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At least 1,207 records · Page 67
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Armillaria root rot fungi host single-stranded RNA viruses

Species of Armillaria are distributed globally and include some of the most important pathogens of forest and ornamental trees. Some of them form large long-living clones that are considered as one of the largest organisms on earth and are capable of long-range spore-mediated transfer as well as vegetative spread by drought-resistant hyphal cords called rhizomorphs. However, the virus community infecting these species has remained unknown. In this study we used dsRNA screening and high-throughput sequencing to search for possible virus infections in a collection of Armillaria isolates representing three different species: Armillaria mellea from South Africa, A. borealis from Finland and Russia (Siberia) and A. cepistipes from Finland. Our analysis revealed the presence of both negative-sense RNA viruses and positive-sense RNA viruses, while no dsRNA viruses were detected. The viruses included putative new members of virus families Mymonaviridae, Botourmiaviridae and Virgaviridae and members of a recently discovered virus group tentatively named “ambiviruses” with ambisense bicistronic genomic organization. We demonstrated that Armillaria isolates can be cured of viruses by thermal treatment, which enables the examination of virus effects on host growth and phenotype using isogenic virus-infected and virus-free strains.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Helium-electrospray improves sample delivery in X-ray single-particle imaging experiments

Abstract Imaging the structure and observing the dynamics of isolated proteins using single-particle X-ray diffractive imaging (SPI) is one of the potential applications of X-ray free-electron lasers (XFELs). Currently, SPI experiments on isolated proteins are limited by three factors: low signal strength, limited data and high background from gas scattering. The last two factors are largely due to the shortcomings of the aerosol sample delivery methods in use. Here we present our modified electrospray ionization (ESI) source, which we dubbed helium-ESI (He-ESI). With it, we increased particle delivery into the interaction region by a factor of 10, for 26 nm-sized biological particles, and decreased the gas load in the interaction chamber corresponding to an 80% reduction in gas scattering when compared to the original ESI. These improvements have the potential to significantly increase the quality and quantity of SPI diffraction patterns in future experiments using He-ESI, resulting in higher-resolution structures.

Science & Technology - Other Topics↗
DOE OSTI2025

Impact of gas background on XFEL single-particle imaging

Abstract Single-particle imaging (SPI) using X-ray free-electron Lasers (XFELs) offers the potential to determine protein structures at high spatial and temporal resolutions without the need for crystallization or vitrification. However, the technique faces challenges due to weak diffraction signals from single proteins and significant background scattering from gases used for sample delivery. A recent observation of a diffraction pattern from an isolated GroEL protein complex Ekeberg T et al. (Light Sci Appl 13:15, 2024.https://doi.org/10.1038/274s41377-023-01352-7) had similar numbers of signal and background photons. Ongoing efforts aim to reduce the background created by sample delivery, with one approach replacing most of the used gas with helium Yenupuri T et al. (Sci Rep 14:4401, 2024.https://doi.org/10.1038/s41598-024-54605-9). In this study, we investigate the effects of a reduced background on the resolution limits for SPI of isolated proteins under different experiment conditions. As a test case, we used GroEL, and we used experimentally derived parameters for our simulations. We observe that background significantly impacts the achievable resolution, particularly when the signal strength is comparable to the background. This is best exemplified at 6.0 keV, where a background reduction by a factor of 10 leads to a resolution improvement from 1.9 to 1.2 nm, for a dataset of$$10^4$$patterns.

Science & Technology - Other Topics↗
DOE OSTI2019

Insights into the κ/ι-carrageenan metabolism pathway of some marine Pseudoalteromonas species

Pseudoalteromonas is a globally distributed marine-associated genus that can be found in a broad range of aquatic environments, including in association with macroalgal surfaces where they may take advantage of these rich sources of polysaccharides. The metabolic systems that confer the ability to metabolize this abundant form of photosynthetically fixed carbon, however, are not yet fully understood. Through genomics, transcriptomics, microbiology, and specific structure-function studies of pathway components we address the capacity of newly isolated marine pseudoalteromonads to metabolize the red algal galactan carrageenan. The results reveal that the κ/ι-$\underline{car}$rageenan specific $\underline{p}$olysaccharide utilization $\underline{l}$ocus (CarPUL) enables isolates possessing this locus the ability to grow on this substrate. Biochemical and structural analysis of the enzymatic components of the CarPUL promoted the development of a detailed model of the κ/ι-carrageenan metabolic pathway deployed by pseudoalteromonads, thus furthering our understanding of how these microbes have adapted to a unique environmental niche.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Potentiating antibiotic efficacy via perturbation of non-essential gene expression

