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At least 1,243 records · Page 69

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DOE OSTI2022

Using Macro- and Microscale Preservation in Vertebrate Fossils as Predictors for Molecular Preservation in Fluvial Environments

Exceptionally preserved fossils retain soft tissues and often the biomolecules that were present in an animal during its life. The majority of terrestrial vertebrate fossils are not traditionally considered exceptionally preserved, with fossils falling on a spectrum ranging from very well-preserved to poorly preserved when considering completeness, morphology and the presence of microstructures. Within this variability of anatomical preservation, high-quality macro-scale preservation (e.g., articulated skeletons) may not be reflected in molecular-scale preservation (i.e., biomolecules). Excavation of the Hayden Quarry (HQ; Chinle Formation, Ghost Ranch, NM, USA) has resulted in the recovery of thousands of fossilized vertebrate specimens. This has contributed greatly to our knowledge of early dinosaur evolution and paleoenvironmental conditions during the Late Triassic Period (~212 Ma). The number of specimens, completeness of skeletons and fidelity of osteohistological microstructures preserved in the bone all demonstrate the remarkable quality of the fossils preserved at this locality. Because the Hayden Quarry is an excellent example of good preservation in a fluvial environment, we have tested different fossil types (i.e., bone, tooth, coprolite) to examine the molecular preservation and overall taphonomy of the HQ to determine how different scales of preservation vary within a single locality. We used multiple high-resolution mass spectrometry techniques (TOF-SIMS, GC-MS, FT-ICR MS) to compare the fossils to unaltered bone from extant vertebrates, experimentally matured bone, and younger dinosaurian skeletal material from other fluvial environments. FT-ICR MS provides detailed molecular information about complex mixtures, and TOF-SIMS has high elemental spatial sensitivity. Using these techniques, we did not find convincing evidence of a molecular signal that can be confidently interpreted as endogenous, indicating that very good macro- and microscale preservation are not necessarily good predictors of molecular preservation.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

DNA adducts form in mouse lung and liver after oral naphthalene exposure

Naphthalene is a ubiquitous combustion product and environmental contaminant with known human exposure. Chronic exposure to naphthalene vapor leads to respiratory tumor formation in rodents. Naphthalene forms DNA adducts (precursors to genotoxicity) in tissue explants but it is unclear if this occurs in vivo. Wild-type C57BL/6 mice were orally exposed to 50 mg/kg 14 C-naphthalene. Naphthalene-DNA adducts were detected by accelerator mass spectrometry at 2- to 72-h post-exposure in both lung and liver, with decreasing abundance over time. Adducts persisted even at 72-h after exposure, which indicates possible evasion of DNA repair and potential to contribute to mutagenesis.

60 APPLIED LIFE SCIENCES↗

NASA NTRS2016

Characterization of Low Pressure Cold Plasma in the Cleaning of Contaminated Surfaces

The characterization of low pressure cold plasma is a broad topic which would benefit many different applications involving such plasma. The characterization described in this paper focuses on cold plasma used as a medium in cleaning and disinfection applications. Optical Emission Spectroscopy (OES) and Mass Spectrometry (MS) are the two analytical methods used in this paper to characterize the plasma. OES analyzes molecules in the plasma phase by displaying the light emitted by the plasma molecules on a graph of wavelength vs. intensity. OES was most useful in identifying species which may interact with other molecules in the plasma, such as atomic oxygen or hydroxide radicals. Extracting useful data from the MS is done by filtering out the peaks generated by expected molecules and looking for peaks caused by foreign ones leaving the plasma chamber. This paper describes the efforts at setting up and testing these methods in order to accurately and effectively characterize the plasma.

cold plasma characterization↗

DOE OSTI2021

Composition and Structure of Fluorescent Graphene Quantum Dots Generated by Enzymatic Degradation of Graphene Oxide

The broad applications of carbon nanomaterials (CNMs) in both materials and life sciences necessitate investigation of their metabolites due to the inevitable contact of CNMs and biological systems. Graphene oxide (GO), along with other types of CNMs, can be enzymatically degraded by myeloperoxidase (MPO), an enzyme released during the innate immune response. However, the enzymatic degradation products are neither well-defined nor well-understood. Some products generated during MPO-catalyzed degradation of GO could emit blue photoluminescence (PL) and were simply dubbed graphene quantum dots (GQDs) without further elucidating their structures. In this work, we use liquid chromatography-mass spectrometry (LC-MS) to isolate and elucidate chemical structures of the MPO-catalyzed degradation products. A general chemical formula screening workflow was developed for the GQDs, which are in the form of polyaromatic hydrocarbons (PAHs), obtained in the degradation products. Structures of the PAHs responsible for the blue PL were further proposed using density functional theory (DFT) calculations. Our results indicated that structures with several conjugated benzene rings are likely to generate the observed PL. This work provides insights into the mechanism of enzymatic degradation and open opportunities for fluorescence imaging of GO in biological systems.

