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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 775 records · Page 43
All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

Acetylation of lysine residues in the recombinant nucleoprotein and VP40 matrix protein of Zaire Ebolavirus by eukaryotic histone acetyltransferases

Acetylation of histones and other proteins plays crucial roles in transcriptional regulation, chromatin organization, and other biological processes. It has been recently reported that the nucleoprotein (NP) of influenza virus is acetylated in infected cells, and this modification contributes to the RNA polymerization activity of the virus. As the influenza virus, the Ebolavirus contains single-stranded negative-sense RNA as its viral genome, which interacts with NP and other viral proteins. In this study, we performed a series of biochemical experiments and revealed that the recombinant Ebolavirus NP and the viral matrix protein VP40, which binds with NP, were acetylated by eukaryotic histone acetyltransferases, such as P300/CREB-binding protein (P300/CBP) and P300/CBP-associated factor (PCAF), in vitro. Mass spectrometry was used to identify the lysine residues that were potential acetylation targets in NP and VP40. The identified lysine residues in NP were located in the RNA-binding cleft and the VP35-binding domain. Potentially acetylated lysine targets in VP40 were identified in the basic patch, which is necessary for constructing oligomers. These results suggest that the acetylation of these lysine residues is involved in the interactions between viral proteins.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Cooperative and bifunctional Ga-Ca-Cr 2 O 3 @CaO structured monoliths as versatile platform for reactive capture of CO 2 and its subsequent conversion to ethylene

Cooperative and bifunctional materials (BFMs) that integrate adsorbents and catalysts offer a promising strategy for the reactive capture of CO 2 to produce valuable fuels and chemicals. In this study, we developed structured BFMs via 3D printing that combine CaO as an adsorbent with Ga–Ca–Cr 2 O 3 metal oxides as the catalyst for the reactive capture of CO 2 and its subsequent conversion to C 2 H 4 via the oxidative dehydrogenation of C 2 H 6 (CO 2 -ODHE). Three different Ga–Ca compositions were used to modify the catalyst surface characteristics and enhance C 2 H 4 selectivity. In these formulations, Ga ions stabilize the oxygen lattice of the BFM, while Ca ions interact strongly with Cr to form CaCrO 4 , thereby altering the oxygen species and enhancing the material’s basic properties. Under adsorption–reaction conditions at 600–650 °C, the optimal BFM achieved an excellent C 2 H 4 selectivity of 96.4 %, attributed to a balanced redox process and improved basicity that facilitate efficient C 2 H 6 conversion and rapid desorption of C 2 H 4 without excessive oxidation. Overall, this work provides new insights into the formulation of BFMs monoliths and highlights the critical role of catalytic surface modification in enhancing C 2 H 4 selectivity in the CO 2 -ODHE reactive capture process.

C2H4 production↗
DOE OSTI2021

Data on erosion and hydrogen fuel retention in Beryllium plasma-facing materials

ITER will use beryllium as a plasma-facing material in the main chamber, covering a total surface area of about 620 m 2 . Given the importance of beryllium erosion and co-deposition for tritium retention in ITER, significant efforts have been made to understand the behaviour of beryllium under fusion-relevant conditions with high particle and heat loads. This paper provides a comprehensive report on the state of knowledge of beryllium behaviour under fusion-relevant conditions: the erosion mechanisms and their consequences, beryllium migration in JET, fuel retention and dust generation. The paper reviews basic laboratory studies, advanced computer simulations and experience from laboratory plasma experiments in linear simulators of plasma–wall interactions and in controlled fusion devices using beryllium plasma-facing components. A critical assessment of analytical methods and simulation codes used in beryllium studies is given. The overall objective is to review the existing set of data with a broad literature survey and to identify gaps and research needs to broaden the database for ITER.

