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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 379 records · Page 21
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Data for Development of Vegetative Oil Sorghum: From Lab-to-Field

Biomass crops engineered to accumulate energy-dense triacylglycerols (TAG or ‘vegetable oils’) in their vegetative tissues have emerged as potential feedstocks to meet the growing demand for renewable diesel and sustainable aviation fuel (SAF). Unlike oil palm and oilseed crops, the current commercial sources of TAG, vegetative tissues, such as leaves and stems, only transiently accumulate TAG. In this report, we used grain (Texas430 or TX430) and sugar-accumulating ‘sweet’ (Ramada) genotypes of sorghum, a high-yielding, environmentally resilient biomass crop, to accumulate TAG in leaves and stems. We initially tested several gene combinations for a ‘push-pull-protect’ strategy. The top TAG-yielding constructs contained five oil transgenes for a sorghum WRINKLED1 transcription factor (‘push’), a Cuphea viscosissima diacylglycerol acyltransferase (DGAT; ‘pull’), a modified sesame oleosin (‘protect’) and two combinations of specialized Cuphea lysophosphatidic acid acyltransferases and medium-chain acyl-acyl carrier protein thioesterases. Though intended to generate oils with medium-chain fatty acids, engineered lines accumulated oleic acid-rich oil to amounts of up to 2.5% DW in leaves and 2.0% DW in stems in the greenhouse, 36-fold and 49-fold increases relative to wild-type (WT) plants, respectively. Under field conditions, the top-performing event accumulated TAG to amount to 5.5% DW in leaves and 3.5% DW in stems, 78-fold and 58-fold increases, respectively, relative to WT TX430. Transcriptomic and fluxomic analyses revealed potential bottlenecks for increased TAG accumulation. Overall, our studies highlight the utility of a lab-to-field pipeline coupled with systems biology studies to deliver high vegetative oil sorghum for SAF and renewable diesel production.

Biofuels↗
DOE OSTI2024

Enabling high-throughput enzyme discovery and engineering with a low-cost, robot-assisted pipeline

Abstract As genomic databases expand and artificial intelligence tools advance, there is a growing demand for efficient characterization of large numbers of proteins. To this end, here we describe a generalizable pipeline for high-throughput protein purification using small-scale expression in E. coli and an affordable liquid-handling robot. This low-cost platform enables the purification of 96 proteins in parallel with minimal waste and is scalable for processing hundreds of proteins weekly per user. We demonstrate the performance of this method with the expression and purification of the leading poly(ethylene terephthalate) hydrolases reported in the literature. Replicate experiments demonstrated reproducibility and enzyme purity and yields (up to 400 µg) sufficient for comprehensive analyses of both thermostability and activity, generating a standardized benchmark dataset for comparing these plastic-degrading enzymes. The cost-effectiveness and ease of implementation of this platform render it broadly applicable to diverse protein characterization challenges in the biological sciences.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Predicting transcription factor activity using prior biological information

Dysregulation of normal transcription factor activity is a common driver of disease. Therefore, the detection of aberrant transcription factor activity is important to understand disease pathogenesis. We have developed Priori, a method to predict transcription factor activity from RNA sequencing data. Priori has two key advantages over existing methods. First, Priori utilizes literature-supported regulatory information to identify transcription factor-target gene relationships. It then applies linear models to determine the impact of transcription factor regulation on the expression of its target genes. Second, results from a third-party benchmarking pipeline reveals that Priori detects aberrant activity from 124 single-gene perturbation experiments with higher sensitivity and specificity than 11 other methods. We applied Priori and other top-performing methods to predict transcription factor activity from two large primary patient datasets. Our work demonstrates that Priori uniquely discovered significant determinants of survival in breast cancer and identified mediators of drug response in leukemia.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Scalable production of recombinant three-finger proteins: from inclusion bodies to high quality molecular probes

