemical contributions of microbial communities become more predictable, and our ability to both understand the effects of environmental change on microbial activity and build synthetic communities with desired functions will increase substantially. In this project, we advanced this broad, ambitious goal in two substantial ways: we developed a multiplexed Fluorescence In Situ Hybridization (FISH) approach that links microbial identity with metabolic function, and we established a novel Bio-Orthogonal Non-Canonical Amino acid Tagging (BONCAT) technique that can resolve the timing of anabolic activity, providing new resolution of when microbial constituents are growing. We deployed both of these techniques in multiple environmental settings to demonstrate their versatility. At the Little Sippewissett Salt Marsh, we combined a novel dual-BONCAT technique with fluorescence activated cell sorting to determine which population of cells was metabolically active during the day and which was active during the night. We found that Methylobacterium was active during daylight hours, potentially feeding on carbon-rich molecules released from plant roots. Sulfur-cycling microbes dominate the population active during the dark night-time hours. Overall, the work conducted under the auspices of this project developed two promising new techniques for identifying the “hot spots” and “hot moments” of microbial activity in complex communities with taxonomic and functional resolution. We focused largely on a salt marsh sediment context, but are confident that microbial ecologists seeking to understand the microbial role in biogeochemical cycles in a wide range of settings will find our newly developed techniques useful in future work.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

BONCAT-FACS-Seq reveals the active fraction of a biocrust community undergoing a wet-up event

Determining which microorganisms are active within soil communities remains a major technical endeavor in microbial ecology research. One promising method to accomplish this is coupling bioorthogonal non-canonical amino acid tagging (BONCAT) with fluorescence activated cell sorting (FACS) which sorts cells based on whether or not they are producing new proteins. Combined with shotgun metagenomic sequencing (Seq), we apply this method to profile the diversity and potential functional capabilities of both active and inactive microorganisms in a biocrust community after being resuscitated by a simulated rain event. We find that BONCAT-FACS-Seq is capable of discerning the pools of active and inactive microorganisms, especially within hours of applying the BONCAT probe. The active and inactive components of the biocrust community differed in species richness and composition at both 4 and 21 h after the wetting event. The active fraction of the biocrust community is marked by taxa commonly observed in other biocrust communities, many of which play important roles in species interactions and nutrient transformations. Among these, 11 families within the Firmicutes are enriched in the active fraction, supporting previous reports indicating that the Firmicutes are key early responders to biocrust wetting. We highlight the apparent inactivity of many Actinobacteria and Proteobacteria through 21 h after wetting, and note that members of the Chitinophagaceae, enriched in the active fraction, may play important ecological roles following wetting. Based on the enrichment of COGs in the active fraction, predation by phage and other bacterial members, as well as scavenging and recycling of labile nutrients, appear to be important ecological processes soon after wetting. To our knowledge, this is the first time BONCAT-FACS-Seq has been applied to biocrust samples, and therefore we discuss the potential advantages and shortcomings of coupling metagenomics to BONCAT to intact soil communities such as biocrust. In all, by pairing BONCAT-FACS and metagenomics, we are capable of highlighting the taxa and potential functions that typifies the microbes actively responding to a rain event.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Improving an Acoustic Vehicle Detector Using an Iterative Self-Supervision Procedure

In many non-canonical data science scenarios, obtaining, detecting, attributing, and annotating enough high-quality training data is the primary barrier to developing highly effective models. Moreover, in many problems that are not sufficiently defined or constrained, manually developing a training dataset can often overlook interesting phenomena that should be included. To this end, we have developed and demonstrated an iterative self-supervised learning procedure, whereby models are successfully trained and applied to new data to extract new training examples that are added to the corpus of training data. Successive generations of classifiers are then trained on this augmented corpus. Using low-frequency acoustic data collected by a network of infrasound sensors deployed around the High Flux Isotope Reactor and Radiochemical Engineering Development Center at Oak Ridge National Laboratory, we test the viability of our proposed approach to develop a powerful classifier with the goal of identifying vehicles from continuously streamed data and differentiating these from other sources of noise such as tools, people, airplanes, and wind. Using a small collection of exhaustively manually labeled data, we test several implementation details of the procedure and demonstrate its success regardless of the fidelity of the initial model used to seed the iterative procedure. Finally, we demonstrate the method’s ability to update a model to accommodate changes in the data-generating distribution encountered during long-term persistent data collection.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
NASA NTRS1980

A note on a Lagrangian formulation for motion about the collinear points

A Lagrangian formulation for the three-dimensional motion of a satellite in the vicinity of the collinear points of the circular-restricted problem is reconsidered. It is shown that the influence of the primaries can be expressed in the form of two third-body disturbing functions. By use of this approach, the equations for the Lagrangian and for the motion itself are readily developed into highly compact expressions. All orders of the non-linear developments are shown to be easily obtainable using well-known recursive relationships. The resulting forms for these equations are well suited for use in the initial phase of canonical or non-canonical investigations.