Erosion–deposition↗
DOE OSTI2015

Switchgrass rhizospheres stimulate microbial biomass but deplete microbial necromass in agricultural soils of the upper Midwest, USA

Rhizosphere microbial communities play an essential role in determining plant productivity, particularly in agriculturally marginal environments. Perennial plants like switchgrass (Panicum virgatum) are thought to particularly influence microbial community composition and function within their rhizosphere. We compared microbial communities in switchgrass rhizospheres and their associated bulk soils in two regions of the U.S. upper Midwest (Michigan and Wisconsin) with contrasting soil types, and at two site types with differing switchgrass establishment ages and management intensities. We characterized microbial communities with a range of culture-independent methods, including amplicon sequencing of 16S/18S rRNA and nifH genes, and membrane lipid profiling. In addition, we quantified abundances of soil amino sugars, a time-integrative indicator of microbial necromass. We found that amino sugar contents and microbial lipid profiles differed between rhizosphere and bulk soils, while DNA-based assays did not provide this discriminatory power. Differences between rhizosphere and bulk soils were not significantly affected by region or site type. Rhizosphere soils had higher microbial lipid abundances, particularly those associated with arbuscular mycorrhizal fungi and Gram-negative bacteria, while amino sugar abundances decreased in the rhizosphere. In conclusion, our findings suggest switchgrass rhizospheres systematically stimulate microbial growth and microbial residue turnover.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

A Structural, Functional, and Computational Analysis of BshA, the First Enzyme in the Bacillithiol Biosynthesis Pathway

Bacillithiol is a compound produced by several Gram-positive bacterial species, including the human pathogens Staphylococcus aureus and Bacillus anthracis. It is involved in maintaining cellular redox balance as well as the destruction of reactive oxygen species and harmful xenobiotic agents, including the antibiotic fosfomycin. BshA, BshB, and BshC are the enzymes involved in bacillithiol biosynthesis. BshA is a retaining glycosyltransferase responsible for the first committed step in bacillithiol production, namely the addition of N-acetylglucosamine to l-malate. Retaining glycosyltransferases like BshA are proposed to utilize an S N i-like reaction mechanism in which leaving group departure and nucleophilic attack occur on the same face of the hexose. However, significant questions regarding the details of how BshA and similar enzymes accommodate their substrates and facilitate catalysis persist. Here we report X-ray crystallographic structures of BshA from Bacillus subtilis 168 bound with UMP and/or GlcNAc-mal at resolutions of 2.15 and 2.02 Å, respectively. These ligand-bound structures, along with our functional and computational studies, provide clearer insight into how BshA and other retaining GT-B glycosyltransferases operate, corroborating the substrate-assisted, S N i-like reaction mechanism. In conclusion, the analyses presented herein can serve as the basis for the design of inhibitors capable of preventing bacillithiol production and, subsequently, help combat resistance to fosfomycin in various pathogenic Gram-positive microorganisms.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Crystal Structures of Wild-Type and F448A Mutant Citrobacter freundii Tyrosine Phenol-Lyase Complexed with a Substrate and Inhibitors: Implications for the Reaction Mechanism

Tyrosine phenol-lyase (TPL; EC 4.1.99.2) is a pyridoxal 5'-phosphate-dependent enzyme that catalyzes the reversible hydrolytic cleavage of l-tyrosine to phenol and ammonium pyruvate. We have shown previously that F448A TPL has k cat and k cat /K m values for l-tyrosine reduced by ~10 4 -fold. We have now obtained crystal structures of F448A TPL and complexes with l-alanine, l-methionine, l-phenylalanine, and 3-F-l-tyrosine at 2.05–2.27 Å and the complex of wild-type TPL with l-phenylalanine at 1.8 Å. The small domain of F448A TPL, where Phe-448 is located, is more disordered in chain A than in wild-type TPL. The complexes of F448A TPL with l-alanine and l-phenylalanine are in an open conformation in both chains, while the complex with l-methionine is a 52:48 open:closed equilibrium mixture in chain A. Wild-type TPL with l-alanine is closed in chain A and open in chain B, and the complex with l-phenylalanine is a 56:44 open:closed mixture in chain A. Thus, the Phe-448 to alanine mutation affects the conformational equilibrium of open and closed active sites. The structure of the 3-F-l-tyrosine quinonoid complex of F448A TPL is unstrained and in an open conformation, with a hydrogen bond from the phenolic OH to Thr-124. Furthermore, these results support our previous conclusion that ground-state strain plays a critical role in the mechanism of TPL.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Sub-picomolar Inhibition of HIV-1 Protease with a Boronic Acid

