Controls of nature: Secondary, tertiary, and quaternary structure of the enamel protein amelogenin in solution and on hydroxyapatite
Not Available
Shaw, Wendy J. (ORCID:0000000246967415)↗
SEARCH · Search NASA
Results for “LABELLED COMPOUNDS”
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.
Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.
Naphthalene genotoxicity: DNA adducts in primate and mouse airway explants
Naphthalene (NA) is a ubiquitous environmental pollutant and possible human carcinogen that forms tumors in rodents with tissue/regional and species selectivity. This study seeks here to determine whether NA is able to directly adduct DNA in an ex vivo culture system. Metabolically active lung tissue was isolated and incubated in explant culture with carbon-14 labeled NA (0, 25, 250 μM) or 1,2-naphthoquinone (NQ), followed by AMS analyses of metabolite binding to DNA. Despite relatively low metabolic bioactivation in the primate airway, dose-dependent NA-DNA adduct formation was detected. More airway adducts were detected in female mice (4.7-fold) and primates (2.1-fold) than in males of the same species. Few adducts were detected in rat airway or nasal epithelium. NQ, which is a metabolic product of NA, proved to be even more potent, with levels of adduct formation 70–80-fold higher than seen when tissues were incubated with the parent compound NA. This is the first study to demonstrate NA-DNA adduct formation at a site of carcinogenesis, the mouse lung. Adducts were also detected in non-human primate lung and with a NQ metabolite of NA. Taken together, this suggests that NA may contribute to in vivo carcinogenesis through a genotoxic mechanism.
59 BASIC BIOLOGICAL SCIENCES↗
DeePKS: A Comprehensive Data-Driven Approach toward Chemically Accurate Density Functional Theory
We propose a general machine learning-based framework for building an accurate and widely applicable energy functional within the framework of generalized Kohn–Sham density functional theory. To this end, we develop a way of training self-consistent models that are capable of taking large datasets from different systems and different kinds of labels. Here, we demonstrate that the functional that results from this training procedure gives chemically accurate predictions on energy, force, dipole, and electron density for a large class of molecules. It can be continuously improved when more and more data are available.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Metal-Tuned Ligand Reactivity Enables CX 2 (X = O, S) Homocoupling with Spectator Cu Centers
Ligand non-innocence is ubiquitous in catalysis with ligands in synthetic complexes contributing as electron reservoirs or co-sites for substrate activation. The latter chemical non-innocence is manifested in H + storage or relay at sites beyond the metal primary coordination sphere. Reaction of a competent CO 2 -to-oxalate reduction catalyst, namely, [K(THF) 3 ](Cu 3 SL), where L 3– is a tris(β-diketiminate) cyclophane, with CS 2 affords tetrathiooxalate at long reaction times or at high CS 2 concentrations, where otherwise an equilibrium is established between the starting species and a complex–CS 2 adduct in which the CS 2 is bound to the C atom on the ligand backbone. X-ray diffraction analysis of this adduct reveals no apparent metal participation, suggesting an entirely ligand-based reaction controlled by the charge state of the cluster. Here, thermodynamic parameters for the formation of the aforementioned Cligand–CS 2 bond were experimentally determined, and trends with cation Lewis acidity were studied, where more acidic cations shift the equilibrium toward the adduct. Relevance of such an adduct in the reduction of CO 2 to oxalate by this complex is supported by DFT studies, similar effects of countercation Lewis acidity on product formation, and the homocoupled heterocumulene product speciation as determined by isotopic labeling studies. Taken together, this system extends chemical non-innocence beyond H + to effect catalytic transformations involving C–C bond formation and represents the rarest example of metal–ligand cooperativity, that is, spectator metal ion(s) and the ligand as the reaction center.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Methane Upgrading of Acetic Acid as a Model Compound for a Biomass-Derived Liquid over a Modified Zeolite Catalyst