The three-finger proteins are a collection of disulfide bond rich proteins of great biomedical interests. Scalable recombinant expression and purification of bioactive three-finger proteins is quite difficult. We introduce a working pipeline for expression, purification and validation of disulfide-bond rich three-finger proteins using E. coli as the expression host. With this pipeline, we have successfully obtained highly purified and bioactive recombinant α-Βungarotoxin, k-Bungarotoxin, Hannalgesin, Mambalgin-1, α-Cobratoxin, MTα, Slurp1, Pate B etc. Milligrams to hundreds of milligrams of recombinant three finger proteins were obtained within weeks in the lab. The recombinant proteins showed specificity in binding assay and six of them were crystallized and structurally validated using X-ray diffraction protein crystallography. Our pipeline allows refolding and purifying recombinant three finger proteins under optimized conditions and can be scaled up for massive production of three finger proteins. As many three finger proteins have attractive therapeutic or research interests and due to the extremely high quality of the recombinant three finger proteins we obtained, our method provides a competitive alternative to either their native counterparts or chemically synthetic ones and should facilitate related research and applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Combinatorial Glycomic Analyses to Direct CAZyme Discovery for the Tailored Degradation of Canola Meal Non-Starch Dietary Polysaccharides

Canola meal (CM), the protein-rich by-product of canola oil extraction, has shown promise as an alternative feedstuff and protein supplement in poultry diets, yet its use has been limited due to the abundance of plant cell wall fibre, specifically non-starch polysaccharides (NSP) and lignin. The addition of exogenous enzymes to promote the digestion of CM NSP in chickens has potential to increase the metabolizable energy of CM. We isolated chicken cecal bacteria from a continuous-flow mini-bioreactor system and selected for those with the ability to metabolize CM NSP. Of 100 isolates identified, Bacteroides spp. and Enterococcus spp. were the most common species with these capabilities. To identify enzymes specifically for the digestion of CM NSP, we used a combination of glycomics techniques, including enzyme-linked immunosorbent assay characterization of the plant cell wall fractions, glycosidic linkage analysis (methylation-GC-MS analysis) of CM NSP and their fractions, bacterial growth profiles using minimal media supplemented with CM NSP, and the sequencing and de novo annotation of bacterial genomes of high-efficiency CM NSP utilizing bacteria. The SACCHARIS pipeline was used to select plant cell wall active enzymes for recombinant production and characterization. This approach represents a multidisciplinary innovation platform to bioprospect endogenous CAZymes from the intestinal microbiota of herbivorous and omnivorous animals which is adaptable to a variety of applications and dietary polysaccharides.

glycome profiling↗
DOE OSTI2022

CORAL: A framework for rigorous self-validated data modeling and integrative, reproducible data analysis

Abstract Background Many organizations face challenges in managing and analyzing data, especially when relevant datasets arise from multiple sources and methods. Analyzing heterogeneous datasets and additional derived data requires rigorous tracking of their interrelationships and provenance. This task has long been a Grand Challenge of data science and has more recently been formalized in the FAIR principles: that all data objects be Findable, Accessible, Interoperable, and Reusable, both for machines and for people. Adherence to these principles is necessary for proper stewardship of information, for testing regulatory compliance, for measuring the efficiency of processes, and for facilitating reuse of data-analytical frameworks. Findings We present the Contextual Ontology-based Repository Analysis Library (CORAL), a platform that greatly facilitates adherence to all 4 of the FAIR principles, including the especially difficult challenge of making heterogeneous datasets Interoperable and Reusable across all parts of a large, long-lasting organization. To achieve this, CORAL's data model requires that data generators extensively document the context for all data, and our tools maintain that context throughout the entire analysis pipeline. CORAL also features a web interface for data generators to upload and explore data, as well as a Jupyter notebook interface for data analysts, both backed by a common API. Conclusions CORAL enables organizations to build FAIR data types on the fly as they are needed, avoiding the expense of bespoke data modeling. CORAL provides a uniquely powerful platform to enable integrative cross-dataset analyses, generating deeper insights than are possible using traditional analysis tools.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Fixed-target serial crystallography at the Structural Biology Center

