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At least 217 records · Page 12
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

A Rhodopseudomonas strain with a substantially smaller genome retains the core metabolic versatility of its genus

ABSTRACT Rhodopseudomonas are a group of phototrophic microbes with a marked metabolic versatility and flexibility that underpins their potential use in the production of value-added products, bioremediation, and plant growth promotion. Members of this group have an average genome size of about 5.5 Mb, but two closely related strains have genome sizes of about 4.0 Mb. To identify the types of genes missing in a reduced genome strain, we compared strain DSM127 with other Rhodopseudomonas isolates at the genomic and phenotypic levels. We found that DSM127 can grow as well as other members of the Rhodopseudomonas genus and retains most of their metabolic versatility, but it has many fewer genes associated with high-affinity transport of nutrients, iron uptake, nitrogen metabolism, and biodegradation of aromatic compounds. This analysis indicates genes that can be deleted in genome reduction campaigns and suggests that DSM127 could be a favorable choice for biotechnology applications using Rhodopseudomonas or as a strain that can be engineered further to reside in a specialized natural environment. IMPORTANCE Rhodopseudomonas are a cohort of phototrophic bacteria with broad metabolic versatility. Members of this group are present in diverse soil and water environments, and some strains are found associated with plants and have plant growth-promoting activity. Motivated by the idea that it may be possible to design bacteria with reduced genomes that can survive well only in a specific environment or that may be more metabolically efficient, we compared Rhodopseudomonas strains with typical genome sizes of about 5.5 Mb to a strain with a reduced genome size of 4.0 Mb. From this, we concluded that metabolic versatility is part of the identity of the Rhodopseudomonas group, but high-affinity transport genes and genes of apparent redundant function can be dispensed with.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Effect of Stress on Irradiation Responses of Highly Oriented Pyrolytic Graphite

The effect of stress on irradiation responses of highly oriented pyrolytic graphite (HOPG) was studied by combing molecular dynamics (MD) simulation, proton irradiation, and Raman characterization. MD simulations of carbon knock-on at energies < 60 eV were used to obtain average threshold displacement energies (E¯d) as a function of strain ranging from 0 to 10%. Simulations at a higher irradiation energy of 2–5 keV were used to study the effect of strain on damage cascade evolution. With increasing tensile strain, E¯d was reduced from 35 eV at 0% strain to 31 eV at 10% strain. The strain-reduced E¯d led to a higher damage peak and more surviving defects (up to 1 ps). Furthermore, high strains induced local cleavage around the cavities, as one additional mechanism of damage enhancement. Experimentally, HOPG film was folded, and the folded region with the maximum tensile stress was irradiated by a 2 MeV proton beam. Raman characterization showed significantly enhanced D to G modes in comparison to the stress-free irradiation. Based on the strain dependence of E¯d and the Kinchin–Pease model, a formula for displacement estimation under different tensile strains is proposed. The stress effects need to be considered in graphite applications in a reactor’s harsh environment where both neutron damage and stress are present.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Investigation of experimental observables in search of the chiral magnetic effect in heavy-ion collisions in the STAR experiment *

The chiral magnetic effect (CME) is a novel transport phenomenon, arising from the interplay between quantum anomalies and strong magnetic fields in chiral systems. In high-energy nuclear collisions, the CME may survive the expansion of the quark-gluon plasma fireball and be detected in experiments. Over the past two decades, experimental searches for the CME have attracted extensive interest at the Relativistic Heavy Ion Collider (RHIC) and the Large Hadron Collider (LHC). The main goal of this study is to investigate three pertinent experimental approaches: the $γ$ correlator, the R correlator, and the signed balance functions. We exploit simple Monte Carlo simulations and a realistic event generator (EBE-AVFD) to verify the equivalence of the core components among these methods and to ascertain their sensitivities to the CME signal and the background contributions for the isobar collisions at the RHIC.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

Zng1 is a GTP-dependent zinc transferase needed for activation of methionine aminopeptidase

