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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 1,297 records · Page 72
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Root carbon interation with soil minerals is dynamic, leaving a legacy of microbially derived residues

Minerals preserve the oldest most persistent soil carbon, and mineral characteristics appear to play a critical role in the formation of soil organic matter (SOM) associations. To test the hypothesis that carbon source and soil microorganisms also influence mineral-SOM associations, we incubated permeable minerals bags in soil microcosms with and without plants, in a 13CO2 labelling chamber. Mineral bags contained quartz, ferrihydrite, kaolinite, or native soil minerals isolated via density separation. Using 13C-NMR, FTICR-MS, and lipidomics, we traced plant-derived carbon onto minerals harvested from microcosms at three plant growth stages, characterizing total carbon, 13C enrichment, and SOM chemistry. While C accumulation was rapid and mineral-dependent, the accumulated amount was not significantly affected by the presence of plant roots. However, the rhizosphere did shape the chemistry of mineral-associated SOM. Minerals incubated in the rhizosphere were associated with a more diverse array of compounds with different C functional groups (carbonyl, aromatics, carbohydrates, lipids) than minerals incubated in a bulk soil control. These diverse rhizosphere-derived compounds may represent a “transient fraction” of mineral SOM, rapidly exchanging with mineral surfaces. Our results also suggest that many of the lipids which persist on minerals are microbially-derived with a large fraction of fungal lipids.

Rhizosphere, soil organic matter, grassland, 13C-N↗
DOE OSTI2022

Searches for light dark matter using condensed matter systems

Identifying the nature of dark matter (DM) has long been a pressing question for particle physics. In the face of ever-more-powerful exclusions and null results from large-exposure searches for TeV-scale DM interacting with nuclei, a significant amount of attention has shifted to lighter (sub-GeV) DM candidates. Direct detection of the light DM in our galaxy by observing DM scattering off a target system requires new approaches compared to prior searches. Lighter DM particles have less available kinetic energy, and achieving a kinematic match between DM and the target mandates the proper treatment of collective excitations in condensed matter systems, such as charged quasiparticles or phonons. In this context, the condensed matter physics of the target material is crucial, necessitating an interdisciplinary approach. In this review, we provide a self-contained introduction to direct detection of keV–GeV DM with condensed matter systems. We give a brief survey of DM models and basics of condensed matter, while the bulk of the review deals with the theoretical treatment of DM-nucleon and DM-electron interactions. Here, we also review recent experimental developments in detector technology, and conclude with an outlook for the field of sub-GeV DM detection over the next decade.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
NASA NTRS1974

Non-relativistic solar electrons

Summary of both the direct spacecraft observations of nonrelativistic solar electrons, and observations of the X-ray and radio emission generated by these particles at the sun and in the interplanetary medium. These observations bear on three physical processes basic to energetic particle phenomena: (1) the acceleration of particles in tenuous plasmas; (2) the propagation of energetic charged particles in a disordered magnetic field, and (3) the interaction of energetic charged particles with tenuous plasmas to produce electromagnetic radiation. Because these electrons are frequently accelerated and emitted by the sun, mostly in small and relatively simple flares, it is possible to define a detailed physical picture of these processes. In many small solar flares nonrelativistic electrons accelerated during flash phase constitute the bulk of the total flare energy. Thus the basic flare mechanism in these flares essentially converts the available flare energy into fast electrons. Nonrelativistic electrons exhibit a wide variety of propagation modes in the interplanetary medium, ranging from diffusive to essentially scatter-free. This variability in the propagation may be explained in terms of the distribution of interplanetary magnetic field fluctuations.

