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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 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
DOE OSTI2017

A novel puromycin decorporation method to quantify skeletal muscle protein breakdown: A proof-of-concept study

Highlights: • Limitations exist in the techniques used to quantify muscle protein breakdown (MPB). • We developed a method for assessing MPB through loss of puromycin labelling in cells. • We validated the method using selected compounds known to dynamically modulate MPB. The precise roles that the major proteolytic pathways play in the regulation of skeletal muscle mass remain incompletely understood, in part due to technical limitations associated with current techniques used to quantify muscle protein breakdown (MPB). We aimed to develop a method to assess MPB in cells, based on loss of puromycin labelling of translated polypeptide chains. Following an initial 24 h incubation period with puromycin (1 μM), loss of puromycin labelling from murine C2C12 myotubes was assessed over 48 h, both in the presence or absence of protein synthesis inhibitor cycloheximide (CHX). To validate the method, loss of puromycin labelling was determined from cells treated with selected compounds known to influence MPB (e.g. serum starvation, Dexamethasone (Dex), tumour necrosis factor alpha (TNF-α) and MG-132)). Reported established (static) markers of MPB were measured following each treatment. Loss of puromycin labelling from cells pre-incubated with puromycin was evident over a 48 h period, both with and without CHX. Treatment with Dex (−14 ± 2% vs. Ctl; P P P P in vitro using an established muscle cell line. It is anticipated this non isotopic-tracer alternative to measuring MPB will facilitate insight into the mechanisms that regulate muscle mass/MPB both in vitro, and perhaps, in vivo.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2026

Comparison of automated chemical-guided segmentation and human annotation of soil organic matter in X-ray microcomputed tomography imaging in contrasted soil types

Soil organic matter (OM) formation and persistence is strongly influenced by the spatial distribution of organic substrates and microscale soil heterogeneity by dictating OM accessibility to microorganisms. However, traditional size and/or density fractionation techniques disrupt aggregate architecture, eliminating spatial information needed to fully understand intra-aggregate OM distribution. To quantify three-dimensional OM spatial distribution and automate segmentation in X-ray microcomputed tomography (µCT) imaging without human annotation bias, we developed an iodine gas vapor (I2) based staining workflow that eliminates labor-intensive manual annotation while maintaining segmentation accuracy, using aggregates from four taxonomically diverse soils (Xerofluvent, Haploxeroll Sphagnofibrist, Palehumult) with an 8-fold range of soil organic carbon. Human annotation of 10 µCT slices by the experienced and inexperienced annotators resulted in variations up to 3% in the Dice similarity coefficient (DSC), reflecting a degree of inherent subjectivity of manual labeling. Such inconsistencies are expected to compound as the number of manually annotated slices increases. Dual-energy µCT imaging at 33.1 keV (below the iodine (I) K-edge) and 33.2 keV (above the I K-edge) was used to resolve aggregate microstructure following I2 staining. The automated image subtraction pipeline identified OM regions by the I Kedge induced brightness increases, achieving DSC values of 0.58–0.83 relative to an experienced annotator. Sensitivity analyses revealed that the reconstruction alpha value—optimized via the open-source tool TomocuPy—and the 3D registration slice count were the primary determinants of accuracy, providing a novel benchmark for dual-energy soil imaging. The pipeline without GPU acceleration achieved 9.6 to 43.2 times faster than manual annotation. Using GPU-accelerated image post-processing and affine transformation matrices, the pipeline successfully segmented OM elements for large-scale datasets (3232×3232 pixel, 2048 slices) within ~5200 s from raw file acquisition to segmented output. The high-throughput approach enables the quantification of OM spatial distribution across diverse and heterogeneous soil.

