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At least 721 records · Page 40
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Locating Methyl-Etherified and Methyl-Esterified Uronic Acids in the Plant Cell Wall Pectic Polysaccharide Rhamnogalacturonan II

Rhamnogalacturonan II (RG-II) is a structurally complex pectic polysaccharide that exists as a borate ester cross-linked dimer in the cell walls of all vascular plants. The glycosyl sequence of RG-II is largely conserved, but there is evidence that galacturonic acid (GalA) methyl etherification and glucuronic acid (GlcA) methyl esterification vary in the A sidechain across plant species. Methyl esterification of the galacturonan backbone has also been reported but not confirmed. Here we describe a new procedure, utilizing aq. sodium borodeuteride (NaBD4)-reduced RG-II, to identify the methyl esterification status of backbone GalAs. Our data suggest that up to two different GalAs are esterified in the RG-II backbone. We also adapted a procedure based on methanolysis and NaBD4 reduction to identify 3-, 4-, and 3,4-O-methyl GalA in RG-II. These data, together with matrix-assisted laser desorption/ionization–time-of-flight mass spectrometry (MALDI-TOF) MS analysis of sidechain A generated from selected RG-IIs and their NaBD4-reduced counterparts, suggest that methyl etherification of the ß-linked GalA and methyl esterification of the GlcA are widespread. Nevertheless, the extent of these modifications varies between plant species. Our analysis of the sidechain B glycoforms in RG-II from different dicots and nonpoalean monocots suggests that this sidechain has a minimum structure of an O-acetylated hexasaccharide (Ara-[MeFuc]-Gal-AceA-Rha-Api-). To complement these studies, we provide further evidence showing that dimer formation and stability in vitro is cation and borate dependent. Taken together, our data further refine the primary sequence and sequence variation of RG-II and provide additional insight into dimer stability and factors controlling dimer self-assembly.

BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Organic amendments change soil organic C structure and microbial community but not total organic matter on sub-decadal scales

Organic C has many benefits for soil, but it is depleted by tillage and crop harvest, and especially so for biofuel crops. Accordingly, strategies such as partially retaining stover or planting a cover crop can help ameliorate the negative effect of C removal. We used a long-term field experiment to study the impacts of stover retention and planting cover crop on soil organic matter (SOM), its extractable components and the soil microbial community. SOM chemical composition characterization was determined by electrospray ionization (ESI) coupled with Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) in sequential water, methanol (MeOH), and chloroform (CHCl3) extracts. The characteristics of the soil bacterial community were measured by phospholipid fatty acid (PLFA), real-time quantitative PCR, and 16S rRNA gene sequence. The variations in total SOM content, total microbial biomass, and bacterial population were slight among treatments, but SOM chemical compounds, arbuscular mycorrhizal fungi (AMF) biomass, and bacterial structure changed significantly, and especially so in the coupled application of stover retention and cover crop. Specifically, stover retention enriched more lignin-like compounds in soil, whereas cover crop enriched more condensed hydrocarbons, and had more compounds with an aromaticity index (AI) >0.5. The bacterial community was not altered by the cover crop, but the corn stover retention increased the relative abundances of Myxococcales (Deltaproteobacteria) and decreased that of Actinobacteria. Redundancy analysis (RDA) further unveiled that the bacterial community in the stover treatments had significantly positive association with CHCl3-extracted chemical classes, i.e. unsaturated hydrocarbon and lipid with the coupled application (stover and cover crop), and lignin and protein with the single corn stover treatment. Taken together, our study shows how different C addition practices influence the molecular composition of SOM and the structure of soil microbial communities.

