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At least 397 records · Page 22
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Weibel-mediated filamentary structures observed in the ICF context

Here, in light of novel and past experimental results, we demonstrate how Weibel-mediated filamentary structures can develop in the expanding plasma plume of a laser-irradiated foil. The transverse ballistic cooling that occurs during the quasi-spherical plasma expansion naturally drives an electron pressure anisotropy, resulting in the growth of electron current filaments. This effect competes with electron–ion Coulomb collisions, which tend to isotropize the electron distribution function. Based on theoretical and particle-in-cell modeling, we provide estimates of the dominant wavelength and amplitude of the self-generated magnetic fluctuations, which are found to explain experimental data obtained at the OMEGA and Laser Megajoule facilities.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2021

Electrochromic shift supports the membrane destabilization model of Tat-mediated transport and shows ion leakage during Sec transport

Significance Due to the transient nature of the active Tat complex, much of the knowledge available has been hard won. Electric-field-indicating absorbance transients allow investigation of transmembrane ion movement using native electric potential in thylakoids while circumventing challenges of reconstitution. Electrical behavior of transiently and/or constitutively assembled complexes suggests that Sec translocation occurs through a barrel-stave-type proteinaceous pore, while Tat translocation likely occurs through a toroidal pore. This would be the first instance of toroidal pores being exploited by a general protein translocation system. Our electrochemical analysis offers insight into how protein transport might be linked to light stimulation. Localized membrane destabilization presents a rational link between the proton motive force, membrane thinning, and Tat-mediated transport of substrates critical to photosynthesis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

A protease-mediated switch regulates the growth of magnetosome organelles in Magnetospirillum magneticum

Magnetosomes are lipid-bound organelles that direct the biomineralization of magnetic nanoparticles in magnetotactic bacteria. Magnetosome membranes are not uniform in size and can grow in a biomineralization-dependent manner. However, the underlying mechanisms of magnetosome membrane growth regulation remain unclear. Using cryoelectron tomography, we systematically examined mutants with defects at various stages of magnetosome formation to identify factors involved in controlling membrane growth. We found that a conserved serine protease, MamE, plays a key role in magnetosome membrane growth regulation. When the protease activity of MamE is disrupted, magnetosome membrane growth is restricted, which, in turn, limits the size of the magnetite particles. Consistent with this finding, the upstream regulators of MamE protease activity, MamO and MamM, are also required for magnetosome membrane growth. We then used a combination of candidate and comparative proteomics approaches to identify Mms6 and MamD as two MamE substrates. Mms6 does not appear to participate in magnetosome membrane growth. However, in the absence of MamD, magnetosome membranes grow to a larger size than the wild type. Furthermore, when the cleavage of MamD by MamE protease is blocked, magnetosome membrane growth and biomineralization are severely inhibited, phenocopying the MamE protease-inactive mutant. We therefore propose that the growth of magnetosome membranes is controlled by a protease-mediated switch through processing of MamD. Overall, our work shows that, like many eukaryotic systems, bacteria control the growth and size of biominerals by manipulating the physical properties of intracellular organelles.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

FDX1-dependent and independent mechanisms of elesclomol-mediated intracellular copper delivery

Recent studies have uncovered the therapeutic potential of elesclomol (ES), a copper-ionophore, for copper deficiency disorders. However, we currently do not understand the mechanism by which copper brought into cells as ES–Cu(II) is released and delivered to cuproenzymes present in different subcellular compartments. Here, we have utilized a combination of genetic, biochemical, and cell-biological approaches to demonstrate that intracellular release of copper from ES occurs inside and outside of mitochondria. The mitochondrial matrix reductase, FDX1, catalyzes the reduction of ES–Cu(II) to Cu(I), releasing it into mitochondria where it is bioavailable for the metalation of mitochondrial cuproenzyme— cytochrome c oxidase. Consistently, ES fails to rescue cytochrome c oxidase abundance and activity in copper-deficient cells lacking FDX1. In the absence of FDX1, the ES-dependent increase in cellular copper is attenuated but not abolished. Thus, ES-mediated copper delivery to nonmitochondrial cuproproteins continues even in the absence of FDX1, suggesting alternate mechanism(s) of copper release. Importantly, we demonstrate that this mechanism of copper transport by ES is distinct from other clinically used copper-transporting drugs. Our study uncovers a unique mode of intracellular copper delivery by ES and may further aid in repurposing this anticancer drug for copper deficiency disorders.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Dual factors required for cytochrome-P450-mediated hydrocarbon ring contraction in bacterial gibberellin phytohormone biosynthesis