composition and structure screening↗

DOE OSTI2025

Challenges in the study of chemistry and photochemistry at air–water interfaces: Toward in situ monitoring of reaction kinetics with spectroscopic techniques

Air–water interfaces, including those on droplet surfaces, have been the subject of many recent experiments due to their propensity for unique chemistry. Here, in this study, an overview of some recent advancements in understanding interfacial reaction kinetics is provided, highlighting non-surface-specific methods—such as mass spectrometry—compared with the advantages of surface-specific techniques—such as reflection–absorption spectroscopy, sum frequency generation, and photoelectron spectroscopy. This Perspective discusses the information depth and time constraints of common surface-specific spectroscopic methods that need to be addressed to monitor interfacial chemistry in situ and uses a few key examples from the literature as case studies. It concludes by advocating for the continued development of advanced spectroscopic methods to further investigate interfacial chemistry, underscoring the need for interdisciplinary collaboration to bridge the gap between molecular-level insights and macroscopic observations in future research.

Air-water interface↗

DOE OSTI2024

Phosphorus recycling by mineral-catalyzed ribonucleotide cleavage on iron and manganese oxides

Abstract Phosphorus is an essential element influencing both food security via plant fertilization, and water pollution through excessive phosphorus use, yet the phosphorus cycle in ecosystems is poorly known. In particular, beyond adsorption, the role of iron and manganese oxides in catalyzing the abiotic dephosphorylation of biomolecules is debated. Here, we studied the reactions of ribonucleotides, containing different phosphate bonding, with goethite, hematite, and birnessite. We employed both high-resolution mass spectrometry of solution species and molecular modeling simulations of ribonucleotide-mineral complexes. Results disclose an up to fivefold preferential hydrolytic cleavage of a phosphoanhydride bond over a phosphoester bond, indicating that mineral-catalyzed reactions reflect the hierarchy reported for the activity of phosphatase enzymes. The fourfold higher catalytic reactivity of goethite and birnessite versus hematite is explained by mineral-specific binding rather than surface area differences. Corresponding simulated adsorbate conformations at the water–mineral interfaces are proposed. Overall, our findings provide new insights on the catalytic recycling of organic phosphorus species by mineral oxides.

58 GEOSCIENCES↗

DOE OSTI2025

Growth and structure of alpha-Ta films for quantum circuit integration

Tantalum films incorporated into superconducting circuits have exhibited low surface losses, resulting in long-lived qubit states. The remaining loss pathways originate in microscopic defects that manifest as two level systems (TLSs) at low temperatures. These defects limit performance, so careful attention to tantalum film structures is critical for optimal use in quantum devices. In this work, we investigate the growth of tantalum using magnetron sputtering on sapphire, Si, and photoresist substrates. In the case of sapphire, we present procedures for the growth of fully-oriented films with α-Ta [1 1 1]//Al2O3 [0 0 0 1] and α-Ta [1 −1 0]//Al2O3 [1 0 −1 0] orientational relationships and having residual resistivity ratio (RRR) ∼ 60 for 220 nm thick films. On Si, we find a complex grain texturing with Ta [1 1 0] normal to the substrate and RRR ∼ 30. We further demonstrate airbridge fabrication using Nb to nucleate α-Ta on photoresist surfaces. For the films on sapphire, resonators show TLS-limited quality factors of 1.3 ± 0.3 × 106 at 10 mK (for a waveguide gap and conductor width of 3 and 6 μm, respectively). Structural characterization using scanning electron microscopy, x-ray diffraction, low temperature transport, secondary ion mass spectrometry, and transmission electron microscopy reveal the dependence of residual impurities and screw dislocation density on processing conditions. The results provide practical insights into the fabrication of advanced superconducting devices including qubit arrays and guide future works on crystallographically deterministic qubit fabrication.