Proliferation of multidrug-resistant (MDR) bacteria poses a threat to human health, requiring new strategies. Here we propose using fitness neutral gene expression perturbations to potentiate antibiotics. We systematically explored 270 gene knockout-antibiotic combinations in Escherichia coli, identifying 90 synergistic interactions. Identified gene targets were subsequently tested for antibiotic synergy on the transcriptomic level via multiplexed CRISPR-dCas9 and showed successful sensitization of E. coli without a separate fitness cost. These fitness neutral gene perturbations worked as co-therapies in reducing a Salmonella enterica intracellular infection in HeLa. Finally, these results informed the design of four antisense peptide nucleic acid (PNA) co-therapies, csgD, fnr, recA and acrA, against four MDR, clinically isolated bacteria. PNA combined with sub-minimal inhibitory concentrations of trimethoprim against two isolates of Klebsiella pneumoniae and E. coli showed three cases of re-sensitization with minimal fitness impacts. Our results highlight a promising approach for extending the utility of current antibiotics.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Arctic sea-ice loss drives a strong regional atmospheric response over the North Pacific and North Atlantic on decadal scales

Previous studies have suggested that Arctic sea-ice loss can have a profound influence on atmospheric circulation far away from the Arctic. However, there is little scientific consensus on the features of these remote responses, with the opposite impacts reported. Here we present a multi-model analysis of the decadal climate response to Arctic sea-ice loss using state-of-the-art energy conserving methodologies to isolate the impacts of sea-ice decline. We observe weakening of the Aleutian Low and development of a geopotential ridge in the North Pacific, associated with drier winter conditions over the southwest United States. Over the Atlantic, a negative NAO-like response drives wetter winter conditions across the western Mediterranean. These decadal-scale impacts substantially differ from reported centennial-scale responses to Arctic sea-ice loss simulated using non-energy conserving methodologies. Factors such as the timescale of the response and methodologies used to isolate the impacts of disappearing sea-ice cover should be carefully considered when consolidating scientific understanding on the future impacts of changing Arctic.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Phenotypic plasticity of fungal traits in response to moisture and temperature

Phenotypic plasticity of traits is commonly measured in plants to improve understanding of organismal and ecosystem responses to climate change but is far less studied for microbes. Specifically, decomposer fungi are thought to display high levels of phenotypic plasticity and their functions have important implications for ecosystem dynamics. Assessing the phenotypic plasticity of fungal traits may therefore be important for predicting fungal community response to climate change. Here, we assess the phenotypic plasticity of 15 fungal isolates (12 species) from a Southern California grassland. Fungi were incubated on litter at five moisture levels (ranging from 4–50% water holding capacity) and at five temperatures (ranging from 4–36 °C). After incubation, fungal biomass and activities of four extracellular enzymes (cellobiohydrolase (CBH), β -glucosidase (BG), β -xylosidase (BX), and N-acetyl- β - D -glucosaminidase (NAG)) were measured. We used response surface methodology to determine how fungal phenotypic plasticity differs across the moisture-temperature gradient. We hypothesized that fungal biomass and extracellular enzyme activities would vary with moisture and temperature and that the shape of the response surface would vary between fungal isolates. We further hypothesized that more closely related fungi would show more similar response surfaces across the moisture-temperature gradient. In support of our hypotheses, we found that plasticity differed between fungi along the temperature gradient for fungal biomass and for all the extracellular enzyme activities. Plasticity also differed between fungi along the moisture gradient for BG activity. These differences appear to be caused by variation mainly at the moisture and temperature extremes. We also found that more closely related fungi had more similar extracellular enzymes activities at the highest temperature. Altogether, this evidence suggests that with global warming, fungal biodiversity may become increasingly important as functional traits tend to diverge along phylogenetic lines at higher temperatures.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Synthesis of core/shell nanocrystals with ordered intermetallic single-atom alloy layers for nitrate electroreduction to ammonia

