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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 109 records · Page 6
All sourcesNASA NTRSDOE OSTI
DOE OSTI2017

Optimized Extraction Method To Remove Humic Acid Interferences from Soil Samples Prior to Microbial Proteome Measurements

The microbial composition and their activities in soil environments play a critical role in organic matter transformation and nutrient cycling, perhaps most specifically with respect to impact on plant growth but also more broadly to global impact on carbon and nitrogen-cycling. Liquid chromatography coupled to high performance mass spectrometry provides a powerful approach to characterize soil microbiomes; however, the limited microbial biomass and the presence of abundant interferences in soil samples present major challenges to soil proteome extraction and subsequent MS measurement. To address some of the major issues, we have designed and optimized an experimental method to enhance microbial proteome extraction concomitant with minimizing the soil-borne humic substances co-extraction from soils. Among the range of interferences, humic substances are often the worst in terms of adversely impacting proteome extraction and mass spectrometry measurement. Our approach employs an in-situ detergent-based microbial lysis / TCA precipitation coupled with an additional acidification precipitation step at the peptide level which efficiently removes humic acids. By combing filtration and pH adjustment of the final peptide solution, the remaining humic acids can be differentially precipitated and removed with a membrane filter, thereby leaving much cleaner proteolytic peptide samples for MS measurement. As a result, this modified method is a reliable and straight-forward protein extraction method that efficiently removes soil-borne humic substances without inducing proteome sample loss or reducing or biasing protein identification in mass spectrometry.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Nanoscale imaging of hydrogen and sodium in alteration layers of corroded glass using ToF-SIMS: Is an auxiliary sputtering ion beam necessary?

The hydrogen (H)/sodium (Na) interface is of great interest in glass corrosion research. Time-of-flight secondary ion mass spectrometry (ToF-SIMS) is one of the few techniques that can provide nanoscale H and Na imaging simultaneously. However, the optimized condition for ToF-SIMS imaging of H in glass is still unclear. In H depth profiling using ToF-SIMS, H background control is a key, in which an analysis ion beam and a sputtering ion beam work together in an interlaced mode to minimize it. Therefore, it is of great interest to determine if an auxiliary sputtering ion beam is also necessary to control H background in ToF-SIMS imaging of H. In this study, a Bi+ primary ion beam with different auxiliary sputtering beams (Cs+, O2+ and Arn+) were compared on a corroded International Simple Glass (ISG). It was surprising that the H/Na interface could be directly imaged using positive ion imaging without any auxiliary sputtering ion beam under a vacuum of 2-3 × 10-8 mbar. The H+ background was about 5% atomic percent on the pristine ISG glass, which was significantly lower than the H concentration in the alteration layer (~15%). Moreover, positive ion imaging could show distributions of other interesting species simultaneously, providing more comprehensive information of the glass corrosion. The H+ background could be reduced with an auxiliary O2+ sputtering ion beam; however, significant loss of signal intensities was observed. In addition, a higher H background in ToF-SIMS imaging than that in the depth profiling was observed.

Zhang, Jiandong↗
DOE OSTI2021

Using MALDI-FTICR-MS Imaging to Track Low-Molecular-Weight Aromatic Derivatives of Fungal Decayed Wood

Low-molecular-weight (LMW) aromatics are crucial in meditating fungal processes for plant biomass decomposition. Some LMW compounds are employed as electron donors for oxidative degradation in brown rot (BR), an efficient wood-degrading strategy in fungi that selectively degrades carbohydrates but leaves modified lignins. Previous understandings of LMW aromatics were primarily based on “bulk extraction”, an approach that cannot fully reflect their real-time functions during BR. Here, we applied an optimized molecular imaging method that combines matrix-assisted laser desorption ionization (MALDI) with Fourier-transform ion cyclotron resonance mass spectrometry (FTICR-MS) to directly measure the temporal profiles of BR aromatics as Rhodonia placenta decayed a wood wafer. We found that some phenolics were pre-existing in wood, while some (e.g., catechin-methyl ether and dihydroxy-dimethoxyflavan) were generated immediately after fungal activity. These pinpointed aromatics might be recruited to drive early BR oxidative mechanisms by generating Fenton reagents, Fe2+ and H2O2. As BR progressed, ligninolytic products were accumulated and then modified into various aromatic derivatives, confirming that R. placenta depolymerizes lignin. Together, this work confirms aromatic patterns that have been implicated in BR fungi, and it demonstrates the use of MALDI-FTICR-MS imaging as a new approach to monitor the temporal changes of LMW aromatics during wood degradation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Characterization of uraninite using a FIB–SEM approach and its implications for LA–ICP–MS analyses