The evolution of zinc (Zn) as a protein cofactor altered the functional landscape of biology, but dependency on Zn also created an Achilles' heel, necessitating adaptive mechanisms to ensure Zn availability to proteins. A debated strategy is whether metallochaperones exist to prioritize essential Zn-dependent proteins. Here, we present evidence for a conserved family of putative metal transferases in human and fungi, which interact with Zn-dependent methionine aminopeptidase type I (MetAP1/Map1p/Fma1). Deletion of the putative metal transferase in Saccharomyces cerevisiae (ZNG1; formerly YNR029c) leads to defective Map1p function and a Zn-deficiency growth defect. In vitro, Zng1p can transfer Zn 2+ or Co 2+ to apo-Map1p, but unlike characterized copper chaperones, transfer is dependent on GTP hydrolysis. Proteomics reveal mis-regulation of the Zap1p transcription factor regulon due to loss of ZNG1 and Map1p activity, suggesting that Zng1p is required to avoid a compounding effect of Map1p dysfunction on survival during Zn limitation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Location and thermal evolution of the pseudogap due to spin fluctuations

We study pseudogap behavior in a metal near a spin density wave (SDW) instability due to thermal magnetic fluctuations. We consider the t–t' Hubbard model on a square lattice at a finite doping, at intermediate coupling strength, and analyze the thermal evolution of the electron spectral function between a SDW ordered state at low temperatures and a normal Fermi liquid at high temperatures. We argue that for proper description of the pseudogap one needs to sum up infinite series of diagrams for both the fermionic self-energy and the SDW order parameter in the SDW state or the magnetic correlation length in the paramagnetic state. We use the eikonal approach to sum up an infinite series of diagrammatic contributions from thermal fluctuations. Earlier studies found that in the SDW state the spectral function A k (ω) of a hot fermion at a finite T is exponentially small below the energy scale Δ(T), which scales with SDW order and vanishes at the ordering temperature T N , and has a hump at a larger frequency Δ PG , comparable to the zero-temperature SDW gap Δ(T = 0). We argue that the hump, which we associate with the pseudogap, survives in some T range above T N . We show that this range is split by regions of strong and weak pseudogap behavior. In the first region, Δ PG is weakly temperature dependent, despite the fact that it comes from thermal fluctuations. Such a behavior has been seen in numerical studies of the Hubbard model. We show that to obtain it one needs to go beyond the one-loop approximation and sum up the infinite series of diagrams. In the second regime, Δ PG decreases with increasing T and eventually vanishes. Here, we further argue that a magnetic pseudogap at a finite T emerges only if the ground state is magnetically ordered. We present the phase diagram and apply the results to high-T c cuprates.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Drug providers’ perspectives on antibiotic misuse practices in eastern Ethiopia: a qualitative study

Objective Antibiotic misuse includes using them to treat colds and influenza, obtaining them without a prescription, not finishing the prescribed course and sharing them with others. Although drug providers are well positioned to advise clients on proper stewardship practices, antibiotic misuse continues to rise in Ethiopia. It necessitates an understanding of why drug providers failed to limit such risky behaviours. This study aimed to explore drug providers’ perspectives on antibiotic misuse practices in eastern Ethiopia. Setting The study was conducted in rural Haramaya district and Harar town, eastern Ethiopia. Design and participants An exploratory qualitative study was undertaken between March and June 2023, among the 15 drug providers. In-depth interviews were conducted using pilot-tested, semistructured questions. The interviews were transcribed verbatim, translated into English and analysed thematically. The analyses considered the entire dataset and field notes. Results The study identified self-medication pressures, non-prescribed dispensing motives, insufficient regulatory functions and a lack of specific antibiotic use policy as the key contributors to antibiotic misuse. We found previous usage experience, a desire to avoid extra costs and a lack of essential diagnostics and antibiotics in public institutions as the key drivers of non-prescribed antibiotic access from private drug suppliers. Non-prescribed antibiotic dispensing in pharmacies was driven by client satisfaction, financial gain, business survival and market competition from informal sellers. Antibiotic misuse in the setting has also been linked to traditional and ineffective dispensing audits, inadequate regulatory oversights and policy gaps. Conclusion This study highlights profits and oversimplified access to antibiotics as the main motivations for their misuse. It also identifies the traditional antibiotic dispensing audit as an inefficient regulatory operation. Hence, enforcing specific antibiotic usage policy guidance that entails an automated practice audit, a responsible office and insurance coverage for persons with financial limitations can help optimise antibiotic use while reducing resistance consequences.

