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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 559 records · Page 31
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Effect of X-ray free-electron laser-induced shockwaves on haemoglobin microcrystals delivered in a liquid jet

X-ray free-electron lasers (XFELs) enable obtaining novel insights in structural biology. The recently available MHz repetition rate XFELs allow full data sets to be collected in shorter time and can also decrease sample consumption. However, the microsecond spacing of MHz XFEL pulses raises new challenges, including possible sample damage induced by shock waves that are launched by preceding pulses in the sample-carrying jet. We explored this matter with an X-ray-pump/X-ray-probe experiment employing haemoglobin microcrystals transported via a liquid jet into the XFEL beam. Diffraction data were collected using a shock-wave-free single-pulse scheme as well as the dual-pulse pump-probe scheme. The latter, relative to the former, reveals significant degradation of crystal hit rate, diffraction resolution and data quality. Crystal structures extracted from the two data sets also differ. Since our pump-probe attributes were chosen to emulate EuXFEL operation at its 4.5 MHz maximum pulse rate, this prompts concern about such data collection.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Visualizing metagenomic and metatranscriptomic data: A comprehensive review

The fields of Metagenomics and Metatranscriptomics involve the examination of complete nucleotide sequences, gene identification, and analysis of potential biological functions within diverse organisms or environmental samples. Despite the vast opportunities for discovery in metagenomics, the sheer volume and complexity of sequence data often present challenges in processing analysis and visualization. This article highlights the critical role of advanced visualization tools in enabling effective exploration, querying, and analysis of these complex datasets. Emphasizing the importance of accessibility, the article categorizes various visualizers based on their intended applications and highlights their utility in empowering bioinformaticians and non-bioinformaticians to interpret and derive insights from meta-omics data effectively.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Engineering Escherichia coli for selective 1-decanol production using the reverse β-oxidation (rBOX) pathway

1-Decanol has great value in the pharmaceutical and fragrance industries and plays an important role in the chemical industry. Here, in this study, we engineered Escherichia coli to selectively synthesize 1-decanol by using enzymes of the core reverse β-oxidation (rBOX) pathway and termination module with overlapping chain-length specificity. Through screening for acyl-CoA reductase termination enzymes and proper regulation of rBOX pathway expression, a 1-decanol titer of 1.4 g/L was achieved. Further improvements were realized by engineering pyruvate dissimilation to ensure the generation of NADH through pyruvate dehydrogenase (PDH) and reducing byproduct synthesis via a tailored YigI thioesterase knockout, increasing 1-decanol titer to 1.9 g/L. The engineered strain produced about 4.4 g/L 1-decanol with a yield of 0.21 g/g in 36 hours in a bi-phasic fermentation that used a dodecane overlay to increase 1-decanol transport and reduce its toxicity. Adjustment of pathway expression (varying inducer concentration) and cell growth (oxygen availability) enabled 1-decanol production at 6.1 g/L (0.26 g/g yield) and 10.05 g/L (0.2 g/g yield) using rich in shake flasks and bioreactor, respectively. Remarkably, the use of minimal medium resulted in 1-decanol production at 100% specificity at 2.8 g/L (0.14 g/g yield) and a per cell mass yield higher than rich medium. These 1-decanol titers, yields and purity are at least 10-fold higher than others reported to date and the engineered strain shows great potential for industrial production. Taken together, our findings suggest that using rBOX pathway and termination enzymes of proper chain-length specificity in combination with optimal chassis engineering should be an effective approach for the selective production of alcohols.