The technical feasibility of coaromatization of acetic acid derived from biomass and methane was investigated under mild reaction conditions (400 °C and 30 bar) over silver-, zinc-, and/or gallium-modified zeolite catalysts. On the basis of GC-MS, Micro-GC, and TGA analysis, more light aromatic hydrocarbons, less phenol formation, lower coke production, and higher methane conversion are observed over 5%Zn-1%Ga/ZSM-5 catalyst in comparison with catalytic performance over the other catalysts. Direct evidence of methane incorporation into aromatics over 5%Zn-1%Ga/ZSM-5 catalyst is witnessed in 1 H, 2 H, and 13 C NMR spectra, revealing that the carbon from methane prefers to occupy the phenyl carbon sites and the benzylic carbon sites, and the hydrogen of methane favors the aromatic and benzylic substitutions of product molecules. In combination with the 13 C NMR results for isotopically labeled acetic acid ( 13 CH 3 COOH and CH 3 13 COOH), it can be seen that the methyl and carbonyl carbons of acetic acid are equally involved in the formation of ortho, meta and para carbons of the aromatics, whereas the phenyl carbons directly bonded with alkyl substituent groups and benzylic carbons are derived mainly from the carboxyl carbon of acetic acid. After various catalyst characterizations by using TEM, XRD, DRIFT, NH 3 -TPD, and XPS, the excellent catalytic performance might be closely related to the highly dispersed zinc and gallium species on the zeolite support, moderate surface acidity, and an appropriate ratio of weak acidic sites to strong acidic sites as well as the fairly stable oxidation state during acetic acid conversion under a methane environment. Two mechanisms of the coaromatization of acetic acid and methane have also been proposed after consulting all the collected data in this study. In conclusion, the results reported in this paper could potentially lead to more cost-effective utilization of abundant natural gas and biomass.
09 BIOMASS FUELS↗
Graph-based featurization methods for classifying small molecule compounds
For over a decade, drug-induced liver injury (DILI) has posed significant drawbacks in the synthesis and development of drugs and remains a consequential concern. With finite success within the existing preclinical models, DILI is one of the main causes of drug withdrawal or termination from the market. Particularly, this withdrawal occurs during the late stages of drug development (Kullak-Ublick, 2017). Since DILI is difficult to diagnose and treat, it has become an obstacle in the drug production market that in turn affects clinicians, pharmaceutical companies, and consumers. We propose a method for learning features of DILI-positive drugs based on the graphical relationships and patterns they possess within a network of biological databases. We also train various statistical and machine learning models on these learned features in order to classify the drugs as DILI-positive or negative. Our methods include Random Forest, Neural networks, and logistic regression classification. We utilize labeled DILI-positive and DILI-negative datasets, which were developed by the FDA and the National center for toxicological research, as well as additional literature datasets (Thakkar, 2020) in order to validate our results and assess our featurization and model accuracy.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Identification of the Tyrosine- and Phenylalanine-Derived Soluble Metabolomes of Sorghum
The synthesis of small organic molecules, known as specialized or secondary metabolites, is one mechanism by which plants resist and tolerate biotic and abiotic stress. Many specialized metabolites are derived from the aromatic amino acids phenylalanine (Phe) and tyrosine (Tyr). In addition, the improved characterization of compounds derived from these amino acids could inform strategies for developing crops with greater resilience and improved traits for the biorefinery. Sorghum and other grasses possess phenylalanine ammonia-lyase (PAL) enzymes that generate cinnamic acid from Phe and bifunctional phenylalanine/tyrosine ammonia-lyase (PTAL) enzymes that generate cinnamic acid and p -coumaric acid from Phe and Tyr, respectively. Cinnamic acid can, in turn, be converted into p -coumaric acid by cinnamate 4-hydroxylase. Thus, Phe and Tyr are both precursors of common downstream products. Not all derivatives of Phe and Tyr are shared, however, and each can act as a precursor for unique metabolites. In this study, 13 C isotopic-labeled precursors and the recently developed Precursor of Origin Determination in Untargeted Metabolomics (PODIUM) mass spectrometry (MS) analytical pipeline were used to identify over 600 MS features derived from Phe and Tyr in sorghum. These features comprised 20% of the MS signal collected by reverse-phase chromatography and detected through negative-ionization. Ninety percent of the labeled mass features were derived from both Phe and Tyr, although the proportional contribution of each precursor varied. In addition, the relative incorporation of Phe and Tyr varied between metabolites and tissues, suggesting the existence of multiple pools of p -coumaric acid that are fed by the two amino acids. Furthermore, Phe incorporation was greater for many known hydroxycinnamate esters and flavonoid glycosides. In contrast, mass features derived exclusively from Tyr were the most abundant in every tissue. The Phe- and Tyr-derived metabolite library was also utilized to retrospectively annotate soluble MS features in two brown midrib mutants ( bmr6 and bmr12 ) identifying several MS features that change significantly in each mutant.