General & Internal Medicine↗
DOE OSTI2022

Hydrous SiO 2 in subducted oceanic crust and H 2 O transport to the core-mantle boundary

Subduction of oceanic lithosphere transports surface H 2 O into the mantle. Recent studies show that dense SiO 2 in the form of stishovite, an abundant mineral in subducted oceanic crust at depths greater than ~270 km, has the potential to host and transport a considerable amount of H 2 O into the lower mantle, but the H 2 O storage capacity of SiO 2 phases at high pressure and temperature remains uncertain. We investigate the hydration of stishovite and its higher-pressure polymorphs, β-stishovite and seifertite, with in situ X-ray diffraction experiments at high pressures and temperatures. The H 2 O contents in SiO 2 phases are quantified based on observed increases in unit cell volume relative to the anhydrous SiO 2 system. Density functional theory (DFT) computations permit calibration of water content as a function of volume change based on interstitial substitution of H 2 O. Regression of our experimental data indicates an H 2 O storage capacity in stishovite of ~3.5 wt% in the transition zone and shallow lower mantle, decreasing to about 0.8 wt% at the base of the mantle. We find that SiO 2 -bearing subducted oceanic crust can accommodate all the H 2 O in slab lithosphere that survives sub-arc dehydration. Hydration of silica phases in subducted oceanic crust and their unparalleled capacity to host significant amounts of H 2 O even at high mantle temperatures provides a unique mechanism for transport and storage of water in the deepest mantle.

58 GEOSCIENCES↗
DOE OSTI2023

Direct Synthesis of Ammonia from Nitrate on Amorphous Graphene with Near 100% Efficiency

Abstract Ammonia is an indispensable commodity in the agricultural and pharmaceutical industries. Direct nitrate‐to‐ammonia electroreduction is a decentralized route yet challenged by competing side reactions. Most catalysts are metal‐based, and metal‐free catalysts with high nitrate‐to‐ammonia conversion activity are rarely reported. Herein, it is shown that amorphous graphene synthesized by laser induction and comprising strained and disordered pentagons, hexagons, and heptagons can electrocatalyze the eight‐electron reduction of NO 3 − to NH 3 with a Faradaic efficiency of ≈100% and an ammonia production rate of 2859 µg cm −2 h −1 at −0.93 V versus reversible hydrogen electrode. X‐ray pair‐distribution function analysis and electron microscopy reveal the unique molecular features of amorphous graphene that facilitate NO 3 − reduction. In situ Fourier transform infrared spectroscopy and theoretical calculations establish the critical role of these features in stabilizing the reaction intermediates via structural relaxation. The enhanced catalytic activity enables the implementation of flow electrolysis for the on‐demand synthesis and release of ammonia with >70% selectivity, resulting in significantly increased yields and survival rates when applied to plant cultivation. The results of this study show significant promise for remediating nitrate‐polluted water and completing the NO x cycle.

Huang, Libei↗
DOE OSTI2021

Responding to the US national pollinator plan: a case study in Michigan

The long‐term health of pollinators is a critical issue for the functioning of natural habitats and for agricultural production. In response to widespread public concern about the future of these ecologically and economically important animals, in 2015 the US Government released a national strategy to support pollinators, including research priorities, directives for funding, and timelines for achieving three overarching goals. Five years after this strategic plan was released, we evaluate progress toward the national targets for improved honey bee ( Apis mellifera ) overwintering survival, expanded pollinator habitat, and larger monarch butterfly ( Danaus plexippus ) populations, and find that the three goals of the plan have not yet been reached. Our research and extension programs to improve the health of honey bees, wild bees, and monarch butterflies in the US state of Michigan are described, providing opportunities to contribute to the national pollinator goals.

Bloom, Elias H.↗
DOE OSTI2020

Influence of hydrogenation on the vibrational density of states of magnetocaloric LaFe 11.4 Si 1.6 H 1.6

We report on the impact of magnetoelastic coupling on the magnetocaloric properties of LaFe 11.4 Si 1.6 H 1.6 in terms of the vibrational (phonon) density of states (VDOS), which we determined with 57 Fe nuclear resonant inelastic x-ray scattering (NRIXS) measurements and with density functional theory (DFT) based first-principles calculations in the ferromagnetic (FM) low-temperature and paramagnetic (PM) high-temperature phase. In experiments and calculations, we observe pronounced differences in the shape of the Fe-partial VDOS between nonhydrogenated and hydrogenated samples. Furthermore, this shows that hydrogen not only shifts the temperature of the first-order phase transition, but also affects the elastic response of the Fe subsystem significantly. In turn, the anomalous redshift of the Fe VDOS, observed by going to the low-volume PM phase, survives hydrogenation. As a consequence, the change in the Fe-specific vibrational entropy ΔS lat across the phase transition has the same sign as the magnetic and electronic contribution. DFT calculations show that the same mechanism, which is a consequence of the itinerant electron metamagnetism associated with the Fe subsystem, is effective in both the hydrogenated and the hydrogen-free compounds. Although reduced by 50% as compared to the hydrogen-free system, the measured change ΔS lat of 3.2 ± 1.9)J/ kg K across the FM-to-PM transition contributes with ~35 % significantly and cooperatively to the total isothermal entropy change ΔS iso . Hydrogenation is observed to induce an overall blueshift of the Fe VDOS with respect to the H-free compound; this effect, together with the enhanced Debye temperature observed, is a fingerprint of the hardening of the Fe sublattice by hydrogen incorporation. In addition, the mean Debye velocity of sound of LaFe 11.4 Si 1.6 H 1.6 was determined from the NRIXS and the DFT data.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

