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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 1,027 records · Page 57
All sourcesNASA NTRSDOE OSTI
DOE OSTI2014

Molecular insights into RNA and DNA helicase evolution from the determinants of specificity for a DEAD-box RNA helicase

How different helicase families with a conserved catalytic ‘helicase core’ evolved to function on varied RNA and DNA substrates by diverse mechanisms remains unclear. In this study, we used Mss116, a yeast DEAD-box protein that utilizes ATP to locally unwind dsRNA, to investigate helicase specificity and mechanism. Our results define the molecular basis for the substrate specificity of a DEAD-box protein. Additionally, they show that Mss116 has ambiguous substrate-binding properties and interacts with all four NTPs and both RNA and DNA. The efficiency of unwinding correlates with the stability of the ‘closed-state’ helicase core, a complex with nucleotide and nucleic acid that forms as duplexes are unwound. Crystal structures reveal that core stability is modulated by family-specific interactions that favor certain substrates. This suggests how present-day helicases diversified from an ancestral core with broad specificity by retaining core closure as a common catalytic mechanism while optimizing substrate-binding interactions for different cellular functions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2011

Structural Insights into Ligand Recognition by a Sensing Domain of the Cooperative Glycine Riboswitch

Glycine riboswitches regulate gene expression by feedback modulation in response to cooperative binding to glycine. Here, we report on crystal structures of the second glycine-sensing domain from the Vibrio cholerae riboswitch in the ligand-bound and unbound states. This domain adopts a three-helical fold that centers on a three-way junction and accommodates glycine within a bulge-containing binding pocket above the junction. Glycine recognition is facilitated by a pair of bound Mg{sup 2+} cations and governed by specific interactions and shape complementarity with the pocket. A conserved adenine extrudes from the binding pocket and intercalates into the junction implying that glycine binding in the context of the complete riboswitch could impact on gene expression by stabilizing the riboswitch junction and regulatory P1 helix. Analysis of riboswitch interactions in the crystal and footprinting experiments indicates that adjacent glycine-sensing modules of the riboswitch could form specific interdomain interactions, thereby potentially contributing to the cooperative response.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2011

In vitro and in vivo Analysis of the Binding of the C Terminus of the HDL Receptor Scavenger Receptor Class B type I (SR-BI) to the PDZ1 Domain of its Cytoplasmic Adaptor Protein PDZK1

The PDZ1 domain of the four PDZ domain-containing protein PDZK1 has been reported to bind the C terminus of the HDL receptor scavenger receptor class B, type I (SR-BI), and to control hepatic SR-BI expression and function. We generated wild-type (WT) and mutant murine PDZ1 domains, the mutants bearing single amino acid substitutions in their carboxylate binding loop (Lys(14)-Xaa(4)-Asn(19)-Tyr-Gly-Phe-Phe-Leu(24)), and measured their binding affinity for a 7-residue peptide corresponding to the C terminus of SR-BI ((503)VLQEAKL(509)). The Y20A and G21Y substitutions abrogated all binding activity. Surprisingly, binding affinities (K(d)) of the K14A and F22A mutants were 3.2 and 4.0 ?M, respectively, similar to 2.6 ?M measured for the WT PDZ1. To understand these findings, we determined the high resolution structure of WT PDZ1 bound to a 5-residue sequence from the C-terminal SR-BI ((505)QEAKL(509)) using x-ray crystallography. In addition, we incorporated the K14A and Y20A substitutions into full-length PDZK1 liver-specific transgenes and expressed them in WT and PDZK1 knock-out mice. In WT mice, the transgenes did not alter endogenous hepatic SR-BI protein expression (intracellular distribution or amount) or lipoprotein metabolism (total plasma cholesterol, lipoprotein size distribution). In PDZK1 knock-out mice, as expected, the K14A mutant behaved like wild-type PDZK1 and completely corrected their hepatic SR-BI and plasma lipoprotein abnormalities. Unexpectedly, the 10-20-fold overexpressed Y20A mutant also substantially, but not completely, corrected these abnormalities. The results suggest that there may be an additional site(s) within PDZK1 that bind(s) SR-BI and mediate(s) productive SR-BI-PDZK1 interaction previously attributed exclusively to the canonical binding of the C-terminal SR-BI to PDZ1.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2011

