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At least 631 records · Page 35
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Cyanobacteria from marine oxygen-deficient zones encode both form I and form II Rubiscos

Cyanobacteria are highly abundant in the marine photic zone and primary drivers of the conversion of inorganic carbon into biomass. To date, all studied cyanobacterial lineages encode carbon fixation machinery relying upon form I Rubiscos within a CO 2 -concentrating carboxysome. Here, we report that the uncultivated anoxic marine zone (AMZ) IB lineage ofProchlorococcusfrom pelagic oxygen-deficient zones (ODZs) harbors both form I and form II Rubiscos, the latter of which are typically noncarboxysomal and possess biochemical properties tuned toward low-oxygen environments. We demonstrate that these cyanobacterial form II enzymes are functional in vitro and were likely acquired from proteobacteria. Metagenomic analysis reveals that AMZ IB are essentially restricted to ODZs in the Eastern Pacific, suggesting that form II acquisition may confer an advantage under low-O 2 conditions. AMZ IB populations express both forms of Rubisco in situ, with the highest form II expression at depths where oxygen and light are low, possibly as a mechanism to increase the efficiency of photoautotrophy under energy limitation. Our findings expand the diversity of carbon fixation configurations in the microbial world and may have implications for carbon sequestration in natural and engineered systems.

Science & Technology - Other Topics↗
DOE OSTI2025

The C2 domain augments Ras GTPase-activating protein catalytic activity

Regulation of Ras GTPases by GTPase-activating proteins (GAPs) is essential for their normal signaling. Nine of the ten GAPs for Ras contain a C2 domain immediately proximal to their canonical GAP domain, and in RasGAP (p120GAP, p120RasGAP;RASA1) mutation of this domain is associated with vascular malformations in humans. Here, we show that the C2 domain of RasGAP is required for full catalytic activity toward Ras. Analyses of the RasGAP C2-GAP crystal structure, AlphaFold models, and sequence conservation reveal direct C2 domain interaction with the Ras allosteric lobe. This is achieved by an evolutionarily conserved surface centered around RasGAP residue R707, point mutation of which impairs the catalytic advantage conferred by the C2 domain in vitro. In mice,R707Cmutation phenocopies the vascular and signaling defects resulting from constitutive disruption of theRASA1gene. In SynGAP, mutation of the equivalent conserved C2 domain surface impairs catalytic activity. Our results indicate that the C2 domain is required to achieve full catalytic activity of GAPs for Ras.

Science & Technology - Other Topics↗
DOE OSTI2025

Enzymatic carbon–fluorine bond cleavage by human gut microbes

Fluorinated compounds are used for agrochemical, pharmaceutical, and numerous industrial applications, resulting in global contamination. In many molecules, fluorine is incorporated to enhance the half-life and improve bioavailability. Fluorinated compounds enter the human body through food, water, and xenobiotics including pharmaceuticals, exposing gut microbes to these substances. The human gut microbiota is known for its xenobiotic biotransformation capabilities, but it was not previously known whether gut microbial enzymes could break carbon-fluorine bonds, potentially altering the toxicity of these compounds. Here, through the development of a rapid, miniaturized fluoride detection assay for whole-cell screening, we identified active gut microbial defluorinases. We biochemically characterized enzymes from diverse human gut microbial classes including Clostridia, Bacilli, and Coriobacteriia, with the capacity to hydrolyze (di)fluorinated organic acids and a fluorinated amino acid. Whole-protein alanine scanning, molecular dynamics simulations, and chimeric protein design enabled the identification of a disordered C-terminal protein segment involved in defluorination activity. Domain swapping exclusively of the C-terminus conferred defluorination activity to a nondefluorinating dehalogenase. To advance our understanding of the structural and sequence differences between defluorinating and nondefluorinating dehalogenases, we trained machine learning models which identified protein termini as important features. Models trained on 41-amino acid segments from protein C termini alone predicted defluorination activity with 83% accuracy (compared to 95% accuracy based on full-length protein features). This work is relevant for therapeutic interventions and environmental and human health by uncovering specificity-determining signatures of fluorine biochemistry from the gut microbiome.