Cytochromes P450 (CYPs) are heme-thiolate monooxygenases that prototypically catalyze the insertion of oxygen into unactivated C–H bonds but are capable of mediating more complex reactions. One of the most remarked-upon alternative reactions occurs during biosynthesis of the gibberellin A (GA) phytohormones, involving hydrocarbon ring contraction with coupled aldehyde extrusion of ent-kaurenoic acid to form the first gibberellin intermediate. While the unusual nature of this reaction has long been noted, its mechanistic basis has remained opaque. Building on identification of the relevant CYP114 from bacterial GA biosynthesis, detailed structure–function studies are reported here, including development of in vitro assays as well as crystallographic analyses both in the absence and presence of substrate. These structures provided insight into enzymatic catalysis of this unusual reaction, as exemplified by identification of a key role for the “missing” acid from an otherwise highly conserved acid–alcohol pair of residues. Notably, the results demonstrate that ring contraction requires dual factors, both the use of a dedicated ferredoxin and absence of the otherwise conserved acidic residue, with exclusion of either limiting turnover to just the initiating and more straightforward hydroxylation. The results provide detailed insight into the enzymatic structure–function relationships underlying this fascinating reaction and support the use of a semipinacol mechanism for the unusual ring contraction reaction.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Real-space visualization of a defect-mediated charge density wave transition

Here, we study the coupled charge density wave (CDW) and insulator-to-metal transitions in the 2D quantum material 1T-TaS 2 . By applying in situ cryogenic 4D scanning transmission electron microscopy with in situ electrical resistance measurements, we directly visualize the CDW transition and establish that the transition is mediated by basal dislocations (stacking solitons). We find that dislocations can both nucleate and pin the transition and locally alter the transition temperature T c by nearly ~75 K. This finding was enabled by the application of unsupervised machine learning to cluster five-dimensional, terabyte scale datasets, which demonstrate a one-to-one correlation between resistance—a global property—and local CDW domain-dislocation dynamics, thereby linking the material microstructure to device properties. This work represents a major step toward defect-engineering of quantum materials, which will become increasingly important as we aim to utilize such materials in real devices.

4D-STEM↗
DOE OSTI2020

A requirement for an active proton delivery network supports a compound I-mediated C–C bond cleavage in CYP51 catalysis

CYP51 enzymes (sterol 14α-demethylases) are cytochromes P450 that catalyze multistep reactions. The CYP51 reaction occurs in all biological kingdoms and is essential in sterol biosynthesis. It removes the 14α-methyl group from cyclized sterol precursors by first forming an alcohol, then an aldehyde, and finally eliminating formic acid with the introduction of a Δ14–15 double bond in the sterol core. The first two steps are typical hydroxylations, mediated by an electrophilic compound I mechanism. The third step, C–C bond cleavage, has been proposed to involve either compound I (i.e. FeO 3+ ) or, alternatively, a proton transfer-independent nucleophilic ferric peroxo anion (compound 0, i.e. Fe 3+ O 2 – ). In this work, using comparative crystallographic and biochemical analyses of WT human CYP51 (CYP51A1) and its D231A/H314A mutant, whose proton delivery network is destroyed (as evidenced in a 1.98-Å X-ray structure in complex with lanosterol), we demonstrate that deformylation of the 14α-carboxaldehyde intermediate requires an active proton relay network to drive the catalysis. These results indicate a unified, compound I-based mechanism for all three steps of the CYP51 reaction, as previously established for CYP11A1 and CYP19A1. We anticipate that our approach can be applied to mechanistic studies of other P450s that catalyze multistep reactions, such as C–C bond cleavage.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

