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At least 793 records · Page 44
All sourcesNASA NTRSDOE OSTI
DOE OSTI2012

Reconstitution of the cellular response to DNA damage in vitro using damage-activated extracts from mammalian cells

In proliferating mammalian cells, DNA damage is detected by sensors that elicit a cellular response which arrests the cell cycle and repairs the damage. As part of the DNA damage response, DNA replication is inhibited and, within seconds, histone H2AX is phosphorylated. Here we describe a cell-free system that reconstitutes the cellular response to DNA double strand breaks using damage-activated cell extracts and naieve nuclei. Using this system the effect of damage signalling on nuclei that do not contain DNA lesions can be studied, thereby uncoupling signalling and repair. Soluble extracts from G1/S phase cells that were treated with etoposide before isolation, or pre-incubated with nuclei from etoposide-treated cells during an in vitro activation reaction, restrain both initiation and elongation of DNA replication in naieve nuclei. At the same time, H2AX is phosphorylated in naieve nuclei in a manner that is dependent upon the phosphatidylinositol 3-kinase-like protein kinases. Notably, phosphorylated H2AX is not focal in naieve nuclei, but is evident throughout the nucleus suggesting that in the absence of DNA lesions the signal is not amplified such that discrete foci can be detected. This system offers a novel screening approach for inhibitors of DNA damage response kinases, which we demonstrate using the inhibitors wortmannin and LY294002. -- Highlights: Black-Right-Pointing-Pointer A cell free system that reconstitutes the response to DNA damage in the absence of DNA lesions. Black-Right-Pointing-Pointer Damage-activated extracts impose the cellular response to DNA damage on naieve nuclei. Black-Right-Pointing-Pointer PIKK-dependent response impacts positively and negatively on two separate fluorescent outputs. Black-Right-Pointing-Pointer Can be used to screen for inhibitors that impact on the response to damage but not on DNA repair. Black-Right-Pointing-Pointer LY294002 and wortmannin demonstrate the system's potential as a pathway focused screening approach.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2026

Development of a Flow-through Cell for Ultrasonic Extraction (UE)─Single Particle (SP)─ICP-MS─an Approach for Nano/Microparticle Elemental and Isotopic Analysis

Nanotechnology is a salient part of the scientific landscape, and analytical approaches are rapidly evolving to enable small-scale characterization of nano- and microparticle compositions and impurities. Here, a flow-through sonicating cell was developed for direct particle extraction from a silicon wafer and integrated with an inductively coupled plasma–mass spectrometer (ICP-MS) for subsequent elemental and isotopic characterization of the released particles. Ultrasonic extraction (UE)─single particle (SP)─ICP-MS offers controlled particle mobilization from solid substrates and allows for increased sample throughput by eliminating the need for pre-extraction of particles and decreasing sample preparation steps. Coupling this device to an ICP-MS with a time-of-flight (TOF) mass analyzer, it is possible to distinguish unique isotopic compositions of the particles. Both tungsten and nickel isotopically tagged particles, which were deposited on Si wafers, are presented here with analysis via UE─SP─ICP-MS. This approach could support efforts in the fields of particle synthesis, nuclear safeguards and forensics, environmental monitoring, and semiconductor industries in which the detection of particles from substrates and wafers is critical.

Paul, Molly [ORNL] (ORCID:0009000009672055)↗
DOE OSTI2023

Investigation of Electron Extraction and Protection Layers on Cu 2 O Photocathodes