Richardson, D. L.↗
NASA NTRS1982

Equivalence of the generalized Lie-Hori method and the method of averaging

In this investigation, a comparison is made of two methods for developing perturbation theories for non-canonical dynamical systems. The methods compared are the generalized Lie-Hori method and the method of averaging. In the comparison presented here, the equivalence of the methods up to the second order in the small parameter is shown. However, the approach used can be extended to demonstrate the equivalence for higher orders. To illustrate the equivalence both Duffing's equation and the van der Pol equation are solved using each method.

Ahmed, A.↗
NASA NTRS1984

Equivalence of the generalized Lie-Hori method and the method of averaging

In this investigation, a comparison is made of two methods for developing perturbation theories for non-canonical dynamical systems. The methods compared are the generalized Lie-Hori method and the method of averaging. In the comparison presented here, the equivalence of the methods up to the second order in the small parameter is shown. However, the approach used can be extended to demonstrate the equivalence for higher orders. To illustrate the equivalence Duffing's equation, the van der Pol equation and the oscillator with quadratic damping problem are solved using each method.

Ahmed, A. H.↗
NASA NTRS2006

Observations of the Hot Horizontal Branch Stars in the Metal-Rich Bulge Globular Cluster NGC 6388

The metal-rich bulge globular cluster NGC 6388 shows a distinct blue horizontal-branch tail in its colour-magnitude diagram (Rich et al. 1997) and is thus a strong case of the well-known 2nd Parameter Problem. In addition, its horizontal branch (HB) shows an upward tilt toward bluer colours, which cannot be explained by canonical evolutionary models. Several non-canonical scenarios have been proposed to explain these puzzling observations. In order to test the predictions of these scenarios, we have obtained medium resolution spectra to determine the atmospheric parameters of a sample of the blue HB stars in NGC 6388.Using the medium resolution spectra, we determine effective temperatures, surface gravities and helium abundances by fitting the observed Balmer and helium lines with appropriate theoretical stellar spectra. As we know the distance to the cluster, we can verify our results by determining masses for the stars. During the data reduction we took special care to correctly subtract the background, which is dominated by the overlapping spectra of cool stars. The cool blue tail stars in our sample with T(sub eff) approximately 10000 K have lower than canonical surface gravities, suggesting that these stars are, on average, approximately equal to 0.4 mag brighter than canonical HB stars in agreement with the observed upward slope of the HB in NGC 6388. Moreover, the mean mass of these stars agrees well with theoretical predictions. In contrast, the hot blue tail stars in our sample with T(sub eff) greater than or equal to 12000 K show significantly lower surface gravities than predicted by any scenario, which can reproduce the photometric observations. Their masses are also too low by about a factor of 2 compared to theoretical predictions. The physical parameters of the blue HB stars at about 10,000 K support the helium pollution scenario. The low gravities and masses of the hot blue tail stars, however, are probably caused by problems with the data reduction, most likely due to remaining background light in the spectra, which would affect the fainter hot blue tail stars much more strongly than the brighter cool blue tail stars. Our study of the hot blue tail stars in NGC 6388 illustrates the obstacles which are encountered when attempting to determine the atmospheric parameters of hot HB stars in very crowded fields using ground-based observations. We discuss these obstacles and offer possible solutions for future projects.

Moehler, S.↗
NASA NTRS2006

Deep HST Photometry of NGC 6388: Age and Horizontal Branch Luminosity

We present the first deep color-magnitude diagram (CMD) of the Galactic globular cluster NGC 6388, obtained with the Hubble Space Telescope, that is able to reach the main-sequence turnoff point of the cluster. From a detailed comparison between the cluster CMD and that of 47 Tucanae (NGC 104), we find that the bulk of the stars in these two clusters have nearly the same age and chemical composition. On the other hand, our results indicate that the blue horizontal branch and RR Lyrae components in NGC 6388 are intrinsically over-luminous, which must be due to one or more, still undetermined, non-canonical second parameter(s) affecting a relatively minor fraction of the stars in NGC 6388.