Probst, Silke I↗
DOE OSTI2026

Rubisco kinetic acclimation at the holoenzyme level

Kinetic acclimation enables proteins to adjust their activity in response to environmental perturbations. For the CO 2 -fixing enzyme Rubisco, kinetic acclimation may be conferred by its small subunits. Plants express multiple small subunits and vary their expression with temperature. Here, we demonstrate that different small subunits can bind to the same Rubisco to form a heterogeneous holoenzyme. These small subunits had distinct kinetic effects which aligned with changes in holoenzyme structure and stability. Our findings indicate that small subunits enable Rubisco kinetic acclimation via manipulation of flexibility. By assembling a more rigid active site in higher temperatures and a more flexible one in lower temperatures, plants maximize the efficiency of their Rubisco, and thus photosynthesis, over a wide range of temperatures.

CO2 fixation↗
DOE OSTI2026

Depth of nutrient uptake by deep-rooted plants is regulated by water availability

The capacity of some plants to access water and nutrients at depths greater than one meter is a critical functional trait that confers resistance to drought and impacts both belowground and shallow soil processes. Here, we report water and strontium isotopic data from an alpine meadow transect showing the correlation between water and nutrient acquisition depths. The isotopic compositions of Sr ( 87 Sr/ 86 Sr ratio) and water in rock and soil, and in plant leaf tissues, reveal that deeper-rooted plants acquire a higher proportion of water, Sr, and cation nutrients that are derived from the saprolite, a zone of silicate weathering, than shallow-rooted grass. A three-decade dendrochemical record reveals that reductions of wet precipitation drive deep-rooted plants to acquire cation nutrients from deeper saprolite or bedrock regions. Thus, the depth of cation nutrient acquisition by deep-rooted plant species at this site is tightly coupled with, and likely determined by, water availability in soil, saprolite, and bedrock. The enhanced uptake of cations as well as water from deeper saprolite zones could impact the rate of bedrock weathering and watershed chemistry during drought.

biogeochemistry↗
DOE OSTI2020

Mutations in penicillin-binding protein 2 from cephalosporin-resistant Neisseria gonorrhoeae hinder ceftriaxone acylation by restricting protein dynamics

The global incidence of the sexually transmitted disease gonorrhea is expected to rise due to the spread of Neisseria gonorrhoeae strains with decreased susceptibility to extended-spectrum cephalosporins (ESCs). ESC resistance is conferred by mosaic variants of penicillin-binding protein 2 (PBP2) that have diminished capacity to form acylated adducts with cephalosporins. To elucidate the molecular mechanisms of ESC resistance, we conducted a biochemical and high-resolution structural analysis of PBP2 variants derived from the decreased-susceptibility N. gonorrhoeae strain 35/02 and ESC-resistant strain H041. Our data reveal that mutations both lower affinity of PBP2 for ceftriaxone and restrict conformational changes that normally accompany acylation. Specifically, we observe that a G545S substitution hinders rotation of the β3 strand necessary to form the oxyanion hole for acylation and also traps ceftriaxone in a noncanonical configuration. In addition, F504L and N512Y substitutions appear to prevent bending of the β3–β4 loop that is required to contact the R1 group of ceftriaxone in the active site. Other mutations also appear to act by reducing flexibility in the protein. Overall, our findings reveal that restriction of protein dynamics in PBP2 underpins the ESC resistance of N. gonorrhoeae.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

The first DEP domain of the RhoGEF P-Rex1 autoinhibits activity and contributes to membrane binding