1-decanol↗
DOE OSTI2022

Revealing low-temperature plasma efficacy through a dose-rate assessment by DNA damage detection combined with machine learning models

Low-temperature plasmas have quickly emerged as alternative and unconventional types of radiation that offer great promise for various clinical modalities. As with other types of radiation, the therapeutic efficacy and safety of low-temperature plasmas are ubiquitous concerns, and assessing their dose rates is crucial in clinical settings. Unfortunately, assessing the dose rates by standard dosimetric techniques has been challenging. To overcome this difficulty, we proposed a dose-rate assessment framework that combined the predictive modeling of plasma-induced damage in DNA by machine learning with existing radiation dose-DNA damage correlations. Our results indicated that low-temperature plasmas have a remarkably high dose rate that can be tuned by various process parameters. This attribute is beneficial for inducing radiobiological effects in a more controllable manner.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Progress in the development of an ultrafast pulsed ponderomotive phase plate for cryo-electron tomography

Cryo-electron tomography (cryo-ET) is a powerful modality for resolving cellular structures in their native state. While single-particle cryo-electron microscopy excels in determining protein structures purified from recombinant or endogenous sources due to an abundance of particles, weak contrast issues are accentuated in cryo-ET by low copy numbers in crowded cellular milieux. Continuous laser phase plates offer improved contrast in cryo-ET; however, their implementation demands exceptionally high-peak optical intensities. Instead, a novel experimental approach to enhance contrast in cryo-ET is to manipulate the phase of scattered pulsed electrons using ultrafast pulsed photons. Here, we outline the experimental design of a proof-of-concept electron microscope and demonstrate synchronization between electron packets and laser pulses. Furthermore, we show ultrabright photoemission of electrons from an alloy field emission tip using femtosecond ultraviolet pulses. These experiments pave the way toward exploring the utility of the ponderomotive effect using pulsed radiation to increase phase contrast in cryo-ET of subcellular protein complexes in situ, thus advancing the field of cell biology.

Du, Daniel X. [Columbia Univ., New York, NY (Unite↗
DOE OSTI2022

Radius measurement via super-resolution microscopy enables the development of a variable radii proximity labeling platform

The elucidation of protein interaction networks is critical to understanding fundamental biology as well as developing new therapeutics. Proximity labeling platforms (PLPs) are state-of-the-art technologies that enable the discovery and delineation of biomolecular networks through the identification of protein-protein interactions. These platforms work via catalytic generation of reactive probes at a biological region of interest; these probes then diffuse through solution and covalently “tag” proximal biomolecules. The physical distance that the probes diffuse determines the effective labeling radius of the PLP and is a critical parameter that influences the scale and resolution of interactome mapping. As such, by expanding the degrees of labeling resolution offered by PLPs, it is possible to better capture the various size scales of interactomes. At present, however, there is little quantitative understanding of the labeling radii of different PLPs. Here, we report the development of a superresolution microscopy-based assay for the direct quantification of PLP labeling radii. Using this assay, we provide direct extracellular measurements of the labeling radii of state-of-the-art antibody-targeted PLPs, including the peroxidase-based phenoxy radical platform (269 ± 41 nm) and the high-resolution iridium-catalyzed µMap technology (54 ± 12 nm). Last, we apply these insights to the development of a molecular diffusion-based approach to tuning PLP resolution and introduce a new aryl-azide-based µMap platform with an intermediate labeling radius (80 ± 28 nm).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Drought–induced increase in tree mortality and corresponding decrease in the carbon sink capacity of Canada's boreal forests from 1970 to 2020

Canada's boreal forests, which occupy approximately 30% of boreal forests world wide, play an important role in the global carbon budget. However, there is lit tle quantitative information available regarding the spatiotemporal changes in the drought-induced tree mortality of Canada's boreal forests overall and their associ ated impacts on biomass carbon dynamics. Here, we develop spatiotemporally ex plicit estimates of drought-induced tree mortality and corresponding biomass carbon sink capacity changes in Canada's boreal forests from 1970 to 2020. We show that the average annual tree mortality rate is approximately 2.7%. Approximately 43% of Canada's boreal forests have experienced significantly increasing tree mortality trends (71% of which are located in the western region of the country), and these trends have accelerated since 2002. This increase in tree mortality has resulted in sig nificant biomass carbon losses at an approximate rate of 1.51±0.29 MgC ha -1 year -1 (95% confidence interval) with an approximate total loss of 0.46±0.09 PgC year -1 (95% confidence interval). Under the drought condition increases predicted for this century, the capacity of Canada's boreal forests to act as a carbon sink will be further reduced, potentially leading to a significant positive climate feedback effect