Focused ion beam (FIB) coupled with scanning electron microscopy (SEM) investigations were performed here on pristine and altered areas of two uraninite samples in order to better understand their 3-dimensional mineralogical and chemical nature, and their impact on trace element abundances obtained by laser ablation inductively coupled plasma mass spectrometry (LA–ICP–MS) analyses. Trace element contents determined by both LA- and solution mode (SM)–ICP–MS analyses together with FIB results identify Pb as the optimal internal standard for LA–ICP–MS analyses of uraninite since it is a major chemical constituent, part of the structure, and similar in abundance to the trace elements of interest.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
DOE OSTI2019

Accelerating Lipidomic Method Development through in Silico Simulation

Judicious selection of mass spectrometry (MS) acquisition parameters is essential for effectively profiling the broad diversity and dynamic range of biomolecules. Typically, acquisition parameters are individually optimized to maximally characterize analytes from each new sample matrix. This time-consuming process often ignores the synergistic relationship between MS method parameters, producing suboptimal results. Here in this paper, we detail the creation of an algorithm which accurately simulates LC-MS/MS lipidomic data acquisition performance for a benchtop quadrupole-Orbitrap MS system. By coupling this simulation tool with a genetic algorithm for constrained parameter optimization, we demonstrate the efficient identification of LC-MS/MS method parameter sets individually suited for specific sample matrices. Finally, we utilize the in silico simulation to examine how continued developments in MS acquisition speed and sensitivity will further increase the power of MS lipidomics as a vital tool for impactful biochemical analysis.

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

Exosomal proteome analysis of human plasma to monitor sepsis progression

Highlights: • As low as 300 μL human plasma is sufficient for exosome isolation using our one-step density gradient ultracentrifugation. • Protein profiling of septic plasma exosomes are closely related to immune responses. • SPTLC3 may play important roles in development of sepsis. Exosomes are cell-derived vesicles containing RNA, lipid, and protein, which act in body immune response, intercellular signaling and some other important biological processes. Exosomes have been extensively studied in the past several years on their disease related mechanisms and potential roles to monitor disease progression as biomarkers. Compared with analyzing exosome RNA, comprehensive proteome profiling of exosomes in clinical samples (e.g. blood) are highly demanded but limited mainly due to lack of a reproducible method for efficient exosome extraction. In this study, we evaluated and optimized an exosome preparation approach using one-step ultracentrifugation through an Optiprep™ cushion. Exosomes prepared via this method and analyzed by mass spectrometry using Q-Exactive plus, has led to reproducible identification and quantification of 200 + proteins from human plasma samples of as little as 300 μL. Therefore, such a straightforward exosome extract method has enable us to deeply profile exosome proteomes from human blood at a scale of clinical studies. As a proof of principal, we practiced this approach in analyzing the exosome proteomic profiles of blood samples collected from a sepsis patient during six time points after diagnosis. Among the 238 proteins identified and quantified across the 6 samples, protein SPTLC3 involved in the sphingolipid metabolism, shows a negative correlation (p = 0.02, correlation coefficient = −0.984) with disease progression indicated by body temperature (BD) and C-reactive protein (CRP). Therefore, SPTLC3 could be an interesting target for future study on molecular mechanism of sepsis development, as well as potential classifier to monitor clinical progression of sepsis.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Efficient discrimination of natural stereoisomers of chicoric acid, an HIV-1 integrase inhibitor

