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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 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

Enrichment methods for inflow turbulence generation in the atmospheric boundary layer

Here, we investigate the feasibility of introducing synthetic turbulence into finite-domain large-eddy simulations (LES) of the wind plant operating environment. This effort is motivated by the need for a robust mesoscale-to-microscale coupling strategy in which a microscale (wind plant) simulation is driven by mesoscale data without any resolved microscale turbulence. A neutrally stratified atmospheric boundary layer was simulated in an LES with 10-m grid spacing. We show how such a fully developed turbulence field may be reproduced with spectral enrichment starting from an under-resolved coarse LES field (with 20-m and 40-m grid spacing). The velocity spectra of the under-resolved fields are enriched by superimposing a fluctuating velocity field calculated by two turbulence simulators: TurbSim and Gabor Kinematic Simulation. Both forms of enrichment accurately simulated the autospectra of all three velocity components at high wavenumbers, with agreement between the enriched fields and the full-resolution LES observed at 400 m from the inflow boundary. In contrast, the spectra of the unenriched fields reached the same fully developed state at four times the downstream distance.

17 WIND ENERGY↗
DOE OSTI2024

Automated Immunoprecipitation Workflow for Comprehensive Acetylome Analysis

Immunoprecipitation is one of the most effective methods for enrichment of lysine-acetylated peptides for comprehensive acetylome analysis using mass spectrometry. Manual acetyl peptide enrichment method using non-conjugated antibodies and agarose beads has been developed and applied in various studies. However, it is time consuming, and can introduce contaminants and variability that leads to potential sample loss and decreased sensitivity and robustness of the analysis. Here we describe a fast, automated enrichment protocol that enables reproducible and comprehensive acetylome analysis using a magnetic bead-based immunoprecipitation reagent.

Lysine acetylation, Acetylome, Acetyl peptide enri↗
DOE OSTI2024

Physics-preserving enriched Galerkin method for a fully-coupled thermo-poroelasticity model

This paper proposes a new numerical method for a fully-coupled, quasi-static thermo-poroelasticity model in a unified enriched Galerkin (EG) method framework. In our method, the mechanics sub-problem is solved using a locking-free EG method, and the flow and heat sub-problems are solved using a locally-conservative EG method. The proposed method offers mass and energy conservation properties with much lower costs than other methods with the same properties, including discontinuous Galerkin methods and mixed finite element methods. The well-posedness and optimal a priori error estimates are carefully derived. Here, several numerical tests confirm the theoretical optimal convergence rates and the mass and energy conservation properties of the new method.

15 GEOTHERMAL ENERGY↗
DOE OSTI2022

Selective Whole-Genome Amplification as a Tool to Enrich Specimens with Low Treponema pallidum Genomic DNA Copies for Whole-Genome Sequencing

Downstream next-generation sequencing (NGS) of the syphilis spirochete Treponema pallidum subspecies pallidum (T. pallidum) is hindered by low bacterial loads and the overwhelming presence of background metagenomic DNA in clinical specimens. In this study, we investigated selective whole-genome amplification (SWGA) utilizing multiple displacement amplification (MDA) in conjunction with custom oligonucleotides with an increased specificity for the T. pallidum genome and the capture and removal of 5'-C-phosphate-G-3' (CpG) methylated host DNA using the NEBNext Microbiome DNA enrichment kit followed by MDA with the REPLI-g single cell kit as enrichment methods to improve the yields of T. pallidum DNA in isolates and lesion specimens from syphilis patients. Sequencing was performed using the Illumina MiSeq v2 500 cycle or NovaSeq 6000 SP platform. These two enrichment methods led to 93 to 98% genome coverage at 5 reads/site in 5 clinical specimens from the United States and rabbit-propagated isolates, containing >14 T. pallidum genomic copies/μL of sample for SWGA and >129 genomic copies/μL for CpG methylation capture with MDA. Variant analysis using sequencing data derived from SWGA-enriched specimens showed that all 5 clinical strains had the A2058G mutation associated with azithromycin resistance. SWGA is a robust method that allows direct whole-genome sequencing (WGS) of specimens containing very low numbers of T. pallidum, which has been challenging until now.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Human Gut Microbiota from Autism Spectrum Disorder Promote Behavioral Symptoms in Mice