Soil microbial biomass↗
DOE OSTI2017

Mechanism of Me–Re Bond Addition to Platinum(II) and Dioxygen Activation by the Resulting Pt–Re Bimetallic Center

Unusual cis-oxidative addition of methyltrioxorhenium (MTO) to [PtMe 2 (bpy)], (bpy = 2,2'-bipyridine) (1) is described. Addition of MTO to 1 first gives the Lewis acid–base adduct [(bpy)Me 2 Pt–Re(Me)(O) 3 ] (2) and subsequently affords the oxidative addition product [(bpy)Me 3 PtReO 3 ] (3). All complexes 1, MTO, 2, and 3 are in equilibrium in solution. The structure of 2 was confirmed by X-ray crystallography, and its dissociation constant in solution is 0.87 M. The structure of 3 was confirmed by extended X-ray absorption fine structure and X-ray absorption near-edge structure in tandem with one- and two-dimensional NMR spectroscopy augmented by deuterium and 13 C isotope-labeling studies. Kinetics of formation of compound 3 revealed saturation kinetics dependence on [MTO] and first-order in [Pt], complying with prior equilibrium formation of 2 with oxidative addition of Me–Re being the rate-determining step. Exposure of 3 to molecular oxygen or air resulted in the insertion of an oxygen atom into the platinum–rhenium bond forming [(bpy)Me 3 PtOReO 3 ] (4) as final product. In conclusion, density functional theory analysis on oxygen insertion pathways leading to complex 4, merited on the basis of Russell oxidation pathway, revealed the involvement of rhenium peroxo species.'

Pichaandi, Kothanda Rama↗
DOE OSTI2017

High-sensitivity infrared vibrational nanospectroscopy in water

Mid-infrared vibrational spectroscopy is a universal label-free tool for identifying molecular compounds in chemical and biological samples on the basis of their ‘fingerprint’ vibrational absorption lines. Vibrational spectroscopy with nanometer spatial resolution can reveal the chemical composition of samples at the nanoscale, and several scanning-probe techniques have been developed to address this need. It is also highly desirable to study biological and chemical samples in their native aqueous environments rather than in air. In aqueous environments, however, the sensitivity of the current vibrational nanospectroscopy techniques deteriorates dramatically . Here, we report the first mid-infrared nanospectroscopy technique that retains nanoscale sensitivity and spatial resolution when the sample and the scanning probe are completely immersed in water. This method overcomes challenges including water absorption and scattering and the mechanical damping of cantilever vibrations. We further demonstrate spectroscopy and imaging of 20- to 50-nm-thick polymer samples with a 25-nm spatial resolution in the biologically relevant Amide I and II spectral regions.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
NASA NTRS1990

A predictive theoretical model for electron tunneling pathways in proteins

A practical method is presented for calculating the dependence of electron transfer rates on details of the protein medium intervening between donor and acceptor. The method takes proper account of the relative energetics and mutual interactions of the donor, acceptor, and peptide groups. It also provides a quantitative search scheme for determining the important tunneling pathways (specific sequences of localized bonding and antibonding orbitals of the protein which dominate the donor-acceptor electronic coupling) in native and tailored proteins, a tool for designing new proteins with prescribed electron transfer rates, and a consistent description of observed electron transfer rates in existing redox labeled metalloproteins and small molecule model compounds.

