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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 469 records · Page 26
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Asymmetric dimerization of adenosine deaminase acting on RNA facilitates substrate recognition

Abstract Adenosine deaminases acting on RNA (ADARs) are enzymes that convert adenosine to inosine in duplex RNA, a modification that exhibits a multitude of effects on RNA structure and function. Recent studies have identified ADAR1 as a potential cancer therapeutic target. ADARs are also important in the development of directed RNA editing therapeutics. A comprehensive understanding of the molecular mechanism of the ADAR reaction will advance efforts to develop ADAR inhibitors and new tools for directed RNA editing. Here we report the X-ray crystal structure of a fragment of human ADAR2 comprising its deaminase domain and double stranded RNA binding domain 2 (dsRBD2) bound to an RNA duplex as an asymmetric homodimer. We identified a highly conserved ADAR dimerization interface and validated the importance of these sequence elements on dimer formation via gel mobility shift assays and size exclusion chromatography. We also show that mutation in the dimerization interface inhibits editing in an RNA substrate-dependent manner for both ADAR1 and ADAR2.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Crystal structure of MutYX: a novel clusterless adenine DNA glycosylase with a distinct C-terminal domain and 8-oxoguanine recognition sphere

Abstract The [4Fe–4S] cluster is an important cofactor of the base excision repair (BER) adenine DNA glycosylase MutY to prevent mutations associated with 8-oxoguanine (OG). Several MutYs lacking the [4Fe–4S] cofactor have been identified. Phylogenetic analysis shows that clusterless MutYs are distributed in two clades suggesting cofactor loss has occurred in multiple independent evolutionary events. Herein, we determined the first crystal structure of a clusterless MutY complexed with DNA. On the basis of the dramatic structural divergence from canonical MutYs, we refer to this as representative of a clusterless MutY subgroup “MutYX.” Interestingly, MutYX compensates for the missing [4Fe–4S] cofactor to maintain positioning of catalytic residues by expanding a pre-existing α-helix and acquisition of a new α-helix. Surprisingly, MutYX also acquired a new C-terminal domain that uniquely recognizes OG using residues Gln201 and Arg209. Adenine glycosylase assays and binding affinity measurements indicate that Arg209 is the primary residue responsible for OG:A lesion specificity, while Gln201 assists by bridging OG and Arg209. Surprisingly, replacement of Arg209 and Gln201 with Ala increased activity toward G:A mismatches. The MutYX structure serves as an example of devolution, capturing structural features required to retain function in the absence of a metal cofactor considered indispensable.

Trasviña-Arenas, Carlos H [University of Californi↗
DOE OSTI2021

Singlet Oxygen Leads to Structural Changes to Chloroplasts during their Degradation in the Arabidopsis thaliana plastid ferrochelatase two Mutant

Abstract During stress, chloroplasts produce large amounts of reactive oxygen species (ROS). Chloroplasts also contain many nutrients, including 80% of a leaf’s nitrogen supply. Therefore, to protect cells from photo-oxidative damage and to redistribute nutrients to sink tissues, chloroplasts are prime targets for degradation. Multiple chloroplast degradation pathways are induced by photo-oxidative stress or nutrient starvation, but the mechanisms by which damaged or senescing chloroplasts are identified, transported to the central vacuole and degraded are poorly defined. Here, we investigated the structures involved with degrading chloroplasts induced by the ROS singlet oxygen (1O2) in the Arabidopsis thaliana plastid ferrochelatase two (fc2) mutant. Under mild 1O2 stress, most fc2 chloroplasts appeared normal, but had reduced starch content. A subset of chloroplasts was degrading, and some protruded into the central vacuole via ‘blebbing’ structures. A 3D electron microscopy analysis demonstrated that up to 35% of degrading chloroplasts contained such structures. While the location of a chloroplast within a cell did not affect the likelihood of its degradation, chloroplasts in spongy mesophyll cells were degraded at a higher rate than those in palisade mesophyll cells. To determine if degrading chloroplasts have unique structural characteristics, allowing them to be distinguished from healthy chloroplasts, we analyzed fc2 seedlings grown under different levels of photo-oxidative stress. A correlation was observed among chloroplast swelling, 1O2 signaling and the state of degradation. Finally, plastoglobule (PG) enzymes involved in chloroplast disassembly were upregulated while PGs increased their association with the thylakoid grana, implicating an interaction between 1O2-induced chloroplast degradation and senescence pathways.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Adrenal Stress Hormone Regulation of Hepatic Homeostatic Function After an Acute Ozone Exposure in Wistar-Kyoto Male Rats