Phosphatidylinositol (3,4,5)-trisphosphate (PIP 3 )-dependent Rac exchanger 1 (P-Rex1) catalyzes the exchange of GDP for GTP on Rac GTPases, thereby triggering changes in the actin cytoskeleton and in transcription. Its overexpression is highly correlated with the metastasis of certain cancers. P-Rex1 recruitment to the plasma membrane and its activity are regulated via interactions with heterotrimeric Gβγ subunits, PIP 3 , and protein kinase A (PKA). Deletion analysis has further shown that domains C-terminal to its catalytic Dbl homology (DH) domain confer autoinhibition. Among these, the first dishevelled, Egl-10, and pleckstrin domain (DEP1) remains to be structurally characterized. DEP1 also harbors the primary PKA phosphorylation site, suggesting that an improved understanding of this region could substantially increase our knowledge of P-Rex1 signaling and open the door to new selective chemotherapeutics. Here we show that the DEP1 domain alone can autoinhibit activity in context of the DH/PH-DEP1 fragment of P-Rex1 and interacts with the DH/PH domains in solution. The 3.1 Å crystal structure of DEP1 features a domain swap, similar to that observed previously in the Dvl2 DEP domain, involving an exposed basic loop that contains the PKA site. Using purified proteins, we show that although DEP1 phosphorylation has no effect on the activity or solution conformation of the DH/PH-DEP1 fragment, it inhibits binding of the DEP1 domain to liposomes containing phosphatidic acid. Thus, we propose that PKA phosphorylation of the DEP1 domain hampers P-Rex1 binding to negatively charged membranes in cells, freeing the DEP1 domain to associate with and inhibit the DH/PH module.

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

First-principles calculation of excited states of diatomic molecules: a benchmark for the Gutzwiller conjugate gradient minimisation method

We recently proposed the Gutzwiller conjugate gradient minimisation (GCGM) method for efficient and accurate calculation of the ground state total energy of molecular and bulk systems. The GCGM method is developed under the framework of Gutzwiller wave function but goes beyond the commonly adopted Gutzwiller approximation to improve the accuracy and flexibility in treating the correlation effects. In this conference proceeding, we benchmark the GCGM method with the calculation of excited state potential energy curves of three diatomic molecules, namely H 2 , N 2 , and O 2 . Our calculations demonstrate the flexibility and reasonable accuracy of the method.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2021

Nuclear Science for the Manhattan Project and Comparison to Today’s ENDF Data

Nuclear physics advances in the United States and Britain from 1939 to 1945 are described. The Manhattan Project’s work led to an explosion in our knowledge of nuclear science. A conference in April 1943 at Los Alamos provided a simple formula used to compute critical masses and laid out the research program needed to determine the key nuclear constants. In short order, four university accelerators were disassembled and reassembled at Los Alamos, and methods were established to make measurements on extremely small samples owing to the initial lack of availability of enriched 235U and plutonium. I trace the program that measured fission cross sections, fission-emitted neutron multiplicities and their energy spectra, and transport cross sections, comparing the measurements with our best understanding today as embodied in the Evaluated Nuclear Data File ENDF/B-VIII.0. The large nuclear data uncertainties at the beginning of the project, which often exceeded 25% to 50%, were reduced by 1945 often to less than 5% to 10%. Uranium-235 and plutonium-239 fission cross-section assessments in the fast mega-electron-volt range were reduced following more accurate measurements, and the neutron multiplicity $\overline{v}$ increased. By a lucky coincidence of canceling errors, the initial critical mass estimates were close to the final estimated masses. Some images from historical documents from our Los Alamos archives are shown. Many of the original measurements from these early years have not previously been widely available. Through this work, these data have now been archived in the international experimental nuclear reaction data library (EXFOR) in a collaboration with the International Atomic Energy Agency and Brookhaven National Laboratory.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2021