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

The older plant gets the sun: Age-related changes in Miscanthus × giganteus phenology

Age-related changes are usually overlooked in perennial grass research; when they are considered it is usually as a change in plant size (e.g., biomass). Whether other physiological or developmental aspects change as stands age, and how those aspects may impact long-term stand dynamics, remains unclear. Conventional experimental designs study a single stand over multiple growing seasons and thereby confound age-related changes with growing season conditions. Here we used a staggered-start experimental design with three repeated planting years over two growing seasons to isolate growing season effects. We studied changes in Miscanthus × giganteus phenology during its yield-building stage (first 3 years) and estimated age, growing season and nitrogen (N) effects on development using nonlinear regression parameters. Stand age clearly changed plant growth; faster developmental rates were usually seen in 1-year-old stands (young), but because 2- and 3-year-old stands (mature) emerged 3 months earlier than newly planted stands they produced ~30% more stems with 30%–60% more leaves. Nitrogen fertilization modulated some age-related phenological changes. Fertilized 2-year-old stands reached similar stem densities as unfertilized 3-year-old stands and had fewer number of senesced leaves like 1-year-old stands. In addition, N fertilization had no effect on young M. × giganteus , but extended mature stands’ growing season more than 2 weeks by hastening emergence and delaying senescence. It also delayed flowering regardless of stand age. Our results suggest that, along with changes in size, M. × giganteus stands showed shifts in developmental strategies: young stands emerged later and developed faster, while mature stands grew for longer but more slowly. In temperate regions, where hard frost events are likely to interrupt development in late autumn, rapid early development is critical to plant survival. Nonlinear regression parameter differences proved effective in identifying phenological shifts.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Managing Climate-Driven Zoonotic Risk Interagency Workshop Report

In July 2022, Sandia National Laboratories hosted a workshop in Washington, D.C., bringing together representatives from eleven Federal Government agencies, responsible for public health, environmental security, and biodefense, as well as six Department of Energy (DOE) National Laboratories, to discuss how to work together to address climate-driven zoonotic disease risk. The primary goal of this workshop was to provide a forum for Federal and DOE National Lab attendees to share their missions, programs, and capabilities relevant to zoonotic disease emergence, to discuss how to best leverage these collective resources, identify key gaps, and to determine an effective path forward.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Molecular Regulatory Mechanisms Drive Emergent Pathogenetic Properties of Neisseria gonorrhoeae

Neisseria gonorrhoeae is the causative agent of the sexually transmitted infection (STI) gonorrhea, with an estimated 87 million annual cases worldwide. N. gonorrhoeae predominantly colonizes the male and female genital tract (FGT). In the FGT, N. gonorrhoeae confronts fluctuating levels of nutrients and oxidative and non-oxidative antimicrobial defenses of the immune system, as well as the resident microbiome. One mechanism utilized by N. gonorrhoeae to adapt to this dynamic FGT niche is to modulate gene expression primarily through DNA-binding transcriptional regulators. Here, we describe the major N. gonorrhoeae transcriptional regulators, genes under their control, and how these regulatory processes lead to pathogenic properties of N. gonorrhoeae during natural infection. We also discuss the current knowledge of the structure, function, and diversity of the FGT microbiome and its influence on gonococcal survival and transcriptional responses orchestrated by its DNA-binding regulators. We conclude with recent multi-omics data and modeling tools and their application to FGT microbiome dynamics. Understanding the strategies utilized by N. gonorrhoeae to regulate gene expression and their impact on the emergent characteristics of this pathogen during infection has the potential to identify new effective strategies to both treat and prevent gonorrhea.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Disruption of Very-Long-Chain-Fatty Acid Synthesis Has an Impact on the Dynamics of Cellulose Synthase in Arabidopsis thaliana