Ozone-induced lung injury, inflammation, and pulmonary/hypothalamus gene expression changes are diminished in adrenalectomized (AD) rats. Acute ozone exposure induces metabolic alterations concomitant with increases in epinephrine and corticosterone. We hypothesized that adrenal hormones are responsible for observed hepatic ozone effects, and in AD rats, these changes would be diminished. In total, 5–7 days after sham (SH) or AD surgeries, male Wistar-Kyoto rats were exposed to air or 0.8-ppm ozone for 4 h. Serum samples were analyzed for metabolites and liver for transcriptional changes immediately post-exposure. Ozone increased circulating triglycerides, cholesterol, free fatty-acids, and leptin in SH but not AD rats. Ozone-induced inhibition of glucose-mediated insulin release was absent in AD rats. Unlike diminution of ozone-induced hypothalamus and lung mRNA expression changes, AD in air-exposed rats (AD-air/SH-air) caused differential hepatic expression of ~1000 genes. Likewise, ozone in AD rats caused differential expression of ~1000 genes (AD-ozone/AD-air). Ozone-induced hepatic changes in SH rats reflected enrichment for pathways involving metabolic processes, including acetyl-CoA biosynthesis, TCA cycle, and sirtuins. Upstream predictor analysis identified similarity to responses produced by glucocorticoids and pathways involving forskolin. These changes were absent in AD rats exposed to ozone. However, ozone caused unique changes in AD liver mRNA reflecting activation of synaptogenesis, neurovascular coupling, neuroinflammation, and insulin signaling with inhibition of senescence pathways. In these rats, upstream predictor analysis identified numerous microRNAs likely involved in glucocorticoid insufficiency. These data demonstrate the critical role of adrenal stress hormones in ozone-induced hepatic homeostasis and necessitate further research elucidating their role in propagating environmentally driven diseases.

Toxicology↗
DOE OSTI2021

δ 13 C methane source signatures from tropical wetland and rice field emissions

The atmospheric methane (CH 4 ) burden is rising sharply, but the causes are still not well understood. One factor of uncertainty is the importance of tropical CH 4 emissions into the global mix. Isotopic signatures of major sources remain poorly constrained, despite their usefulness in constraining the global methane budget. Here, a collection of new δ 13 C CH 4 signatures is presented for a range of tropical wetlands and rice fields determined from air samples collected during campaigns from 2016 to 2020. Long-term monitoring of δ 13 C CH 4 in ambient air has been conducted at the Chacaltaya observatory, Bolivia and Southern Botswana. Both long-term records are dominated by biogenic CH 4 sources, with isotopic signatures expected from wetland sources. From the longer-term Bolivian record, a seasonal isotopic shift is observed corresponding to wetland extent suggesting that there is input of relatively isotopically light CH 4 to the atmosphere during periods of reduced wetland extent. This new data expands the geographical extent and range of measurements of tropical wetland and rice δ 13 C CH 4 sources and hints at significant seasonal variation in tropical wetland δ 13 C CH 4 signatures which may be important to capture in future global and regional models.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Binding profiles for 961 Drosophila and C. elegans transcription factors reveal tissue-specific regulatory relationships