Critical Assemblies: Dragon Burst Assembly and Solution Assemblies

This work reviews the historical literature associated with the Dragon experiment and water boiler reactors operated at Los Alamos during the Manhattan Project. Frisch’s invited talk given at the American Nuclear Society’s Fast Burst Reactor Conference held at the University of New Mexico in Albuquerque, New Mexico, in 1969 is quoted. From the literature review, basic models for the Dragon experiment and for a water boiler–type assembly (aqueous homogeneous reactor) were created that can be used for conducting multiphysics simulations for criticality excursion studies. This methodology utilizes the coupled neutronic-hydrodynamic method to perform a time-dependent dynamic simulation of a criticality excursion. MCNP® was utilized to calculate important nuclear kinetic parameters that were incorporated into the models. Simulation results compare reasonably well with historic data.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2025

NEUWAVE-12 at ESS: Workshop Series on Wavelength Dependent Neutron Imaging Back in Full Swing

The NEUWAVE workshop series, a cornerstone for advancements in energy- or wavelength-resolved neutron imaging, held its 12th meeting at the European Spallation Source (ESS) in Lund from September 1 to 5, 2024. The participants can be seen in Figure 1 during the site visit. The series focuses on developments in techniques using phenomena such as Bragg-edges, incoherent and inelastic scattering, or neutron absorption resonances as contrast mechanisms and is therefore far more specialized than more general conferences for neutron imaging such as the WCNR or ITMNR series [Citation1]. After a break during the pandemic and record attendance at NEUWAVE-11 in Tokyo in 2023, which underscored the immense interest in wavelength dependent neutron imaging, NEUWAVE returned to its roots with a focus on a smaller group of specialists meeting in a workshop format, allowing for in-depth discussions and the exchange of new ideas.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2026

A New Shutdown Dose Rate Benchmark Problem for Representative Fusion Applications

Here, this work introduces a new benchmark problem for calculating shutdown dose rates (SDDRs) aimed at fusion reactor applications. The model is designed to represent a simplified version of a typical ITER port plug. The responses of interest include neutron flux, gamma flux, and gamma SDDR at 12 different locations scattered throughout the port. This article outlines the geometry specifications of the problem, provides material definitions for the components, specifies the required responses to be calculated, and presents the source definition information. The need for this benchmark arises from the limited availability of publicly accessible references, with only one benchmark representing the typical dimensions and materials found in fusion systems. This existing benchmark has been cited extensively, reflecting the demand within the scientific community to test both established and novel workflows for SDDR calculations. However, since its presentation at a conference in 2011, the results have become increasingly well known. Moreover, the absence of formal publication and peer review has led to the details of this benchmark being extracted from secondary sources, such as subsequent studies that reference it. As a result, analysts are left with significant flexibility in interpreting the key parameters, which can be adjusted to account for unknown systematic errors, ultimately reproducing the already well-known responses. This new benchmark serves as an updated version of that earlier work, with the aim of providing a more reliable description of the materials and their impurities, which is crucial for assessing activation and subsequent gamma emission. Additionally, it seeks to provide a geometry that more closely represents an ITER port plug. The improvements in the problem definition will lead to a more reproducible benchmark problem, while also presenting the radiation transport community with a completely new challenge. The results will be published in a future article to allow analysts adequate time to analyze this problem independently.

Benchmark↗
DOE OSTI2024

Investigating the mechanism of chloroplast singlet oxygen signaling in the Arabidopsis thaliana accelerated cell death 2 mutant