Xu, Jiangbin↗
DOE OSTI2023

Multiple highly expressed phospho enol pyruvate carboxylase genes have divergent enzyme kinetic properties in two C4 grasses

Abstract Background and Aims Phosphoenolpyruvate (PEP) carboxylase (PEPC) catalyses the irreversible carboxylation of PEP with bicarbonate to produce oxaloacetate. This reaction powers the carbon-concentrating mechanism (CCM) in plants that perform C4 photosynthesis. This CCM is generally driven by a single PEPC gene product that is highly expressed in the cytosol of mesophyll cells. We found two C4 grasses, Panicum miliaceum and Echinochloa colona, that each have two highly expressed PEPC genes. We characterized the kinetic properties of the two most abundant PEPCs in E. colona and P. miliaceum to better understand how the enzyme’s amino acid structure influences its function. Methods Coding sequences of the two most abundant PEPC proteins in E. colona and P. miliaceum were synthesized by GenScript and were inserted into bacteria expression plasmids. Point mutations resulting in substitutions at conserved amino acid residues (e.g. N-terminal serine and residue 890) were created via site-directed PCR mutagenesis. The kinetic properties of semi-purified plant PEPCs from Escherichia coli were analysed using membrane-inlet mass spectrometry and a spectrophotometric enzyme-coupled reaction. Key Results The two most abundant P. miliaceum PEPCs (PmPPC1 and PmPPC2) have similar sequence identities (>95 %), and as a result had similar kinetic properties. The two most abundant E. colona PEPCs (EcPPC1 and EcPPC2) had identities of ~78 % and had significantly different kinetic properties. The PmPPCs and EcPPCs had different responses to allosteric inhibitors and activators, and substitutions at the conserved N-terminal serine and residue 890 resulted in significantly altered responses to allosteric regulators. Conclusions The two, significantly expressed C4Ppc genes in P. miliaceum were probably the result of genomes combining from two closely related C4Panicum species. We found natural variation in PEPC’s sensitivity to allosteric inhibition that seems to bypass the conserved 890 residue, suggesting alternative evolutionary pathways for increased malate tolerance and other kinetic properties.

DiMario, Robert J. (ORCID:0000000250566868)↗
DOE OSTI2025

Influence of counterion substitution on the properties of imidazolium-based ionic liquid clusters

Due to their unique physiochemical properties that may be tailored for specific purposes, ionic liquids (ILs) have been investigated for various applications, including chemical separations, catalysis, energy storage, and space propulsion. The different cations and anions comprising ILs may be selected to optimize a range of desired properties, such as thermal stability, ionic conductivity, and volatility, leading to the designation of certain ILs as designer “green” solvents. The effect of counterions on the properties of ILs is of both fundamental scientific interest and technological importance. Herein, we report a systematic experimental and theoretical investigation of the size, charge, stability toward dissociation, and geometric/electronic structure of 1-ethyl-3-methyl imidazolium (EMIM)-based IL clusters containing two different atomic counterions (i.e., bromide [Br − ] and iodide [I − ]). This work extends our studies of EMIM + cations with atomic chloride (Cl − ) and molecular tetrafluoroborate (BF 4 − ) anions reported previously by Baxter et al. [Chem. Mater. 34, 2612 (2022)] and Zhang et al . [J. Phys. Chem. Lett. 11, 6844 (2020)], respectively. Distributions of anionic IL clusters were generated in the gas phase using electrospray ionization and characterized by high mass resolution mass spectrometry, energy-resolved collision-induced dissociation, and negative ion photoelectron spectroscopy experiments. The experimental results reveal anion-dependent trends in the size distribution, relative abundance, ionic charge state, stability toward dissociation, and electron binding energies of the IL clusters. Complementary global optimization theory provides molecular-level insights into the bonding and electronic structure of a selected subset of clusters, including their low energy structures and electrostatic potential maps, and how these fundamental characteristics are influenced by anion substitution. Collectively, our findings demonstrate how the fundamental properties of ILs, which determine their suitability for many applications, may be tuned by substituting counterions. These observations are critical in the sub-nanometer cluster size regime where phenomena do not scale predictably to the bulk phase, and each atom counts toward determining behavior.

cluster↗
DOE OSTI2025

Evaluation of normalization strategies for mass spectrometry-based multi-omics datasets