A catalog of transcription factor (TF) binding sites in the genome is critical for deciphering regulatory relationships. Here, we present the culmination of the efforts of the modENCODE (model organism Encyclopedia of DNA Elements) and modERN (model organism Encyclopedia of Regulatory Networks) consortia to systematically assay TF binding events in vivo in two major model organisms,Drosophila melanogaster(fly) andCaenorhabditis elegans(worm). These data sets comprise 605 TFs identifying 3.6 M sites in the fly and 356 TFs identifying 0.9 M sites in the worm, and represent the majority of the regulatory space in each genome. We demonstrate that TFs associate with chromatin in clusters termed “metapeaks,” that larger metapeaks have characteristics of high-occupancy target (HOT) regions, and that the importance of consensus sequence motifs bound by TFs depends on metapeak size and complexity. Combining ChIP-seq data with single-cell RNA-seq data in a machine-learning model identifies TFs with a prominent role in promoting target gene expression in specific cell types, even differentiating between parent–daughter cells during embryogenesis. These data are a rich resource for the community that should fuel and guide future investigations into TF function. To facilitate data accessibility and utility, all strains expressing green fluorescent protein (GFP)-tagged TFs are available at the stock centers for each organism. The chromatin immunoprecipitation sequencing data are available through the ENCODE Data Coordinating Center, GEO, and through a direct interface that provides rapid access to processed data sets and summary analyses, as well as widgets to probe the cell-type-specific TF–target relationships.

Biochemistry & Molecular Biology↗
DOE OSTI2026

Lattice vacancy migration barriers in Fe-Ni alloys, and an indication as to why Ni atoms diffuse slowly: A first-principles study

Lattice vacancy migration barriers in ferromagnetic Fe 𝑥 ⁢Ni 1−𝑥 alloys (0.4 ≤ 𝑥 ≤ 0.6) are accurately quantified within the framework of ab initio electronic structure calculations using the nudged elastic band (NEB) method. Both the atomically disordered (A1) fcc phase, as well as the atomically ordered, tetragonal L⁢1 0 phase—which is under consideration as a material for a rare-earth-free gap magnet for advanced engineering applications—are investigated. Across an ensemble of NEB calculations performed on supercell configurations spanning a range of compositions and containing disordered, partially ordered, and fully ordered structures, we find that Ni-vacancy interchanges encounter significantly higher energetic barriers than do Fe-vacancy interchanges. We contend that this aspect is a key factor in determining the differences in mobility between Fe and Ni atoms in this ferromagnetic alloy. Moreover, we are able to interpret these findings in terms of the ferromagnetic alloy's underlying spin-polarized electronic structure. Specifically, we report a coupling between the size of local lattice distortions and the magnitude of the local electronic spin polarization around vacancies. This causes Fe atoms to relax into lattice vacancies, while Ni atoms remain rigidly fixed to their original lattice positions. These results give atomic-scale insight into the longstanding experimental observation that Ni exhibits remarkably slow atomic diffusion in Fe-Ni alloys.

density functional theory↗
DOE OSTI2026

Evolution of charge density wave soft phonon modes in Pd 𝑥 ⁢ErTe 3

Here, we investigated the lattice dynamics of quasi-two-dimensional Pd-intercalated ErTe 3 in relation to its charge-density-wave (CDW) transitions by means of x-ray diffuse and meV-resolution inelastic x-ray scattering. In pristine ErTe 3 , CDW order develops at orthogonal in-plane wave vectors q$^𝑐_1$ =(0,0,0.29) (the 𝑐−CDW ) and q$^𝑎_2 $= (0.31,0,0) (the 𝑎−CDW ), with transition temperatures $𝑇^𝑐_1$ = 270K and $𝑇^𝑎_2$ = 160K, respectively. Remarkably, we observe diffuse x-ray scattering already near the higher transition temperature $𝑇^𝑐_1$ along 𝑎−CDW but at a slightly different wave vector q$^𝑎_1$ = (0.29,0,0). Inelastic x-ray scattering for Pd 0.01 ⁢ErTe 3 shows that a partial phonon softening at q$^𝑎_1$, underscoring the strong competition between ordering tendencies along the nearly equivalent in-plane axes of the orthorhombic lattice. For intercalation levels 𝑥 ≥ 0.02, the 𝑎−CDW state is suppressed. Nevertheless, a similar correlation between phonon softening and diffuse scattering persists along the [100] direction, again observed at q$^𝑎_1$ = (0.29,0,0) and $𝑇^𝑐_1$. These findings suggest that the 𝑎−CDW is fully suppressed for 𝑥 ≥ 0.02, and that the residual diffuse scattering at originates from the partial phonon softening associated with the 𝑐−CDW, reflected by the near equality of the absolute size of q$^𝑐_1$ and q$^𝑎_1$.