Lin, R. P.↗
DOE OSTI2016

Structural basis of recognition of farnesylated and methylated KRAS4b by PDEδ

Farnesylation and carboxymethylation of KRAS4b (Kirsten rat sarcoma isoform 4b) are essential for its interaction with the plasma membrane where KRAS-mediated signaling events occur. Phosphodiesterase-δ (PDEδ) binds to KRAS4b and plays an important role in targeting it to cellular membranes. We solved structures of human farnesylated–methylated KRAS4b in complex with PDEδ in two different crystal forms. In these structures, the interaction is driven by the C-terminal amino acids together with the farnesylated and methylated C185 of KRAS4b that binds tightly in the central hydrophobic pocket present in PDEδ. In crystal form II, we see the full-length structure of farnesylated–methylated KRAS4b, including the hypervariable region. Crystal form I reveals structural details of farnesylated–methylated KRAS4b binding to PDEδ, and crystal form II suggests the potential binding mode of geranylgeranylated–methylated KRAS4b to PDEδ. We identified a 5-aa-long sequence motif (Lys-Ser-Lys-Thr-Lys) in KRAS4b that may enable PDEδ to bind both forms of prenylated KRAS4b. Structure and sequence analysis of various prenylated proteins that have been previously tested for binding to PDEδ provides a rationale for why some prenylated proteins, such as KRAS4a, RalA, RalB, and Rac1, do not bind to PDEδ. Comparison of all four available structures of PDEδ complexed with various prenylated proteins/peptides shows the presence of additional interactions due to a larger protein–protein interaction interface in KRAS4b–PDEδ complex. Here, this interface might be exploited for designing an inhibitor with minimal off-target effects.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2004

Fourth Computational Aeroacoustics (CAA) Workshop on Benchmark Problems

This publication contains the proceedings of the Fourth Computational Aeroacoustics (CAA) Workshop on Benchmark Problems. In this workshop, as in previous workshops, the problems were devised to gauge the technological advancement of computational techniques to calculate all aspects of sound generation and propagation in air directly from the fundamental governing equations. A variety of benchmark problems have been previously solved ranging from simple geometries with idealized acoustic conditions to test the accuracy and effectiveness of computational algorithms and numerical boundary conditions; to sound radiation from a duct; to gust interaction with a cascade of airfoils; to the sound generated by a separating, turbulent viscous flow. By solving these and similar problems, workshop participants have shown the technical progress from the basic challenges to accurate CAA calculations to the solution of CAA problems of increasing complexity and difficulty. The fourth CAA workshop emphasized the application of CAA methods to the solution of realistic problems. The workshop was held at the Ohio Aerospace Institute in Cleveland, Ohio, on October 20 to 22, 2003. At that time, workshop participants presented their solutions to problems in one or more of five categories. Their solutions are presented in this proceedings along with the comparisons of their solutions to the benchmark solutions or experimental data. The five categories for the benchmark problems were as follows: Category 1:Basic Methods. The numerical computation of sound is affected by, among other issues, the choice of grid used and by the boundary conditions. Category 2:Complex Geometry. The ability to compute the sound in the presence of complex geometric surfaces is important in practical applications of CAA. Category 3:Sound Generation by Interacting With a Gust. The practical application of CAA for computing noise generated by turbomachinery involves the modeling of the noise source mechanism as a vortical gust interacting with an airfoil. Category 4:Sound Transmission and Radiation. Category 5:Sound Generation in Viscous Problems. Sound is generated under certain conditions by a viscous flow as the flow passes an object or a cavity.

Dahl, Milo D.↗
DOE OSTI2015

Rice phytochrome-interacting factor protein OsPIF14 represses OsDREB1B gene expression through an extended N-box and interacts preferentially with the active form of phytochrome B

DREB1/CBF genes, known as major regulators of plant stress responses, are rapidly and transiently induced by low temperatures. Using a yeast one-hybrid screening, we identified a putative Phytochrome-Interacting bHLH Factor (OsPIF14), as binding to the OsDREB1B promoter. bHLH proteins are able to bind to hexameric E-box (CANNTG) or N-box (CACG(A/C)G) motifs, depending on transcriptional activity. We have shown that OsPIF14 binds to the OsDREB1B promoter through two N-boxes and that the flanking regions of the hexameric core are essential for protein–DNA interaction and stability. We also showed that OsPIF14 down-regulates OsDREB1B gene expression in rice protoplasts, corroborating the OsPIF14 repressor activity observed in the transactivation assays using Arabidopsis protoplasts. Additionally, we showed that OsPIF14 is indeed a phytochrome interacting factor, which preferentially binds to the active form (Pfr) of rice phytochrome B. This raises the possibility that OsPIF14 activity might be modulated by light. However, we did not observe any regulation of the OsDREB1B gene expression by light under control conditions. Moreover, OsPIF14 gene expression was shown to be modulated by different treatments, such as drought, salt, cold and ABA. Interestingly, OsPIF14 showed also a specific cold-induced alternative splicing. Our results suggest the possibility that OsPIF14 is involved in cross-talk between light and stress signaling through interaction with the OsDREB1B promoter. Finally, although in the absence of stress, OsDREB1B gene expression was not regulated by light, given previous reports, it remains possible that OsPIF14 has a role in light modulation of stress responses.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Role of the highly conserved G68 residue in the yeast phosphorelay protein Ypd1: implications for interactions between histidine phosphotransfer (HPt) and response regulator proteins