42 ENGINEERING↗

DOE OSTI2020

CO as a Probe Molecule to Study Surface Adsorbates during Electrochemical Oxidation of Propene

A major challenge in the electrochemical oxidation of hydrocarbons is understanding the formation of intermediate species, some of which continue to react, while others are non-reactive or poisonous species that block adsorption of further reactants. Herein we investigate the identity and behavior of adsorbates formed during partial oxidation of propene. We employ two techniques: Electrochemistry-Mass Spectrometry (EC-MS) and Attenuated Total Reflection Infrared Spectroscopy (ATR-FTIR). In both cases, we use CO as a probe molecule, to perturb the ad-layer of propene intermediates. In the EC-MS experiments, propene and its intermediates were quantified by triggering their desorption via displacement with CO. We show evidence for at least two distinct classes of propene adsorbates, via CO displacement and electrochemical stripping. A redshift in the ν(C–O) mode was observed, during IR spectroscopy, reflecting the chemical environment arising from strongly bound propene intermediates.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Tocopherol controls D1 amino acid oxidation by oxygen radicals in Photosystem II

Photosystem II (PSII) is an intrinsic membrane protein complex that functions as a light-driven water:plastoquinone oxidoreductase in oxygenic photosynthesis. Electron transport in PSII is associated with formation of reactive oxygen species (ROS) responsible for oxidative modifications of PSII proteins. In this study, oxidative modifications of the D1 and D2 proteins by the superoxide anion (O 2 •- ) and the hydroxyl (HO•) radicals were studied in WT and a tocopherol cyclase (vte1) mutant, which is deficient in the lipid-soluble antioxidant α-tocopherol. In the absence of this antioxidant, high-resolution tandem mass spectrometry was used to identify oxidation of D1: 130 E to hydroxyglutamic acid by O 2 •- at the Pheo D1 site. Additionally, D1: 246 Y was modified to either tyrosine hydroperoxide or dihydroxyphenylalanine by O 2 •- and HO • , respectively, in the vicinity of the nonheme iron. We propose that α-tocopherol is localized near PheoD1 and the nonheme iron, with its chromanol head exposed to the lipid–water interface. This helps to prevent oxidative modification of the amino acid’s hydrogen that is bonded to PheoD1 and the nonheme iron (via bicarbonate), and thus protects electron transport in PSII from ROS damage.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Differences in the dynamics of the tandem-SH2 modules of the Syk and ZAP-70 tyrosine kinases

The catalytic activity of Syk-family tyrosine kinases is regulated by a tandem Src homology 2 module (tSH2 module). In the autoinhibited state, this module adopts a conformation that stabilizes an inactive conformation of the kinase domain. The binding of the tSH2 module to phosphorylated immunoreceptor tyrosine-based activation motifs necessitates a conformational change, thereby relieving kinase inhibition and promoting activation. We determined the crystal structure of the isolated tSH2 module of Syk and find, in contrast to ZAP-70, that its conformation more closely resembles that of the peptide-bound state, rather than the autoinhibited state. Hydrogen–deuterium exchange by mass spectrometry, as well as molecular dynamics simulations, reveal that the dynamics of the tSH2 modules of Syk and ZAP-70 differ, with most of these differences occurring in the C-terminal SH2 domain. Our data suggest that the conformational landscapes of the tSH2 modules in Syk and ZAP-70 have been tuned differently, such that the autoinhibited conformation of the Syk tSH2 module is less stable. This feature of Syk likely contributes to its ability to more readily escape autoinhibition when compared to ZAP-70, consistent with tighter control of downstream signaling pathways in T cells.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

The development and evolution of biological AMS at Livermore: a perspective

Biological accelerator mass spectrometry (AMS) provides ultrasensitive carbon-14 isotopic analysis enabling a deeper understanding of human health concerns by enabling quantification of pharmacokinetics and other molecular endpoints directly in humans. It enables environmentally and human relevant studies of metabolic pathways through the use of very low concentrations of labeled metabolic substrates in cells and organisms. Here, we discuss why AMS is an important tool for the biosciences, the development and evolution of biological AMS at Livermore and discuss technical refinements that will improve the efficiency of operation for the measurement of ultra-trace levels of 14 C, which, long term, will enable greater ease of use and sample throughput.