09 BIOMASS FUELS↗
Bio-distribution and deposition of wildfire smoke chemicals into olfactory bulb and brain of rats after intranasal instillation
Epidemiological and experimental studies suggest wildfire smoke is a potential contributor to neurological dysfunction and associated with neuroinflammation. Using doses comparable to those encountered during intense wildfire events (200-300 μg/m 3 ), we explore the absorption, distribution, metabolism, and elimination (ADME) and pharmacokinetics of representative members of major chemical classes (acid, phenol, PAH, aldehyde) in inhaled wood smoke condensates. Male Sprague Dawley rats were intranasally instilled with smoldering eucalyptus woodsmoke extract (WSE) reconstituted in saline spiked with 14 C-labeled palmitic acid (PA), benzo[a]pyrene (B[a]P), catechol (CAT) or benzaldehyde (BZ). Serum was collected from 5 min to 2 weeks after exposure and tissues were collected at 0.5, 2, 4, 24 h and 2 weeks after exposure. Urine was collected over the 24 h exposure. Tissues were collected, rinsed in PBS and analyzed by accelerator mass spectrometry (AMS) for 14C-labeled chemicals. PA and B[a]P entered circulation slowly, reached maximum concentration (C max ) near 15 ng/mL at 2 h, and had circulating concentrations near 1/3 C max 24 h after exposure. CAT and BZ rapidly entered circulation and were mostly cleared at 2 h. Excess 14 C from all four chemicals was detected in olfactory bulb and brain over the first 24 h but only PA (or its metabolites) was retained in olfactory bulb, brain and kidney at 2 weeks post exposure. All excess 14 C was cleared from the lung at 2 weeks. Metabolite analysis of urine (CAT, BZ and B(a)P) dosed samples did not detect any parent compound. CAT and BZ were rapidly cleared. The slower uptake and clearance of PA or B[a]P or their reactive metabolites when dosed with WSE in brain and olfactory bulb potentially provide greater opportunity for inflammatory response. This study suggests that wildfire smoke chemicals can enter the brain directly from the nasal cavity to the olfactory bulb and via systemic circulation.
63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗
Ammonia synthesis by photocatalytic hydrogenation of a N 2 -derived molybdenum nitride
Although metal complexes are known to split dinitrogen at ambient temperature and pressure, the synthesis of ammonia from these compounds and using H 2 as the terminal reductant has been rarely achieved. Here, we report photocatalytic ammonia synthesis from a N 2 -derived terminal molybdenum nitride and by using H 2 as the terminal reductant. An iridium hydride photocatalyst mediates the reaction upon irradiation with blue light. A molybdenum pentahydride was identified as the principal metal product arising following ammonia release. Conversion of the molybdenum pentahydride back to the terminal molybdenum nitride was accomplished in three-steps and completes a synthetic cycle for NH3 formation from N 2 and H 2 . Mechanistic investigations support a pathway involving photoexcitation of the iridium hydride and subsequent energy transfer rather than electron transfer. Deuterium labelling confirmed H 2 as the source of the N–H bonds. This photodriven, proton coupled electron transfer allows the use of H 2 as the terminal reductant for catalytic formation of NH 3 from N 2 using metal catalysts.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Two-bond 13 C– 13 C spin-coupling constants in saccharides: dependencies on exocyclic hydroxyl group conformation
Seven doubly 13 C-labeled isotopomers of methyl β-D-glucopyranoside, methyl β-D-xylopyranoside, methyl β-D-galactopyranoside, methyl β-D-galactopyranosyl-(1→4)-β-D-glucopyranoside and methyl β-D-galactopyranosyl-(1→4)-β-D-xylopyranoside were prepared, crystallized, and studied by single-crystal X-ray crystallography and solid-state 13 C NMR spectroscopy to determine experimentally the dependence of 2 J C1,C3 values in aldopyranosyl rings on the C1–C2–O2–H torsion angle, θ 2 , involving the C2 carbon of the C1–C2–C3 coupling pathway. Using X-ray crystal structures to determine θ 2 in crystalline samples and by selecting compounds that exhibit a relatively wide range of θ 2 values in the crystalline state, 2 J C1,C3 values measured in crystalline samples were plotted against θ 2 and the resulting plot compared to that obtained from density functional theory (DFT) calculations. For