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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 127 records · Page 7
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Circadian rhythmicity of amyloid‐beta‐related molecules is disrupted in the choroid plexus of a female Alzheimer's disease mouse model

Abstract The choroid plexus (CP) is part of the blood‐cerebrospinal fluid barrier (BCSFB) and was recently described as an important component of the circadian clock system. It is the principal source of cerebrospinal fluid (CSF) and responsible for the synthesis and secretion of various neuroprotective peptides including those involved in amyloid‐β (Aβ) transport/degradation, contributing to Aβ homeostasis. Inadequate Aβ metabolic clearance and transport across the BCSFB have been associated with circadian dysfunctions in Alzheimer's disease (AD) patients. To investigate whether AD pathology influences Aβ scavengers circadian expression, we collected CP at different time points from an AD mouse model (APP/PS1) (female and male animals, aged 6‐ and 12‐months‐old) and analyzed their mRNA expression by Real‐time RT‐PCR. Only angiotensin‐converting enzyme (Ace) expression in 6‐month‐old female wild‐type mice and transthyretin (Ttr) expression in 12‐month‐old female wild‐type mice presented significant rhythmicity. The circadian rhythmicity of Ace and Ttr, prompt us to analyze the involvement of circadian rhythm in Aβ uptake. A human CP papilloma (HIBCPP) cell line was incubated with Aβ‐488 and uptake was evaluated at different time points using flow cytometry. Aβ uptake displayed circadian rhythmicity. Our results suggest that AD might affect Aβ scavengers rhythmicity and that Aβ clearance is a rhythmic process possibly regulated by the rhythmic expression of Aβ scavengers.

Furtado, André↗
DOE OSTI2022

Effect of bacterial cell addition on Fe(III) reduction and soil organic matter transformation in a farmland soil

The coupled biogeochemical processes of Fe(III) reduction and organic matter transformation profoundly impact terrestrial carbon cycling. However, little is known about the microbial role in soil organic matter (SOM) transformation during Fe(III) bio-reduction. Here we investigated the bio-reduction behavior of a black farmland soil and corresponding SOM transformation under circumneutral and anoxic conditions. A model dissimilatory Fe reducing bacterium, Geobacter sulfurreducens, was added in either live or dead form in order to enhance Fe(III) reduction in soil and to evaluate the accompanying transformation of SOM. The progress of Fe reduction was monitored and SOM transformation was characterized by various spectroscopy methods. Results showed that addition of either dead or live G. sulfurreducens cells increased the Fe(III) reduction rate and extent. Without cell addition, SOM transformation was insignificant within 13 days of incubation, only with some consumption of aliphatic/protein compounds, apparently due to their higher bio-degradability. Addition of dead or live cells resulted in more drastic SOM transformation, but through different mechanisms. With dead cell amendment, cell necromass and debris stimulated the activity of indigenous soil microbes by serving as extra carbon/energy sources. During Fe(III) reduction, the aliphatic/protein compounds were preferentially consumed by indigenous microbial communities, similar to the treatment without cell addition but with a greater extent of consumption. In comparison, addition of live G. sulfurreducens cells stimulated degradation of less bioavailable compounds, including more saturated and higher molecular weight SOM. It is possible that fast depletion of labile SOM by live G. sulfurreducens cells favored utilization of less bioavailable molecules (such as those with more aromatic structures) by the originally dormant species in native microbial community, suggesting an active role of live Fe(III)-reducing bacteria in affecting SOM transformation. In addition, fast assimilation of microbial related carbon, such as aromatic proteins and microbial byproducts, into SOM pools was also observed. Overall, our results suggest that addition of Fe(III)-reducing bacteria to a native soil can enhance Fe(III) reduction and accelerate the turnover of SOM through various mechanisms. The study provides new insights into coupled Fe(III) reduction and SOM transformation, as well as the “priming effect” of SOM using microbial cells as substrate.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