Large-scale phosphoproteomics with coverage of over 10,000 sites of phosphorylation have now been routinely achieved with advanced mass spectrometry (MS)-based workflows. However, accurate targeted MS-based quantification of phosphorylation dynamics, an important direction for gaining quantitative understanding of signaling pathways or networks, has been much less investigated. Herein, we report an assessment of the targeted workflow in the context of signal transduction pathways, using the epidermal growth factor receptor (EGFR)–mitogen-activated protein kinase (MAPK) pathway as our model. 43 phosphopeptides from the EGFR–MAPK pathway were selected for the study. The recovery and sensitivity of a workflow consisted of two commonly used enrichment methods, immobilized metal affinity chromatography (IMAC) and titanium oxide (TiO2), combined with selected reaction monitoring (SRM)-MS, were evaluated. The recovery of phosphopeptides by IMAC and TiO2 enrichment was quantified to be 38 ± 5% and 58 ± 20%, respectively, based on internal standards. Moreover, both enrichment methods provided comparable sensitivity from 1-100 g starting peptides. Robust quantification was consistently achieved for most targeted phosphopeptides when starting with 25-100 g peptides. However, the numbers of quantified targets significantly dropped when peptide samples were in the 1-25g range. Finally, IMAC-SRM was applied to quantify signaling dynamics of EGFR-MAPK pathway in Hs578T cells following 3 ng/mL EGF treatment. The kinetics of phosphorylation clearly revealed early and late phases of phosphorylation, even for very low abundance proteins. These results demonstrate the feasibility of robust targeted quantification of phosphorylation dynamics for specific pathways, even starting with relatively small amounts of protein.

Sharon, Gil↗
DOE OSTI2018

Targeted Quantification of Phosphorylation Dynamics in the Context of EGFR-MAPK Pathway

Large-scale phosphoproteomics with coverage of over 10,000 sites of phosphorylation have now been routinely achieved with advanced mass spectrometry (MS)-based workflows. However, accurate targeted MS-based quantification of phosphorylation dynamics, an important direction for gaining quantitative understanding of signaling pathways or networks, has been much less investigated. Herein, we report an assessment of the targeted workflow in the context of signal transduction pathways, using the epidermal growth factor receptor (EGFR)–mitogen-activated protein kinase (MAPK) pathway as our model. 43 phosphopeptides from the EGFR–MAPK pathway were selected for the study. The recovery and sensitivity of a workflow consisted of two commonly used enrichment methods, immobilized metal affinity chromatography (IMAC) and titanium oxide (TiO2), combined with selected reaction monitoring (SRM)-MS, were evaluated. The recovery of phosphopeptides by IMAC and TiO2 enrichment was quantified to be 38 ± 5% and 58 ± 20%, respectively, based on internal standards. Moreover, both enrichment methods provided comparable sensitivity from 1-100 g starting peptides. Robust quantification was consistently achieved for most targeted phosphopeptides when starting with 25-100 g peptides. However, the numbers of quantified targets significantly dropped when peptide samples were in the 1-25g range. Finally, IMAC-SRM was applied to quantify signaling dynamics of EGFR-MAPK pathway in Hs578T cells following 3 ng/mL EGF treatment. The kinetics of phosphorylation clearly revealed early and late phases of phosphorylation, even for very low abundance proteins. These results demonstrate the feasibility of robust targeted quantification of phosphorylation dynamics for specific pathways, even starting with relatively small amounts of protein.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2026

Bioorthogonal Click Chemistry for Antibody-Free Profiling of Acetylation, Propionylation, and Butyrylation in Pseudomonas aeruginosa and Methicillin-Resistant Staphylococcus aureus

Lysine acylation is a posttranslational modification (PTM) conserved in all domains of life and is essential for regulating diverse biological processes. Traditional methods for investigating acylation rely on anti-acyl-lysine antibodies, which are costly and time-consuming and often exhibit variable affinity. To remedy these pitfalls, we developed an antibody-free method for bacterial acylome enrichment using bioorthogonal click chemistry coupled with tandem mass spectrometry. We applied this approach to the pathogens Pseudomonas aeruginosa and methicillin-resistant Staphylococcus aureus (MRSA) to explore the biological significance of acylation in each organism. We characterized the acetylome, propionylome, and butyrylome in P. aeruginosa UCBPP-PA14 and the acetylome and propionylome in MRSA. Comparative analyses revealed unique PTM dynamics showing that acylation regulated a wide range of cellular functions, including metabolism, antibiotic resistance, virulence, and stress response. This work establishes the first antibody-free enrichment method for defining bacterial acylomes and provides new insight into global lysine acylation networks in pathogenic bacteria.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Evaluation of Protein Extraction Methods for Metaproteomic Analyses of Root-Associated Microbes