NO 2 -mediated voloxidation for iodine separation from cesium iodide surrogates

Heterogeneous NO 2 -mediated oxidation of uranium, also known as advanced voloxidation, is a proposed head-end reprocessing method for used nuclear fuel. An advantage of advanced voloxidation is the removal of volatile fission products, which complicate downstream separation and containment challenges leading to increased processing economics. Iodine, one of the volatile species of interest, has exhibited varied results in this process. Using CsI as a surrogate material, this work mimics the effect of NO 2 -based voloxidation on iodine and sheds light on the factors that influence the solid–gas phase reaction. Solid-state analysis using Fourier transform infrared attenuated total reflectance spectroscopy and scanning electron microscopy with energy-dispersive X-ray spectroscopy confirmed the conversion of CsI to CsNO 3 . Iodine separation ranged from 46% to 100% across multiple tests. Iodine separation was most effective when multiple recharges of NO 2 were administered. In conclusion, at the bench scale, liberating iodine from CsI appears to occur within 1 h, but the presence of surface H 2 O and the composition of the NO x reagent mixtures greatly influence its success.

advanced voloxidation↗
DOE OSTI2023

Plasmoid-mediated reconnection during nonlinear peeling–ballooning edge-localized modes

Abstract Plasmoid-mediated reconnection is investigated for nonlinear peeling–ballooning edge-localized modes (P-B ELMs). The formation of current sheets and the transition to 3D current sheet instability is demonstrated through fully nonlinear resistive MHD simulations of P-B ELMs in DIII-D discharges. Large-scale axisymmetric current sheets, as well as small-scale poloidally extended current sheets, are formed as the coherent P-B ELM filaments nonlinearly evolve. It is observed that, at high Lundquist numbers, these current sheets break during a reconnection burst, i.e. a secondary exponential growth of intermediate modes followed by relaxation due to the suppression of P-B drive.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2021

Climate-Mediated Changes to Linked Terrestrial and Marine Ecosystems across the Northeast Pacific Coastal Temperate Rainforest Margin

Coastal margins are important areas of materials flux that link terrestrial and marine ecosystems. Consequently, climate-mediated changes to coastal terrestrial ecosystems and hydrologic regimes have high potential to influence nearshore ocean chemistry and food web dynamics. Research from tightly coupled, high-flux coastal ecosystems can advance understanding of terrestrial–marine links and climate sensitivities more generally. In the present article, we use the northeast Pacific coastal temperate rainforest as a model system to evaluate such links. We focus on key above- and belowground production and hydrological transport processes that control the land-to-ocean flow of materials and their influence on nearshore marine ecosystems. We evaluate how these connections may be altered by global climate change and we identify knowledge gaps in our understanding of the source, transport, and fate of terrestrial materials along this coastal margin. Finally, we propose five priority research themes in this region that are relevant for understanding coastal ecosystem links more broadly.

temperate rainforest, coastal margin, climate chan↗
DOE OSTI2020

Genotype-Specific Neutralization of Norovirus Is Mediated by Antibodies Against the Protruding Domain of the Major Capsid Protein

Abstract Human noroviruses are the most common viral agents of acute gastroenteritis. Recently, human intestinal enteroids were shown to be permissive for norovirus infection. We tested their suitability as a system to study norovirus neutralization. Hyperimmune sera raised against virus-like particles (VLPs) representing different genotypes showed highly specific neutralization activity against GII.4 and GII.6 noroviruses. Carbohydrate blocking assays and neutralization exhibited similar patterns in antibody responses. Notably, sera produced against chimeric VLPs that presented swapped structural shell and protruding (P) domains, from different genotypes showed that neutralization is primarily mediated by antibodies mapping to the P domain of the norovirus capsid protein. This study provides empirical information on the antigenic differences among genotypes as measured by neutralization, which could guide vaccine design.

Ford-Siltz, Lauren A.↗
DOE OSTI2021

Impact of PrsA on membrane lipid composition during daptomycin-resistance-mediated β-lactam sensitization in clinical MRSA strains

Abstract Background The cyclic anionic lipopeptide daptomycin is used in the treatment of severe infections caused by Gram-positive pathogens, including MRSA. Daptomycin resistance, although rare, often results in treatment failure. Paradoxically, in MRSA, daptomycin resistance is usually accompanied by a concomitant decrease in β-lactam resistance in what is known as the ‘see-saw effect’. This resensitization is extensively used for the treatment of MRSA infections, by combining daptomycin and a β-lactam antibiotic, such as oxacillin. Objectives We aimed: (i) to investigate the combined effects of daptomycin and oxacillin on the lipid composition of the cellular membrane of both daptomycin-resistant and -susceptible MRSA strains; and (ii) to assess the involvement of the post-translocational protein PrsA, which plays an important role in oxacillin resistance in MRSA, in membrane lipid composition and remodelling during daptomycin resistance/β-lactam sensitization. Results The combination of microbiological and biochemical studies, with fluorescence microscopy using lipid probes, showed that the lipid composition and surface charge of the daptomycin-resistant cells exposed to daptomycin/oxacillin were dependent on antibiotic concentration and directly associated with PrsA, which influenced cardiolipin remodelling/relocation. Conclusions Our findings show that PrsA, in addition to its post-transcriptional role in the maturation of PBP 2a, is a key mediator of cell membrane remodelling connected to the see-saw effect and may have a key role in the resensitization of daptomycin-resistant strains to β-lactams, such as oxacillin.