High-throughput screening of multifunctional nanocoatings based on combinations of polyphenols and catecholamines

Biomimetic surface coatings based on plant polyphenols and catecholamines have been used broadly in a variety of applications. However, the lack of a rational cost-effective platform for screening these coatings and their properties limits the true potential of these functional materials to be unleashed. Here, we investigated the oxidation behavior and coating formation ability of a library consisting of 45 phenolic compounds and catecholamines. UV–vis spectroscopy demonstrated significant acceleration of oxidation and polymerization under UV irradiation. We discovered that several binary mixtures resulted in non-additive behavior (synergistic or antagonistic effect) yielding much thicker or thinner coatings than individual compounds measured by ellipsometry. To investigate the properties of coatings derived from new combinations, we used a miniaturized high-throughput strategy to screen 2,532 spots coated with single, binary, and ternary combinations of coating precursors in one run. We evaluated the use of machine learning models to learn the relation between the chemical structure of the precursors and the thickness of the nanocoatings. Formation and stability of nanocoatings were investigated in a high-throughput manner via discontinuous dewetting. 30 stable combinations (hits) were used to tune the surface wettability and to form water droplet microarray and spot size gradients of water droplets on the coated surface. No toxicity was observed against eukaryotic HeLa cells and Pseudomonas aeruginosa (strain PA30) bacteria after 24 h incubation at 37 C. The strategy introduced here for high-throughput screening of nanocoatings derived from combinations of coating precursors enables the discovery of new functional materials for various applications in science and technology in a cost-effective miniaturized manner.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Hole formation effect on surface morphological response of plasma-facing tungsten

We report simulation results on the effect of helium (He) bubble bursting-mediated surface hole formation on the surface morphological response of tungsten plasma-facing components (PFCs) in nuclear fusion devices. Our analysis is based on an atomistically informed, continuum-scale model, which is capable of accessing the spatiotemporal scales relevant to the fuzz nanostructure formation process on the surface of PFC tungsten. Our simulations account, in an empirical fashion, for two types of subsurface bubble dynamical phenomena in the nanobubble region of PFC tungsten during He plasma irradiation, involving bubble bursting and surface crater formation. We demonstrate that the hole formation effect on the PFC tungsten surface accelerates the growth rate of nanotendrils and the onset of fuzz formation. As a result, the predicted incubation time for surface nanotendril growth is shortened, in agreement with experimental data of incubation fluence at comparable plasma exposure conditions. We also explore systematically the dependence of the PFC surface morphological response on the areal density of holes introduced at regular time intervals onto the He-implanted tungsten surface, a parameter in our analysis that serves as a proxy for the rate of He bubble bursting. More importantly, our simulations capture fine surface features in the PFC tungsten surface morphology and predict that the average spacing between nanotendrils is on the order of 100 nm, consistent with the experimental findings.

Chen, Chao-Shou (ORCID:0000000307910042)↗
DOE OSTI2024

Substantial and overlooked greenhouse gas emissions from deep Arctic lake sediment - supporting data and code

This data package contains data, descriptions, and code-based analyses that were used to support conclusions drawn in “Substantial and overlooked greenhouse gas emissions from deep Arctic lake sediment”, by Freitas et al. (2025) (https://doi.org/10.1038/s41561-024-01614-y). The study evaluated greenhouse gas production along a deep sediment core (20 m) taken in 2018 from below Goldstream Lake, a field site approximately 15 km north of Fairbanks, Alaska.The file “ESSDive_NFreitas_2024_flmd.csv” includes an overview of all other csv files in this data package, namely: sediment descriptions (depth and type of sediment), sediment characterizations (bulk density, gravimetric water content, total carbon, etc.), calculated respiration and temperature sensitivity values associated with year-long incubations of the sediment core, and the R code used to process the dataset. Additional details regarding the content of these files and how the calculations were performed are described in the Methods section of this archive. The “data_dictionary_ESSDive_NFreitas_2024_dd.csv” is a data dictionary for all files included in the data package. Each row in the data dictionary represents a column name in a given file. The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research. The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska.Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).Data package updates- August 2024: Title was updated, R code now includes a process for calculating potential production across the whole sediment column, the "sediment_column_production_potentials_ESSDive_NFreitas_2024.csv" is the associated data output file, and the file level metadata and data dictionaries were updated to reflect the contents of the additional csv file.- October 2024: Title was updated, and a statement was added to Step 2 of the Methods that describes that samples were collected (and exported) in a responsible manner and in accordance with relevant permits and local laws.- January 2025: Updated the associated manuscript details in the Abstract (manuscript title, publication date, DOI link) and in the Related References section (full citation).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