Structurally ordered intermetallic nanocrystals (NCs) and single-atom catalysts (SACs) are two emerging catalytic motifs for sustainable chemical production and energy conversion. However, both have synthetic limitations which can lead to the aggregation of NCs or metal atoms. Single-atom alloys (SAAs), which contain isolated metal atoms in a host metal, can overcome the aggregation concern because of the thermodynamic stabilization of single atoms on host metal surfaces. We report a direct solution-phase synthesis of Cu/CuAu core/shell NCs with tunable SAA layers. This synthesis can be extended to other Cu/CuM (M = Pt, Pd) systems, in which M atoms are isolated in the copper host. Using this method, the density of SAAs on a copper surface can be controlled, resulting in both low and high densities of single atoms. Alloying gold into the copper matrix introduced ligand effects that optimized the chemisorption of *NO 3 and *N. As a result, the densely packed Cu/CuAu material demonstrated a high selectivity toward NH 3 from the electrocatalytic nitrate reduction reaction with an 85.5% Faradaic efficiency while maintaining a high yield rate of 8.47 mol h -1 g -1 . This work advances the design of atomically precise catalytic sites by creating core/shell NCs with SAA atomic layers, opening an avenue for broad catalytic applications.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Surface chemical trapping of optical cycling centers

Quantum information processors based on trapped atoms utilize laser-induced optical cycling transitions for state preparation and measurement. These transitions consist of an electronic excitation from the ground to an excited state and a decay back to the initial ground state, associated with a photon emission. While this technique has been used primarily with atoms, it has also recently been shown to work for some divalent metal hydroxides ( e.g. SrOH) and alkoxides ( e.g. SrOCH 3 ). Additionally, this extension to molecules is possible because these molecules feature nearly isolated, atomic-like ground and first-excited electronic states centered on the radical metal atom. We theoretically investigate the extension of this idea to a larger scale by growing the alkyl group, R, beyond the initial methyl group, CH 3 , while preserving the isolated and highly vertical character of the electronic excitation on the radical metal atom, M. Theory suggests that in the limit as the size of the ligand carbon chain increases, it can be considered a functionalized diamond (or cubic boron nitride) surface. Several requirements must be observed for the cycling centers to function when bound to the surface. First, the surface must have a significant band gap that fully encapsulates both the ground and excited states of the cycling center. Second, while the surface lattice imposes strict limits on the achievable spacing between the SrO– groups, at high coverage, SrO– centers can interact, and show geometric changes and/or electronic state mixing. We show that the coverage of the diamond surface with SrO– cycling centers needs to be significantly sub-monolayer for the functionality of the cycling center to be preserved. Having the lattice-imposed spatial control of SrO– placements will allow nanometer-scale proximity between qubits and will eliminate the need for atom traps for localized cycling emitters. Our results also imply that a functionalization could be done on a scanning microscope tip for local quantum sensing or on photonic structures for optically-mediated quantum information processing.

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

Isocyanide adducts of tri- and tetravalent uranium metallocenes supported by tetra(isopropyl)cyclopentadienyl ligands

In this work, reaction of the uranium( III ) metallocenium salt [(Cp iPr4 ) 2 U][B(C 6 F 5 ) 4 ] with tert-butyl isocyanide ( t BuNC) yielded the dicationic uranium( IV ) complex [(Cp iPr4 ) 2 U(CN t Bu) 4 ][B(C 6 F 5 ) 4 ] 2 (1), which displays a linear metallocene geometry. Use of crude mixtures of [(Cp iPr4 ) 2 U][B(C 6 F 5 ) 4 ], which contain a soluble source of iodide, led instead to isolation of the monocationic uranium( IV ) iodide complex [(Cp iPr4 ) 2 U(I)(CN t Bu) 2 ][B(C 6 F 5 ) 4 ] (2). Adduct formation with no change in oxidation state was observed upon addition of t BuNC to the neutral uranium( III ) species (Cp iPr4 ) 2 UI, resulting in isolation of (Cp iPr4 ) 2 U(I)(CN t Bu) (3). X-ray crystallographic and IR spectroscopic studies both showed effects ascribed to the presence of multiple strongly donating isocyanide ligands in 1.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
DOE OSTI2020

Correlations of the physicochemical properties of organosolv lignins from Broussonetia papyrifera with their antioxidant activities

To understand the influence of lignin characteristics on their antioxidant activities, lignins were isolated from Broussonetia papyrifera by organosolv pretreatment at different temperatures. The physicochemical features of the lignins were investigated by GPC, 31 P NMR and 2D HSQC NMR analyses. An increase of organosolv pretreatment temperature resulted in a decrease of M w and an increase of the phenolic hydroxyl group content in the isolated lignin. The lignins extracted at higher organosolv pretreatment temperature showed higher antioxidant activity according to the IC 50 determined using DPPH and ABTS. The correlations between the physicochemical properties of organosolv lignins and their antioxidant activities were studied. The contents of phenolic hydroxyl groups, especially syringyl and guaiacyl, and double bonds in the C α position had positive effects on the antioxidant activity of the lignins. Finally, on the other hand, M w and aliphatic hydroxyl groups of the lignins exhibited negative correlations with the antioxidant activity.