Many semiconductor photoelectrodes used for solar fuel production require the addition of buffer and protection layers to enhance their solar-to-fuel conversion efficiency and long-term stability. For example, Cu 2 O, which is the most efficient oxide-based photocathode but suffers from photocorrosion, has been assembled with various buffer and protection layers to suppress photocorrosion and use more photoexcited electrons for useful reactions such as water reduction to H 2 . However, the abilities of various buffer and protection layers to extract electrons from Cu 2 O have never been directly evaluated. Instead, their abilities were estimated based on the photocurrent for water reduction after adding a hydrogen evolution catalyst on top of them. In these evaluations, as the photocurrent is affected not only by the buffer or protection layer but also by the catalyst, the ability of the buffer or protection layer to extract electrons from Cu 2 O could not be accurately determined or compared. Here, in this study, we demonstrate that 4-hydroxy-2,2,6,6-tetramethylpiperidine-1-oxyl (TEMPOL), whose reduction rate is faster than the photocorrosion rate of Cu 2 O, can be used as an effective electron scavenger to directly evaluate any change caused by a buffer or protection layer in electron-hole separation in Cu 2 O. In particular, we compared the performances of ZnO and TiO 2 layers on Cu 2 O for extracting electrons and suppressing photocorrosion. We also compared the performances of TiO 2 layers prepared by electrodeposition and atomic layer deposition (ALD) to show that the deposition method can make a striking impact on the performance of the same TiO 2 because it can affect the critical characteristics of the layer (e.g., defect levels, conductivity, interfacial atomic arrangements) that govern interfacial charge transfer in multilayer photoelectrodes.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Electrochemical Recovery of Rare-Earth Elements from Coal Fly Ash Using Ionic Liquids as both Extractant and Electrolyte

Rare-earth elements (REEs) are critical for medical technologies, electronics, and clean energy. Coal fly ash (CFA), a byproduct of coal combustion, offers a promising alternative REE source. However, efficient extraction and separation of REEs from CFA remain challenging due to the complex composition of CFA. This study introduces a sustainable method for REE recovery using a recyclable ionic liquid, betainium bis(trifluoromethylsulfonyl)imide ([Hbet]- [Tf 2 N]), which serves both as the extractant from CFA and as the electrolyte in electrodeposition. In the first stage, [Hbet][Tf 2 N] preferentially extracts REEs from CFA through leaching. In the second stage, the REE-enriched ionic liquid undergoes electrochemical deposition using amperometry techniques, where REEs are reduced and deposited onto the electrode. The deposition experiments were conducted from −0.5 to −2.0 V vs a Pt quasireference electrode in a three-electrode setup comprising titanium as the working electrode and platinum as both the reference and counter electrodes. Varying the applied potential enabled potential-dependent preferential REE deposition. At −0.5 V, neodymium (Nd) showed preferential recovery, reaching 25% with a separation factor of 37 over other REEs. In contrast, applying a more negative potential increased overall deposition, yielding ∼50% Nd recovery and 10−20% recovery for the remaining REEs. After recovery, the ionic liquid was regenerated and reused for a subsequent electrochemical recovery cycle. Overall, this study demonstrates a feasible approach for REE recovery from CFA waste, with potential to enhance resource utilization within the REE supply chain.

coal fly ash↗
DOE OSTI2019

Results of an Ocean Trial of the Symbiotic Machine for Ocean uRanium Extraction

Amidoxime-based adsorbents have become highly promising for seawater uranium extraction. However, current deployment schemes are stand-alone, intermittent operation systems that have significant practical and economic challenges. This paper presents two 1/10th scale prototypes of a Symbiotic Machine for Ocean uRanium Extraction (SMORE) which pairs with an existing offshore structure. This pairing reduces mooring and deployment costs while enabling continuous, autonomous uranium extraction. Utilizing a shell enclosure to decouple the mechanical and chemical requirements of the adsorbent, one design concept prototyped continuously moves the shells through the water while the other keeps them stationary. Water flow in the shells on each prototype was determined using the measurement of radium adsorbed by MnO 2 impregnated acrylic fibers. The results from a nine-week ocean trial show that while movement of the shells through the water may not have an effect on uranium adsorption by the fibers encased, it could help reduce biofouling if above a certain threshold speed (resulting in increased uptake), while also allowing for the incorporation of design elements to further mitigate biofouling such as bristle brushes and UV lamps. The trace metal uptake by the AI8 adsorbents in this trial also varied greatly from previous marine deployments, suggesting that uranium uptake may depend greatly upon the seawater concentrations of other elements such as vanadium and copper. Lastly, the results from this study will be used to inform future work on the seawater uranium production cost from a full-scale SMORE system.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2022