As sessile organisms, plants have evolved complex signaling mechanisms to sense stress and acclimate. This includes the use of reactive oxygen species (ROS) generated during dysfunctional photosynthesis to initiate signaling. One such ROS, singlet oxygen ( 1 O 2 ), can trigger retrograde signaling, chloroplast degradation, and programmed cell death. However, the signaling mechanisms are largely unknown. Several proteins (e.g. PUB4, OXI1, EX1) are proposed to play signaling roles across three Arabidopsis thaliana mutants that conditionally accumulate chloroplast 1 O 2 (fluorescent in blue light (flu), chlorina 1 (ch1), and plastid ferrochelatase 2 (fc2)). We previously demonstrated that these mutants reveal at least two chloroplast 1 O 2 signaling pathways (represented by flu and fc2/ch1). Here, we test if the 1 O 2 -accumulating lesion mimic mutant, accelerated cell death 2 (acd2), also utilizes these pathways. The pub4–6 allele delayed lesion formation in acd2 and restored photosynthetic efficiency and biomass. Conversely, an oxi1 mutation had no measurable effect on these phenotypes. acd2 mutants were not sensitive to excess light (EL) stress, yet pub4–6 and oxi1 both conferred EL tolerance within the acd2 background, suggesting that EL-induced 1 O 2 signaling pathways are independent from spontaneous lesion formation. Thus, 1 O 2 signaling in acd2 may represent a third (partially overlapping) pathway to control cellular degradation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

National Council on Radiation Protection (NCRP) 2024 annual meeting: advanced and small modular nuclear power reactors

On 25–26 March 2023, the U.S. National Council on Radiation Protection and Measurements (NCRP) held its 2024 annual meeting in Bethesda, Maryland, USA. The NCRP dates from 1929, and this meeting celebrated the 60th anniversary of receiving a U.S. Congressional Charter. For this annual meeting the NCRP felt it was essential to provide a briefing about advanced and small modular nuclear reactors (SMRs). The Journal of Radiological Protection is delighted to publish the following synopsis of material presented at the U.S. NCRP meeting. This synopsis is divided into five sections. The first section provides an overview of the whole meeting together with summaries of two context setting overview papers. The following four sessions of this synopsis are specific to advanced and small modular nuclear power reactors. The meeting also included keynote presentations by three of NCRP annual award recipients. The meeting topical areas were Technology Overview and Critical Issues. The individual papers laid the groundwork to understanding reactor technologies, terminology, and the fundamental concepts and processes for electrical generation. The perspectives of the U.S. Environmental Protection Agency and states, through the Conference of Radiation Control Program Directors were provided. The papers included a discussion of diverse topics including potential emergency preparedness considerations, radiological survey requirements, an evaluation of the future of nuclear power, the economics of reactors (both large and small), and the critical issues identified by the recent National Academies of Sciences’ study on advanced reactors. Here, the summary papers were developed to briefly document the major points and concepts presented during the oral papers presented at the 2024 NCRP Annual Meeting. The meeting heralded the dawn of a new era for commercial nuclear power.

61 RADIATION PROTECTION AND DOSIMETRY↗
DOE OSTI2021

The NUBASE2020 evaluation of nuclear physics properties *

The NUBASE2020 evaluation contains the recommended values of the main nuclear physics properties for all nuclei in their ground and excited, isomeric (T-1/2 >= 100 ns) states. It encompasses all experimental data published in primary (journal articles) and secondary (mainly laboratory reports and conference proceedings) references, together with the corresponding bibliographical information. In cases where no experimental data were available for a particular nuclide, trends in the behavior of specific properties in neighboring nuclei were examined and estimated values are proposed. Evaluation procedures and policies that were used during the development of this evaluated nuclear data library are presented, together with a detailed table of recommended values and their uncertainties.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

Advances in the long-pulse steady-state high beta H-mode scenario with active controls of divertor heat and particle fluxes in EAST