Binding of [alpha, alpha]-Disubstituted Amino Acids to Arginase Suggests New Avenues for Inhibitor Design

Arginase is a binuclear manganese metalloenzyme that hydrolyzes L-arginine to form L-ornithine and urea, and aberrant arginase activity is implicated in various diseases such as erectile dysfunction, asthma, atherosclerosis, and cerebral malaria. Accordingly, arginase inhibitors may be therapeutically useful. Continuing our efforts to expand the chemical space of arginase inhibitor design and inspired by the binding of 2-(difluoromethyl)-L-ornithine to human arginase I, we now report the first study of the binding of {alpha},{alpha}-disubstituted amino acids to arginase. Specifically, we report the design, synthesis, and assay of racemic 2-amino-6-borono-2-methylhexanoic acid and racemic 2-amino-6-borono-2-(difluoromethyl)hexanoic acid. X-ray crystal structures of human arginase I and Plasmodium falciparum arginase complexed with these inhibitors reveal the exclusive binding of the L-stereoisomer; the additional {alpha}-substituent of each inhibitor is readily accommodated and makes new intermolecular interactions in the outer active site of each enzyme. Therefore, this work highlights a new region of the protein surface that can be targeted for additional affinity interactions, as well as the first comparative structural insights on inhibitor discrimination between a human and a parasitic arginase.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Mechanism of endosomal escape by p H -responsive nucleic-acid vectors

Successful intracellular delivery of nucleic acids (NAs) hinges on many factors, one of them being NAs’ efficacious escape from endosomes. As competent NA vectors, pH-responsive gemini surfactants (GSs) might achieve high efficacy by facilitating endosomal escape. However, how the GSs assist the escape remains debated as many proposed mechanisms still lack experimental support, which hinders replication and further improvement of the efficient delivery. Here, via UV, fluorescence spectroscopy, and small-angle neutron scattering (SANS), we examined a pH-responsive GS's and a pH-unresponsive GS's capabilities to compact DNA and withstand binding competition, and their interactions with model endosomal and lysosomal membranes, at varied pHs. Acidification-driven enhancement of DNA-compaction capability and of stability against binding competition were found specific to the pH-responsive GS. Alongside the pH-responsive GS's structural perturbation to the membranes as observed with SANS, the features suggest that pH-responsive GSs facilitate endosomal escape by releasing excess GS molecules from DNA-GS complexes upon acidification in endosome maturation, with the released GS molecules disrupting endosomal and lysosomal membranes and thereby assisting the escape. Here a general design principle for NA vectors is proposed on the basis of this experimental finding.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Deriving spatially explicit direct and indirect interaction networks from animal movement data

Abstract Quantifying spatiotemporally explicit interactions within animal populations facilitates the understanding of social structure and its relationship with ecological processes. Data from animal tracking technologies (Global Positioning Systems [“GPS”]) can circumvent longstanding challenges in the estimation of spatiotemporally explicit interactions, but the discrete nature and coarse temporal resolution of data mean that ephemeral interactions that occur between consecutive GPS locations go undetected. Here, we developed a method to quantify individual and spatial patterns of interaction using continuous‐time movement models (CTMMs) fit to GPS tracking data. We first applied CTMMs to infer the full movement trajectories at an arbitrarily fine temporal scale before estimating interactions, thus allowing inference of interactions occurring between observed GPS locations. Our framework then infers indirect interactions—individuals occurring at the same location, but at different times—while allowing the identification of indirect interactions to vary with ecological context based on CTMM outputs. We assessed the performance of our new method using simulations and illustrated its implementation by deriving disease‐relevant interaction networks for two behaviorally differentiated species, wild pigs ( Sus scrofa ) that can host African Swine Fever and mule deer ( Odocoileus hemionus ) that can host chronic wasting disease. Simulations showed that interactions derived from observed GPS data can be substantially underestimated when temporal resolution of movement data exceeds 30‐min intervals. Empirical application suggested that underestimation occurred in both interaction rates and their spatial distributions. CTMM‐Interaction method, which can introduce uncertainties, recovered majority of true interactions. Our method leverages advances in movement ecology to quantify fine‐scale spatiotemporal interactions between individuals from lower temporal resolution GPS data. It can be leveraged to infer dynamic social networks, transmission potential in disease systems, consumer–resource interactions, information sharing, and beyond. The method also sets the stage for future predictive models linking observed spatiotemporal interaction patterns to environmental drivers.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Dynamic transcriptome profiling of Bean Common Mosaic Virus (BCMV) infection in Common Bean ( Phaseolus vulgaris L.)