Flow-Assisted Selective Mineral Extraction from Seawater

The sustainable production of critical materials from natural sources requires a paradigm shift away from currently used resource-intensive processes. In this paper, we report a single-step, laminar co-flow method (LCM) that leverages non-equilibrium conditions to selectively extract pure Mg(OH) 2 from natural seawater. Conventional seawater-based Mg extraction involves adding individual or a combination of precipitants to obtain Mg(OH) 2 , but the co-existence of Ca 2+ unavoidably results in CaCO 3 impurities requiring additional purification steps. Here we show that the non-equilibrium conditions in LCM achieved using a microfluidics device and by simply co-injecting a NaOH solution with seawater can result in improved selectivity for Mg(OH) 2 unlike in conventional bulk mixing method. The resulting precipitates are characterized for composition and the process yield and purity are optimized through systematic variations of the reaction time and the concentration of NaOH. This is the first demonstration of LCM for selective separation, and as a one-step process that does not rely on novel sorbents, membranes, or external stimuli, it is easy to scale-up. LCM has the potential to be broadly relevant to selective separations from complex feed streams and diverse chemistries—enabling more sustainable materials extraction and processing.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2016

Potential impact of seawater uranium extraction on marine life

A variety of adsorbent materials have been developed to extract uranium from seawater as an alternative traditional terrestrial mining. A large-scale deployment of these adsorbents would be necessary to recover useful quantities of uranium and this raises a number of concerns regarding potential impacts on the surrounding marine environment. Two concerns are whether or not the adsorbent materials are toxic and any potentially harmful effects that may result from depleting uranium or vanadium (also highly concentrated by the adsorbents) from the local environment. To test the potential toxicity of the adsorbent with or without bound metals, Microtox assays were used to test both direct contact toxicity and the toxicity of any leachate in the seawater. The Microtox assay was chosen because it the detection of non-specific mechanisms of toxicity. Toxicity was not observed with leachates from any of 68 adsorbent materials that were tested, but direct contact with some adsorbents at very high adsorbent con-centrations exhibited toxicity. These concentrations are, however, very unlikely to be seen in the actual marine deployment. Adsor-bents that accumulated uranium and trace metals were also tested for toxicity, and no toxic effect was observed. Biofouling on the adsorbents and in columns or flumes containing the adsorbents also indicates that the adsorbents are not toxic and that there may not be an obvious deleterious effect resulting from removing uranium and vanadium from seawater. An extensive literature search was also performed to examine the potential impact of uranium and vanadium extraction from seawater on marine life using the Pacific Northwest National Laboratory’s (PNNL’s) document analysis tool, IN-SPIRE™. Although other potential environmental effects must also be considered, results from both the Microtox assay and the literature search provide preliminary evidence that uranium extraction from seawater could be performed with minimal impact on marine fauna.

environment↗
DOE OSTI2020

Nanomaterial Synthesis Insights from Machine Learning of Scientific Articles by Extracting, Structuring, and Visualizing Knowledge