A prion-like protein regulator of seed germination undergoes hydration-dependent phase separation

Many organisms evolved strategies to survive desiccation. Plant seeds protect dehydrated embryos from various stressors and can lay dormant for millennia. Hydration is the key trigger to initiate germination, but the mechanism by which seeds sense water remains unresolved. Here we identified an uncharacterized Arabidopsis thaliana prion-like protein we named FLOE1, which phase separates upon hydration and allows the embryo to sense water stress. We demonstrate that biophysical states of FLOE1 condensates modulate its biological function in vivo in suppressing seed germination under unfavorable environments. We find intragenic, intraspecific, and interspecific natural variation in FLOE1 expression and phase separation and show that intragenic variation is associated with adaptive germination strategies in natural populations. This combination of molecular, organismal, and ecological studies uncovers FLOE1 as a tunable environmental sensor with direct implications for the design of drought-resistant crops, in the face of climate change.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Experimental evolution reveals nitrate tolerance mechanisms in Desulfovibrio vulgaris

Elevated nitrate in the environment inhibits sulfate reduction by important microorganisms of sulfate-reducing bacteria (SRB). Several SRB may respire nitrate to survive under elevated nitrate, but how SRB that lack nitrate reductase survive to elevated nitrate remains elusive. To understand nitrate adaptation mechanisms, we evolved 12 populations of a model SRB (i.e., Desulfovibrio vulgaris Hildenborough, DvH) under elevated NaNO 3 for 1000 generations, analyzed growth and acquired mutations, and linked their genotypes with phenotypes. Nitrate-evolved (EN) populations significantly (p < 0.05) increased nitrate tolerance, and whole-genome resequencing identified 119 new mutations in 44 genes of 12 EN populations, among which six functional gene groups were discovered with high mutation frequencies at the population level. In this work, we observed a high frequency of nonsense or frameshift mutations in nitrosative stress response genes (NSR: DVU2543, DVU2547, and DVU2548), nitrogen regulatory protein C family genes (NRC: DVU2394-2396, DVU2402, and DVU2405), and nitrate cluster (DVU0246-0249 and DVU0251). Mutagenesis analysis confirmed that loss-of-functions of NRC and NSR increased nitrate tolerance. Also, functional gene groups involved in fatty acid synthesis, iron regulation, and two-component system (LytR/LytS) known to be responsive to multiple stresses, had a high frequency of missense mutations. Additionally, mutations in those gene groups could increase nitrate tolerance through regulating energy metabolism, barring entry of nitrate into cells, altering cell membrane characteristics, or conferring growth advantages at the stationary phase. This study advances our understanding of nitrate tolerance mechanisms and has important implications for linking genotypes with phenotypes in DvH.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Time-dependent relaxation of observables in complex quantum systems

Abstract We consider time-dependent relaxation of observables in quantum systems of chaotic and regular type. Using statistical arguments and exact numerical solutions we show that the spread of the initial wave function in the Hilbert space and the main characteristics of evolution of observables have certain generic features. The study compares examples of regular dynamics, a completely chaotic case of the Gaussian orthogonal ensemble, a bosonic system with random interactions, and a fully realistic case of the time evolution of various initial non-stationary states in the nuclear shell model. In the case of the Gaussian orthogonal ensemble we show that the survival probability obtained analytically also fully defines the relaxation timescale of observables. This is not the case in general. Using the realistic nuclear shell model and the quadrupole moment as an observable we demonstrate that the relaxation time is significantly longer than defined by the survival probability of the initial state. The full analysis does not show the presence of an analog of the Lyapunov exponent characteristic for examples of classical chaos.