Background: Bean common mosaic virus (BCMV) is widespread, with Phaseolus species as the primary host plants. Numerous BCMV strains have been identified on the basis of a panel of bean varieties that distinguish the pathogenicity types with respect to the viral strains. The molecular responses in Phaseolus to BCMV infection have not yet been well characterized. Results: We report the transcriptional responses of a widely susceptible variety of common bean ( Phaseolus vulgaris L., cultivar ‘Stringless green refugee’) to two BCMV strains, in a time-course experiment. We also report the genome sequence of a previously unreported BCMV strain. The interaction with the known strain NL1-Iowa causes moderate symptoms and large transcriptional responses, and the newly identified strain (Strain 2 or S2) causes severe symptoms and moderate transcriptional responses. The transcriptional profiles of host plants infected with the two isolates are distinct, and involve numerous differences in splice forms in particular genes, and pathway specific expression patterns. Conclusions: We identified differential host transcriptome response after infection of two different strains of Bean common mosaic virus (BCMV) in common bean ( Phaseolus vulgaris L.). Virus infection initiated a suite of changes in gene expression level and patterns in the host plants. Pathways related to defense, gene regulation, metabolic processes, photosynthesis were specifically altered after virus infection. Results presented in this study can increase the understanding of host-pathogen interactions and provide resources for further investigations of the biological mechanisms in BCMV infection and defense.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Interactive Effects of Microbes and Nitrogen on Panicum virgatum Root Functional Traits and Patterns of Phenotypic Selection

Premise of research. Plants in natural and agricultural systems are influenced in myriad ways by their microbial communities, particularly by providing goods and services that change plant functional traits. Microbes are considered an influential part of the environmental context that change plant trait expression, but often, microbe-mediated effects are contingent on local resources, such as nitrogen. Here, we ask how microbes and nitrogen affect belowground functional traits and patterns of phenotypic selection. Methodology. We performed a fully factorial greenhouse experiment with switchgrass (Panicum virgatum), manipulating microbial community composition and nitrogen availability. We measured plant performance and belowground functional traits and performed 16S amplicon sequencing of the root-associated microbial communities. We looked for correlations between microbial taxa and root functional traits, and we performed phenotypic selection analysis on five belowground functional traits to determine how traits affect plant relative performance across biotic and abiotic contexts. Pivotal results. All belowground plant functional traits except root tissue density were affected by adding nitrogen. We found that a microbial taxon (amplicon sequence variant [ASV]) in the genus Micromonospora correlated with shorter root lengths. We also found strong positive selection for longer roots regardless of the abiotic or biotic environment. In contrast, selection favored lower root-to-shoot ratios in high-nitrogen conditions, and selection on root tissue density was highest in treatments that had high nitrogen levels and perturbed microbial communities. Conclusions. We did not detect microbial effects on the expression of plant traits (ecological effects); however, patterns of phenotypic selection (evolutionary effects) on root tissue density differed depending on the biotic and abiotic environment. Additionally, we detected strong selection for increased root length across treatments; we also found that one ASV correlated with decreased root length, indicating potential conflict between root microbiome components and plant fitness. Future work would be to include microbial taxa in phenotypic selection analysis and to conduct manipulations of the microbes correlated with functional traits to determine causality.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2012

Molecular Mechanism of Specific Ion Interactions Between Alkali Cations and Acetate Anion in Aqueous Solution: A Molecular Dynamics Study