The effect of heat treatment on the defect evolution in LPBF 316H stainless steel

This work investigates the effect of processing and heat treatment on defect evolution and irradiation response of laser powder bed fusion (LPBF) 316H stainless steel, with comparisons to LPBF 316L and wrought 316L/316H. Using in-situ and ex-situ ion irradiations across a wide parameter space—temperature (300–675 °C), dose (0.2–25 dpa), dose rate (10 -3 –10 -5 dpa/s), and helium co-implantation (20–2500 appm)—we correlated void swelling, dislocation loop evolution, and segregation behavior with pre-irradiation microstructures (as-built, stress-relieved, solution-annealed, and cold-worked). Results show that swelling is strongly controlled by dislocation density: intermediate densities maximize swelling, while solution annealing or cold working reduce susceptibility to levels comparable to wrought alloys. Low dose rates and helium both promote cavity nucleation and lower the incubation barrier, with helium suppressing the role of dislocation density and driving swelling behavior toward wrought-like response. Loop evolution in SA LPBF 316H resembles wrought 316L but shows localized denuded zones near low-angle grain boundaries. STEM-EDS mapping further revealed Ni segregation at voids and sparse Al-rich oxides, without evidence of Ni–Si precipitates. Collectively, these findings identify dislocation density, helium content, and dose rate as the factors governing swelling in LPBF 316H and provide mechanistic datasets for model validation, supporting LAIN and the qualification of AM austenitic steels for nuclear service.

316 stainless steel↗
DOE OSTI2024

Data and Scripts associated with “Lambda-PFLOTRAN: Workflow for Incorporating Organic Matter Chemistry Informed by Ultra High Resolution Mass Spectrometry into Biogeochemical Modeling.”

This data package is associated with the publication “Lambda-PFLOTRAN: Workflow for Incorporating Organic Matter Chemistry Informed by Ultra High Resolution Mass Spectrometry into Biogeochemical Modeling” submitted to Geoscientific Model Development (Muller et al., 2024). In this manuscript, organic matter chemistry and thermodynamics are directly connected to reactive transport simulators through the newly developed Lambda-PFLOTRAN (Parallel Reactive Flow and Transport model) workflow tool that succinctly incorporates organic matter chemistry data generated from Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) into reaction networks to simulate aerobic respiration of the organic matter and the resulting biogeochemistry. Lambda-PFLOTRAN is a python-based workflow, executed through a Jupyter Notebook interface, that digests raw FTICR-MS data, develops a representative reaction network based on substrate-explicit thermodynamic modeling (also termed lambda modeling due to its key thermodynamic parameter λ used therein), and completes a biogeochemical simulation with the open source, reactive flow, and transport code PFLOTRAN. This data package contains Jupyter Notebook based workflows for two test cases for running biogeochemical simulations of organic matter oxidation identified by FTICR-MS. It contains four primary folders (workflow, data, src, and analysis), a file-level metadata file (Muller_2024_Lambda_PFLOTRAN_Manuscript_Data_Package_flmd.csv) that lists all the files contained in this data package with a short description of each, and a data dictionary (Muller_2024_Lambda_PFLOTRAN_Manuscript_Data_Package_dd.csv) file that describes the tabular column headers. The ‘workflow’ folder contains the Jupyter Notebook based workflows for running the lambda analysis, PFLOTRAN simulation, sensitivity analysis and parameter estimation. The ‘data’ folder contains the FTICR-MS data, initial conditions, and incubation data for test cases 1 and 2 in folders titled ‘WHONDRS’ and ‘Colloids’, respectively. The data folder also has a ‘Database’ folder containing a reaction network for bulk organic matter (assumed to be CH2O) and a general database for PFLOTRAN (hanford_rxn_network). The CH2O reaction network defines bulk organic matter oxidation. Biogeochemical simulations are completed for both the lambda binned organic matter and bulk organic matter reaction networks. The ‘hanford_rxn_network’ database includes information required for PFLTORAN simulations including ion size, molar mass, and charge of the aqueous species, gases, and minerals phases. The ‘src’ folder contains python source codes for performing lambda analysis, PFLOTRAN simulation, sensitivity analysis and parameter estimation. The ‘analysis’ folder contains outputs from the test cases 1 and 2 including lambda analysis, PFLOTRAN runs and the calibration results.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Organic sulfur from source to sink in low‐sulfate Lake Superior