Plants from the Asteraceae family are known to contain a wide spectrum of phytochemicals with various nutraceutical properties. One important phytochemical, chicoric acid (CA), is reported to exist in plants, such as Sonchus oleraceus and Bidens pilosa, as stereoisomers. They occur either as the naturally abundant RR-chicoric acid (RR-CA), or the less abundant RS-chicoric acid (RS-CA), also known as meso-chicoric acid. To date, little is known about the biological activity of RS-CA, but there is evidence of its anti-HIV (human immunodeficiency virus) properties. In this study, a reliable analytical method was developed to distinguish between the two stereoisomers detected in S. oleraceus and B. pilosa. Structure identification used liquid chromatography–mass spectrometry (LC-MS) in combination with ultraviolet radiation (UV) -induced geometrical isomerization, molecular dynamics (MD) simulations, and density functional theory (DFT) models. Optimized structures from DFT calculations were used for docking studies against the HIV-1 integrase enzyme. Different retention times on the reverse phase chromatograms revealed the plants produce two different CA stereoisomers: S. oleraceus produced the RR-CA isomer, while B. pilosa produced the RS-CA isomer. DFT results demonstrated the RR-CA molecule was more stable than RS-CA due to the stabilizing force of intra-molecular hydrogen bonding. Differences in the HIV-1 integrase enzyme binding modes were observed, with the RR-CA being a more potent inhibitor than the RS-CA molecule. The results highlight the significance of plant metabolite structural complexity from both chemical and biological perspectives. Artificial formation of geometrical isomers, in combination with the predictive ability of DFT models and the resolving power of the LC-MS, can be exploited to distinguish closely related compounds, in particular stereoisomers.

chicoric acid, RR-chicoric acid, RS-chicoric acid,↗
DOE OSTI2017

Ambient aging of rhenium filaments used in thermal ionization mass spectrometry: Growth of oxo-rhenium crystallites and anti-aging strategies

Degassing is a common preparation technique for rhenium filaments used for thermal ionization mass spectrometric analysis of actinides, including plutonium. Although optimization studies regarding degassing conditions have been reported, little work has been done to characterize filament aging after degassing. In this study, the effects of filament aging after degassing were explored to determine a “shelf-life” for degassed rhenium filaments, and methods to limit filament aging were investigated. Zone-refined rhenium filaments were degassed by resistance heating under high vacuum before exposure to ambient atmosphere for up to 2 months. After degassing the nucleation and preferential growth of oxo-rhenium crystallites on the surface of polycrystalline rhenium filaments was observed by atomic force microscopy and scanning electron microscopy (SEM). Compositional analysis of the crystallites was conducted using SEM-Raman spectroscopy and SEM energy dispersive X-ray spectroscopy, and grain orientation at the metal surface was investigated by electron back-scatter diffraction mapping. Spectra collected by SEM-Raman suggest crystallites are composed primarily of perrhenic acid. The relative extent of growth and crystallite morphology were found to be grain dependent and affected by the dissolution of carbon into filaments during annealing (often referred to as carbonization or carburization). Crystallites were observed to nucleate in region specific modes and grow over time through transfer of material from the surface. Factors most likely to affect the rates of crystallite growth include rhenium substrate properties such as grain size, orientation, levels of dissolved carbon, and relative abundance of defect sites; as well as environmental factors such as length of exposure to oxygen and relative humidity. Thin (~180 nm) hydrophobic films of poly(vinylbenzyl chloride) were found to slow the growth of oxo-rhenium crystallites on the filament surfaces and may serve as an alternative carbon source for filament carburization.