Specific ion interactions between the alkali cations (i.e., Li+, Na+ and K+) and an acetate anion in aqueous solution were studied using molecular dynamics simulation techniques and polarizable potential models. The ions-acetate systems were used as a model for understanding the interactions between ions and protein surfaces. We computed free energy profiles for different ion pairs using constrained mean force methods. Upon analyzing the computed free energy profiles for the Na+/K+-acetate ion-pairs, we observed a deeper contact ion minimum and also a larger association constant for the Na+-acetate pair compared to the corresponding K+-acetate pair. These observations help to demonstrate the preferential binding of Na+ over K+ to protein surfaces.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Effect of Cysteine Substitutions on the Structural and Magnetic Properties of Fe{sub 3}O{sub 4}–Cysteine/RGO and Fe{sub 3}O{sub 4}/RGO–Cysteine Nanocomposites

We synthesized by electrostatic self-assembly route in basic solution Fe{sub 3}O{sub 4}–cysteine/RGO and Fe{sub 3}O{sub 4}/RGO–cysteine nanocomposites. In this method, electrostatic interaction was created via negatively charged surface of the reduced graphene oxide and reduced graphene oxide–cysteine sheets and positively charged surface of the Fe{sub 3}O{sub 4} and Fe{sub 3}O{sub 4}–Cys nanoparticles in aqueous solution. The structural and magnetic properties of the prepared samples were analyzed by x-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), Raman spectroscopy, transmission electron microscopy (TEM), and vibrating sample magnetometer (VSM), respectively. The dependences of magnetization as a function of applied field using a vibrating sample magnetometer exhibit S-like curves, indicating a magnetic hysteresis behavior for all samples. It clearly showed that, the nanocomposites showed a reduction of saturation magnetization to the Fe{sub 3}O{sub 4} nanoparticles.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2018

Characterization of Pharmaceutical Cocrystals and Salts by Dynamic Nuclear Polarization-Enhanced Solid-State NMR Spectroscopy

Multicomponent solids such as cocrystals have emerged as a way to control and engineer the stability, solubility and manufacturability of solid active pharmaceutical ingredients (APIs). Cocrystals are typically formed by solution- or solid-phase reactions of APIs with suitable cocrystal coformers, which are often weak acids. One key structural question about a given multicomponent solid is whether it should be classified as a salt, where the basic API is protonated by the acid, or as a cocrystal, where the API and coformer remain neutral and engage in hydrogen bonding interactions. It has previously been demonstrated that solid-state NMR spectroscopy is a powerful probe of structure in cocrystals and salts of APIs, however, the poor sensitivity of solid-state NMR spectroscopy usually restricts the types of experiments that can be performed. Here relayed dynamic nuclear polarization (DNP) was applied to reduce solid-state NMR experiments by one to two orders of magnitude for salts and cocrystals of a complex API. The large sensitivity gains from DNP facilitates rapid acquisition of natural isotopic abundance 13C and 15N solid-state NMR spectra. Critically, DNP enables double resonance 1H-15N solid-state NMR experiments such as 2D 1H-15N HETCOR, 1H-15N CP-build up, 15N{1H} J-resolved/attached proton tests, 1H-15N DIPSHIFT and 1H-15N PRESTO. The latter two experiments allow 1H-15N dipolar coupling constants and H-N bond lengths to be accurately measured, providing an unambiguous assignment of nitrogen protonation state and definitive classification of the multi-component solids as cocrystals or salts. In conclusion, these types of measurements should also be extremely useful in the context of polymorph discrimination, NMR crystallography structure determination and for probing hydrogen bonding in a variety of organic materials.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Ambient-Temperature Hydrogen Storage via Vanadium(II)-Dihydrogen Complexation in a Metal-Organic Framework