Serial synchrotron crystallography enables the study of protein structures under physiological temperature and reduced radiation damage by collection of data from thousands of crystals. The Structural Biology Center at Sector 19 of the Advanced Photon Source has implemented a fixed-target approach with a new 3D-printed mesh-holder optimized for sample handling. The holder immobilizes a crystal suspension or droplet emulsion on a nylon mesh, trapping and sealing a near-monolayer of crystals in its mother liquor between two thin Mylar films. Data can be rapidly collected in scan mode and analyzed in near real-time using piezoelectric linear stages assembled in an XYZ arrangement, controlled with a graphical user interface and analyzed using a high-performance computing pipeline. Here, the system was applied to two β-lactamases: a class D serine β-lactamase from Chitinophaga pinensis DSM 2588 and L1 metallo-β-lactamase from Stenotrophomonas maltophilia K279a.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Integrated Mid-Continent Stacked Carbon Storage Hub Project Phase II (Final Summary Report)

The Phase II Integrated Midcontinent Stacked Carbon Storage Hub (IMSCS-HUB) is part of the Carbon Storage Assurance Facility Enterprise (CarbonSAFE) established by the United States Department of Energy (DOE) National Energy Technology Laboratory (NETL). CarbonSAFE is phased to support the development of commercial-scale (50 million metric tonnes [Mt] over a 30-year period) carbon capture, utilization, and storage (CCUS) in the United States. The IMSCS-HUB study area comprises carbon dioxide (CO 2 ) sources in Iowa, Kansas, and Nebraska (the source corridor), and CO 2 sinks in Kansas and Nebraska (the storage corridor), representing the first large-scale project for the Midcontinent region. The stacked storage corridor is characterized by alternating sequences of deep saline formations, oil-bearing reservoirs, shale, and evaporite units that are conducive to vertically stacked CO 2 injection for geologic storage and enhanced oil recovery (EOR). Three sites within the IMSCS-HUB stacked storage corridor were evaluated in Phase II for commercial CCUS feasibility: one in southwest-central Nebraska, Sleepy Hollow Field (SHF), a second in southwestern Nebraska near Madrid (Madrid), and a third in southwestern Kansas, the Patterson Site (composed of the Patterson, Heinitz, Hartland, and Oslo fields). In Phase II, the team assessed the feasibility of storage complexes at the potential storage sites in Nebraska and Kansas to support a commercial-scale storage hub that integrates proven CO 2 capture technology and transport from nearby ethanol sources. Building on lessons learned from the DOE-NETL Regional Carbon Sequestration Partnerships (RCSPs), the Project Team has identified a clear strategy to meet DOE’s 2025 objective of commercial carbon capture and storage (CCS) implementation by developing a CO 2 market and infrastructure that relies on multiple ethanol-based CO 2 sources in the short term and the incorporation of multiple coal-fired power plant CO 2 sources when commercial capture is economically viable. The team also leveraged the updated 45Q tax credit to develop capture and transport infrastructure. Commercial-scale CCUS is feasible at two candidate storage sites studied, the Madrid, Nebraska Site and the Patterson Site in Kearny County, Kansas. The Sleepy Hollow Field in Nebraska was found to be an attractive candidate for stacked storage with CO 2 -EOR (Battelle 2020e). Outreach efforts facilitated engagement from industry, government, and research sectors (Battelle and GPI, 2020) and an outreach plan for future phases of the project was developed to address issues that are of concern in the IMSCS-HUB project area (Battelle, 2020f). All components of a CCUS project were determined to be feasible in the IMSCS-HUB region and Risk Mitigation Plan was developed and includes strategies to mitigate risks associated with each project component (Battelle, 2020j). A roadmap was developed to obtain the required UIC permits for an integrated CCUS project (Battelle, 2020k). The regional storage resource characterization demonstrated significant opportunity for commercial-scale projects in the IMSCS-HUB storage corridor with 577.4 Mt of stacked CO 2 storage capacity and the potential to produce 181.9 MMbbls of oil via EOR across 17 individual storage areas (Battelle and ARI, 2020). The pipeline assessment study found viable pipeline routes that connected 45Q-eligible ethanol plants, coal fired power plants, and other sources in the IMSCS-HUB corridor. The comprehensive results of subsurface characterization, modeling efforts, outreach assessment, and regulatory analysis from were integrated to develop a Detailed Commercial Development Plan for the IMSCS-HUB (Battelle, 2020n). Commercialization efforts will involve obtaining Class VI UIC permits, establishing and finalizing the pipeline route, and evaluating capture projects at participating CO 2 sources. Phases I and II of the IMSCS-HUB CarbonSAFE provide a strong foundation for safely, efficiently, and cost-effectively characterizing and permitting commercial-scale project sites in the region. The plan for implementation of commercial-scale CCUS projects in the IMSCS-HUB is aligned with the objectives of CarbonSAFE Phase III: Site Characterization and CO 2 Capture Assessment.