Many bacteria and certain eukaryotes utilize multi-step His-to-Asp phosphorelays for adaptive responses to their extracellular environments. Histidine phosphotransfer (HPt) proteins function as key components of these pathways. HPt proteins are genetically diverse, but share a common tertiary fold with conserved residues near the active site. A surface-exposed glycine at the H + 4 position relative to the phosphorylatable histidine is found in a significant number of annotated HPt protein sequences. Furthermore previous reports demonstrated that substitutions at this position result in diminished phosphotransfer activity between HPt proteins and their cognate signaling partners.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Temperature-dependent oxygen isotope fractionation in otoliths of juvenile Chinook salmon ( Oncorhynchus tshawytscha )

Oxygen thermometry has become a widely used technique for reconstructing thermal history in calcifying organisms but interpretation can be subject to predictive error from vital effects. To better understand these processes in Chinook salmon (Oncorhynchus tshawytscha) we experimentally constructed a temperature-dependent, otolith–water fractionation relationship for oxygen isotopes (δ 18 O) by rearing post-yolk absorptive juvenile fish at nominal temperatures from 6 to 21 °C. Temperature and otolith precipitation rate had significant effects on the otolith–water δ 18 O fractionation, but somatic growth rate did not. The slope of the δ 18 O fractionation equation also differed significantly from that of synthetic aragonite. Furthermore, our results suggest the expression of kinetic effects on δ 18 O fractionation in otoliths of Chinook salmon that are increasingly constrained at higher temperatures by other physical and physiological processes involved in mineral formation. Species-specific δ 18 O fractionation equations have considerable utility to reconstruct temperature history in Pacific salmon, but applications should recognize the potential for inferential uncertainty arising from interacting vital effects.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Phosphatidylserine Asymmetry Promotes the Membrane Insertion of a Transmembrane Helix

The plasma membrane (PM) contains an asymmetric distribution of lipids between the inner and outer bilayer leaflets. A lipid of special interest in eukaryotic membranes is the negatively charged phosphatidylserine (PS). In healthy cells, PS is actively sequestered to the inner leaflet of the PM, but PS redistributes to the outer leaflet when the cell is damaged or at the onset of apoptosis. Yet, the influence of PS asymmetry on membrane protein structure and folding are poorly understood. The pH low insertion peptide (pHLIP) adsorbs to the membrane surface at a neutral pH, but it inserts into the membrane at an acidic pH. We have previously observed that in symmetric vesicles, PS affects the membrane insertion of pHLIP by lowering the pH midpoint of insertion. In this work, we researched the effect of PS asymmetry on the membrane interaction of pHLIP. We developed a modified protocol to create asymmetric vesicles containing PS and employed Annexin V labeled with an Alexa Fluor 568 fluorophore as a new probe to quantify PS asymmetry. We observed that the membrane insertion of pHLIP was promoted by the asymmetric distribution of negatively charged PS, which causes a surface charge difference between bilayer leaflets. Our results indicate that lipid asymmetry can modulate the formation of an α-helix on the membrane. A corollary is that model studies using symmetric bilayers to mimic the PM may fail to capture important aspects of protein-membrane interactions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Structures of two novel crystal forms of Aspergillus oryzae alpha amylase (taka-amylase)

The structures of Aspergillus oryzae α-amylase were determined in a tetragonal crystal, having one molecule as asymmetric unit, and a monoclinic crystal with two molecules as asymmetric unit. Both crystal forms were obtained from trace contaminants of an old commercial lipase preparation. Structures were determined and refined to 1.65 Å and 1.43 Å resolution respectively. The latter crystal has a non-crystallographic (NCS) twofold axis within the asymmetric unit. Glycosylation at Asn197 is evident, and in the tetragonal crystal can be seen to include three, partially disordered sugar residues following the initial N-acetyl glucosamine (NAG). Superposition of the tetragonal crystal model on the α-amylases from Bacillus subtilis (PDB:1BAG), pig pancreas (PDB:3L2L), and barley (PDB:1AMY), show a high degree of coincidence, particularly for the (β/α)8-barrel domains, and especially within the active site. Using this structural agreement between amylases, we extrapolated the binding model of a six residue, limit dextrin found in pig pancreas α-amylase to the A. oryzae enzyme model, which predicts substrate interacting amino acid residues.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Synthesis and Function of Complex Sphingolipid Glycosylation