In this report, the widespread implementation of H 2 as a fuel is currently hindered by the high pressures or cryogenic temperatures required to achieve reasonable storage densities. In contrast, the realization of materials that strongly and reversibly adsorb hydrogen at ambient temperatures and moderate pressures could transform the transportation sector and expand adoption of fuel cells in other applications. To date, however, no adsorbent has been identified that exhibits a binding enthalpy within the optimal range of -15 to -25 kJ/mol for ambient-temperature hydrogen storage. Here, we report the hydrogen adsorption properties of the metal-organic framework (MOF) V 2 Cl 2.8 (btdd) (H 2 btdd, bis(1 H -1,2,3-triazolo[4,5- b ],[4',5'- i ])dibenzo[1,4]dioxin), which features exposed vanadium(II) sites capable of backbonding with weak π acids. Significantly, gas adsorption data reveal that this material binds H 2 with an enthalpy of -21 kJ/mol. This binding energy enables usable hydrogen capacities that exceed that of compressed storage under the same operating conditions. The Kubas-type vanadium(II)-dihydrogen complexation is characterized by a combination of techniques. From powder neutron diffraction data, a V-D 2 (centroid) distance of 1.966(8) Å is obtained, the shortest yet reported for a MOF. Using in situ infrared spectroscopy, the H-H stretch was identified, and it displays a red shift of 242 cm -1 . Electronic structure calculations show that a main contribution to bonding stems from the interaction between the vanadium d π and H 2 σ* orbital. Ultimately, the pursuit of MOFs containing high densities of weakly π-basic metal sites may enable storage capacities under ambient conditions that far surpass those accessible with compressed gas storage.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Spin waves and spin-state transitions in a ruthenate high-temperature antiferromagnet

Ruthenium compounds serve as a platform for fundamental concepts such as spin-triplet superconductivity, Kitaev spin liquids and solid-state analogues of the Higgs mode in particle physics. However, basic questions about the electronic structure of ruthenates remain unanswered, because several key parameters (including Hund’s coupling, spin–orbit coupling and exchange interactions) are comparable in magnitude and their interplay is poorly understood, partly due to difficulties in synthesizing large single crystals for spectroscopic experiments. Here we introduce a resonant inelastic X-ray scattering (RIXS) technique capable of probing collective modes in microcrystals of 4d electron materials. We observe spin waves and spin-state transitions in the honeycomb antiferromagnet SrRu 2 O 6 (ref. 10) and use the extracted exchange interactions and measured magnon gap to explain its high Néel temperature. We expect that the RIXS method presented here will enable momentum-resolved spectroscopy of a large class of 4d transition-metal compounds.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2022

EIC Detector Overview

The Electron Ion Collider will have two interaction regions that can be instrumented with detectors. Here, the first region will be instrumented as part of the project and needs to be capable of delivering the physics that has been outlined by the National Academy of Sciences and ready at the start of beam commissioning near the end of this decade. Plans for a second complementary detector to be located at a second interaction region are already in progress and will hopefully come to fruition just few years after the first detector comes online. While the basic parameters of these detectors are being selected using conventional approaches, the optimization of the detectors is already being enhanced by making use of advanced optimization techniques.

47 OTHER INSTRUMENTATION↗
DOE OSTI2014

WE-G-12A-01: High Intensity Focused Ultrasound Surgery and Therapy

More and more emphasis is being made on alternatives to invasive surgery and the use of ionizing radiation to treat various diseases including cancer. Novel screening, diagnosis, treatment and monitoring of response to treatment are also hot areas of research and new clinical technologies. Ultrasound(US) has gained traction in all of the aforementioned areas of focus. Especially with recent advances in the use of ultrasound to noninvasively treat various diseases/organ systems. This session will focus on covering MR-guided focused ultrasound and the state of the art clinical applications, and the second speaker will survey the more cutting edge technologies e.g. Focused Ultrasound (FUS) mediated drug delivery, principles of cavitation and US guided FUS. Learning Objectives: Fundamental physics and physical limitations of US interaction with tissue and nanoparticles The alteration of tissue transport using focused ultrasound US control of nanoparticle drug carriers for targeted release The basic principles of MRI-guided focused ultrasound (MRgFUS) surgery and therapy the current state of the art clinical applications of MRgFUS requirements for quality assurance and treatment planning.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

Solid-state-based analog of optomechanics

In this study, we investigate a semiconductor quantum dot as a microscopic analog of a basic optomechanical setup. We show that optomechanical features can be reproduced by the solid-state platform, arising from parallels of the underlying interaction processes, which in the optomechanical case is the radiation pressure coupling and in the semiconductor case the electron–phonon coupling. We discuss bistabilities, lasing, and phonon damping, and recover the same qualitative behaviors for the semiconductor and the optomechanical cases expected for low driving strengths. However, in contrast to the optomechanical case, distinct signatures of higher order processes arise in the semiconductor model.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