Introduction Data normalization is crucial for multi-omics integration, reducing systematic errors and maximizing the likelihood of discovering true biological variation. Most studies assess normalization for a single omics type or use datasets from separate experiments. Few address time-course data, where normalization might bias temporal differentiation. In this study, we compared common normalization methods and a machine learning approach, Systematical Error Removal using Random Forest (SERRF), using multi-omics datasets generated from the same experiment—even from the same cell lysate. Objectives To develop a straightforward process to assess normalization effects and identify the most robust methods across multi-omics datasets. Methods We analyzed metabolomics, lipidomics, and proteomics datasets from primary human cardiomyocytes and motor neurons exposed to acetylcholine-active compounds over time. Normalization effectiveness was evaluated based on improvement in QC features consistency and observing the change in treatment and time-related variance. Results Probabilistic Quotient Normalization (PQN) and Locally Estimated Scatterplot Smoothing (LOESS) QC were identified as optimal for metabolomics and lipidomics, while PQN, Median, and LOESS normalization excelled for proteomics. These methods consistently enhanced QC feature consistency in metabolomics and lipidomics, and preserved time-related variance or treatment-related variance in proteomics, demonstrating their effectiveness and robustness. SERRF normalization, applied only to metabolomics in this study, outperformed other methods in some datasets but inadvertently masked treatment-related variance in others. Conclusion Our evaluation identified PQN and LoessQC as the top methods for metabolomics and lipidomics, and PQN, Median, and Loess normalization for proteomics, in multi-omics integration in a temporal study.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Airborne Release Fractions from Surrogate Nuclear Waste Fires Containing Lanthanide Nitrates and Depleted Uranium Nitrate in 30% Tributyl Phosphate in Kerosene

Airborne contaminants from fires containing nuclear waste represent significant health hazards and shape the design and operation of nuclear facilities. Much of the data used to formulate DOE-HDBK-3010-94, “Airborne Release Fractions/Rates and Respirable Fractions for Nonreactor Nuclear Facilities,” from the U.S. Department of Energy, were taken over 40 years ago. The objectives of this study were to reproduce experiments from Pacific Northwest Laboratories conducted in June 1973 employing current aerosol measurement methods and instrumentation, develop an enhanced understanding of particulate formation and transport from fires containing nuclear waste, and provide modeling and experimental capabilities for updating current standards and practices in nuclear facilities. A special chamber was designed to conduct small fires containing 25 mL of flammable waste containing lutetium nitrate, ytterbium nitrate, or depleted uranium nitrate. Carbon soot aerosols showed aggregates of primary particles ranging from 20 to 60 nm in diameter. In scanning electron microscopy, ~200-nm spheroidal particles were also observed dispersed among the fractal aggregates. The 200-nm spherical particles were composed of metal phosphates. Airborne release fractions (ARFs) were characterized by leaching filter deposits and quantifying metal concentrations with mass spectrometry. The average mass-based ARF for 238 U experiments was 1.0 × 10 -3 with a standard deviation of 7.5 × 10 -4 . For the original experiments, DOE-HDBK-3010-94 states, “Uranium ARFs range from 2 × 10 -4 to 3 × 10 -3 , an uncertainty of approximately an order of magnitude.” Therefore, current measurements were consistent with DOE-HDBK-3010-94 values. ARF values for lutetium and ytterbium were approximately one to two orders of magnitude lower than 238 U. Furthermore, metal nitrate solubility may have varied with elemental composition and temperature, thereby affecting ARF values for uranium surrogates (Yb and Lu). In addition to ARF data, solution boiling temperatures and evaporation rates can also be deduced from experimental data.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2022

A catalytic dyad modulates conformational change in the CO 2 -fixing flavoenzyme 2-ketopropyl coenzyme M oxidoreductase/carboxylase