θ 2 values ranging from ~90° to ~240°, very good agreement was observed between the experimental and theoretical plots, providing strong validation of DFT-calculated spin-coupling dependencies on exocyclic C–O bond conformation involving the central carbon of geminal C–C–C coupling pathways. we report that these findings provide new experimental evidence supporting the use of 2 J CCC values as non-conventional spin-coupling constraints in MA'AT conformational modeling of saccharides in solution, and the use of NMR spin-couplings not involving coupled hydroxyl hydrogens as indirect probes of C–O bond conformation. Solvomorphism was observed in crystalline βGal-(1→4)-βGlcOCH 3 wherein the previously-reported methanol solvate form was found to spontaneously convert to a monohydrate upon air-drying, leading to small but discernible conformational changes in, and a new crystalline form of, this disaccharide.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Carbon dioxide fixation by Metallosphaera yellowstonensis and acidothermophilic iron-oxidizing microbial communities from Yellowstone National Park
The fixation of inorganic carbon (as carbon dioxide) has been documented in all three domains of life and results in the biosynthesis of a diverse suite of organic compounds that support the growth of heterotrophic organisms. The primary aim of this study was to assess the importance of carbon dioxide fixation in high-temperature Fe(III)-oxide mat communities and in pure cultures of one of the dominant Fe(II)-oxidizing organisms (Metallosphaera yellowstonensis strain MK1) present in situ. Protein-encoding genes of the complete 3-hydroxypropionate/4-hydroxybutyrate (3-HP/4-HB) carbon fixation pathway were identified in pure-cultures of M. yellowstonensis strain MK1. Metagenome sequencing from the same environments also revealed genes for the 3-HP/4-HB pathway belonging to M. yellowstonensis populations, as well as genes for a complete reductive TCA cycle from Hydrogenobaculum spp. (Aquificales). Stable isotope (13CO2) labeling was used to measure the fixation of CO2 by M. yellowstonensis strain MK1, and in ex situ assays containing live Fe(III)-oxide microbial mats. Results showed that M. yellowstonensis strain MK1 fixes CO2 via the 3-HP/4-HB pathway with a fractionation factor of ~ 2.5 ‰. Direct analysis of the 13C composition of dissolved inorganic C (DIC), dissolved organic C (DOC), landscape C and microbial mat C showed that mat C is comprised of both DIC and non-DIC sources. The estimated contribution of DIC carbon to biomass C (> ~ 35%) is reasonably consistent with the relative abundance of known chemolithoautotrophs and corresponding CO2 fixation pathways detected in metagenome sequence. The significance of DIC as a major source of carbon for Fe-oxide mat communities provides a foundation for examining microbial interactions in these systems that are dependent on the activity of autotrophic organisms such as Hydrogenobaculum and Metallosphaera spp.
Sulfolobales, Crenarchaeota, stable isotope analys↗
Catalytic Hydrotreatment of Humins to Bio‐Oil in Methanol over Supported Metal Catalysts
Abstract Valorization of humins, the polymeric byproducts formed during the acid‐catalyzed production of HMF (5‐hydroxymethylfurfural) or furfural, is necessary to improve process economics and make biorefineries viable. We report the one‐step catalytic hydrotreatment of humins in methanol to humin oil containing fully or partially deoxygenated compounds. First, we compare four commercial noble‐metal catalysts (Ru/C, Rh/C, Pt/C, and Pd/C). Aromatic hydrocarbons, phenols, and esters are the main products detected by GC. Rh/C achieves the best GC‐detectable oil yield and 75 % humins conversion in 3 h at 400 °C, 30 bar H 2 , and a catalyst‐to‐humins mass ratio of 1:10. High H 2 pressures and intermediate temperatures, reaction times, and catalyst loadings enhance GC‐detectable oil yields. In contrast, high temperatures and long reaction times enhance gasification. Aromatics and phenols are found at high temperatures and long reaction times, whereas esters are the major species at short reaction times and high catalyst loading. 13 C‐isotopic labeling studies confirm, for the first time, that methanol participates in the alkylation and esterification reactions to form aromatic, phenolic and ester products. The reactivity in isopropanol is also discussed.