36 MATERIALS SCIENCE↗
NASA NTRS1986

Dry etching of beta-SiC in CF4 and CF4 + O2 mixtures

Dry etching of cubic (100) beta-SiC single-crystal thin films produced via chemical-vapor deposition (CVD) has been performed in CF4 and CF4 + O2 mixtures, in both the reactive-ion-etching (RIE) and plasma-etching modes. The latter process yielded measurable etch rates, but produced a dark surface layer which appears, from the results of secondary-ion mass spectrometry, to be residual SiC. The RIE samples had no residual layer, but Auger electron spectroscopy did reveal a C-rich surface. The optimal RIE conditions were obtained with 10 sccm of pure CF4 at 40 mtorr and a power density of 0.548 W/sq cm, giving an etch rate of 23.3 nm/min. Neither the increase of temperature between 293 and 573 K, nor the incremental addition of O2 to CF4 to 50 percent, produced any strong effect on the etch rates of SiC during RIE. Pictorial evidence of fine line structures produced by RIE of beta-SiC films are also presented.

Palmour, J. W.↗
NASA NTRS2000

A DNA enzyme with N-glycosylase activity

In vitro evolution was used to develop a DNA enzyme that catalyzes the site-specific depurination of DNA with a catalytic rate enhancement of about 10(6)-fold. The reaction involves hydrolysis of the N-glycosidic bond of a particular deoxyguanosine residue, leading to DNA strand scission at the apurinic site. The DNA enzyme contains 93 nucleotides and is structurally complex. It has an absolute requirement for a divalent metal cation and exhibits optimal activity at about pH 5. The mechanism of the reaction was confirmed by analysis of the cleavage products by using HPLC and mass spectrometry. The isolation and characterization of an N-glycosylase DNA enzyme demonstrates that single-stranded DNA, like RNA and proteins, can form a complex tertiary structure and catalyze a difficult biochemical transformation. This DNA enzyme provides a new approach for the site-specific cleavage of DNA molecules.

Non-NASA Center↗
DOE OSTI2023

Integrated data-driven and experimental approaches to accelerate lead optimization targeting SARS-CoV- 2 main protease

Identification of potential therapeutic candidates can be expedited by integrating computational modeling with domain aware machine learning (ML) approaches followed by experimental validation. Generative deep learning models have been recently developed that can generate thousands of new candidates, but their physiochemical properties are typically not optimized. Using our deep learning models and a scaffold as a starting point, we generated tens of thousands of compounds for SARS-CoV-2 M pro that preserve the core scaffold. Here we utilized and implemented several computational tools such as structural alert and toxicity analysis, high throughput virtual screening, ML-based 3D quantitative structure–activity relationships, multi-parameter optimization, and graph neural networks on libraries of generated candidates to predict biological activity and binding affinity a priori. From these collective computational results, eight promising candidates were identified and tested experimentally using Native Mass Spectrometry (MS) and FRET-based functional assays. Two compounds, with quinazoline-2-thiol and acetylpiperidine core moiety showed IC 50 values in the low micromolar range: 2.95±0.0017 µM and 3.41±0.0015 µM, respectively. The molecular dynamics simulations further highlight that binding of these compounds results in allosteric modulations in the chain B and the interface domains of the M pro . The key fragments from these top hits can be used as input for closed loop lead optimization in the integrated pipeline.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

Photovoltaic Properties of Selenized CuGa/In Films with Varied Compositions

Thin CuGa/In films with varied compositions were deposited by co-evaporation and then selenized in situ with evaporated selenium. The selenized Cu(In, Ga)Se2 absorbers were used to fabricate 390 solar cells. Cu/(Ga+In) and Ga/(Ga+In) (Cu/III and Ga/III) were independently varied, and photovoltaic performance was optimal at Cu/III of 77-92% for all Ga/III compositions studied (Ga/III ~ 30, 50, and 70%). The best absorbers at each Ga/III composition were characterized with time-resolved photoluminescence, scanning electron microscopy, and secondary ion mass spectrometry, and devices were studied with temperature-dependent current density-voltage, light and electrical biased quantum efficiency, and capacitance-voltage. The best cells with Ga/III ~ 30, 50, and 70% had efficiencies of 14.5, 14.4, and 12.2% and maximum power temperature coefficients of -0.496, -0.452, and -0.413%/degrees C, respectively. This resulted in the Ga/III ~ 50% champion having the highest efficiency at temperatures greater than 40 degrees C, making it the optimal composition for practical purposes. This optimum is understood as a result of the absorber's band gap grading- where minimum band gap dominates short-circuit current density, maximum space charge region band gap dominates open-circuit voltage, and average absorber band gap dominates maximum power temperature coefficient.