Volya, Alexander (ORCID:0000000217656466)↗
DOE OSTI2023

Dynamic Aperture of the PIP-II Accumulator Ring (PAR)

The Proton Improvement Plan-II (PIP-II) will include a superconducting linear accelerator which will accelerate H- ions to 800MeV, at an intensity never seen before. A proposed PIP-II Accumulator Ring (PAR) can reduce the injection losses to the booster, enhance the ramp up of the Long Baseline Neutrino Facility (LBNF) and support experiments in Dark Sector Physics. When the beam is circulating in PAR at its full intensity, it will then be transferred to the Booster via single turn injection. Strong PAR focusing results in larger phase advances, shorter focal lengths and higher machine tunes, which creates robust beam envelope control. Particles will be able to survive modest excursions from the elliptical phase-space trajectories of linear optics, and any loss of particles would be due to reduced dynamic aperture. The values for tunes and chromaticities are flexible and will continue to evolve as the lattice matures. Since there will be non-linear terms impacting the particles’ trajectories, tracking will include realistic magnetic field errors and installation alignment errors to determine the dynamic aperture as a function of the machine tunes. This will allow us to determine the optimum operating point in phase-space.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2025

Investigation of a gallium alloy liquid metal mirror for application in inertial fusion energy systems

The final optic in future inertial fusion energy plants must maintain high performance and survivability under gigashot laser irradiation while exposed to fusion byproducts. Although no practical solution has been demonstrated, a self-healing final turning mirror based on a grazing-incidence liquid metal mirror has been theoretically explored. This work investigates the suitability of a gallium alloy. The experimental system simulates key conditions, including vacuum exposure and 10-Hz, 355-nm, and 6-ns laser pulses. Experiments address reflectivity, damage, and response as a function of pressure. Results highlight the potential of liquid metal gallium alloys for robust final optics in laser-based fusion power plants and inform non-traditional optics for intense laser systems.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2020

Molecular subtyping reveals immune alterations in IDH wild‐type lower‐grade diffuse glioma

Abstract Isocitrate dehydrogenase ( IDH ) wild‐type diffuse lower‐grade glioma (LGG) is usually associated with poor outcome, but there have been disputes over its clinical outcome and classification. We present here a robust gene expression‐based molecular classification of IDH wild‐type diffuse LGG into two subtypes with distinct biological and clinical features. A discovery cohort of 49 IDH wild‐type diffuse LGGs from the Chinese Glioma Genome Atlas (CGGA) was subjected to clustering and function analysis. Seventy‐three tumors from The Cancer Genome Atlas (TCGA) were used to validate our findings. Consensus clustering of transcriptional data uncovered concordant classification of two robust and prognostically significant subtypes of IDH wild‐type LGG. Subtype 1, associated with poorer outcomes, was characterized by significantly higher immune and cytolytic scores, M2 macrophages, and up‐regulation of immune exhaustion markers, while Subtype 2, which had elevated lymphocytes and plasma cells, showed relatively favorable survival. Somatic alteration analysis revealed that Subtype 1 showed more frequently deleted regions, such as the locus of CDKN2A / CDKN2B , DMRTA1 , C9orf53 , and MTAP . Furthermore, we developed and validated a five‐gene signature for better application of this acquired stratification. Our data demonstrate the biological and prognostic heterogeneity within IDH wild‐type diffuse LGGs and deepen our molecular understandi‐g of this tumor entity. © 2020 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

Wu, Fan↗
DOE OSTI2021

WISP3 suppresses ESCC progression by inhibiting the IGF-2-IGF1R-AKT signaling cascade

Esophageal squamous cell carcinoma (ESCC) is a major health problem worldwide, especially in the Chinese population. However, the intrinsic molecular mechanisms of ESCC progression are largely unclear, thus there is an unmet need to identify essential genes governing this disease. Here, we discovered WISP3, an important member of the CCN family, is markedly downregulated in ESCC tissues compared to the normal esophageal epithelium. Downregulation of WISP3 in cancer tissue correlates with worse overall survival of ESCC patients. Using ESCC cell lines as models, we found that forced expression of WISP3 not only suppressed proliferation and migration of cancer cells in vitro, but also inhibited ESCC tumor growth and metastasis in vivo. On the contrary, WISP3 depletion strongly promoted the tumorigenicity of ESCC cells. Mechanistically, we found that WISP3 negates the activity of AKT via inhibiting the IGF-2-IGF1R signaling cascade, which mediates the tumor-suppressive function of WISP3 in esophageal cancers. Together, we identified a novel factor driving the development of ESCC, and revealed a potential therapeutic target for ESCC treatment.

60 APPLIED LIFE SCIENCES↗