47 OTHER INSTRUMENTATION↗

DOE OSTI2023

Arsenic Exposure Causes Global Changes in the Metalloproteome of Escherichia coli

Arsenic is a toxic metalloid with differential biological effects, depending on speciation and concentration. Trivalent arsenic (arsenite, AsIII) is more toxic at lower concentrations than the pentavalent form (arsenate, AsV). In E. coli, the proteins encoded by the arsRBC operon are the major arsenic detoxification mechanism. Our previous transcriptional analyses indicate broad changes in metal uptake and regulation upon arsenic exposure. Currently, it is not known how arsenic exposure impacts the cellular distribution of other metals. This study examines the metalloproteome of E. coli strains with and without the arsRBC operon in response to sublethal doses of AsIII and AsV. Size exclusion chromatography coupled with inductively coupled plasma mass spectrometry (SEC-ICPMS) was used to investigate the distribution of five metals (56Fe, 24Mg, 66Zn, 75As, and 63Cu) in proteins and protein complexes under native conditions. Parallel analysis by SEC-UV-Vis spectroscopy monitored the presence of protein cofactors. Together, these data reveal global changes in the metalloproteome, proteome, protein cofactors, and soluble intracellular metal pools in response to arsenic stress in E. coli. This work brings to light one outcome of metal exposure and suggests that metal toxicity on the cellular level arises from direct and indirect effects.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Gas-phase stability of large lanthanide:diglycolamide clusters evaluated using collision-induced dissociation

Efficient utilization of long-term deep geologic storage repositories is critical for the large-scale deployment of nuclear energy. As the minor actinides (americium and curium) are the largest contributor to the decay heat of used nuclear fuel after a few hundred years, their removal from used fuel prior to disposal can significantly increase the amount of waste that can be stored in a given volume. The development of ligands that can effectively separate the minor actinides from other components of used nuclear fuel are crucial to efficient utilization of geological storage repositories. N,N,N’,N’-tetraoctyl diglycolamide (TODGA) is a promising extractant for the separation of lanthanides and the minor actinides from other components of used nuclear fuel. While the use of TODGA in f-element separations has been investigated in process-based formulations, gas-phase metal ion cluster experiments enable the study of covalent interactions in reprocessing systems absent from solvent effects. Exploring fundamental differences in lanthanide-ligand covalent interactions can impact the development and implementation of actinide-lanthanide separation systems in nuclear fuels reprocessing. In this study, lanthanide-TODGA clusters were synthesized in the gas-phase and identified using mass spectrometry fragmentation experiments. Large europium and samarium clusters were identified that contained up to 8 and 10 bound TODGA ligands, respectively; this was surprising due to the size and multidentate binding that is normal for TODGA. In addition, while smaller clusters showed evidence of sequential ligand fragmentation, larger clusters displayed the loss of neutral TODGA with applied collision voltage. Interestingly, the voltage required for this removal decreased as more TODGA ligands were bound to the metal, suggesting that the metal coordination sphere was becoming more saturated and TODGA ligands were more weakly bound as the clusters got larger.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2025

Real-Time Measurements of Gas-Phase Medium-Chain Chlorinated Paraffins Reveal Daily Changes in Gas-Particle Partitioning Controlled by Ambient Temperature

Chlorinated paraffins (CPs) are synthetic polychlorinated n-alkanes produced as mixtures of a range of C x Cl y H 2x–y+2 formulas. CPs have numerous industrial applications but are toxic, long-lived, and environmentally ubiquitous with environmental releases occurring throughout their production, use, and disposal. Short-chain chlorinated paraffins (SCCPs, C 10–13 ) have been regulated by the United States Environmental Protection Agency since 2009 and by the Stockholm Convention since 2017. SCCP regulation is expected to cause increased production of medium-chain chlorinated paraffins (MCCPs; C 14–17 ), which are currently under consideration for Stockholm Convention regulations. Thus, there is a need to improve the understanding of MCCP environmental transport, distribution, and fate. Existing measurements are limited in their spatial and temporal coverage. Measurements of CP atmospheric loading are particularly scarce. Historically, these measurements have required long sampling times, obscuring the temporal behavior of atmospheric CPs. We report real-time in situ measurements of 18 gas-phase MCCPs. These measurements were made in the United States Southern Great Plains with nitrate ion chemical ionization mass spectrometry (NO 3 –CIMS). Here, the estimated average lower-limit concentration of MCCPs is on the order of single-digit ng/m 3 . MCCP diel behavior is partially explained by gas-particle partitioning with implications for MCCP transport and lifetimes.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Following O and OH in He/O 2 and He/H 2 O gas mixtures—from the gas phase through the liquid phase to modifications on a biological sample