Nanomaterials of varying compositions and morphologies are of interest for many applications from catalysis to optics, but the synthesis of nanomaterials and their scale-up are most often time-consuming and Edisonian processes. Information gleaned from the scientific literature can help inform and accelerate nanomaterials development, but again, searching the literature and digesting the information are time-consuming manual processes for researchers. To help address these challenges, here we developed scientific article-processing tools that extract and structure information from the text and figures of nanomaterials articles, thereby enabling the creation of a personalized knowledgebase for nanomaterials synthesis that can be mined to help inform further nanomaterials development. Starting with a corpus of ~35k nanomaterials-related articles, we developed models to classify articles according to the nanomaterial composition and morphology, extract synthesis protocols from within the articles’ text, and extract, normalize, and categorize chemical terms within synthesis protocols. We demonstrate the efficiency of the proposed pipeline on an expert-labeled set of nanomaterials synthesis articles, achieving 100% accuracy on composition prediction, 95% accuracy on morphology prediction, 0.99 AUC on protocol identification, and up to a 0.87 F1-score on chemical entity recognition. In addition to processing articles’ text, microscopy images of nanomaterials within the articles are also automatically identified and analyzed to determine the nanomaterials’ morphologies and size distributions. To enable users to easily explore the database, we developed a complementary browser-based visualization tool that provides flexibility in comparing across subsets of articles of interest. We use these tools and information to identify trends in nanomaterials synthesis, such as the correlation of certain reagents with various nanomaterial morphologies, which is useful in guiding hypotheses and reducing the potential parameter space during experimental design.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Impact of Water Extraction on Malonamide Aggregation: A Molecular Dynamics and Graph Theoretic Approach

Solution structure in liquid-liquid extraction affects the efficacy of separation; however, even for simplified organic phases, structural characterization and attribution of aggregation to intermolecular interactions are fundamental challenges. We investigate water uptake into organic phases for two malonamides commonly applied to actinide and lanthanide separations. Extracted water induces reorganization of the amphiphilic extractant molecules, although we find this rearrangement is not strongly manifested in small-angle X-ray scattering making it challenging to probe without methods such as atomistic simulation. Using a graph theoretic approach to define hydrogen bonded water/malonamide aggregates from molecular dynamics simulations, we find evidence of a characteristic aggregate size by water number that results from geometric accommodation of the surrounding malonamide molecules. Furthermore, this implies a degree of size selectivity inherent to these water-in-oil aggregates. Conversely, we find no evidence of a characteristic size of the aggregates with respect to their malonamide number. By defining a separate graphical representation of self-association of the amphiphilic malonamides, we quantify how water affects the local and nonlocal topology of the malonamide network, providing a basis for characterization of the structure and impact of polar solutes in increasingly complex organic phases.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Bacillus subtilis Lipid Extract, A Branched-Chain Fatty Acid Model Membrane

Lipid extracts are an excellent choice of model biomembrane; however at present, there are no commercially available lipid extracts or computational models that mimic microbial membranes containing the branched-chain fatty acids found in many pathogenic and industrially relevant bacteria. Here, we advance the extract of Bacillus subtilis as a standard model for these diverse systems, providing a detailed experimental description and equilibrated atomistic bilayer model included as Supporting Information to this Letter and at (http://cmb.ornl.gov/members/cheng). The development and validation of this model represents an advance that enables more realistic simulations and experiments on bacterial membranes and reconstituted bacterial membrane proteins.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Rational Construction of Porous Metal–Organic Frameworks for Uranium(VI) Extraction: The Strong Periodic Tendency with a Metal Node

Although metal-organic frameworks (MOFs) have been reported as important porous materials for the potential utility in metal ion separation, coordinating the functionality, structure, and component of MOFs remains a great challenge. Herein, a series of anionic rare earth MOFs (RE-MOFs) were synthesized via a solvothermal template reaction and for the first time explored for uranium(VI) capture from an acidic medium. The unusually high extraction capacity of UO2 2 + (e.g., 538 mg U per g of Y-MOF) was achieved through ion-exchange with the concomitant release of Me 2 NH 2 + , during which the uranium(VI) extraction in the series of isostructural RE-MOFs was found to be highly sensitive to the ionic radii of the metal nodes. That is, the uranium(VI) adsorption capacities continuously increased as the ionic radii decreased. Finally, in-depth mechanism insight was obtained from molecular dynamics simulations, suggesting that both the accessible pore volume of the MOFs and hydrogen-bonding interactions contribute to the strong periodic tendency of uranium(VI) extraction.