Abstract Organic sulfur plays a crucial role in the biogeochemistry of aquatic sediments, especially in low sulfate (< 500 μ M) environments like freshwater lakes and the Earth's early oceans. To better understand organic sulfur cycling in these systems, we followed organic sulfur in the sulfate‐poor (< 40 μ M) iron‐rich (30–80 μ M) sediments of Lake Superior from source to sink. We identified microbial populations with shotgun metagenomic sequencing and characterized geochemical species in porewater and solid phases. In anoxic sediments, we found an active sulfur cycle fueled primarily by oxidized organic sulfur. Sediment incubations indicated a microbial capacity to hydrolyze sulfonates, sulfate esters, and sulfonic acids to sulfate. Gene abundances for dissimilatory sulfate reduction ( dsrAB ) increased with depth and coincided with sulfide maxima. Despite these indicators of sulfide formation, sulfide concentrations remain low (< 40 nM) due to both pyritization and organic matter sulfurization. Immediately below the oxycline, pyrite accounted for 13% of total sedimentary sulfur. Both free and intact lipids in this same interval accumulated disulfides, indicating rapid sulfurization even at low concentrations of sulfide. Our investigation revealed a new model of sulfur cycling in a low‐sulfate environment that likely extends to other modern lakes and possibly the ancient ocean, with organic sulfur both fueling sulfate reduction and consuming the resultant sulfide.

Phillips, Alexandra A.↗
DOE OSTI2020

Water-dispersible nanocolloids and higher temperatures promote the release of carbon from riparian soil

Increasing temperatures in alpine regions accompanied by glacial retreat is occurring rapidly due to climate change. This may affect riparian soils by increasing weathering rates, resulting in greater organic carbon (OC) release to rivers via movement of iron-containing colloids and nanonminerals. Increased concentrations of iron- or silcate-nanominerals would result in higher surface area for OC adsorption. To test the influence of temperature on OC leaching, we examined mineral weathering and nanocolloid facilitated release of OC through a series of controlled laboratory batch and column experiments using sediment from the banks of the Nisqually River, Mount Rainier in Washington State (USA). Additional experiments were conduscted using the same sediments, but with an illite amendment added to test the influence of additional surface area and nanominerals that many sediments along the Nisqually River contain. These higher- and lower-surface-area sediments (i.e., sediments with and with the illite amendment) were incubated for three months at 4 or 20 °C, followed by batch and column OC leaching tests. Results show that OC leaching rates for 20 °C were two to three times greater than for 4 °C. Further, our results suggest that nanocolloids are responsible for moving this increased OC load from these sediments. When hydrologically connected, OC is released from back sediments to rivers faster than presently anticipated in fluvial environments experiencing climate change-induced glacial retreat. Further, a one-dimensional, finite-element computational model developed for this study estimates that a 1 °C increase in temperature over a 3-mo summer runoff period increases the OC release rate from sediments by 79%.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Naphthalene-DNA Adduct Formation in a Lung Airway Explant Model: The Role of Bioactivation and Naphthalene Metabolites