20 FOSSIL-FUELED POWER PLANTS↗
DOE OSTI2022

Multiple Mutations Associated with Emergent Variants Can Be Detected as Low-Frequency Mutations in Early SARS-CoV-2 Pandemic Clinical Samples

Genetic analysis of intra-host viral populations provides unique insight into pre-emergent mutations that may contribute to the genotype of future variants. Clinical samples positive for SARS-CoV-2 collected in California during the first months of the pandemic were sequenced to define the dynamics of mutation emergence as the virus became established in the state. Deep sequencing of 90 nasopharyngeal samples showed that many mutations associated with the establishment of SARS-CoV-2 globally were present at varying frequencies in a majority of the samples, even those collected as the virus was first detected in the US. A subset of mutations that emerged months later in consensus sequences were detected as subconsensus members of intra-host populations. Spike mutations P681H, H655Y, and V1104L were detected prior to emergence in variant genotypes, mutations were detected at multiple positions within the furin cleavage site, and pre-emergent mutations were identified in the nucleocapsid and the envelope genes. Because many of the samples had a very high depth of coverage, a bioinformatics pipeline, “Mappgene”, was established that uses both iVar and LoFreq variant calling to enable identification of very low-frequency variants. This enabled detection of a spike protein deletion present in many samples at low frequency and associated with a variant of concern.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

SECARB-USA: A Sub-Basin Framework for Future CO 2 Infrastructure Development

Task 4 of the SECARB-USA Project is designed to evaluate the regional needs and challenges for the development of a safe and environmentally sound CO 2 transport infrastructure. This infrastructure would transport CO 2 capture from power generating plants and/or industrial sources and distribute it to oil fields for associated storage in EOR operations, saline storage, and/or other suitable storage sites. The objective of this report on Sub-Basin Prospective Areas (Deliverable 4.1.a), is to provide the framework for understanding how regional infrastructure development could occur. The sub-basin prospective areas, in conjunction with the locations of CO 2 sources and pipeline infrastructure (for source-sink matching networks), form the basis for the analysis that will be performed in the Techno-Economic Analysis of Infrastructure Buildout Scenarios (Deliverable 4.1.b).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Efficient Synthetic Natural Gas Production from Direct Air Capture Using Titania-Based Dual Function Materials

Converting atmospheric CO2 into methane offers a compelling pathway to store intermittent renewable electricity and enhance energy security using existing natural gas infrastructure. However, current CO2 utilization approaches remain energy- and capital-intensive, largely due to the need for separate capture, purification, and conversion steps. Integrating CO2 capture with catalytic methanation represents a transformative strategy for process intensification on both the unit operation and molecular levels. We report a series of Ru-Na/TiO2 dual function materials (DFMs) for a reactive carbon capture (RCC) process consisting of simulated direct air capture and subsequent CO2 methanation (DACM). Superior methane desorption purity was observed on TiO2-based DFMs (>94 %) relative to state-of-the-art Al2O3-supported DFMs (77 %). Modifying the process to begin CO2 adsorption immediately following the methanation stage, rather than beginning adsorption near ambient temperature, resulted in >97 % methane desorption purity, suitable for injection into the natural gas pipeline without additional CO2 separation steps.