Boronic acids have been typecast as moieties for covalent complexation and are employed only rarely as agents for non-covalent recognition. By exploiting the profuse ability of a boronic acid group to form hydrogen bonds, we have developed an inhibitor of HIV-1 protease with extraordinary affinity. Specifically, we find that replacing an aniline moiety in darunavir with a phenylboronic acid leads to 20-fold greater affinity for the protease. X-ray crystallography demonstrates that the boronic acid group participates in three hydrogen bonds, more than the amino group of darunavir or any other analog. Importantly, the boronic acid maintains its hydrogen bonds and its affinity for the drug-resistant D30N variant of HIV-1 protease. The BOH···OC hydrogen bonds between the boronic acid hydroxy group and Asp30 (or Asn30) of the protease are short (r O···O = 2.2 Å), and density functional theory analysis reveals a high degree of covalency. Furthermore, these data highlight the utility of boronic acids as versatile functional groups in the design of small-molecule ligands.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2012

Single Molecule Kinetics of ENTH Binding to Lipid Membranes

Transient recruitment of proteins to membranes is a fundamental mechanism by which the cell exerts spatial and temporal control over proteins’ localization and interactions. Thus, the specificity and the kinetics of peripheral proteins’ membrane residence are an attribute of their function. In this article, we describe the membrane interactions of the interfacial epsin N-terminal homology (ENTH) domain with its target lipid phosphatidylinositol (4,5)-bisphosphate (PtdIns(4,5)P 2 ). The direct visualization and quantification of interactions of single ENTH molecules with supported lipid bilayers is achieved using total internal reflection fluorescence microscopy (TIRFM) with a time resolution of 13 ms. This enables the recording of the kinetic behavior of ENTH interacting with membranes with physiologically relevant concentrations of PtdIns(4,5)P 2 despite the low effective binding affinity. Subsequent single fluorophore tracking permits us to build up distributions of residence times and to measure ENTH dissociation rates as a function of membrane composition. In addition, due to the high time resolution, we are able to resolve details of the motion of ENTH associated with a simple, homogeneous membrane. In this case ENTH’s diffusive transport appears to be the result of at least three different diffusion processes.

membrane-protein interactions↗
DOE OSTI2023

Structural interplay of anesthetics and paralytics on muscle nicotinic receptors

General anesthetics and neuromuscular blockers are used together during surgery to stabilize patients in an unconscious state. Anesthetics act mainly by potentiating inhibitory ion channels and inhibiting excitatory ion channels, with the net effect of dampening nervous system excitability. Neuromuscular blockers act by antagonizing nicotinic acetylcholine receptors at the motor endplate; these excitatory ligand-gated ion channels are also inhibited by general anesthetics. The mechanisms by which anesthetics and neuromuscular blockers inhibit nicotinic receptors are poorly understood but underlie safe and effective surgeries. Here we took a direct structural approach to define how a commonly used anesthetic and two neuromuscular blockers act on a muscle-type nicotinic receptor. We discover that the intravenous anesthetic etomidate binds at an intrasubunit site in the transmembrane domain and stabilizes a non-conducting, desensitized-like state of the channel. The depolarizing neuromuscular blocker succinylcholine also stabilizes a desensitized channel but does so through binding to the classical neurotransmitter site. Rocuronium binds in this same neurotransmitter site but locks the receptor in a resting, non-conducting state. Together, this study reveals a structural mechanism for how general anesthetics work on excitatory nicotinic receptors and further rationalizes clinical observations in how general anesthetics and neuromuscular blockers interact.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Conservation and divergence of C-terminal domain structure in the retinoblastoma protein family