Abstract Applied cold atmospheric plasma allows for the controlled delivery of reactive oxygen and nitrogen species tailored for specific applications. Through the manipulation of the plasma parameters, feed gases, and careful consideration of the environment surrounding the treatment target, selective chemistries that preferentially influence the target can be produced and delivered. To demonstrate this, the COST reference microscale atmospheric pressure plasma jet is used to study the generation and transport of O and ⋅ OH from the gas phase through the liquid to the biological model target cysteine. Relative and absolute species densities of ⋅ OH and O are measured in the gas phase through laser induced fluorescence (LIF) and two-photon absorption LIF respectively. The transport of these species is followed into the liquid phase by hydrogen peroxide quantification and visualized by a fluorescence assay. Modifications to the model biological sample cysteine exposed to ⋅ OH and H 2 O 2 dominated chemistry (He/H 2 O (0.25%)) and O dominated chemistry (He/O 2 (0.6%)) is measured by FTIR spectroscopy. The origin of these species that modify cysteine is considered through the use of heavy water (H 2 18 O) and mass spectrometry. It is found that the reaction pathways differ significantly for He/O 2 and He/H 2 O. Hydrogen peroxide is formed mainly in the liquid phase in the presence of a substrate for He/O 2 whereas for He/H 2 O it forms in the gas phase. The liquid chemistry resulting from the He/O 2 admixture mainly targets the sulfur moiety of cysteine for oxidation up to irreversible oxidation states, while He/H 2 O treatment leads preferentially to reversible oxidation products. The more O or OH/H 2 O 2 dominated chemistry produced by the two gas admixtures studied offers the possibility to select species for target modification.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2025

Spatial Glycomics and Kidney Disease

Glycans are critical for the kidney's physiological and pathological cellular functions, and our ability to reveal their spatial distributions within tissues has helped us reveal how these carbohydrate moieties are involved in many of these processes. This review discusses the role of different types of glycans in kidney biology and disease, common approaches used for glycan imaging, and how glycan imaging has helped us better understand kidney pathology. Here, we mainly focus on emerging methods using mass spectrometry imaging (MSI) because this technology is untargeted and provides complete information on glycan composition compared to the other methods, such as lectin and metabolite labeling, which are targeted and often inform only on the specific part of a glycan structure. We especially focus on protein N-glycosylation, as this is one of the most common post-translational modifications, and these moieties play a vital role in renal structure and function. The recent advancements in MSI of N-glycans we reviewed have provided new insights into the pathophysiology of the kidney and paved the way for clinical application.

60 APPLIED LIFE SCIENCES↗

NASA NTRS2021

Thermodynamics of the Lu2O3 – SiO2 system and comparison to other Rare Earth Silicates

Environmental barrier coatings are necessary to protect SiC based ceramics and composites from water vapor degradation in harsh engine environments. Currently, rare earth (RE) silicates are the most promising systems to protect SiC based ceramics and composites. This protection is largely based on reduced silica activity in these rare earth silicates which results in a lowered reactivity with water vapor. To that end, previous Knudsen effusion mass spectrometry (KEMS) studies have explored RE = Yb, Y silicates to measure the reduced silica activity and subsequent water vapor reactivity. Similarly, this work employs the KEMS technique to measure the SiO(g) vapor pressure in Lu containing RE silicates to calculate the activity of silica within the monosilicate [log(a(SiO2)) = -2351.1*1/T-1.6731] and the disilicate (log(a(SiO2)) = -4884.0*1/T + 2.2208) as a function of temperature. The enthalpies of formation for Lu monosilicate from the oxides and the elements were calculated to be -45±3 kJ/mol at 1550 K and -2831.1±12 kJ/mol at 298 K, respectively. The measured enthalpy of formation and those found in literature are compared to modeled values from density functional theory and those estimated using electronegativity.

Knudesen Effusion Mass Spectrometry↗

NASA NTRS2015

Thermochemistry of Silicates

The thermodynamic properties of vapor and condensed phases of silicates are crucial in many fields of science. These quantities address fundamental questions on the formation, stability, transformation, and physical properties of silicate minerals and silicate coating compositions. Here the thermodynamic activities of silica and other species in solid solution have been measured by the analysis of the corresponding high temperature vapors using Knudsen Effusion Mass Spectrometry (KEMS). In first set of experiments KEMS has been used to examine the volatility sequence of species (Fe, SiO, Mg, O2 and O) present in the vapor phase during heating of fosterite-rich olivine (Fo93Fa7) up to 2400 C and to measure the Fe, SiO and Mg activities in its solid solution. The data of fosterite-rich olivine are essential for thermochemical equilibrium models to predict the atmospheric and surface composition of hot, rocky exoplanets (Lava Planets). In the second set of experiments the measured thermodynamic activities of the silica in Y2O3-SiO2 and Yb2O3-SiO2 systems are used to assess their reactivity and degradation recession as environmental barrier coatings (EBCs) in combustion environments (e.g. non-moveable parts of gas turbine engine).

Silicates↗