09 BIOMASS FUELS↗
DOE OSTI2020

Computational modeling predicts the stability of both Pd + and Pd2 + ion-exchanged into H-CHA

Passive NO x adsorbers (PNA) using Pd/zeolites have emerged as a promising solution for the reduction of cold-start emissions from vehicle exhaust. However, the nature of the active sites and the mechanisms underlying NO x adsorption in Pd/zeolites remain a subject of ongoing investigation. In this study, we employ quantum chemical simulations to investigate the structure of Pd species in cation-exchange sites at isolated Al and Al pairs in the 6-ring and 8-ring of the CHA framework before the introduction of NO x . Our calculations show that the speciation of Pd in these exchange sites strongly depends on the precise Al arrangement within the framework, as well as the operating conditions. Ionically dispersed Pd is found to be the most favorable species over a wide range of oxidizing and reducing conditions. Small oligomers of PdO and metallic Pd do not appear to be competitive at either isolated Al or Al pairs. Notably, our calculations show that ion exchange sites other than next–next–nearest neighbor Al pairs in the 6-ring will be preferentially occupied by Pd + instead of Pd 2+ . The stability of Pd + in the zeolite environment is an interesting contrast with its rareness in molecular Pd compounds. Nonetheless, a detailed analysis of the electronic structure shows that predicted Pd oxidation states are consistent with chemical intuition for all complexes investigated in this study. We also discuss the potential ambiguity in Pd characterization provided by typical experimental techniques such as XANES, EXAFS and UV-Vis, and highlight the need for additional EPR spectroscopy studies to further elucidate the initial Pd speciation in zeolites for PNA applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Gaseous cyclodextrin- closo -dodecaborate complexes χCD·B 12 X 12 2– (χ = α, β, and γ; X = F, Cl, Br, and I): electronic structures and intramolecular interactions

A fundamental understanding of cyclodextrin- closo -dodecaborate inclusion complexes is of great interest in supramolecular chemistry. Herein, we report a systematic investigation on the electronic structures and intramolecular interactions of perhalogenated closo -dodecaborate dianions B 12 X 12 2– (X = F, Cl, Br and I) binding to α-, β-, and γ-cyclodextrins (CDs) in the gas phase using combined negative ion photoelectron spectroscopy (NIPES) and density functional theory (DFT) calculations. The vertical detachment energy (VDE) of each complex and electronic stabilization of each dianion due to the CD binding (ΔVDE, relative to the corresponding isolated B 12 X 12 2– ) are determined from the experiments along α-, β- and γ-CD in the form of VDE (ΔVDE): 4.00 (2.10), 4.33 (2.43), and 4.30 (2.40) eV in X = F; 4.09 (1.14), 4.64 (1.69), and 4.69 (1.74) eV in X = Cl; 4.11 (0.91), 4.58 (1.38), and 4.70 (1.50) eV in X = Br; and 3.54 (0.74), 3.88 (1.08), and 4.05 (1.25) eV in X = I, respectively. All complexes have significantly higher VDEs than the corresponding isolated dodecaborate dianions with ΔVDE spanning from 0.74 eV at (α, I) to 2.43 eV at (β, F), sensitive to both host CD size and guest substituent X. DFT-optimized complex structures indicate that all B 12 X 12 2– prefer binding to the wide openings of CDs with the insertion depth and binding motif strongly dependent on the CD size and halogen X. Dodecaborate anions with heavy halogens, i.e. , X = Cl, Br, and I, are found outside of α-CD, while B 12 F 12 2– is completely wrapped by γ-CD. Partial embedment of B 12 X 12 2– into CDs is observed for the other complexes via multipronged B–X … H–O/C interlocking patterns. The simulated spectra based on the density of states agree well with those of the experiments and the calculated VDEs well reproduce the experimental trends. Molecular orbital analyses suggest that the spectral features at low binding energies originated from electrons detached from the dodecaborate dianion, while those at higher binding energies are derived from electron detachment from CDs. Energy decomposition analyses reveal that the electrostatic interaction plays a dominating role in contributing to the host–guest interactions for the X = F series partially due to the formation of a O/C–H … X–B hydrogen bonding network, and the dispersion forces gradually become important with the increase of halogen size.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Lithium calix[4]arenes: structural studies and use in the ring opening polymerization of cyclic esters