Humans are widely exposed to naphthalene. Once inhaled or ingested, naphthalene is metabolized by cytochrome P450 and other enzymes to form toxic metabolites known to harm lung epithelial cells. Naphthalene metabolites circulate in the blood. Chronic naphthalene inhalation promotes lesions in the epithelium of the mouse lung and rat nose. Oral naphthalene exposure leads to DNA adduct formation in mouse lung, but the contributions of different enzymatic pathways and the metabolites they generate are not fully understood. This study explores the influence of naphthalene metabolites on DNA adduct formation in the lungs of two species (mice and primates). To isolate the lung response, conducting airway explants containing Club cells, a target for pulmonary naphthalene toxicity, were microdissected from live lung tissue and incubated with 14 C-naphthalene or its metabolites: 14 C-1,2-naphthoquinone or 14 C-naphthalene-1,2-dihydrodiol. Explants were incubated for 1 h, then processed immediately (T1), or were transferred to clean media for the remainder of the 24 h (T24), to monitor 14 C in DNA over time. Accelerator mass spectrometry analysis revealed the formation of DNA adducts by all three radiolabeled compounds by T24. Our results support the notion that P450 enzymes of the Cyp2abfgs subfamily contribute to naphthalene-induced DNA adduct formation (approximately 4-fold reduction in male mice lacking the Cyp2abfgs genes, P < 0.01). The finding that naphthalene-1,2-dihydrodiol, a stable metabolite, formed DNA adducts (102–117 adducts/10 8 nucleotides) at 24 h following addition to the culture media validates the concern that circulating naphthalene metabolites can contribute to DNA adduct formation in the lung. DNA adducts persisted to 24 h after exposure in both mouse and primate airways and at comparable levels between species (77.8 vs 129 adducts/10 8 nucleotides, respectively). Together, these results support the importance of a potential genotoxic mechanism of naphthalene and its metabolites in vivo in both mice and nonhuman primates, and possibly also in humans.

Biological and medical sciences↗
DOE OSTI2024

Twenty Years of Progress, Challenges, and Opportunities in Measuring and Understanding Soil Respiration

Abstract Soil respiration (Rs), the soil‐to‐atmosphere flux of CO 2 , is a dominant but uncertain part of the carbon cycle, even after decades of study. This review focuses on progress in understanding Rs from laboratory incubations to global estimates. We survey key developments of in situ ecosystem‐scale Rs observations and manipulations, synthesize Rs meta‐analyses and global flux estimates, and discuss the most compelling challenges and opportunities for the future. Increasingly sophisticated lab experiments have yielded insights into the interaction among heterotrophic respiration, substrate supply, and enzymatic kinetics, and extended incubation‐based analyses across space and time. Observational and manipulative field‐based experiments have used improved measurement approaches to deepen our understanding of the integrated effects of environmental change and disturbance on Rs. Freely‐available observational databases have enabled meta‐analyses and studies probing the magnitude of, and constraints on, the global Rs flux. Key challenges for the field include expanding Rs measurements, experiments, and opportunities to under‐represented communities and ecosystems; reconciling independent estimates of global respiration fluxes and trends; testing and leveraging the power of machine learning and process‐based models, both independently and in conjunction with each other; and continuing the field's tradition of using novel experiments to explore diverse mechanisms and ecosystems.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Calcium is associated with specific soil organic carbon decomposition products at Blodgett Forest Research Center, Georgetown, California as analysed with scanning transmission X-ray microscopy carbon near-edge X-ray absorption fine structure spectroscopy