The retinoblastoma protein (Rb) and the homologous pocket proteins p107 and p130 negatively regulate cell proliferation by binding and inhibiting members of the E2F transcription factor family. Here, the structural features that distinguish Rb from other pocket proteins have been unclear but are critical for understanding their functional diversity and determining why Rb has unique tumor suppressor activities. We describe here important differences in how the Rb and p107 C-terminal domains (CTDs) associate with the coiled-coil and marked-box domains (CMs) of E2Fs. We find that although CTD–CM binding is conserved across protein families, Rb and p107 CTDs show clear preferences for different E2Fs. A crystal structure of the p107 CTD bound to E2F5 and its dimer partner DP1 reveals the molecular basis for pocket protein–E2F binding specificity and how cyclin-dependent kinases differentially regulate pocket proteins through CTD phosphorylation. Our structural and biochemical data together with phylogenetic analyses of Rb and E2F proteins support the conclusion that Rb evolved specific structural motifs that confer its unique capacity to bind with high affinity those E2Fs that are the most potent activators of the cell cycle.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Analysis of Σ* via isospin selective reaction 𝐾 𝐿 ⁢𝑝 →𝜋 + ⁢Σ 0

The isospin-selective reaction 𝐾 𝐿 ⁢𝑝 →𝜋 + ⁢Σ 0 provides a clean probe for investigating 𝐼 =1 Σ* resonances. In this work, we perform an analysis of this reaction using an effective Lagrangian approach for the first time, incorporating the well-established Σ⁡(1189)⁢1/2 + , Σ⁡(1385)⁢3/2 + , Σ⁡(1670)⁢3/2 − , and Σ⁡(1775)⁢5/2 − states, while also exploring contributions from other unestablished states. By fitting the available differential cross-section and recoil polarization data, adhering to partial-wave phase conventions same as the Particle Data Group, we find that besides the established resonances, contributions from Σ⁡(1660)⁢1/2 + , Σ⁡(1580)⁢3/2 − , and a Σ*⁢(1/2 − ) improve the description. Notably, a Σ*⁢(1/2 − ) resonance with mass around 1.54 GeV, consistent with Σ⁡(1620)⁢1/2 − , is found to be essential for describing the data in this channel, a stronger indication than found in previous analyses focusing on 𝜋⁢Λ final states. While providing complementary support for Σ⁡(1660)⁢1/2 + and Σ⁡(1580)⁢3/2 − , our results highlight the importance of the Σ⁡(1620)⁢1/2 − region in 𝐾 𝐿 ⁢𝑝 →𝜋 + ⁢Σ 0 . Future high-precision measurements are needed to solidify these findings and further constrain the Σ* spectrum.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2015

Plant compartment and biogeography affect microbiome composition in cultivated and native Agave species

Desert plants are hypothesized to survive the environmental stress inherent to these regions in part thanks to symbioses with microorganisms, and yet these microbial species, the communities they form, and the forces that influence them are poorly understood. Here we report the first comprehensive investigation of the microbial communities associated with species of Agave, which are native to semiarid and arid regions of Central and North America and are emerging as biofuel feedstocks. We examined prokaryotic and fungal communities in the rhizosphere, phyllosphere, leaf and root endosphere, as well as proximal and distal soil samples from cultivated and native agaves, through Illumina amplicon sequencing. Phylogenetic profiling revealed that the composition of prokaryotic communities was primarily determined by the plant compartment, whereas the composition of fungal communities was mainly influenced by the biogeography of the host species. Cultivated A. tequilana exhibited lower levels of prokaryotic diversity compared with native agaves, although no differences in microbial diversity were found in the endosphere. Agaves shared core prokaryotic and fungal taxa known to promote plant growth and confer tolerance to abiotic stress, which suggests common principles underpinning Agave-microbe interactions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Brachypodium Phenylalanine Ammonia Lyase (PAL) Promotes Antiviral Defenses against Panicum mosaic virus and Its Satellites

Brachypodium distachyon has recently emerged as a premier model plant for monocot biology, akin to Arabidopsis thaliana. We previously reported genome-wide transcriptomic and alternative splicing changes occurring in Brachypodium during compatible infections with Panicum mosaic virus (PMV) and its satellite virus (SPMV). Here, we dissected the role of Brachypodium phenylalanine ammonia lyase 1 (PAL1), a key enzyme for phenylpropanoid and salicylic acid (SA) biosynthesis and the induction of plant defenses. Targeted metabolomics profiling of PMV-infected and PMV- plus SPMV-infected (PMV/SPMV) Brachypodium plants revealed enhanced levels of multiple defense-related hormones and metabolites such as cinnamic acid, SA, and fatty acids and lignin precursors during disease progression. The virus-induced accumulation of SA and lignin was significantly suppressed upon knockdown of B. distachyon PAL1 (BdPAL1) using RNA interference (RNAi). The compromised SA accumulation in PMV/SPMV-infected BdPAL1 RNAi plants correlated with weaker induction of multiple SA-related defense gene markers (pathogenesis related 1 [PR-1], PR-3, PR-5, and WRKY75) and enhanced susceptibility to PMV/SPMV compared to that of wild-type (WT) plants. Furthermore, exogenous application of SA alleviated the PMV/SPMV necrotic disease phenotypes and delayed plant death caused by single and mixed infections. Together, our results support an antiviral role for BdPAL1 during compatible host-virus interaction, perhaps as a last resort attempt to rescue the infected plant.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Integrating Viral Metagenomics into an Ecological Framework