Onuchic, Jose Nelson↗
NASA NTRS1994

A Coupled Soil-Atmosphere Model of H2O2 on Mars

The Viking Gas Chromatograph Mass Spectrometer failed to detect organic compounds on Mars, and both the Viking Labeled Release and the Viking Gas Exchange experiments indicated a reactive soil surface. These results have led to the widespread belief that there are oxidants in the martian soil. Since H2O2 is produced by photochemical processes in the atmosphere of Mars, and has been shown in the laboratory to reproduce closely the Viking LR results, it is a likely candidate for a martian soil oxidant. Here, we report on the results of a coupled soil/atmosphere transport model for H202 on Mars. Upon diffusing into the soil, its concentration is determined by the extent to which it is adsorbed and by the rate at which it is catalytically destroyed. An analytical model for calculating the distribution of H202 in the martian atmosphere and soil is developed. The concentration of H202 in the soil is shown to go to zero at a finite depth, a consequence of the nonlinear soil diffusion equation. The model is parameterized in terms of an unknown quantity, the lifetime of H202 against heterogeneous catalytic destruction in the soil. Calculated concentrations are compared with a H202 concentration of 30 nmoles/cu cm, inferred from the Viking Labeled Release experiment. A significant result of this model is that for a wide range of H202 lifetimes (up to 105 years), the extinction depth was found to be less than 3 m. The maximum possible concentration in the top 4 cm is calculated to be approx. 240 nmoles/cu cm, achieved with lifetimes of greater than 1000 years. Concentrations higher than 30 nmoles/cu cm require lifetimes of greater than 4.3 terrestrial years. For a wide range of H202 lifetimes, it was found that the atmospheric concentration is only weakly coupled with soil loss processes. Losses to the soil become significant only when lifetimes are less than a few hours. If there are depths below which H202 is not transported, it is plausible that organic compounds, protected from an oxidizing environment, may still exist. They would have been deposited by meteors, or be the organic remains of past life.

Bullock, Mark A.↗
DOE OSTI2021

GHB analogs confer neuroprotection through specific interaction with the CaMKIIα hub domain

Ca 2+ /calmodulin-dependent protein kinase II alpha subunit (CaMKIIα) is a key neuronal signaling protein and an emerging drug target. The central hub domain regulates the activity of CaMKIIα by organizing the holoenzyme complex into functional oligomers, yet pharmacological modulation of the hub domain has never been demonstrated. Here, using a combination of photoaffinity labeling and chemical proteomics, we show that compounds related to the natural substance γ-hydroxybutyrate (GHB) bind selectively to CaMKIIα. By means of a 2.2-Å x-ray crystal structure of ligand-bound CaMKIIα hub, we reveal the molecular details of the binding site deep within the hub. Furthermore, we show that binding of GHB and related analogs to this site promotes concentration-dependent increases in hub thermal stability believed to alter holoenzyme functionality. Selectively under states of pathological CaMKIIα activation, hub ligands provide a significant and sustained neuroprotection, which is both time and dose dependent. This is demonstrated in neurons exposed to excitotoxicity and in a mouse model of cerebral ischemia with the selective GHB analog, HOCPCA (3-hydroxycyclopent-1-enecarboxylic acid). Together, our results indicate a hitherto unknown mechanism for neuroprotection by a highly specific and unforeseen interaction between the CaMKIIα hub domain and small molecule brain-penetrant GHB analogs. This establishes GHB analogs as powerful tools for investigating CaMKII neuropharmacology in general and as potential therapeutic compounds for cerebral ischemia in particular.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Unraveling the Dynamic Network in the Reactions of an Alkyl Aryl Ether Catalyzed by Ni/γ-Al 2 O 3 in 2-Propanol

The reductive cleavage of aryl ether linkages is a key step in the disassembly of lignin to its monolignol components, where selectivity is determined by the kinetics of multiple parallel and consecutive liquid-phase reactions. Triphasic hydrogenolysis of 13 C-labeled benzyl phenyl ether (BPE, a model compound with the same C-O bond energy as the major β-O-4 linkage in lignin), catalyzed by Ni/γ-Al 2 O 3 , was observed directly at elevated temperatures (150 - 175 °C) and pressures (79-89 bar) using operando magic-angle spinning NMR spectroscopy. Liquid-vapor partitioning in the NMR rotor was quantified using the 13 C NMR resonances for the 2-propanol solvent, whose chemical shifts report on the internal reactor temperature. At 170 °C, BPE is converted to toluene and phenol with k 1 = 0.17 s -1 g cat -1 and an apparent activation barrier of (80 ± 8) kJ mol -1 . Subsequent phenol hydrogenation occurs much more slowly (k 2 = 0.0052 s -1 g cat -1 at 170-175 °C), such that cyclohexanol formation is significant only at higher temperatures. Toluene is stable under these reaction conditions, but its methyl group undergoes facile H/D exchange (k 3 = 0.046 s -1 g cat -1 at 175 °C). While the source of the reducing equivalents for both hydrogenolysis and hydrogenation is exclusively H 2 /D 2(g) rather than the alcohol solvent at these temperatures, the initial isotopic composition of adsorbed H/D on the catalyst surface is principally determined by the solvent isotopic composition (2-PrOH/D). All reactions are preceded by a pronounced induction period associated with catalyst activation. In air, Ni nanoparticles are passivated by a surface oxide monolayer, whose removal under H 2 proceeds with an apparent activation barrier of (72 ± 13) kJ mol -1 . Finally ,the operando NMR spectra provide molecularly-specific, time-resolved information about the multiple simultaneous and sequential processes as they occur at the solid-liquid interface.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1979