Cheng, Ziwei↗
Metabolic Incorporation of N ‐Acetyl Muramic Acid Probes into Bacterial Peptidoglycan
Abstract Bacterial cells utilize small carbohydrate building blocks to construct peptidoglycan (PG), a highly conserved mesh‐like polymer that serves as a protective coat for the cell. PG production has long been a target for antibiotics, and its breakdown is a source for human immune recognition. A key component of bacterial PG, N ‐acetyl muramic acid (NAM), is a vital element in many synthetically derived immunostimulatory compounds. However, the exact molecular details of these structures and how they are generated remain unknown due to a lack of chemical probes surrounding the NAM core. A robust synthetic strategy to generate bioorthogonally tagged NAM carbohydrate units is implemented. These molecules serve as precursors for PG biosynthesis and recycling. Escherichia coli cells are metabolically engineered to incorporate the bioorthogonal NAM probes into their PG network. The probes are subsequently modified using copper‐catalyzed azide‐alkyne cycloaddition to install fluorophores directly into the bacterial PG, as confirmed by super‐resolution microscopy and high‐resolution mass spectrometry. Here, synthetic notes for key elements of this process to generate the sugar probes as well as streamlined user‐friendly metabolic labeling strategies for both microbiology and immunological applications are described. © 2019 by John Wiley & Sons, Inc. Basic Protocol 1 : Synthesis of peracetylated 2‐azido glucosamine Basic Protocol 2 : Synthesis of 2‐azido and 2‐alkyne NAM Basic Protocol 3 : Synthesis of 3‐azido NAM methyl ester Basic Protocol 4 : Incorporation of NAM probes into bacterial peptidoglycan Basic Protocol 5 : Confirmation of bacterial cell wall remodeling by mass spectrometry
DeMeester, Kristen E.↗
Emissions of putative isoprene oxidation products from mango branches under abiotic stress
Although several per cent of net carbon assimilation can be re-released as isoprene emissions to the atmosphere by many tropical plants, much uncertainty remains regarding its biological significance. In a previous study, we detected emissions of isoprene and its oxidation products methyl vinyl ketone (MVK) and methacrolein (MACR) from tropical plants under high temperature/light stress, suggesting that isoprene is oxidized not only in the atmosphere but also within plants. However, a comprehensive analysis of the suite of isoprene oxidation products in plants has not been performed and production relationships with environmental stress have not been described. In this study, putative isoprene oxidation products from mango (Mangifera indica) branches under abiotic stress were first identified. High temperature/light and freeze–thaw treatments verified direct emissions of the isoprene oxidation products MVK and MACR together with the first observations of 3-methyl furan (3-MF) and 2-methyl-3-buten-2-ol (MBO) as putative novel isoprene oxidation products. Mechanical wounding also stimulated emissions of MVK and MACR. Photosynthesis under 13 CO 2 resulted in rapid (<30min) labelling of up to five carbon atoms of isoprene, with a similar labelling pattern observed in the putative oxidation products. These observations highlight the need to investigate further the mechanisms of isoprene oxidation within plants under stress and its biological and atmospheric significance.