We have structurally characterized a number of lithiated calix[4]arenes, where the bridge in the calix[4]arene is thia (–S–, L S H 4 ), sulfinyl (–SO–, L SO H 4 ), sulfonyl (–SO 2 –, L SO2 H 4 ), dimethyleneoxa (–CH 2 OCH 2 –, L COC H 4 ) or methylene (–CH 2 –, LH 4 ). In the case of L 4S H 4 , interaction with LiO t Bu led to the isolation of the complex [Li 8 (L 4S ) 2 (THF) 4 ]·5THF ( 1 ·5THF), whilst similar interaction of L 4SO H 4 led to the isolation of [Li 6 (L 4SO H) 2 (THF) 2 ]·5(THF) ( 2 ·5THF). Interestingly, the mixed sulfinyl/sulfonyl complexes [Li 8 (calix[4]arene(SO)(SO 2 )(SO 1.68 ) 2 ) 2 (THF) 6 ]·8(THF) ( 3 ·8THF) and [Li 5 Na(L SO/3SO2 H) 2 (THF) 5 ]·7.5(THF) ( 4 ·7.5(THF) have also been characterized. Interaction of LiO t Bu with L SO2 H 4 and L COC H 4 afforded [Li 5 L 4SO2 (OH)(THF) 4 ]·2THF ( 5 ·2THF) and [Li 6 (L COC ) 2 (HO t Bu) 2 ]·0.78THF·1.22hexane ( 6 ·0.78THF·1.22hexane), respectively. In the case of LH 4 , reaction with LiO t Bu in THF afforded a monoclinic polymorph [LH 2 Li 2 (thf)(OH 2 ) 2 ]·3THF ( 7 ·3THF) of a known triclinic form of the complex, whilst reaction of the de-butylated analogue of LH 4 , namely de-BuLH 4 , afforded a polymeric chain structure {[Li 5 (de-BuL)(OH)(NCMe) 3 ]·2MeCN} n ( 8 ·2MeCN). For comparative catalytic studies, the complex [Li 6 (L Pr ) 2 (H 2 O) 2 ]·hexane ( 9 hexane), where L Pr2 H 2 = 1,3-di- n -propyloxycalix[4]areneH 2 , was also prepared. The molecular crystal structures of 1–9 are reported, and their ability to act as catalysts for the ring opening (co-)/polymerization (ROP) of the cyclic esters ε-caprolactone, δ-valerolactone, and rac -lactide has been investigated. In most of the cases, complex 6 outperformed the other systems, allowing for higher conversions and/or greated polymer M n .

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

The role of complementary shape in protein dimerization

Shape guides colloidal nanoparticles to form complex assemblies, but its role in defining interfaces in biomolecular complexes is less clear. In this work, we isolate the role of shape in protein complexes by studying the reversible binding processes of 46 protein dimer pairs, and investigate when entropic effects from shape complementarity alone are sufficient to predict the native protein binding interface. We employ depletants using a generic, implicit depletion model to amplify the magnitude of the entropic forces arising from lock-and-key binding and isolate the effect of shape complementarity in protein dimerization. For 13% of the complexes studied here, protein shape is sufficient to predict native complexes as equilibrium assemblies. We elucidate the results by analyzing the importance of competing binding configurations and how it affects the assembly. Furthermore, a machine learning classifier, with a precision of 89.14% and a recall of 77.11%, is able to identify the cases where shape alone predicts the native protein interface.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Multivariate zeolitic imidazolate frameworks with an inverting trend in flexibility

Here, through systematic linker substitution in a flexible zeolitic imidazolate framework (ZIF) with step-shaped adsorption–desorption, structural intermediates between the known open and closed phases were isolated. Reflecting this, modulative sorption behaviour with an inverting adsorption pressure trend—in which the step pressure decreases and then increases again with increasing mixed linker concentration—is observed, highlighting how linker substitution modifies the energetic landscape of framework flexibility

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