Viral metagenomics has expanded our knowledge of the ecology of uncultured viruses, within both environmental (e.g., terrestrial and aquatic) and host-associated (e.g., plants and animals, including humans) contexts. Here, we emphasize the implementation of an ecological framework in viral metagenomic studies to address questions in virology rarely considered ecological, which can change our perception of viruses and how they interact with their surroundings. Additionally, an ecological framework explicitly considers diverse variants of viruses in populations that make up communities of interacting viruses, with ecosystem-level effects. It provides a structure for the study of the diversity, distributions, dynamics, and interactions of viruses with one another, hosts, and the ecosystem, including interactions with abiotic factors. An ecological framework in viral metagenomics stands poised to broadly expand our knowledge in basic and applied virology. We highlight specific fundamental research needs to capitalize on its potential and advance the field.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Metagenomic insights into the taxonomy, function, and dysbiosis of prokaryotic communities in octocorals

Background. In octocorals (Cnidaria Octocorallia), the functional relationship between host health and its symbiotic consortium has yet to be determined. Here, we employed comparative metagenomics to uncover the distinct functional and phylogenetic features of the microbiomes of healthy Eunicella gazella, Eunicella verrucosa, and Leptogorgia sarmentosa tissues, in contrast with the microbiomes found in seawater and sediments. We further explored how the octocoral microbiome shifts to a pathobiome state in E. gazella. Results. Multivariate analyses based on 16S rRNA genes, Clusters of Orthologous Groups of proteins (COGs), Protein families (Pfams), and secondary metabolite-biosynthetic gene clusters annotated from 20 Illumina-sequenced metagenomes each revealed separate clustering of the prokaryotic communities of healthy tissue samples of the three octocoral species from those of necrotic E. gazella tissue and surrounding environments. While the healthy octocoral microbiome was distinguished by so-far uncultivated Endozoicomonadaceae, Oceanospirillales, and Alteromonadales phylotypes in all host species, a pronounced increase of Flavobacteriaceae and Alphaproteobacteria, originating from seawater, was observed in necrotic E. gazella tissue. Increased abundances of eukaryotic-like proteins, exonucleases, restriction endonucleases, CRISPR/Cas proteins, and genes encoding for heat-shock proteins, inorganic ion transport, and iron storage distinguished the prokaryotic communities of healthy octocoral tissue regardless of the host species. An increase of arginase and nitric oxide reductase genes, observed in necrotic E. gazella tissues, suggests the existence of a mechanism for suppression of nitrite oxide production by which octocoral pathogens may overcome the host’s immune system. Conclusions. This is the first study to employ primer-less, shotgun metagenome sequencing to unveil the taxonomic, functional, and secondary metabolism features of prokaryotic communities in octocorals. Our analyses reveal that the octocoral microbiome is distinct from those of the environmental surroundings, is host genus (but not species) specific, and undergoes large, complex structural changes in the transition to the dysbiotic state. Host-symbiont recognition, abiotic-stress response, micronutrient acquisition, and an antiviral defense arsenal comprising multiple restriction endonucleases, CRISPR/Cas systems, and phage lysogenization regulators are signatures of prokaryotic communities in octocorals. We argue that these features collectively contribute to the stabilization of symbiosis in the octocoral holobiont and constitute beneficial traits that can guide future studies on coral reef conservation and microbiome therapy.

59 BASIC BIOLOGICAL SCIENCES↗