2-Methyl-3-buten-2-ol↗
The Role of Mass Spectrometry in Structural Studies of Flavin-Based Electron Bifurcating Enzymes
For decades, biologists and biochemists have taken advantage of atomic resolution structural models of proteins from X-ray crystallography, nuclear magnetic resonance spectroscopy, and more recently cryo-electron microscopy. However, not all proteins relent to structural analyses using these approaches, and as the depth of knowledge increases, additional data elucidating a mechanistic understanding of protein function is desired. Flavin-based electron bifurcating enzymes, which are responsible for producing high energy compounds through the simultaneous endergonic and exergonic reduction of two intercellular electron carriers (i.e., NAD + and ferredoxin) are one class of proteins that have challenged structural biologists and in which there is great interest to understand the mechanism behind electron gating. A limited number of X-ray crystallography projects have been successful; however, it is clear that to understand how these enzymes function, techniques that can reveal detailed in solution information about protein structure, dynamics, and interactions involved in the bifurcating reaction are needed. In this review, we cover a general set of mass spectrometry-based techniques that, combined with protein modeling, are capable of providing information on both protein structure and dynamics. Techniques discussed include surface labeling, covalent cross-linking, native mass spectrometry, and hydrogen/deuterium exchange. We cover how biophysical data can be used to validate computationally generated protein models and develop mechanistic explanations for regulation and performance of enzymes and protein complexes. Our focus will be on flavin-based electron bifurcating enzymes, but the broad applicability of the techniques will be showcased.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
The Regulation of Photosynthetic Structure and Function during Nitrogen Deprivation in Chlamydomonas reinhardtii
The accumulation of carbon storage compounds by many unicellular algae after nutrient deprivation occurs despite declines in their photosynthetic apparatus. To understand the regulation and roles of photosynthesis during this potentially bioenergetically valuable process, we analyzed photosynthetic structure and function after nitrogen deprivation in the model alga Chlamydomonas reinhardtii. Transcriptomic, proteomic, metabolite, and lipid profiling and microscopic time course data were combined with multiple measures of photosynthetic function. Levels of transcripts and proteins of photosystems I and II and most antenna genes fell with differing trajectories; thylakoid membrane lipid levels decreased, while their proportions remained similar and thylakoid membrane organization appeared to be preserved. Cellular chlorophyll (Chl) content decreased more than 2-fold within 24 h, and we conclude from transcript protein and 13 C labeling rates that Chl synthesis was down-regulated both pre- and posttranslationally and that Chl levels fell because of a rapid cessation in synthesis and dilution by cellular growth rather than because of degradation. Photosynthetically driven oxygen production and the efficiency of photosystem II as well as P700 + reduction and electrochromic shift kinetics all decreased over the time course, without evidence of substantial energy overflow. The results also indicate that linear electron flow fell approximately 15% more than cyclic flow over the first 24 h. Comparing Calvin-Benson cycle transcript and enzyme levels with changes in photosynthetic 13 CO 2 incorporation rates also pointed to a coordinated multilevel down-regulation of photosynthetic fluxes during starch synthesis before the induction of high triacylglycerol accumulation rates.
59 BASIC BIOLOGICAL SCIENCES↗
GLBRC Soil Yearlong Incubation 13C-SIP-Lipidomics
Data package for Lipids represent a dynamic, yet stable pool of microbially-derived soil carbon This data is published under a CC0 license. The authors encourage data reuse and request attribution by referencing the below citations for the data packages and associated manuscript. Please cite as: Rempfert KR, Bell SL, Kasanke CP, Kyle JE, Hofmockel KS. 2025. GLBRC Soil Yearlong Incubation 13C-SIP-Lipidomics. [Data Set] PNNL DataHub. doi: Rempfert KR, Bell SL, Kasanke CP, Kyle JE, Hofmockel KS. 2025. MSV000097435: GLBRC soil yearlong incubation 13C-SIP-Lipidomics [Data Set] MassIVE. doi:10.25345/C57659T3K Rempfert KR, Bell SL, Kasanke CP, Kyle JE, Hofmockel KS. 2025. Lipids represent a dynamic, yet stable pool of microbially-derived soil carbon. In Prep This data package consists of compound-specific 13C SIP-lipidomics data from a yearlong tracer incubation experiment designed to investigate microbial lipid persistence in switchgrass bioenergy crop soils. In order to explore how lipid structure may modulate the persistence of C in soil lipids, we leveraged soils from two sites (Michigan - sandy texture, Wisconsin - silty texture) operated by the U.S. Department of Energy-funded Great Lakes Bioenergy Research Center (GLBRC). These sites had comparable climates, identical