14 SOLAR ENERGY↗
DOE OSTI2019

Effect of Chemical Composition on the Microstructure and Properties of the Ag-Ga-Ge Alloys

This study presents a comparison of thermodynamically calculated phase compositions of Ag-Ga-Ge alloys at fixed temperatures with phase analysis results of alloys annealed at respective temperatures. Three isothermal sections of the Ag-Ga-Ge system at 25, 100 and 300 °C have been extrapolated using optimized thermodynamic parameters from the literature. An experimental analysis of the microstructure was carried out using optical microscopy, scanning electron microscopy and energy-dispersive spectrometry. Results obtained by x-ray powder diffraction methods (identified phases and lattice parameters) were compared with the results of the predicted phase equilibria. Good overall agreement between experimental and calculated values was obtained. The Brinell hardness and electrical conductivity of selected alloys were measured and obtained results were analyzed with respect to their overall compositions and phase constituents.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Screening of the Suzuki Cross-Coupling Reaction Using Desorption Electrospray Ionization in High-Throughput and in Leidenfrost Droplet Experiments

Suzuki cross-coupling is a widely performed reaction, typically using metal catalysts under heated conditions. Acceleration of the Suzuki cross-coupling reaction has been previously explored in microdroplets using desorption electrospray ionization mass spectrometry (DESI-MS). Building upon previous work, presented here is the use of a high-throughput DESI-MS screening system to identify optimal reaction conditions. Multiple reagents, bases, and stoichiometries were screened using the automated system at rates that approach 10,000 reaction mixture systems per hour. The DESI-MS system utilizes reaction acceleration in microdroplets to allow rapid screening. The results of screening of an array of reaction mixtures using this technique are presented as product ion images via standard MS imaging software, facilitating quick readout. Instructive comparisons are provided with another method of generating droplets for reaction acceleration—the Leidenfrost technique. Acceleration factors greater than 200 were measured for brominated substrates, paralleling the DESI-MS results. Acceleration factors dropped to near unity with highly substituted pyridines, attributable to a steric effect. The reaction proceeded in the absence of a base in Leidenfrost droplets although no product formation was seen without base in the bulk or in the DESI-MS screening experiments. These differences between Leidenfrost chemistry and the bulk and in droplets formed in high-throughput DESI are tentatively attributed to extremes of pH associated with the surfaces of Leidenfrost droplets. .

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Metabolic Source Isotopic Pair Labeling and Genome-Wide Association Are Complementary Tools for the Identification of Metabolite-Gene Associations in Plants

The optimal extraction of information from untargeted metabolomics analyses is a continuing challenge. Here, we describe an approach that combines stable isotope labeling, liquid chromatography– mass spectrometry (LC–MS), and a computational pipeline to automatically identify metabolites produced from a selected metabolic precursor. Here, we identified the subset of the soluble metabolome generated from phenylalanine (Phe) in Arabidopsis thaliana, which we refer to as the Phe-derived metabolome (FDM) In addition to identifying Phe-derived metabolites present in a single wild-type reference accession, the FDM was established in nine enzymatic and regulatory mutants in the phenylpropanoid pathway. To identify genes associated with variation in Phe-derived metabolites in Arabidopsis, MS features collected by untargeted metabolite profiling of an Arabidopsis diversity panel were retrospectively annotated to the FDM and natural genetic variants responsible for differences in accumulation of FDM features were identified by genome-wide association. Large differences in Phe-derived metabolite accumulation and presence/absence variation of abundant metabolites were observed in the nine mutants as well as between accessions from the diversity panel. Many Phe-derived metabolites that accumulated in mutants also accumulated in non-Col-0 accessions and was associated to genes with known or suspected functions in the phenylpropanoid pathway as well as genes with no known functions. Overall, we show that cataloguing a biochemical pathway’s products through isotopic labeling across genetic variants can substantially contribute to the identification of metabolites and genes associated with their biosynthesis.