Glycosylinositol phosphorylceramides (GIPCs) constitute an important class of plasma-membrane lipids in plants. The complex glycan headgroups of GIPCs vary between plant species and tissues. Recent studies show that the structure of the glycan headgroup is important for plant development, abiotic stress tolerance, and interactions with pathogenic and symbiotic microorganisms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Conformational Equilibria of Multimodal Chromatography Ligands in Water and Bound to Protein Surfaces

Multimodal chromatography uses small ligands with multiple modes of interaction, e.g., charged, hydrophobic or hydrogen bonding, to separate proteins from complex mixtures. The mechanism by which multimodal ligands interact with proteins is expected to be affected by ligand conformations, among other factors. In this report, we determine conformational equilibria of two commercially used multimodal cation exchange ligands, Capto MMC and Nuvia cPrime, in a range of solvents, a Lennard-Jones (LJ) liquid, ethanol, and water, using molecular dynamics (MD) simulations. By mapping ligand conformations onto two key torsion angles, ω and φ, in these solvents and in low and high dielectric media, we quantify the relative importance of intramolecular and solvent-mediated interactions. In a high dielectric medium, Capto MMC preferentially samples three conformations, which are stabilized by a combination of an intramolecular torsion potential (on ω) and LJ interactions. In an LJ liquid, solvent molecules compete with intramolecular interactions while simultaneously providing an osmotic force, stabilizing both closer and farther distances between ligand sites. This has the overall result of “flattening out” the conformational landscape. Interestingly, in ethanol and water, hydrogen bonding among the amide hydrogen and solvent molecules stabilizes two additional conformations of Capto MMC in which ω takes on less favorable cis-like configurations. MD simulations of ligands in free solution with three therapeutic antibody fragments show that ligand conformational equilibria remain effectively unchanged upon binding to proteins. Although, there is 20–30% dehydration of the overall ligand upon binding, the hydrogen-bonding sites are dehydrated to a much smaller extent, particularly in cis-like configurations. Conformational preferences of Nuvia cPrime are similar to that of Capto MMC, except for the effect of symmetry arising from the absence of an alkyl thiol tail. Characterizing the conformational equilibria of these two ligands in free solution and bound to a protein provides a foundation for developing a mechanistic understanding of protein–multimodal ligand interactions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Understanding the Structure and Dynamics of Complex Biomembrane Interactions by Neutron Scattering Techniques

The membrane is one of the key structural materials of biology at the cellular level. Composed predominantly of a bilayer of lipids with embedded and bound proteins, it defines the boundaries of the cell and many organelles essential to life and therefore is involved in almost all biological processes. Membrane-specific interactions, such as drug binding to a membrane receptor or the interactions of an antimicrobial compound with the lipid matrix of a pathogen membrane, are of interest across the scientific disciplines. Herein we present a review, aimed at nonexperts, of the major neutron scattering techniques used in membrane studies: small-angle neutron scattering, neutron membrane diffraction, neutron reflectometry, quasielastic neutron scattering, and neutron spin echo. Neutron scattering techniques are well suited to studying biological membranes. The nondestructive nature of cold neutrons means that samples can be measured for long periods without fear of beam damage from ultraviolet, electron, or X-ray radiation, and neutron beams are highly penetrating, thus offering flexibility in samples and sample environments. Most important is the strong difference in neutron scattering lengths between the two most abundant forms of hydrogen, protium and deuterium. Changing the relative amounts of protium/deuterium in a sample allows the production of a series of neutron scattering data sets, enabling the observation of differing components within complex membrane architectures. This approach can be as simple as using the naturally occurring neutron contrast between different biomolecules to study components in a complex by changing the solution H 2 O/D 2 O ratio or as complex as selectively labeling individual components with hydrogen isotopes. This review presents an overview of each experimental technique with the neutron instrument configuration, related sample preparation and sample environment, and data analysis, highlighted by a special emphasis on using prominent neutron contrast to understand structure and dynamics. This review gives researchers a practical introduction to the often enigmatic suite of neutron beamlines, thereby lowering the barrier to taking advantage of these large-facility techniques to achieve new understandings of membranes and their interactions with other molecules.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2012