de Carvalho, Carla C. C. R.↗
DOE OSTI2022

The role of plasma instabilities in relativistic radiation-mediated shocks: stability analysis and particle-in-cell simulations

ABSTRACT Relativistic radiation-mediated shocks are likely formed in prodigious cosmic explosions. The structure and emission of such shocks are regulated by copious production of electron–positron pairs inside the shock-transition layer. It has been pointed out recently that substantial abundance of positrons inside the shock leads to a velocity separation of the different plasma constituents, which is expected to induce a rapid growth of plasma instabilities. In this paper, we study the hierarchy of plasma microinstabilities growing in an electron-ion plasma loaded with pairs and subject to a radiation force. Linear stability analysis indicates that such a system is unstable to the growth of various plasma modes which ultimately become dominated by a current filamentation instability driven by the relative drift between the ions and the pairs. These results are validated by particle-in-cell simulations that further probe the non-linear regime of the instabilities, and the pair-ion coupling in the microturbulent electromagnetic field. Based on this analysis, we derive a reduced-transport equation for the particles via pitch-angle scattering in the microturbulence and demonstrate that it can couple the different species and lead to non-adiabatic compression via a Joule-like heating. The heating of the pairs and, conceivably, the formation of non-thermal distributions, arising from the microturbulence, can affect the observed shock-breakout signal in ways unaccounted for by current single-fluid models.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

CRISPR–Cas9-mediated nuclear transport and genomic integration of nanostructured genes in human primary cells

DNA nanostructures are a promising tool to deliver molecular payloads to cells. DNA origami structures, where long single-stranded DNA is folded into a compact nanostructure, present an attractive approach to package genes; however, effective delivery of genetic material into cell nuclei has remained a critical challenge. Here, we describe the use of DNA nanostructures encoding an intact human gene and a fluorescent protein encoding gene as compact templates for gene integration by CRISPR-mediated homology-directed repair (HDR). Our design includes CRISPR–Cas9 ribonucleoprotein binding sites on DNA nanostructures to increase shuttling into the nucleus. We demonstrate efficient shuttling and genomic integration of DNA nanostructures using transfection and electroporation. These nanostructured templates display lower toxicity and higher insertion efficiency compared to unstructured double-stranded DNA templates in human primary cells. Furthermore, our study validates virus-like particles as an efficient method of DNA nanostructure delivery, opening the possibility of delivering nanostructures in vivo to specific cell types. Together, these results provide new approaches to gene delivery with DNA nanostructures and establish their use as HDR templates, exploiting both their design features and their ability to encode genetic information. This work also opens a door to translate other DNA nanodevice functions, such as biosensing, into cell nuclei.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Group VII ethylene response factors forming distinct regulatory loops mediate submergence responses

Group VII ethylene response factors (ERFVIIs), whose stability is oxygen concentration-dependent, play key roles in regulating hypoxia response genes in Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) during submergence. To understand the evolution of flooding tolerance in cereal crops, we evaluated whether Brachypodium distachyon ERFVII genes (BdERFVIIs) are related to submergence tolerance. We found that three BdERFVIIs, BdERF108, BdERF018, and BdERF961, form a feedback regulatory loop to mediate downstream responses. BdERF108 and BdERF018 activated the expression of BdERF961 and PHYTOGLOBIN 1 (PGB1), which promoted nitric oxide turnover and preserved ERFVII protein stability. The activation of PGB1 was subsequently counteracted by increased BdERF961 accumulation through negative feedback regulation. Interestingly, we found that OsERF67, the orthologue of BdERF961 in rice, activated PHYTOGLOBIN (OsHB2) expression and formed distinct regulatory loops during submergence. Overall, the divergent regulatory mechanisms exhibited by orthologs collectively offer perspectives for the development of submergence-tolerant crops.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Endophyte mediated Populus trichocarpa water use efficiency is dependent on time of day and plant water status