Metaproteomics is a powerful tool for the characterization of metabolism, physiology, and functional interactions in microbial communities, including plant-associated microbiota. However, the metaproteomic methods that have been used to study plant-associated microbiota are very laborious and require large amounts of plant tissue, hindering wider application of these methods. We optimized and evaluated different protein extraction methods for metaproteomics of plant-associated microbiota in two different plant species (Arabidopsis and maize). Our main goal was to identify a method that would work with low amounts of input material (40 to 70 mg) and that would maximize the number of identified microbial proteins. We tested eight protocols, each comprising a different combination of physical lysis method, extraction buffer, and cell-enrichment method on roots from plants grown with synthetic microbial communities. We assessed the performance of the extraction protocols by liquid chromatography-tandem mass spectrometry–based metaproteomics and found that the optimal extraction method differed between the two species. For Arabidopsis roots, protein extraction by beating whole roots with small beads provided the greatest number of identified microbial proteins and improved the identification of proteins from gram-positive bacteria. For maize, vortexing root pieces in the presence of large glass beads yielded the greatest number of microbial proteins identified. Based on these data, we recommend the use of these two methods for metaproteomics with Arabidopsis and maize. Furthermore, detailed descriptions of the eight tested protocols will enable future optimization of protein extraction for metaproteomics in other dicot and monocot plants.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Oxygen enrichment combustion to reduce fossil energy consumption and emissions in hot rolling steel production

The reheating furnace operation in the hot mill is natural gas- and electricity-intensive. Oxygen enrichment combustion for reheating furnaces has been proposed to curb and replace natural gas use. In this study, heat transfer in steel slabs in the combustion environment of a push-type reheating furnace was simulated using a computational fluid dynamics (CFD) model. Two oxygen enrichment methods that optimized for performance were selected— a medium oxygen enrichment (MOE) case and an oxy-fuel (OF) case. A life cycle analysis (LCA) characterized the energy and emission profiles of an integrated iron and steel manufacturing process using the two oxygen enrichment cases for the hot mill. These conditions were evaluated for energy use and carbon intensity and compared with a baseline case. Results show that with oxygen enrichment, natural gas consumption can decrease by 19.6%–26.8%, total energy consumption (natural gas and electricity) can decrease by 15.1%–20.7% in the hot mill. Emissions of greenhouse gases can decrease by 11.1%–15.2% in the two optimized cases with 14%–27% reductions in regulated criteria pollutants (nitrogen oxides, carbon monoxide, particulate matter, volatile organic compounds, black carbon, organic carbon, and volatile organic carbons). There is a tradeoff between reducing natural gas consumption and increasing electricity demand from a life cycle perspective. Although the OF case resulted in higher energy- and emissions-related benefits, the MOE case showed the more desirable heat flux uniformity, which is key to maintaining product quality. The analysis suggests that oxygen enrichment in the reheating furnace process can have a significant impact on hot mill environmental performance and become a contributing factor in transitioning to low-carbon steel manufacturing.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Methods of producing enriched scandium-47, and related systems and apparatuses

A method of producing enriched 47 Sc comprises irradiating a V structure comprising 51 V with at least one incident photon beam having an endpoint energy within a range of from about 14 MeV to about 44 MeV to convert at least some of the 51 V to 47 Sc and form a 47 Sc-containing structure. The 47 Sc of the 47 Sc-containing structure is separated from additional components of the 47 Sc-containing structure using a chromatography process. Systems and apparatuses for producing enriched 47 Sc are also described.

Snow, Mathew S.↗
DOE OSTI2023

Whole genome sequencing of Mycobacterium bovis directly from clinical tissue samples without culture

Advancement in next generation sequencing offers the possibility of routine use of whole genome sequencing (WGS) for Mycobacterium bovis (M. bovis) genomes in clinical reference laboratories. To date, the M. bovis genome could only be sequenced if the mycobacteria were cultured from tissue. This requirement for culture has been due to the overwhelmingly large amount of host DNA present when DNA is prepared directly from a granuloma. To overcome this formidable hurdle, we evaluated the usefulness of an RNA-based targeted enrichment method to sequence M. bovis DNA directly from tissue samples without culture. Initial spiking experiments for method development were established by spiking DNA extracted from tissue samples with serially diluted M. bovis BCG DNA at the following concentration range: 0.1 ng/μl to 0.1 pg/μl (10 –1 to 10 –4 ). Library preparation, hybridization and enrichment was performed using SureSelect custom capture library RNA baits and the SureSelect XT HS2 target enrichment system for Illumina paired-end sequencing. The method validation was then assessed using direct WGS of M. bovis DNA extracted from tissue samples from naturally (n = 6) and experimentally (n = 6) infected animals with variable Ct values. Direct WGS of spiked DNA samples achieved 99.1% mean genome coverage (mean depth of coverage: 108×) and 98.8% mean genome coverage (mean depth of coverage: 26.4×) for tissue samples spiked with BCG DNA at 10 –1 (mean Ct value: 20.3) and 10 –2 (mean Ct value: 23.4), respectively. The M. bovis genome from the experimentally and naturally infected tissue samples was successfully sequenced with a mean genome coverage of 99.56% and depth of genome coverage ranging from 9.2× to 72.1×. The spoligoyping and M. bovis group assignment derived from sequencing DNA directly from the infected tissue samples matched that of the cultured isolates from the same sample. Our results show that direct sequencing of M. bovis DNA from tissue samples has the potential to provide accurate sequencing of M. bovis genomes significantly faster than WGS from cultures in research and diagnostic settings.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Quantitative phosphoproteomic analysis reveals reciprocal activation of receptor tyrosine kinases between cancer epithelial cells and stromal fibroblasts