This data is from the paper calcium is associated with specific soil organic carbon decomposition products, published in SOIL. DOI: https://doi.org/10.5194/soil-11-381-2025, 2025.This file contains CSVs with spectral data and bulk soil data and there is no specific program required to open this data. The data includes Scanning transmission X-ray microscopy carbon near-edge X-ray absorption fine structure spectroscopy. data from the measurement of samples from the Whole-soil Warming project, run by the Belowground Biogeochemistry team at Blodgett Forest Research Center, Georgetown, California run by the University of California, Berkeley. It also includes bulk soil chemical properties. The University of California's Blodgett Forest Research Station (Forest) is situated in the Sierra Nevada foothills (1370 m a.s.l.) near Georgetown, California. The samples were collected from here: 38.912013, -120.661469, https://maps.app.goo.gl/291bCJ1zVqUhgktz6. The Forest soils were characterised as Alfisols, which are equivalent to Dystric Cambisols (IUSS Working Group WRB, 2015), and formed in granitic parent materials, in a temperate climate, under thinned, mixed-coniferous forest (Fig. S3; Gaudinski et al., 2009). With these analyses we aimed to answer the question, is calcium associated with a specific type of organic matter enriched in aromatic and phenolic carbon at the microscale in samples from Blodgett Forest Research Center? and how does this specific type of carbon respond to experiments targetted at removing and adding calcium to the soils, specifically cation exchange and incubation after calcium addition? Abstract from the paper can be found below: Calcium (Ca) may contribute to the preservation of soil organic carbon (SOC) in more ecosystems than previously thought. Here we provide evidence that Ca is co-located with SOC compounds that are enriched in aromatic and phenolic groups, across different acidic soil-types and locations with different ecosystem properties, differing in terms of climate, parent material, soil type, and vegetation. In turn, this co-localised fraction of Ca-SOC is removed through cation-exchange, and the association is then only re-established during decomposition in the presence of Ca (Ca addition incubation). Thus, highlighting a causative link between decomposition and the co-location of Ca with a characteristic fraction of SOC. Decomposition increases the relative proportion of negatively charged functional groups, which can increase the propensity for the association between SOC and Ca, and in turn, this association inhibits dissolved organic carbon export or further decomposition. We propose that this mechanism could be driven by Ca hotspots on the microscale shifting local decomposition processes and thereby explaining the colocation of Ca with SOC of a specific composition across different acidic soil environments. Incorporating this biogeochemical process into Earth System Models could improve our understanding, predictions, and management of carbon dynamics in soils, and account for their response to Ca-rich amendments.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Calcium is associated with specific soil organic carbon decomposition products

Abstract. Calcium (Ca) may contribute to the preservation of soil organic carbon (SOC) in more ecosystems than previously thought. Here, we provide evidence that Ca is co-located with SOC compounds that are enriched in aromatic and phenolic groups, across different acidic soil types and locations with different ecosystem properties, differing in terms of climate, parent material, soil type, and vegetation. In turn, this co-localised fraction of Ca–SOC is removed through cation exchange, and the association is then only re-established during decomposition in the presence of Ca (Ca addition incubation). Thus, this highlights a causative link between decomposition and the co-location of Ca with a characteristic fraction of SOC. Decomposition increases the relative proportion of negatively charged functional groups, which can increase the propensity for the association between SOC and Ca; in turn, this association can inhibit dissolved organic carbon export or further decomposition. We propose that this mechanism could be driven by Ca hotspots at the microscale shifting local decomposition processes and thereby explaining the co-location of Ca with SOC of a specific composition across different acidic soil environments. Incorporating this biogeochemical process into Earth system models could improve our understanding, predictions, and management of carbon dynamics in soils, as well as accounting for their response to Ca-rich amendments.