organic↗
DOE OSTI2026

Scatter Removal using Black Body Grids and Determining the Minimum Resolvable Hydrogen Concentration at MARS

This dataset was used to develop and validate a scatter-correction pipeline for neutron radiographs acquired at the MARS beamline, based on the methodology of Carminati et al. (2019). Scatter removal was performed using 36 gadolinium black bodies to characterize and remove the spatially varying neutron scatter field that cannot be eliminated by conventional open-beam normalization. The dataset comprises eight samples - four single-crystal nickel and four polycrystalline austenitic 316L stainless steel. Within each material system, samples were pre-charged with hydrogen gas at four charging pressures (1.5, 5, 12.5, and 20 kpsi). Following scatter correction, the pipeline was applied to all radiographs to recover quantitative attenuation maps. After subtracting the known attenuation contribution of the metal matrix, spatial maps of the hydrogen attenuation coefficient were obtained for each sample. This data was then used to construct a calibration curve relating hydrogen attenuation to hydrogen concentration and to determine the minimum resolvable hydrogen concentration at the MARS beamline. The resulting dataset provides a pressure-resolved calibration standard for quantitative hydrogen mapping using neutron radiography.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Industry Partnerships & Their Role In Reducing Natural Gas Supply Chain Greenhouse Gas Emissions – Phase 2

This analysis is the product of collaboration between Our Nation’s Energy Future (ONE Future) and the United States (U.S.) Department of Energy (DOE) National Energy Technology Laboratory (NETL). This analysis is an update to Phase 1 of the collaboration between ONE Future and NETL. Phase 1 had three objectives: 1. Calculate a greenhouse gas (GHG) emission profile representative of ONE Future’s supply chain, including methane (CH 4 ) emission rates. 2. Compare ONE Future’s emission profile to the emission profile for the U.S. natural gas supply chain. 3. Evaluate specific emission reduction opportunities. Phase 2 has two key enhancements over Phase 1: 1. The reporting year of the data is updated from 2016 to 2017. 2. The emission profiles and the specific emission reduction opportunities are regionalized for the ONE Future supply chain. The ONE Future supply chain is based on data provided by ONE Future members for all their U.S. onshore assets. ONE Future’s data are mostly representative of their participation in the Greenhouse Gas Reporting Program (GHGRP) administered by the Environmental Protection Agency (EPA) and is supplemented by ONE Future facilities that are not required to report to GHGRP. The U.S. scenario is based on NETL’s life cycle analysis (LCA) of natural gas extraction and power generation, which also uses data from the GHGRP (but does not include non-GHGRP facilities). In addition to the data from these sources, NETL accounted for uncertainty due to data variability, data limitations, and variability in liquids unloading frequency and event duration. This report is a re-issue of the 2020 study (published on July 28, 2020). It revises the device count in the mitigation strategy “pipeline pump-down before maintenance” in the Marginal Abatement Cost (MAC) Analysis section of the report (Section 7). Please see the addendum for more details on this revision and resultant changes. This revision does not change most of our conclusions and recommendations. It only changes the total methane reduced from all the mitigation opportunities (low cost and high cost) from 6.5 Bcf CH 4 /yr to 4.8 Bcf CH 4 /yr.