Endophytes are potential partners for improving the resource use efficiency of bioenergy feedstock systems such as short rotation coppiced Populus. Endophytes isolated from members of the Salicaceae family have broad host compatibility and can improve water use efficiency (WUE) through decreases in stomatal conductance. However, the literature is inconsistent with regards to the environmental conditions and temporal patterns of these benefits. This study investigates how endophyte mediated changes in Populus trichocarpa (Torr. and Gray) ‘Nisqually-1’ stomatal conductance and WUE shift with time and scale in response to water-deficit stress. Leaf gas exchange and above-ground productivity were used to evaluate the carbon and water balances of glasshouse grown plants in response to endophyte inoculation and water-deficit. Differences in stomatal conductance between control and inoculated plants were more pronounced (39.7 % decrease, Welch’s two-sample t(14.34 dfadj) = -2.358, p-value = 0.033) under water-deficit conditions in the late morning during a period of higher light intensity. The decrease in stomatal conductance accompanied a substantial increase in intrinsic WUE (iWUE) for water-deficit inoculated plants. However, increases in iWUE did not result in improvements in aboveground productivity or shoot biomass WUE (WUEsb) for water-deficit inoculated plants. This decoupling between iWUE and aboveground productivity may be an indicator of assimilate allocation to microbial metabolism as an additional carbon sink or a shift in carbon allocation towards belowground biomass. Future work should take a whole-plant approach that accounts for diurnal patterns in incident irradiance to evaluate the impact of endophyte inoculation on host WUE and stress tolerance.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Mechanism of shape symmetry breaking in surfactant-mediated crystal growth

We present a dynamical model of crystal growth, in which it is possible to reliably achieve asymmetric products, beginning from symmetric initial conditions and growing within an isotropic environment. The asymmetric growth is the result of a positive feedback mechanism that amplifies the effect of thermal fluctuations in the coverage of surfactants on the growing crystalline facets. Within our simple model, we are able to understand the kinetic and thermodynamic factors involved in both the onset of symmetry breaking and the persistence of anisotropic growth. We demonstrate that the mechanism is general by studying models with increasing complexity. We argue that this mechanism of symmetry breaking underpins observations of colloidal, seed-mediated syntheses of single crystalline metal nanorods capped with strongly interacting surfactants. The parameters within our model are related to experimental observables such as the concentration, hydrophobicity, and binding strength of the surfactants, which suggests a potential route to optimize the yield of asymmetric products in colloidal nanoparticle syntheses.

Oaks-Leaf, Sam↗
DOE OSTI2026

Langevin and Fokker-Planck analyses for diffusion-mediated passing of circular and discorectangular species in two-dimensional channels

The propensity for pairs of diffusing species to pass each other within narrow channels or pores is of basic interest as a first-passage-type problem. It is also of relevance for solution-phase transport in nanoporous materials, and in particular for catalytic conversion reactions where high yield requires that product species can efficiently pass reactant species to exit the pores. Here, we analyze a two-dimensional model with nonoverlapping circular and discorectangular species confined to a rectangular channel, and where passing is mediated by Brownian dynamics in an implicit solvent. For narrower channels where passing is still possible, the discorectangle must align with the channel to pass the circular species. Behavior of the passing propensity, 𝑃, can be assessed by strongly damped Langevin simulations, or within an equivalent Fokker-Planck equation (FPE) formalism. The latter corresponds to a diffusion problem in a “higher-dimensional channel” with a constriction. We assess the variation of the passing propensity, 𝑃, for a broad range of channel width including its scaling just above the threshold where passing is sterically blocked. Analysis of 𝑃 versus the rotational diffusion coefficient 𝐷 𝑟 of the discorectangle reveals a significant decrease in 𝑃 for lower 𝐷 𝑟 for moderate channel width. This prompts a direct analysis of the regime where 𝐷 𝑟 → 0 , for which the FPE can be reduced to a three-dimensional diffusion problem, precise analysis of which is facilitated by adaptive-mesh finite element methods. The dependence of 𝑃 on the aspect ratio of the discorectangle is also assessed.

Rahman, Md Khaledur [Ames Laboratory (AMES), Ames,↗