Rowley, Mike C. (ORCID:0000000224407855)↗
DOE OSTI2024

Evaluating the mutagenicity of N-nitrosodimethylamine in 2D and 3D HepaRG cell cultures using error-corrected next generation sequencing

Human liver-derived metabolically competent HepaRG cells have been successfully employed in both two-dimensional (2D) and 3D spheroid formats for performing the comet assay and micronucleus (MN) assay. In the present study, we have investigated expanding the genotoxicity endpoints evaluated in HepaRG cells by detecting mutagenesis using two error-corrected next generation sequencing (ecNGS) technologies, Duplex Sequencing (DS) and High-Fidelity (HiFi) Sequencing. Both HepaRG 2D cells and 3D spheroids were exposed for 72 h to N-nitrosodimethylamine (NDMA), followed by an additional incubation for the fixation of induced mutations. NDMA-induced DNA damage, chromosomal damage, and mutagenesis were determined using the comet assay, MN assay, and ecNGS, respectively. The 72-h treatment with NDMA resulted in concentration-dependent increases in cytotoxicity, DNA damage, MN formation, and mutation frequency in both 2D and 3D cultures, with greater responses observed in the 3D spheroids compared to 2D cells. The mutational spectrum analysis showed that NDMA induced predominantly A:T → G:C transitions, along with a lower frequency of G:C → A:T transitions, and exhibited a different trinucleotide signature relative to the negative control. These results demonstrate that the HepaRG 2D cells and 3D spheroid models can be used for mutagenesis assessment using both DS and HiFi Sequencing, with the caveat that severe cytotoxic concentrations should be avoided when conducting DS. With further validation, the HepaRG 2D/3D system may become a powerful human-based metabolically competent platform for genotoxicity testing.

3D spheroids↗
DOE OSTI2020

Autoclave treatment of the classical scrapie agent US No. 13-7 and experimental inoculation to susceptible VRQ/ARQ sheep via the oral route results in decreased transmission efficiency

Scrapie, a prion disease of sheep, is highly resistant to conventional deactivation. Numerous methods to deactivate scrapie have been tested in laboratory animal models, and adequate autoclave treatment can reduce or remove the infectivity of some classical scrapie strains depending on the heating parameters used. In this study, we autoclaved brain homogenate from a sheep with US scrapie strain 13–7 for 30 minutes at 121°C. Genetically susceptible VRQ/ARQ sheep were orally inoculated with 3 grams of the autoclaved brain homogenate. For comparison, a second group of sheep was inoculated with a non-autoclaved brain homogenate. Rectal biopsies were used to assess antemortem scrapie disease progression throughout the study. Five out of ten (5/10) sheep that received autoclaved inoculum ultimately developed scrapie after an experimental endpoint of 72 months. These sheep had a mean incubation period of 26.99 months. Two out of five (2/5) positive sheep had detectable PrP Sc in antemortem rectal biopsies, and two (2/5) other sheep had PrP Sc in postmortem rectal tissue. A single sheep (1/5) was positive for scrapie in the CNS, small intestine, and retropharyngeal lymph node but had negative rectal tissue. All of the sheep (10/10) that received non-autoclaved inoculum developed scrapie with a mean incubation period of 20.2 months and had positive rectal biopsies at the earliest timepoint (14.7 months post-inoculation). These results demonstrate that sheep are orally susceptible to US derived classical scrapie strain 13–7 after autoclave treatment at 121°C for 30 minutes. Differences in incubation periods and time interval to first positive rectal biopsies indicate a partial reduction in infectivity titers for the autoclaved inoculum group.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Time-lapse approach to correct deficiencies of 2D soil zymography