management practices, but contrasting soil textures, allowing us to assess the variability of lipid accrual or degradation in soils as well as provide insight regarding the degree to which edaphic properties may regulate the retention of soil lipids. Untargeted lipidomics analyses were performed to identify 13C-labeled lipids in the soil microbiome after long-term incubation. Soils were supplemented with 100 micrograms glucose per gram dry soil (99 atom % 13C or natural abundance for paired control) and incubated; samples were collected two months and one year after glucose addition. Lipid extracts (MPLEx) were analyzed by LC-MS/MS and identified using LIQUID. Calculation of isotopic enrichment of lipids was performed by targeted approach using TarMet to quantify lipid isotopologues and IsoCorrectoR to correct for natural abundance isotopes. Contents: Data package contents reported here are the first version and contain downstream analysis files for the raw LC-MS mass spectrometry files (.mzXML) deposited at the MassIVE database repository under accession MSV000097435 (80 experimental runs; 5.85 GB) | MassIVE DOI: 10.25345/C57659T3K. Support files include the additional data download 'Read Me' file containing data descriptor information. Reported data download contents are structured for compliance with project data sharing guidelines, community standards initiatives, and sponsor stakeholder policies supporting FAIR data principles. Data processing software, analysis tools, and data workflows are listed below corresponding to the host repository long-term location. Available Data Downloads (0.3 GB): "GLBRC soil yearlong incubation 13C-SIP-Lipidomics_readme.txt" - 'Read Me' data package content file (txt) "GLBRC_DataPackage_analysis files" - Data processing files (Rmd) and saved intermediate data processing outputs (rds, csv, xlsx) "GLBRC_13C_lipidomics_dataset.xlsx" - processed data in tabular format (xlsx) Linked Software: LIQUID LC-MS Analysis Software | 10.5281/zenodo.6459462 Lipid Mini-On Software Tools | 10.5281/zenodo.1492803 pmartR Omics Statistical Software | 10.5281/zenodo.6108667 xcms (v4.3.3) TarMet (v1.1.1) IsoCorrectoR (1.24.0) Funding Acknowledgments: This research was supported by an Early Career Research Program award funded by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research (OBER) Genomic Science program under FWP 68292, FWP 07880 and EMSL Exploratory Research Project 51095. A portion of this work was performed in the William R. Wiley Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by OBER and located at Pacific Northwest National Laboratory (PNNL). PNNL is a multi-program national laboratory operated by Battelle for the DOE under Contract DE-AC05-76RLO1830.
Rempfert, Kaitlin R [Pacific Northwest National La↗
Cradle-to-Grave: Assessment Methods for Hazardous Waste Management
The Resource Conservation and Recovery Act (RCRA) was passed to set up a framework for the proper management of waste. The 40CFR260-273 regulation established the regulatory framework to handle solid and hazardous waste, from the point of generation to its disposal; or cradle-to-grave management. Per these regulations, a hazardous waste generator is responsible for its waste from initial generation through its ultimate disposal and beyond. Nothing will relinquish a generator of this responsibility. There is no expiration date or time limit, and hiring a someone else to transport and dispose of waste does not transfer responsibility. If an incident occurs at any point during the life cycle of a waste, the generator can be held liable. The first step to compliance with RCRA is proper characterization of the waste. Waste may either be listed specifically or may show a characteristic as defined in the regulation: Is my waste hazardous? Why is it Hazardous? What should I do as a generator? Plan chemical use: - Create a chemical inventory for your research project. - Use existing chemicals if available instead of ordering new ones. - Brainstorm methods that will help to reduce toxicity and minimize waste. Waste Inventory: - Label all waste bottles with: ID no., What is it, Whose is it, Hazards, and Date. - Add waste containers into the inventory log. - Initiate/complete the container sheet to describe the waste. Satellite Areas: - Store waste in containers compatible with the waste with lids on tight. - Store waste containers properly and segregate them according to their specific hazards. - Use secondary containment for liquids. Store acids and bases separately; apart from cyanides or sulfides. Acids should never be put into steel containers. Water-reactive, strong acids such as organic acid halides, organic acid anhydrides, inorganic acid anhydrides, and strong acidic salts must be kept apart from both alkalis and water. Oxidizing agents must be kept apart from reducing agents and organic compounds. Water-reactive agents must be stored apart from water, aqueous solutions, and acids. Air-reactive materials must be packed in containers that are sealed off from the atmosphere. Explosive and shock-sensitive materials present risks that require special handling.
12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