Stetson, Peter B.↗
NASA NTRS2011

Distinct Purine Distribution in Carbonaceous Chondrites

Carbonaceous chondrite meteorites are known to contain a diverse suite of organic compounds, many of which are essential components of biochemistry. Amino acids, which are the monomers of proteins, have been extensively studied in such meteorites (e.g. Botta and Bada 2002; Pizzarello et aI., 2006). The origin of amino acids in meteorites has been firmly established as extraterrestrial based on their detection typically as racemic mixtures of amino acids, the presence of many non-protein amino acids, and non-terrestrial values for compound-specific deuterium, carbon, and nitrogen isotopic measurements. In contrast to amino acids, nucleobases in meteorites have been far less studied. Nucleobases are substituted one-ring (pyrimidine) or two-ring (purine) nitrogen heterocyclic compounds and serve as the information carriers of nucleic acids and in numerous coenzymes. All of the purines (adenine, guanine, hypoxanthine, and xanthine) and pyrimidines (uracil) previously reported in meteorites are biologically common and could be interpreted as the result of terrestrial contamination (e.g. van del' Velden and Schwartz, 1974.) Unlike other meteoritic organics, there have been no observations of stochastic molecular diversity of purines and pyrimidines in meteorites, which has been a criterion for establishing extraterrestrial origin. Maltins et al. (2008) performed compound-specific stable carbon isotope measurements for uracil and xanthine in the Murchison meteorite. They assigned a non-terrestrial origin for these nucleobases; however, the possibility that interfering indigenous molecules (e.g. carboxylic acids) contributed to the 13C-enriched isotope values for these nucleobases cannot be completely ruled out. Thus, the origin of these meteoritic nucleobases has never been established unequivocally. Here we report on our investigation of extracts of II different carbonaceous chondrites covering various petrographic types (Cl, CM, and CR) and degrees of aqueous alteration (l, 2, and 3) and one ureilite. Analysis via liquid chromatography coupled with electrospray triple-stage mass spectrometry or orbitrap mass spectrometry employed a targeted approach for analysis focused on the five canonical RNA/DNA nucleobases as well as 14 non-canonical pyrimidines and purines, which have bcen observed under plausible prebiotic reactions.

Callahan, Michael P.↗
NASA NTRS2017

Modulation of Bone Marrow Primary Cell Osteoblastogenesis and Cell Senescence by Mechanical Stimulation

Cell and animal studies conducted onboard the International Space Station and formerly the Shuttle flights have provided groundbreaking data illuminating the deleterious biological response of bone to mechanical unloading. Specifically CDKN1A/p-21 a cell senescence protein, was found to be upregulated in osteoprecursor cells of the femur during 15-day spaceflight, leading to the working hypothesis that CDKN1A/p-21 plays a role in inhibition of bone formation via mechanical regulation. To evaluate this hypothesis, utilizing a p-21 knockout mouse-line and relevant wildtype control, we cultured femoral bone marrow primary cells under unloaded (static) and cyclically stretched loading through a 30 day osteoblastogenesis protocol. Morphologic evaluation of the cultures demonstrated that mechanical stretching aligned the cells and increased the presence of defined focal adhesion expressing talin, integrin αvβ3, and PTK2 protein tyrosine kinase 2, also known as focal adhesion kinase (FAK) in both mouse strains. In corroboration with previous investigations of cell survival signals relation to FAK, our study found that with greater concentration of focal adhesions via stretch stimulation the live cell percentage was significantly higher than the unloaded controls (p-21 knockout line: +49.70%, p*=0.009, wildtype control: +18.14%, p*=.01). Also evaluated was the mineralization and ECM secretion capability of the differentiating cells. Von Kossa staining has shown that in the p-21 knockout cells unloaded cells produce more matrix that the stretch stimulated, however the matrix is unorganized presenting in sporadic nodules covering approximately 30% of the culture area at day 14 (n=6 wells) while the stretch stimulated cultures have less mineralization content the surface area containing mineralized matrix is greater (~68% at day 14). Q-PCR evaluation of the p-21 knockout cells revealed that canonical (β-catenin cascade) and non-canonical wnt11 and downstream planar cell polarity (wnt/PCP) pathway molecule RAC1 are prevalently upregulated with mechanical stimulation. Immunofluorescence for β-catenin and RAC1 showed co-localization at the nuclear membrane of the p-21 knockout cells but not the wildtype (n=1) suggesting that molecular communication via the canonical and wnt/PCP pathway are initiated by mechanical loading and experience regulation along the signaling cascade by CDKN1A/p-21. Future investigations will further elucidate this relationship and provide causal data demonstrating mechanical loading’s modulatory effect on p-21 expression change.

Juran, Cassandra M.↗
NASA NTRS2019

A NICER View of PSR J0030+0451: Evidence for a Global-Scale Multipolar Magnetic Field

Recent modeling of Neutron Star Interior Composition Explorer observations of thermal X-ray pulsations from the surface of the isolated millisecond pulsar PSRJ0030+0451 suggests that the hot emitting regions on the pulsar’s surface are far from antipodal, which is at odds with the classical assumption that the magnetic field in the pulsar magnetosphere is predominantly that of a centered dipole. Here, we review these results and examine previous attempts to constrain the magnetospheric configuration of PSRJ0030+0451. To the best of our knowledge, there is in fact no direct observational evidence that PSRJ0030+0451’s magnetic field is a centered dipole. Developing models of physically motivated, non-canonical magnetic field configurations and the currents that they can support poses a challenging task. However, such models may have profound implications for many aspects of pulsar research, including pulsar braking, estimates of birth velocities, and interpretations of multi-wavelength magnetospheric emission.

A V Bilous↗