Membrane zymography is commonly used in rhizosphere ecology to map enzyme activities in intact soil samples and plant roots. The method consists of incubating a membrane saturated with an enzyme-specific fluorogenic substrate on the soil/root surface followed by measurements of fluorescence intensity of the product in the membrane. The traditional zymography is based on assumptions that fluorescence on membrane images is linearly increasing with time during zymography and an increase in product content is numerically equal to enzyme activity in soil below the membrane. These assumptions are unlikely to hold in experimental settings. In this work we introduce a new zymography technique, time-lapse zymography (TLZ); the approach that eliminates the need for assumptions of the traditional zymography and provides more realistic estimates of enzymatic activities. We assessed the new technique in a series of laboratory and modeling experiments, including quantification of the fluorescent product diffusion (e.g. MUF: 4-methylumbelliferone) from plant roots, enzyme activity measurements on the roots, and HYDRUS-2D & HP2 software calibration with obtained data. The calibrated model was used to analyze the processes governing spatial and temporal dynamics of MUF contents in the membrane. The results indicated that the enzyme diffusion within the membrane-soil system was negligible, and measured zymograms were adequately reproduced solely by accounting for substrate and product diffusions and for catalytic enzyme reaction described by the Michaelis-Menten equation. TLZ enabled identifying and using linear parts on MUF time series and accounting for MUF losses in each zymogram pixel, considerably improving the accuracy as compared to the traditional method. Results demonstrated that enzymatic activity from only a thin soil layer (~0.2 mm) is adequately represented in zymograms.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

A Coupled Small and Wide-Angle X-Ray Scattering Study of Phase Transformation Mechanisms in U-6Wt Pct Nb

The elevated temperature phase transformation kinetics of U-6wt%Nb in both wrought and cast conditions were investigated using in-situ high energy synchrotron X-ray scattering. The evolution of the phase content, γ-phase composition, and microstructure morphology was determined through the analysis of simultaneously collected wide-angle diffraction and small-angle scattering (SAXS) data. The results of the wide-angle scattering analysis, especially the phase fractions and average composition of the γ-phase, provide model parameters to enable a quantitative analysis using the SAXS data. Greater clarity regarding the kinetics of different precipitation mechanisms, namely the continuous precipitation (CP) of α-U within the γ-phase matrix and the discontinuous (DP) grain boundary precipitation of a lamellar microstructure, consisting of α-U and Nb-rich γ-phase are obtained from the coupled measurement modes. These results indicate that the CP mechanism is responsible for the initial precipitation of α-U at all temperatures considered. Near the nose in the time-temperature-transformation (TTT) diagram at ~798 K, both mechanisms are active during the early stages of phase transformation. However, the DP mechanism has an increasingly long incubation period with decreasing temperature below the TTT nose. In conclusion, the average interlamellar spacing obtained from the SAXS analysis increases with time, providing further evidence of the so-called divergent DP behavior previously observed in U-6wt%Nb alloys.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Winter warming in Alaska accelerates lignin decomposition contributed by Proteobacteria

Background: In a warmer world, microbial decomposition of previously frozen organic carbon (C) is one of the most likely positive climate feedbacks of permafrost regions to the atmosphere. However, mechanistic understanding of microbial mediation on chemically recalcitrant C instability is limited; thus, it is crucial to identify and evaluate active decomposers of chemically recalcitrant C, which is essential for predicting C-cycle feedbacks and their relative strength of influence on climate change. Using stable isotope probing of the active layer of Arctic tundra soils after depleting soil labile C through a 975-day laboratory incubation, the identity of microbial decomposers of lignin and, their responses to warming were revealed. Results: The β - Proteobacteria genus Burkholderia accounted for 95.1% of total abundance of potential lignin decomposers. Consistently, Burkholderia isolated from our tundra soils could grow with lignin as the sole C source. A 2.2 °C increase of warming considerably increased total abundance and functional capacities of all potential lignin decomposers. In addition to Burkholderia , α - Proteobacteria capable of lignin decomposition (e.g. Bradyrhizobium and Methylobacterium genera) were stimulated by warming by 82-fold. Those community changes collectively doubled the priming effect, i.e., decomposition of existing C after fresh C input to soil. Consequently, warming aggravates soil C instability, as verified by microbially enabled climate-C modeling. Conclusions: Our findings are alarming, which demonstrate that accelerated C decomposition under warming conditions will make tundra soils a larger biospheric C source than anticipated.

54 ENVIRONMENTAL SCIENCES↗