Maity, Avishek [Technische Univ. München, Garching↗
DOE OSTI2026

Properties of Heavy Cosmic Nuclei Phosphorus, Chlorine, Argon, Potassium, and Calcium: Results from the Alpha Magnetic Spectrometer

We report the unique properties of cosmic phosphorus (P), chlorine (Cl), argon (Ar), potassium (K), and calcium (Ca) fluxes in the GV to TV rigidity range collected by the Alpha Magnetic Spectrometer (AMS) on the International Space Station. With a total of one million events collected over 13.5 years, we observed that the rigidity dependencies of the five fluxes are well described by the sums of a primary cosmic ray component and a secondary cosmic ray component. The abundance ratios of all five elements to Si at the source are accurately determined independent of cosmic ray propagation. The source abundance of Ar and Ca (even-𝑍 elements) is larger than P, Cl, and K (odd-𝑍 elements). The secondary components of the P and the Cl fluxes are each ∼1/3 of the F flux, and the secondary components of the Ar, K, and Ca fluxes are each ∼1/2 of the F flux. The twenty elements measured by AMS, from He to Ca and Fe, can be categorized into four classes, two primary and two secondary, based on their rigidity dependence.

cosmic ray acceleration↗
DOE OSTI2025

Stochastic Waveform Estimation at the Fundamental Quantum Limit

Although measuring the deterministic waveform of a weak classical force is a well-studied problem, estimating a random waveform, such as the spectral density of a stochastic signal field, is much less well understood despite it being a widespread task at the frontier of experimental physics. State-of-the-art precision sensors of random forces must account for the underlying quantum nature of the measurement but the optimal quantum protocol for interrogating such linear sensors is not known. We derive the fundamental precision limit: the extended-channel quantum Cramér-Rao bound. In the experimentally relevant regime in which losses dominate, we prove that non-Gaussian-state preparation and measurement are required to achieve this fundamental limit and we determine numerically the optimal non-Gaussian protocol. We discuss how this scheme could accelerate searches for signatures of quantum gravity, stochastic gravitational waves, and axionic dark matter.

Axions↗
DOE OSTI2024

Tapering-enhanced high-efficiency THz waveguide oscillator

Using a waveguide in a THz FEL has been shown to maximize the coupling and enable efficient extraction of relativistic electron beam energy from a single passage through a tapered helical undulator. An oscillator configuration can further boost energy extraction above the single-pass limits and open the door toward very high average power THz sources. Embedding the undulator in an oscillator cavity is particularly useful in combination with high repetition rate electron sources, even if at reduced peak brightness, since recycling a fraction of the radiation as an intense seed can compensate for lower single-pass gain. In this paper, we investigate the efficiency scaling of a tapering-enhanced waveguide oscillator, showcasing its capability for frequency-tuning operation and high-efficiency operation at different wavelengths. Using a thermionic-driven beamline equipped with compression elements, numerical start-to-end simulation results indicate a 16% efficiency at 200 GHz and a 2.1% efficiency at 1.5 THz, resulting in kW-level average power out-coupled in radiation pulses with few hundred μ J energy and tens of MW peak power. Published by the American Physical Society 2024

Yang, Y. N. (ORCID:0009000849540151)↗
DOE OSTI2019

Disorder-induced suppression of charge density wave order: STM study of Pd-intercalated ErTe 3

Pd-intercalated ErTe3 is studied as a model system to explore the effect of increasing disorder on an incommensurate two-component charge density wave (CDW). The ordering vectors of the CDW components lie along the two in-plane principal axes of the nearly tetragonal crystal structure. Using scanning tunneling microscopy (STM), we show that introducing Pd intercalants (i.e., disorder) induces CDW dislocations, which appear to be associated with each CDW component separately. Increasing Pd concentration has a stronger effect on the secondary CDW order, manifested in a higher density of dislocations, and thus increases the anisotropy (nematic character) of the CDW. Suggestive evidence of Bragg glass phases at weak disorder is also discussed.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Interplay of charge density wave states and strain at the surface of CeTe 2