2-Ketopropyl-coenzyme M oxidoreductase/carboxylase (2-KPCC) is a member of the flavin and cysteine disulfide containing oxidoreductase family (DSOR) that catalyzes the unique reaction between atmospheric CO 2 and a ketone/enolate nucleophile to generate acetoacetate. However, the mechanism of this reaction is not well understood. Here, we present evidence that 2-KPCC, in contrast to the well-characterized DSOR enzyme glutathione reductase, undergoes conformational changes during catalysis. Using a suite of biophysical techniques including limited proteolysis, differential scanning fluorimetry, and native mass spectrometry in the presence of substrates and inhibitors, we observed conformational differences between different ligand-bound 2-KPCC species within the catalytic cycle. Analysis of site-specific amino acid variants indicated that 2-KPCC-defining residues, Phe501-His506, within the active site are important for transducing these ligand induced conformational changes. We propose that these conformational changes promote substrate discrimination between H + and CO 2 to favor the metabolically preferred carboxylation product, acetoacetate.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Emergent Chemical Behavior in Mixed Food and Lignocellulosic Green Waste Hydrothermal Liquefaction

Hydrothermal liquefaction (HTL) is a promising strategy for the conversion of energy-dense waste streams to fuels. Mixed-feed HTL aggregates multiple feed streams to achieve greater scales that capitalize on local resources, hence lowering costs. The potential for new pathways and products upon feedstock blending becomes a compounding level of complexity when unlocking emergent chemistries. Here, food and green waste streams were evaluated under HTL conditions (300 °C, 1 h) to understand the effect of feed molecular composition on product distributions and mechanisms. Thousands of emergent chemical compounds were detected via Fourier transform ion cyclotron resonance mass spectrometry, ultimately leading to the emergence of two dominant outcomes. First, the presence of small amounts of food waste into green waste results in substantial decarboxylation and subsequent polymerization to biocrude than chars. Second, in the other limit, small amounts of green waste promote the capping of oxygenates into the biodiesel range, such as with the emergence of fatty acid methyl esters.

09 BIOMASS FUELS↗
DOE OSTI2023

Imaging plant metabolism in situ

Abstract Mass spectrometry imaging (MSI) has emerged as an invaluable analytical technique for investigating the spatial distribution of molecules within biological systems. In the realm of plant science, MSI is increasingly employed to explore metabolic processes across a wide array of plant tissues, including those in leaves, fruits, stems, roots, and seeds, spanning various plant systems such as model species, staple and energy crops, and medicinal plants. By generating spatial maps of metabolites, MSI has elucidated the distribution patterns of diverse metabolites and phytochemicals, encompassing lipids, carbohydrates, amino acids, organic acids, phenolics, terpenes, alkaloids, vitamins, pigments, and others, thereby providing insights into their metabolic pathways and functional roles. In this review, we present recent MSI studies that demonstrate the advances made in visualizing the plant spatial metabolome. Moreover, we emphasize the technical progress that enhances the identification and interpretation of spatial metabolite maps. Within a mere decade since the inception of plant MSI studies, this robust technology is poised to continue as a vital tool for tackling complex challenges in plant metabolism.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2023

Evaluating Linear Ion Trap for MS3-Based Multiplexed Single-Cell Proteomics

There is a growing demand to develop high-throughput and high-sensitivity mass spectrometry methods for single-cell proteomics. The commonly used isobaric labeling-based multiplexed single-cell proteomics approach suffers from distorted protein quantification due to co-isolated interfering ions during MS/MS fragmentation, also known as ratio compression. We reasoned that the use of MS3-based quantification could mitigate ratio compression and provide better quantification. However, previous studies indicated reduced proteome coverages in the MS3 method, likely due to long duty cycle time and ion losses during multilevel ion selection and fragmentation. Here, in this paper, we described an improved MS acquisition method for MS3-based single-cell proteomics by employing a linear ion trap to measure reporter ions. We demonstrated that linear ion trap can increase the proteome coverages for single-cell-level peptides with even higher gain obtained via the MS3 method. The optimized real-time search MS3 method was further applied to study the immune activation of single macrophages. Among a total of 126 single cells studied, over 1200 and 1000 proteins were quantifiable when at least 50 and 75% nonmissing data were required, respectively. Our evaluation also revealed several limitations of the low-resolution ion trap detector for multiplexed single-cell proteomics and suggested experimental solutions to minimize their impacts on single-cell analysis.