Simulation of the Viking biology experiments - An overview

In the present paper, ground-based investigations of the Viking Martian biology data, which have resulted in reasonable simulations of these data, are reviewed. These simulations, which in strong oxidants, UV-treated materials, iron-containing clays, or iron salts were used as Martian analogs, are capable of explaining the ambiguity between the GCMS (gas-chromatography mass-spectrometry) experiments, in which no organic compounds were found on Mars, and the Labeled Release experiments, in which added organics were decomposed.

Klein, H. P.↗
NASA NTRS1989

New insights in the photochemistry of grain mantles: The identification of the 4.62 and 6.87 micron bands

The mid-IR spectral region of molecular clouds is known to show the fingerprints of molecules frozen in the icy mantles of the interstellar grains. To study the complex chemical and physical interactions on the ice mantles accreted on grains in molecular clouds numerous UV irradiation and diffusion experiments were performed. The irradiation of binary ices was studied. Using isotopic labelling on NH3/CO and NH3/O2 ices numerous compounds were identified, of which OCN(-), NO2(-), NO3(-), and NH4(+) ions reveal a new type of chemical reactions. It appeared that these compounds were formed by proton transfer reactions induced by the interaction between an acid (HNCO, HNO2, HNO3) and a base (NH3) through a hydrogen bond. This mechanism was confirmed by a study of photolyzed diluted argon mixtures. The main astrophysically relevant data from the overall study are presented. The 4.62 micron band in W33A can be reproduced with NH3/CO containing irradiated ices and was identified with OCN(-). The 6.87 micron band in W33A and other photostellar objects is reproduced with NH3/O2 containing ices and is identified with NH4(+).

Grim, Ruud↗
NASA NTRS1980

Evaluation of the procedure for separating barley from other spring small grains

The success of the Transition Year procedure to separate and label barley and the other small grains was assessed. It was decided that developers of the procedure would carry out the exercise in order to prevent compounding procedural problems with implementation problems. The evaluation proceeded by labeling the sping small grains first. The accuracy of this labeling was, on the average, somewhat better than that in the Transition Year operations. Other departures from the original procedure included a regionalization of the labeling process, the use of trend analysis, and the removal of time constraints from the actual processing. Segment selection, ground truth derivation, and data available for each segment in the analysis are discussed. Labeling accuracy is examined for North Dakota, South Dakota, Minnesota, and Montana as well as for the entire four-state area. Errors are characterized.

Magness, E. R.↗
NASA NTRS1997

Oxidative Degradation of Nadic-End-Capped Polyimides: Evidence for Reactions Occurring at High Temperatures - 2

The oxidative degradation of PMR (for polymerization of monomeric reactants) polyimides at elevated temperatures was followed by cross-polarized magic angle spinning (Cp-MAS) NMR. C-13 labeling of selected sites in the polymers allowed for direct observation of the transformations arising from oxidation processes. As opposed to model compound studies, the reactions were followed directly in the polymer. The labeling experiments confirm the previously reported oxidation of the methylene carbon to ketone in the methylenedianiline portion of the polymer chain. They also show the formation of two other oxidized species, acid and ester, from this same carbon. In addition, the technique provides the first evidence of the kind of degradation reactions that are occurring in the nadic end caps. Several PMR formulations containing moieties determined to be present after oxidation, as suggested by the labeling study, were synthesized. Weight loss, FTIR, and natural abundance NMR of these derivatives were followed during aging. In this way, weight loss could be related to the observed transformations.