in this work we use scanning tunneling microscopy (STM) to study charge density wave (CDW) states in the rare-earth ditelluride, CeTe 2 . Our STM measurements surprisingly detect a unidirectional CDW with q ~ 0.28 a * , which differs from previous experimental and first-principles studies of the rare-earth ditellurides, and which is very close to what is found in experimental measurements of the related rare-earth tritellurides. Furthermore, in the vicinity of an extended subsurface defect, we find spatially-separated as well as spatially-coexisting unidirectional CDWs at the surface of CeTe 2 . We quantify the nanoscale strain and its variations induced by this defect, and establish a correlation between local lattice strain and the locally-established CDW states; this suggests that lattice strain plays an important role in determining the specific characteristics of the established CDW state. Our measurements probe the fundamental properties of a weakly-bound two-dimensional Te sheet, which experimental and theoretical work has previously established as the fundamental component driving much of the essential physics in both the rare-earth di- and tritelluride compounds.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Magnetic breakdown and charge density wave formation: A quantum oscillation study of the rare-earth tritellurides

The rare-earth tritellurides (RTe 3 , where R = La, Ce, Pr, Nd, Sm, Gd, Tb, Dy, Ho, Er, Tm, Y) form a charge density wave state consisting of a single unidirectional charge density wave for lighter R, with a second unidirectional charge density wave, perpendicular and in addition to the first, also present at low temperatures for heavier R. In this paper, we present a quantum oscillation study in magnetic fields up to 65T that compares the single charge density wave state with the double charge density wave state both above and below the magnetic breakdown field of the second charge density wave. In the double charge density wave state it is observed that there remain several small, light pockets with the largest occupying around 0.5% of the Brillouin zone. By applying magnetic fields above the independently determined magnetic breakdown field, the quantum oscillation frequencies of the single charge density wave state are recovered, as expected in a magnetic breakdown scenario. Measurements of the electronic effective mass do not show any divergence or significant increase on the pockets of Fermi surface observed here as the putative quantum phase transition between the single and double charge density wave states is approached.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Ultrafast formation of domain walls of a charge density wave in SmTe 3

We study ultrafast x-ray diffraction on the charge density wave (CDW) of SmTe 3 using an x-ray free-electron laser. The high momentum and time resolution afforded by the x-ray laser enabled capturing fine wave-vector and time-dependent features of the CDW that originate from fast (in time) and sharp (in real space) variations of the CDW lattice distortion, which we attribute to an inversion of the order parameter. These domain inversions occur near the surface and are caused by the short penetration depth of the near-infrared pump with the wavelength centered at 800 nm, resulting in CDW domain walls perpendicular to the sample surface. These domain walls break the CDW long-range order on the scale of the x-ray probe depth, controlled experimentally by the x-ray incidence angle and suppress the diffraction intensity of the CDW for times much longer than the ~1–ps recovery of the electronic gap observed in time and angle-resolved photoemission spectroscopy. We model the spatial and temporal dependences of the order parameter using a simple Ginzburg-Landau model with all the parameters obtained from the published literature. We find reasonable agreement between the calculated and the measured diffraction across the momentum, time, fluence, and incidence angle dependence without adjusting any parameters. In conclusion, we reconstruct the spatial and temporal dependences of the lattice order parameter and find that at long times, depending on the pump fluence, multiple domain walls remain at distances of a few nanometers from the surface.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Anisotropic quasiparticle coherence in nematic BaFe 2 As 2 studied with strain-dependent ARPES

The hallmark of nematic order in iron-based superconductors is a resistivity anisotropy but it is unclear to which extent quasiparticle dispersions, lifetimes, and coherence contribute. While the lifted degeneracy of the Fe d xz and d yz dispersions has been studied extensively, only little is known about the two other factors. In this work, we combine in situ strain tuning with ARPES and study the nematic response of the spectral weight in BaFe 2 As 2 . The symmetry analysis of the ARPES spectra demonstrates that the d xz band gains quasiparticle spectral weight compared to the d yz band for negative antisymmetric strain Δε yy suggesting the same response inside the nematic phase. Our results are compatible with a different coherence of the d xz and d yz orbital within a Hund's metal picture. We also discuss the influence of orbital mixing.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