Since the last IAEA-Fusion Energy Conference, the Experimental Advanced Superconducting Tokamak (EAST) research program has been, in support of ITER and CFETR, focused on development in terms of the long-pulse steady-state (fully noninductive) high beta H-mode scenario with active controls of the stationary and transient divertor heat and particle fluxes. The operational domain of the steady-state H-mode plasma scenario has been significantly extended with ITER-like tungsten mono-block divertor, plasma control and heating schemes. EAST has achieved several important milestones in the development of high β p H-mode scenario and its key physics and technologies. A 60 s-scale long-pulse steady-state high β p H-mode discharge with the major normalized plasma parameters similar to the designed performance of the CFETR 1GW fusion power operation scenario has been successfully established and sustained by pure RF heating and current drive. Several feedback control schemes have been developed for a sustained detachment with good core confinement. This includes control of the total radiation power, target electron temperature, and particle flux measured using divertor Langmuir probes or a combination of the control of target electron temperature and AXUV radiation near the X point. The detachment feedback control schemes have been integrated with small-ELM regimes and high β p scenario via neon seeding, enabling a core and edge compatible integrated high-beta scenario applicable to long-pulse operations. ELM suppression has been achieved using various methods, including resonant magnetic perturbations and impurity seeding. Full suppression of ELMs by using n=4 RMPs has been demonstrated for ITER for the first time in low input torque plasmas in EAST. Finally, EAST has been operated with helium to support the ITER research requirements for the first time. For a long-pulse, high bootstrap current fraction operation, a new lower tungsten divertor with active water-cooling has been installed, along with improvements in the heating and current drive capability.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

Exploring the effect of ELM and code-coupling frequencies on plasma and material modeling of dynamic recycling in divertors

Abstract Integrated modeling of plasma-surface interactions provides a comprehensive and self-consistent description of the system, moving the field closer to developing predictive and design capabilities for plasma facing components. One such workflow, including descriptions for the scrape-off-layer plasma, ion-surface interactions and the sub-surface evolution, was previously used to address steady-state scenarios and has recently been extended to incorporate time-dependence and two-way information flow. The new model can address dynamic recycling in transient scenarios, such as the application presented in this paper: the evolution of W samples pre-damaged by helium and exposed to ELMy H-mode plasmas in the DIII-D DiMES. A first set of simulations explored the effect of ELM frequency. This study was discussed in detail in this conference’s proceedings and is summarized here. The 2nd set of simulations, which is the focus of this paper, explores the effect of code-coupling frequency. These simulations include initial SOLPS solutions converged to the inter-ELM state, ion impact energy ( E in ) and angles ( A in ) calculated by hPIC2, and an improved heat transfer description in Xolotl. The model predicts increases in particle fluxes and decreases in heat fluxes by 10%–20% with the coupling time-step. Compared with the first set of simulations, the less shallow impact angle leads to smaller reflection rates and significant D implantation. The higher fraction of implanted flux (and deeper), in particular during ELMs, increases the accumulated D content in the W near-surface region. Future expansion of the workflow includes coupling to hPIC2 and GITR to ensure accurate descriptions of E in and A in , and W impurity transport.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

Design improvements to the SNS ion source and diagnostics

The U.S. Spallation Neutron Source (SNS) is a state-of-the-art neutron scattering facility delivering the world's most intense pulsed-neutron beams to a wide array of instruments which are used to conduct investigations in many fields of science and engineering. The accelerator system is fed by an RF-driven, multicusp, H - ion source which nominally provides pulsed beam currents of 50-60 mA (1ms, 60Hz). This report provides a discussion of ongoing design improvements to the SNS ion source and Low Energy Beam Transport (LEBT) as well as diagnostic upgrades undertaken since the previous ICIS conference. These improvements include (i) simple mechanical modifications to the source outlet aperture which resulted in dramatically increased extracted beam current and comparable or lower emittance at similar beam currents, (ii) design improvements to the LEBT chopper target which will enable full power beam-dumping during physics studies, (iii) refinement of the SNS Allison emittance scanner that has enabled the first reliable LEBT beam measurements at full beam power (65kV, 50-100mA, 1ms, 60Hz) on the SNS ion source test stand and (iv) the implementation of a thermal imaging camera for the monitoring the LEBT electrode temperatures. (v) The design of an advanced Cs system, capable of more efficient Cs utilization with significantly lower Cs losses from the source is also presented. Mechanical details, computational simulations and experimental results are discussed within the context of these improvements.

47 OTHER INSTRUMENTATION↗