03 NATURAL GAS↗
DOE OSTI2024

Agora : Multicomponent simulation for cross-survey science

ABSTRACT Next-generation cosmological surveys will observe large portions of the sky, with significant overlap between them. Multi-wavelength observations will enable us to analyse the same large-scale structure from different angles using a variety of tracers and astrophysical effects. The complex interplay between these observables calls for a model that can accurately and coherently describe their collective behaviour, posing a challenge that can only be met through the use of simulations. In this work, a suite of simulated extragalactic skies is presented, including maps and/or catalogues of cosmic microwave background (CMB) lensing, thermal and kinetic Sunyaev–Zel’dovich (tSZ/kSZ) effects, cosmic infrared background (CIB), radio sources, galaxy overdensity and galaxy weak lensing. Each of these probes is implemented in the lightcone using halo catalogues and/or particles from the Multidark-Planck2 ($\small {MDPL2}$) N-body simulation, and the modelling is calibrated using hydrodynamic simulations and publicly available data. The auto and cross-spectra of the individual probes, as well as the cross-spectra between the observables, are shown to be consistent with theoretical models and measurements from data. The simulation is shown to have a wide range of applications, including forecasting, pipeline testing, and evaluating astrophysical biases in cross-correlation measurements. It is further demonstrated that the simulation products produced in this work have sufficient accuracy to recover the input cosmology when subjected to a full cosmological analysis and are ready for application in real-world analyses for ongoing and future surveys. The simulation products presented in this work can be accessed at: https://yomori.github.io/agora/index.html.

Astronomy & Astrophysics↗
DOE OSTI2024

Artificial intelligence to unlock real-world evidence in clinical oncology: A primer on recent advances

Purpose: Real world evidence is crucial to understanding the diffusion of new oncologic therapies, monitoring cancer outcomes, and detecting unexpected toxicities. In practice, real world evidence is challenging to collect rapidly and comprehensively, often requiring expensive and time-consuming manual case-finding and annotation of clinical text. In this Review, we summarise recent developments in the use of artificial intelligence to collect and analyze real world evidence in oncology. Methods: We performed a narrative review of the major current trends and recent literature in artificial intelligence applications in oncology. Results: Artificial intelligence (AI) approaches are increasingly used to efficiently phenotype patients and tumors at large scale. These tools also may provide novel biological insights and improve risk prediction through multimodal integration of radiographic, pathological, and genomic datasets. Custom language processing pipelines and large language models hold great promise for clinical prediction and phenotyping. Conclusions: Despite rapid advances, continued progress in computation, generalizability, interpretability, and reliability as well as prospective validation are needed to integrate AI approaches into routine clinical care and real-time monitoring of novel therapies.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Strangers in a foreign land: ‘Yeastizing’ plant enzymes

Abstract Expressing plant metabolic pathways in microbial platforms is an efficient, cost‐effective solution for producing many desired plant compounds. As eukaryotic organisms, yeasts are often the preferred platform. However, expression of plant enzymes in a yeast frequently leads to failure because the enzymes are poorly adapted to the foreign yeast cellular environment. Here, we first summarize the current engineering approaches for optimizing performance of plant enzymes in yeast. A critical limitation of these approaches is that they are labour‐intensive and must be customized for each individual enzyme, which significantly hinders the establishment of plant pathways in cellular factories. In response to this challenge, we propose the development of a cost‐effective computational pipeline to redesign plant enzymes for better adaptation to the yeast cellular milieu. This proposition is underpinned by compelling evidence that plant and yeast enzymes exhibit distinct sequence features that are generalizable across enzyme families. Consequently, we introduce a data‐driven machine learning framework designed to extract ‘yeastizing’ rules from natural protein sequence variations, which can be broadly applied to all enzymes. Additionally, we discuss the potential to integrate the machine learning model into a full design‐build‐test cycle.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

HiFiAdapterFilt, a memory efficient read processing pipeline, prevents occurrence of adapter sequence in PacBio HiFi reads and their negative impacts on genome assembly

Abstract Background Pacific Biosciences HiFi read technology is currently the industry standard for high accuracy long-read sequencing that has been widely adopted by large sequencing and assembly initiatives for generation of de novo assemblies in non-model organisms. Though adapter contamination filtering is routine in traditional short-read analysis pipelines, it has not been widely adopted for HiFi workflows. Results Analysis of 55 publicly available HiFi datasets revealed that a read-sanitation step to remove sequence artifacts derived from PacBio library preparation from read pools is necessary as adapter sequences can be erroneously integrated into assemblies. Conclusions Here we describe the nature of adapter contaminated reads, their consequences in assembly, and present HiFiAdapterFilt, a simple and memory efficient solution for removing adapter contaminated reads prior to assembly.

59 BASIC BIOLOGICAL SCIENCES↗