Structure of the basal components of a bacterial transporter

Proteins SpoIIQ and SpoIIIAH interact through two membranes to connect the forespore and the mother cell during endospore development in the bacterium Bacillus subtilis. SpoIIIAH consists of a transmembrane segment and an extracellular domain with similarity to YscJ proteins. YscJ proteins form large multimeric rings that are the structural scaffolds for the assembly of type III secretion systems in Gram-negative bacteria. The predicted ring-forming motif of SpoIIIAH and other evidence led to the model that SpoIIQ and SpoIIIAH form the core components of a channel or transporter through which the mother cell nurtures forespore development. Therefore, to understand the roles of SpoIIIAH and SpoIIQ in channel formation, it is critical to determine whether SpoIIIAH adopts a ring-forming structural motif, and whether interaction of SpoIIIAH with SpoIIQ would preclude ring formation. We report a 2.8-{angstrom} resolution structure of a complex of SpoIIQ and SpoIIIAH. SpoIIIAH folds into the ring-building structural motif, and modeling shows that the structure of the SpoIIQ-SpoIIIAH complex is compatible with forming a symmetrical oligomer that is similar to those in type III systems. The inner diameters of the two most likely ring models are large enough to accommodate several copies of other integral membrane proteins. SpoIIQ contains a LytM domain, which is found in metalloendopeptidases, but lacks residues important for metalloprotease activity. Other LytM domains appear to be involved in protein-protein interactions. We found that the LytM domain of SpoIIQ contains an accessory region that interacts with SpoIIIAH.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Visualizing a viral genome with contrast variation small angle X-ray scattering

Despite the threat to human health posed by some single-stranded RNA viruses, little is understood about their assembly. The goal of this work is to introduce a new tool for watching an RNA genome direct its own packaging and encapsidation by proteins. Contrast variation small-angle X-ray scattering (CV-SAXS) is a powerful tool with the potential to monitor the changing structure of a viral RNA through this assembly process. The proteins, though present, do not contribute to the measured signal. As a first step in assessing the feasibility of viral genome studies, the structure of encapsidated MS2 RNA was exclusively detected with CV-SAXS and compared with a structure derived from asymmetric cryo-EM reconstructions. Additional comparisons with free RNA highlight the significant structural rearrangements induced by capsid proteins and invite the application of time-resolved CV-SAXS to reveal interactions that result in efficient viral assembly.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

A minimal motif for sequence recognition by mitochondrial transcription factor A (TFAM)

Abstract Mitochondrial transcription factor A (TFAM) plays a critical role in mitochondrial transcription initiation and mitochondrial DNA (mtDNA) packaging. Both functions require DNA binding, but in one case TFAM must recognize a specific promoter sequence, while packaging requires coating of mtDNA by association with non sequence-specific regions. The mechanisms by which TFAM achieves both sequence-specific and non sequence-specific recognition have not yet been determined. Existing crystal structures of TFAM bound to DNA allowed us to identify two guanine-specific interactions that are established between TFAM and the bound DNA. These interactions are observed when TFAM is bound to both specific promoter sequences and non-sequence specific DNA. These interactions are established with two guanine bases separated by 10 random nucleotides (GN10G). Our biochemical results demonstrate that the GN10G consensus is essential for transcriptional initiation and contributes to facilitating TFAM binding to DNA substrates. Furthermore, we report a crystal structure of TFAM in complex with a non sequence-specific sequence containing a GN10G consensus. The structure reveals a unique arrangement in which TFAM bridges two DNA substrates while maintaining the GN10G interactions. We propose that the GN10G consensus is key to facilitate the interaction of TFAM with DNA.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

A single-cell genome perspective on studying intracellular associations in unicellular eukaryotes

Single-cell genomics (SCG) methods provide a unique opportunity to analyse whole genome information at the resolution of an individual cell. While SCG has been extensively used to investigate bacterial and archaeal genomes, the technique has been rarely used to access the genetic makeup of uncultivated microbial eukaryotes. In this regard, the use of SCG can provide a wealth of information; not only do the methods allow exploration of the genome, they can also help elucidate the relationship between the cell and intracellular entities extant in nearly all eukaryotes. SCG enables the study of total eukaryotic cellular DNA, which in turn allows us to better understand the evolutionary history and diversity of life, and the physiological interactions that define complex organisms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Small RNAs at the Interface of the Plant-Fungal Interactions

Fungi and plants interact in a myriad of ways. These interactions range from mutualism to parasitism, and yet, many plant species appear to use similar tools to deal with both. One recent observation is the role that small RNAs play in mediating the conversation between plant and fungus. Increasingly, many studies demonstrate these RNAs are pivotal modulators, reprogramming gene expression and cellular processes essential to the biogenesis of these inter-kingdom relationships.

59 BASIC BIOLOGICAL SCIENCES↗