Background Cancer-associated fibroblasts (CAFs) are one of the most important components of tumor stroma and play a key role in modulating tumor growth. However, a mechanistic understanding of how CAFs communicate with tumor cells to promote their proliferation and invasion is far from complete. A major reason for this is that most current techniques and model systems do not capture the complexity of signal transduction that occurs between CAFs and tumor cells. Methods In this study, we employed a stable isotope labeling with amino acids in cell culture (SILAC) strategy to label invasive breast cancer cells, MDA-MB-231, and breast cancer patient-derived CAF cells. We used an antibody-based phosphotyrosine peptide enrichment method coupled to LC–MS/MS to catalog and quantify tyrosine phosphorylation-mediated signal transduction events induced by the bidirectional communication between patient-derived CAFs and tumor cells. Results We discovered that distinct signaling events were activated in CAFs and in tumor epithelial cells during the crosstalk between these two cell types. We identified reciprocal activation of a number of receptor tyrosine kinases including EGFR, FGFR1 and EPHA2 induced by this bidirectional communication. Conclusions Our study not only provides insights into the mechanisms of the interaction between CAFs and tumor cells, but the model system described here could be used as a prototype for analysis of intercellular communication in many different tumor microenvironments.

Biochemistry & Molecular Biology↗
DOE OSTI2023

Using nickel-molybdenum cathode catalysts for efficient hydrogen gas production in microbial electrolysis cells

A low-cost cathode catalyst based on a NiMo alloy was examined here to replace noble metals for the hydrogen production in microbial electrolysis cells (MECs). Two NiMo catalysts were synthesized through either an electrochemical assisted (NiMo Elec) or a hydrothermal (NiMo Ht) approach. The NiMo Ht method enriched the electrocatalyst with Mo atoms compared to the NiMo Elec approach, producing a similar current density with a minimal overpotential of 50mV compared to Pt. Further, in MEC tests using the NiMo Ht catalyst, H 2 was generated at a highest rate of 81±3 L H2 /L-d (current density of 44.4 ± 0.9 A/m 2 ) at a cell voltage of -0.86 V, and a Coulombic efficiency of >97%. Modifying the closely stacked MEC design to include a reference electrode, and analysis of the electrode potentials using the electrode potential slope method, revealed a large contribution of the cathode resistance (5.3±0.5mΩm 2 ) compared to the anode (1.4±0.2mΩm 2 ) and ohmic resistance (0.83mΩm 2 ) for a total internal resistance of 7.6±0.5mΩm 2 . The high performance of the NiMo Ht catalyst coupled with its low cost provides an economically viable approach to advance the generation of biohydrogen in MECs.

25 ENERGY STORAGE↗
DOE OSTI2020

The impact of tillage row orientation on physical and chemical sediment enrichment

Abstract This study aimed to better understand how tillage row orientation with respect to dominant flow‐pathway along hillslope impacts runoff and the transport of different sediment size fractions. Experimental plots were constructed in contour ridge till (CRT) and parallel ridge till (PRT) sites to monitor runoff and sediment fluxes. Particle size fractions of the sediment, along with organic C and N contents were measured to quantify physical and chemical enrichment ratios for the two tillage orientations. In the CRT plot, tillage produced large oriented roughness elements along the contours, which acted as little check dams, while in the PRT site, the roughness elements helped confine and concentrate the runoff. In the CRT, the “check dams” resulted in a runoff coefficient of .03, while in the PRT, the flow confinement between rows produced a runoff coefficient of .82. Moreover, the erosion rates at the CRT site were 97% less than those in the PRT plot. Large contours produced finer sediment fractions due to the selective sorting in ponded furrows. More aggregate sediment fractions were present in the PRT site, which was dominated by rill erosion. Physical enrichment revealed selective entrainment of finer sediment particles during erosion. Finer‐grain particles with higher specific surface areas, attached more organic C resulting in chemical enrichment. Physical and chemical enrichment methods were found to be in good agreement. These findings suggest transport models that can simulate size fraction updates to the soil active layer can be used to estimate SOC redistribution and hence more accurate C budgets.

Wacha, Kenneth M.↗