36 MATERIALS SCIENCE↗
DOE OSTI2013

Design criteria for polyazine extractants to separate An III from Ln III

Although polyazine extractants have been extensively studied as agents for partitioning trivalent actinides from lanthanides, an explanation for why certain azine compositions succeed and others fail is lacking. To address this issue, density functional theory calculations were used to evaluate fundamental properties (intrinsic binding affinity for a representative trivalent f-block metal, basicity, and hardness) for prototype azine donors pyridine, pyridazine, pyrimidine, pyrazine, 1,2,3-triazine, 1,2,4-triazine, and 1,3,5-triazine, as well as perform conformational analyses of bisazine chelates formed by directly connecting two donors together. Lastly, the results provide criteria that both rationalize the behavior of known extractants, TERPY, TPTZ, hemi-BTP, BTP, BTBP, and BTPhen, and predict a new class of extractants based on pyridazine donor groups.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Influence of Groundwater Extraction Costs and Resource Depletion Limits on Simulated Global Nonrenewable Water Withdrawals Over the Twenty‐First Century

Abstract Future rates of global groundwater depletion will depend on the economic and environmental viability of extracting water from increasingly stressed aquifers. Here we analyze global groundwater depletion by considering these factors explicitly. Global gridded groundwater availability and extraction cost data are aggregated to produce nonrenewable resource supply curves for 235 major river basins and geopolitical regions. These resources are then exposed to dynamically generated demands for water in a fully coupled, multisectoral, global simulation. As groundwater head levels drop, imposing greater capital and operating costs to bring water to the surface, modeled water use sectors are able to deploy a range of supply‐ and demand‐driven adaptive responses. Results demonstrate large sensitivity in global groundwater depletion rates to adjustments in resource exploitability. Extraction costs moderate demands for nonrenewable water substantially, resulting in the onset of a decline in global groundwater depletion rates within the twenty‐first century. New groundwater depletion hot spots may emerge as crop producers abandon overexploited basins and expand croplands in regions with cheaper, more plentiful water resources.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2019

Extraction of higher-order nonlinear electronic response in solids using high harmonic generation

Nonlinear susceptibilities are key to ultrafast lightwave driven optoelectronics, allowing petahertz scaling manipulation of the signal. Recent experiments retrieved a 3rd order nonlinear susceptibility by comparing the nonlinear response induced by a strong laser field to a linear response induced by the otherwise identical weak field. The highly nonlinear nature of high harmonic generation (HHG) has the potential to extract even higher order nonlinear susceptibility terms. However, up till now, such characterization has been elusive due to a lack of direct correspondence between high harmonics and nonlinear susceptibilities. Here, we demonstrate a regime where such correspondence can be clearly made, extracting nonlinear susceptibilities (7th, 9th, and 11th) from sapphire of the same order as the measured high harmonics. The extracted high order susceptibilities show angular-resolved periodicities arising from variation in the band structure with crystal orientation. Our results open a door to multi-channel signal processing, controlled by laser polarization.

42 ENGINEERING↗
DOE OSTI2021

An integrated in vivo/in vitro framework to enhance cell-free biosynthesis with metabolically rewired yeast extracts

Cell-free systems using crude cell extracts present appealing opportunities for designing biosynthetic pathways and enabling sustainable chemical synthesis. However, the lack of tools to effectively manipulate the underlying host metabolism in vitro limits the potential of these systems. Here, we create an integrated framework to address this gap that leverages cell extracts from host strains genetically rewired by multiplexed CRISPR-dCas9 modulation and other metabolic engineering techniques. As a model, we explore conversion of glucose to 2,3-butanediol in extracts from flux-enhanced Saccharomyces cerevisiae strains. We show that cellular flux rewiring in several strains of S. cerevisiae combined with systematic optimization of the cell-free reaction environment significantly increases 2,3-butanediol titers and volumetric productivities, reaching productivities greater than 0.9 g/L-h. We then show the generalizability of the framework by improving cell-free itaconic acid and glycerol biosynthesis. Our coupled in vivo/in vitro metabolic engineering approach opens opportunities for synthetic biology prototyping efforts and cell-free biomanufacturing.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Metagenome-assembled genome extraction and analysis from microbiomes using KBase