Meador, Mary Ann B.↗
NASA NTRS2003

Formation and Survival of Amino Acids in Space

The detection of deuterium enrichments in meteoritic hydroxy and amino acids demonstrates that there is a connection between organic material in the interstellar medium and in primitive meteorites. It has generally been assumed that such molecules formed via reactions of small deuterium enriched insterstellar precursors in liquid water on a large asteroidal or cometary parent body. We have recently show that the W photolysis of interstellar/presolar ices can produce the amino acids alanine, serine, and glycine, as well as hydroxy acids, and glycerol, all of which have been extracted from the Murchison meteorite. Thus, some of the probiologically interesting organic compounds, compounds found in meteorites may have formed in presolar ice and have not solely been a product of parent body liquid water chemistry. We will report on our isotopic labeling studies of the mechanism of formation of these interesting compounds, and on astrophysically relevant kinetic studies UV photodecomposition of amino acid precursors in the solid state. This is our first year of exobiology funding on this project.

Bernstein, M. P.↗
NASA NTRS2003

Formation and Survival of Amino Acids in Space

The detection of deuterium enrichments in meteoritic hydroxy and amino acids demonstrates that there is a connection between organic material in the interstellar medium and in piimitive meteorites. It has generally been assumed that such molecules formed via reactions of small deuterium enriched insterstellar precursors in liquid water on a large asteroidal or cometary parent body. We have recently show that the W photolysis of interstellar/presolar ices can produce the amino acids alanine, serine, and glycine, as well as hydroxy acids, and glycerol, all of which have been extracted from the Murchison meteorite. Thus, some of the probiologically interesting organic compounds compounds found in meteorites may have formed in presolar ice and have not solely been a product of parent body liquid water chemistry. We will report on our isotopic labeling studies of the mechanism of formation of these inteiesting compounds, and on astrophysically relevant kinetic studies UV photo-decomposition of amino acid precursors in the solid state. This is our first year of exobiology funding on this project.

Bernstein, M. P.↗
DOE OSTI2023

Copper-Mediated Radiobromination of (Hetero)Aryl Boronic Pinacol Esters

Herein, a copper-mediated radiobromination of (hetero)aryl boronic pinacol esters is described. Cyclotron-produced [76/77Br]bromide was isolated using an anion exchange cartridge, wherein the pre-equilibration and elution solutions played a critical role in downstream deboro-bromination. The bromination tolerates a broad range of functional groups, labeling molecules with ranging electronic and steric effects. Bologically active radiopharmaceuticals were synthesized, including two radiobrominated inhibitors of poly ADP ribose polymerase, a clinically relevant chemotherapeutic target for ovarian, breast, and prostate cancers.

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

Increasing the Reproducibility and Replicability of Supervised AI/ML in the Earth Systems Science by Leveraging Social Science Methods

Artificial intelligence (AI) and machine learning (ML) pose a challenge for achieving science that is both reproducible and replicable. The challenge is compounded in supervised models that depend on manually labeled training data, as they introduce additional decision-making and processes that require thorough documentation and reporting. We address these limitations by providing an approach to hand labeling training data for supervised ML that integrates quantitative content analysis (QCA)—a method from social science research. The QCA approach provides a rigorous and well-documented hand labeling procedure to improve the replicability and reproducibility of supervised ML applications in Earth systems science (ESS), as well as the ability to evaluate them. Specifically, the approach requires (a) the articulation and documentation of the exact decision-making process used for assigning hand labels in a “codebook” and (b) an empirical evaluation of the reliability” of the hand labelers. In this paper, we outline the contributions of QCA to the field, along with an overview of the general approach. We then provide a case study to further demonstrate how this framework has and can be applied when developing supervised ML models for applications in ESS. With this approach, we provide an actionable path forward for addressing ethical considerations and goals outlined by recent AGU work on ML ethics in ESS.

58 GEOSCIENCES↗