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

Aircraft Measurements from a U.S. Western Wildfire Demonstrating Day and Night Differences in the Chemical Composition and Optical Properties of Biomass Burning Aerosols and Their Atmospheric Evolution

The composition and transformations of biomass burning aerosols (BBA) have been measured onboard the NOAA Twin Otter research aircraft during the Fire Influence on Regional to Global Environments and Air Quality field study. Here, we analyze real-time aerosol mass spectrometry measurements across three flights during the afternoon, late afternoon, and night of August 28, 2019, for one midsized wildfire. Analysis of several metrics showed that the aerosol composition and optical properties varied depending on the burning conditions at the fire zone and the time of day the BBA was emitted, with substantial variations in the available sunlight. The total aerosol mass loadings were dominated by organic components with a much smaller contribution from inorganic species. A gradual buildup of organic material was observed during the afternoon as the plume aged, indicating the condensation of photochemically formed low-volatility oxidized organic compounds. Highly hygroscopic ammonium nitrate was the main inorganic component, suggesting potential water content in BBA particles and the likelihood of their aqueous-phase reactivity. Depletions of particle-phase NO 3 – and Cl – relative to carbon monoxide were observed in the late afternoon and nighttime plumes, respectively, aligning with known gas-particle partitioning thermodynamics and the heterogeneous chemistry of dissolved nitrate and chloride. The wavelength-dependent light absorption by aerosol species was higher for the plume sampled at night and showed no significant changes with plume age, despite observed trends in composition and mass downwind. These differences in particle composition and optical properties demonstrate that the processes involved in BBA aging are not uniform for the same wildfire over the course of the day and depend highly on when the BBA was emitted, as well as the burning phase at the emissions source.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Manuscript Workflows from and Processed Organic Matter Composition of Experimentally Burned Open Air and Muffle Furnace Vegetation Chars across Differing Burn Severity and Feedstock Types from Pacific Northwest, USA (v3)

This dataset includes processed organic matter chemistry data from an experimental study designed to compare how the chemical composition of organic matter changes across different burn conditions and vegetation materials representative of major land cover types of the Pacific Northwest, USA. Chars were created in a closed muffle furnace or on an open burn table from four different feedstock species representing vegetation commonly impacted by fire regimes across the Pacific Northwest, USA. Source data and associated metadata (including methods and geospatial information) can be found at https://data.ess-dive.lbl.gov/datasets/doi:10.15485/1894135 (Grieger et al. 2022). This dataset provides processing scripts and processed data for both solid and dissolved phase organic matter characterization data from experimentally generated chars. These processed data can be used to compare how different burn conditions may influence resultant organic matter chemistry and help further our understanding of potential biogeochemical impacts on river corridors post-fire. The processed data were subsequently analyzed; and the results and ecological implications of the findings were published in peer-reviewed manuscripts. The scripts and workflows used to develop the manuscripts are also included in this data package.This data package was originally published June 2024. It was updated September 2024 (new and modified files) and in January 2025 (modified files). See the change history section in the readme for more details.This dataset is comprised of one data package readme, one data dictionary (dd), one file level metadata (flmd), and folders containing (A) processed data; (B) general processing scripts; and (C) additional folders with specific manuscript analysis scripts and processed data. Step-by-step instructions to assist the user in recreating the workflow used to generate the results in the manuscripts is also provided. The processed data folder includes (1) a folder of processed Parallel Factor Analysis (PARAFAC) and spectra indices outputs from excitation emissions matrix (EEM) fluorescence and absorbance data; (2) a folder of processed solid state carbon-13 (13-C NMR) integrals; (3) folder of high resolution characterization of organic matter via 21 Tesla Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) generated through the Environmental Molecular Sciences Laboratory (EMSL; https://www.pnnl.gov/environmental-molecular-sciences-laboratory) processed data outputs from Formultitude (https://github.com/PNNL-Comp-Mass-Spec/Formultitude), blank corrections and data aggregation, and calculated molecular indices. All files are .pdf, .csv, .html, .Rmd, .R, or .RData.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