09 BIOMASS FUELS↗
DOE OSTI2025

X-ray crystallographic and hydrogen deuterium exchange studies confirm alternate kinetic models for homolog insulin monomers

Despite the crucial role of various insulin analogs in achieving satisfactory glycemic control, a comprehensive understanding of their in-solution dynamic mechanisms still holds the potential to further optimize rapid insulin analogs, thus significantly improving the well-being of individuals with Type 1 Diabetes. Here, we employed hydrogen-deuterium exchange mass spectrometry to decipher the molecular dynamics of newly modified and functional insulin analog. A comparative analysis of H/D dynamics demonstrated that the modified insulin exchanges deuterium atoms faster and more extensively than the intact insulin aspart. Additionally, we present new insights derived from our 2.5 Å resolution X-ray crystal structure of modified hexamer insulin analog at ambient temperature. Furthermore, we obtained a distinctive side-chain conformation of the Asn3 residue on the B chain (AsnB3) by operating a comparative analysis with a previously available cryogenic rapid-acting insulin structure (PDB_ID: 4GBN). The experimental conclusions have demonstrated compatibility with modified insulin’s distinct cellular activity, comparably to aspart. Additionally, the hybrid structural approach combined with computational analysis employed in this study provides novel insight into the structural dynamics of newly modified and functional insulin vs insulin aspart monomeric entities. It allows further molecular understanding of intermolecular interrelations driving dissociation kinetics and, therefore, a fast action mechanism.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Single-Particle Isotopic Analysis Using the Liquid Sampling-Atmospheric Pressure Glow Discharge Microplasma Coupled to an Orbitrap Mass Spectrometer

Isotope ratio (IR) determinations on individual particles can provide valuable information relative to the sample, including processing and dating, which could be valuable to geological and nuclear material analysis communities. In comparison to “bulk” measurements, in which all particle information is lost and homogenized within a sample, “particle” measurements allow for fingerprinting and can provide unique insights related to the sample’s nano- and micro- compositions. Furthermore, the complex nature of particles, with potential isobaric interferences from either the matrix or other elements within the same particle, poses a significant analytical challenge for conventional mass spectrometry platforms employed for elemental analysis due to their limited mass resolution. Presented here is the first demonstration of an ultrahigh resolution method for single particle (SP) isotopic analysis using the liquid sampling-atmospheric pressure glow discharge (LS-APGD) microplasma ionization source coupled to an Orbitrap mass spectrometer and FTMS Booster X2T acquisition/processing system. For proof of concept, well-characterized CeO 2 microparticles with a nominal diameter of 1.0 μm were analyzed at a mass resolution of ∼330,000. Important instrumental parameters were optimized to enable the detection of single particles. The 142 Ce/ 140 Ce ratio of individual particles and the population average were determined and compared to an SP inductively coupled plasma time-of-flight mass spectrometry (ICP-TOF-MS) analysis. The isotopic accuracy and precision were determined by two methods and found to be in good agreement with the SP-ICP-TOF-MS method, with the linear regression slope method providing a more accurate ratio, showing a ∼1.4% relative difference from the ratio determined from a particle digest. The encouraging performance of the method was further supported by a determined detection limit of 2.9 fg ( 142 Ce). The developed method is anticipated to overcome many of the challenges posed by isobaric interferences encountered in conventional mass spectrometry techniques when analyzing real-world samples for particle isotopic composition.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