Uncultivated Bacteria and Archaea account for the vast majority of species on Earth, but obtaining their genomes directly from the environment, using shotgun sequencing, has only become possible recently. In order to realize the hope of capturing Earth’s microbial genetic complement and to facilitate the investigation of the functional roles of specific lineages in a given ecosystem, technologies that accelerate the recovery of high-quality genomes are necessary. We present a series of analysis steps and data products for the extraction of high-quality metagenome-assembled genomes (MAGs) from microbiomes using the U.S. Department of Energy Systems Biology Knowledgebase (KBase) platform (http://www.kbase.us/). Overall, these steps take about a day to obtain extracted genomes when starting from smaller environmental shotgun read libraries, or up to about a week from larger libraries. In KBase, the process is end-to-end, allowing a user to go from the initial sequencing reads all the way through to MAGs, which can then be analyzed with other KBase capabilities such as phylogenetic placement, functional assignment, metabolic modeling, pangenome functional profiling, RNA-Seq and others. While portions of such capabilities are available individually from other resources, the combination of the intuitive usability, data interoperability and integration of tools in a freely available computational resource makes KBase a powerful platform for obtaining MAGs from microbiomes. While this workflow offers tools for each of the key steps in the genome extraction process, it also provides a scaffold that can be easily extended with additional MAG recovery and analysis tools, via the KBase software development kit (SDK).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Mobility and threshold voltage extraction in transistors with gate-voltage-dependent contact resistance

The mobility of emerging (e.g., two-dimensional, oxide, organic) semiconductors is commonly estimated from transistor current-voltage measurements. However, such devices often experience contact gating, i.e., electric fields from the gate modulate the contact resistance during measurements, which can lead conventional extraction techniques to estimate mobility incorrectly even by a factor >2. Although this error can be minimized by measuring transistors at high gate-source bias |V gs |, this regime is often inaccessible in emerging devices that suffer from high contact resistance or early gate dielectric breakdown. Here, we propose a method of extracting mobility in transistors with gate-dependent contact resistance that does not require operation at high |V gs |, enabling accurate mobility extraction even in emerging transistors with strong contact gating. Our approach relies on updating the transfer length method (TLM) and can achieve <10% error even in regimes where conventional techniques overestimate mobility by >2×

36 MATERIALS SCIENCE↗
DOE OSTI2018

Extraction and biomolecular analysis of dermal interstitial fluid collected with hollow microneedles

Dermal interstitial fluid (ISF) is an underutilized information-rich biofluid potentially useful in health status monitoring applications whose contents remain challenging to characterize. Here, we present a facile microneedle approach for dermal ISF extraction with minimal pain and no blistering for human subjects and rats. Extracted ISF volumes were sufficient for determining transcriptome, and proteome signatures. We noted similar profiles in ISF, serum, and plasma samples, suggesting that ISF can be a proxy for direct blood sampling. Dynamic changes in RNA-seq were recorded in ISF from induced hypoxia conditions. Finally, we report the first isolation and characterization, to our knowledge, of exosomes from dermal ISF. The ISF exosome concentration is 12–13 times more enriched when compared to plasma and serum and represents a previously unexplored biofluid for exosome isolation. This minimally invasive extraction approach can enable mechanistic studies of ISF and demonstrates the potential of ISF for real-time health monitoring applications.

59 BASIC BIOLOGICAL SCIENCES↗