FTICR-MS Data from Multi-continent River Water and Sediment and from Coastal River Fresh and Saline Sediment Associated with: “Dissolved Organic Matter Functional Trait Relationships are Conserved Across Rivers”

This data package is associated with the publication “Dissolved Organic Matter Functional Trait Relationships are Conserved Across Rivers” submitted to PNAS (Stegen et al., 2023). The study aims to understand large-scale spatial structure of the dissolved organic matter (DOM) thermodynamic traits and inter-trait relationships by investigating (1) river water and sediments collected along 97 rivers spanning 3 continents and (2) coastal sediment collected from fresh and saline locations in Pacific and Gulf/Atlantic rivers. Sediment extracts and water samples were analyzed using ultrahigh resolution Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS). This dataset is comprised of three folders (1) Coastal, (2) WHONDR_S19S, and (3) Data_Dictionaries. Coastal contains (1) a subfolder with processed FTICR-MS data as csv files and sample collection metadata, (2) a subfolder with R scripts used to process the data and create associated figures, (3) a subfolder with the raw, unprocessed FTICR-MS data as .xml files, and (4) a readme file with more information about the dataset and instructions for using Formularity (https://omics.pnl.gov/software/formularity). WHONDRS_S19S contains (1) a csv file with processed FTICR data, (2) a csv with sample collection metadata, (3) a csv with sample geospatial data, (4) a csv with simulated lambda model outputs, (5) a subfolder with R scripts used to process the data and create associated figures, and (6) a readme file with more information regarding WHONDRS raw FTICR data and processing scripts. Data_Dictionaries contains data dictionaries for each csv file in the data package. The 97 global river corridors were part of a WHONDRS (https://whondrs.pnnl.gov) study. The raw, unprocessed FTICR-MS data with additional data can be found at doi:10.15485/1729719 for sediments and doi:10.15485/1603775 for water. This data package contains the processed data used in the associated manuscript. The coastal data has not been previously published, and this data package contains both the raw and processed data. Version 3 of this data package published February 2023 includes updates to the title of the manuscript, additional data and data dictionary and updated scripts linked to new analysis.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

In-house synthesized poly(ether ether ketone) ionenes. I. ToF-SIMS spectra in the positive ion mode

Static time-of-flight secondary ion mass spectrometry (ToF-SIMS) was performed for acquiring the high-resolution surface spectra of four types of synthesized imidazolium ionene membranes. These novel membranes have aromatic ether–ketone–ether linkages inspired by poly(ether ether ketone) (PEEK). The PEEK-ionenes synthesized for this study have imidazolium cations placed in the polymeric backbone with bistriflimide [Tf 2 N]- counterions. The attention given to synthetically modified PEEK derivatives, such as PEEK-ionenes, is considerable due to their ability to selectively capture CO 2 molecules and other light gases. Therefore, it is important to characterize the surface of these synthesized novel PEEK-ionenes. In this work, characteristic and unique peaks were identified in the positive spectra of each sample. The differences in mass spectra among the samples provide insights for optimizing or fine-tuning the PEEK-ionenes synthesis to achieve a high-performance CO 2 separation membrane with enhanced permeability, selectivity, and mechanical stability. The SIMS spectra and identified characteristic peaks of these synthesized ionenes will serve as a reference in the positive mode, complementing the corresponding spectra reported in the negative ion mode (Paper II).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