In higher plants, cellulose is synthesized by membrane-spanning large protein complexes named cellulose synthase complexes (CSCs). In this study, the Arabidopsis PASTICCINO2 (PAS2) was identified as an interacting partner of cellulose synthases. PAS2 was previously characterized as the plant 3-hydroxy-acyl-CoA dehydratase, an ER membrane-localized dehydratase that is essential for very-long-chain-fatty acid (VLCFA) elongation. The pas2-1 mutants show defective cell elongation and reduction in cellulose content in both etiolated hypocotyls and light-grown roots. Although disruption of VLCFA synthesis by a genetic alteration had a reduction in VLCFA in both etiolated hypocotyls and light-grown roots, it had a differential effect on cellulose content in the two systems, suggesting the threshold level of VLCFA for efficient cellulose synthesis may be different in the two biological systems. pas2-1 had a reduction in both CSC delivery rate and CSC velocity at the PM in etiolated hypocotyls. Interestingly, Golgi but not post-Golgi endomembrane structures exhibited a severe defect in motility. Experiments using pharmacological perturbation of VLCFA content in etiolated hypocotyls strongly indicate a novel function of PAS2 in the regulation of CSC and Golgi motility. Through a combination of genetic, biochemical and cell biology studies, our study demonstrated that PAS2 as a multifunction protein has an important role in the regulation of cellulose biosynthesis in Arabidopsis hypocotyl.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Mass spectrometry-based proteomics for analysis of hydrophilic phosphopeptides

Protein phosphorylation is a critical post-translational modification (PTM), with cell signaling networks being tightly regulated by protein phosphorylation. Despite recent technological advances in reversed-phase liquid chromatography (RPLC)-mass spectrometry (MS)-based proteomics, comprehensive phosphoproteomic coverage in complex biological systems remains challenging, especially for hydrophilic phosphopeptides that often have multiple phosphorylation sites. Herein we describe an MS-based phosphoproteomics protocol for effective quantitative analysis of hydrophilic phosphopeptides. This protocol was built upon a simple tandem mass tag (TMT)-labeling method for significantly increasing peptide hydrophobicity, thus effectively enhancing RPLC-MS analysis of hydrophilic peptides. Through phosphoproteomic analyses of MCF7 cells, this method was demonstrated to greatly increase the number of identified hydrophilic phosphopeptides and improve MS signal detection. With the TMT labeling method, we were able to identify a previously unreported phosphopeptide from the G protein-coupled receptor (GPCR) CXCR3, QPpSSSR, which is thought to be important in regulating receptor signaling. This protocol is easy to adopt and implement, and thus should have broad utility for effective RPLC-MS analysis of the hydrophilic phosphoproteome as well as other highly hydrophilic analytes.

Hydrophilic phosphopeptide, Phosphoproteomics, TMT↗
DOE OSTI2023

Modelos de riesgo de colision: una herramienta para evaluar los riesgos para las aves rapaces en instalaciones de energia eolica (Spanish)

In January 2022, the International Energy Agency Wind Task 34 - Working Together to Resolve the Environmental Effects of Wind Energy (WREN) - organized a forum to discuss aspects of raptor collision risk with wind turbines. The forum included experts in raptor biology and physiology, collision risk modeling, wind energy development, and atmospheric scientists from seven countries. They represented a range of international stakeholder groups including academia, government agencies, national laboratories, and wildlife consultants. This educational brief summarizes the discussion during the forum and written comments from those who could not attend. Relevant literature was used to provide additional context when needed. For several species of raptors, such as golden eagles (Aquila chrysaetos), griffon vultures (Gyps fulvus) and white-tailed eagles (Haliaatus albicilla), collision risk with wind turbines continues to be a concern among stakeholders. These concerns include the potential population-level impact related to collisions, compliance with regulatory mechanisms for protected species, and the ability to generate renewable energy. To make siting and operational decisions, stakeholders require some level of certainty of the risk associated with a proposed project. Understanding this risk, in part, requires species-specific data on raptors and how they perceive and interact with wind farms or individual wind turbines. Collision risk models (CRMs) are a tool, often used in environmental impact assessments, that can provide estimates of risk relative to specific turbines or an entire wind farm. However, questions associated with the uncertainty in CRM estimates remain. This is the Spanish translation of NREL/FS-5000-84747, "Collision Risk Modeling - A Tool for Assessing Risks to Raptors at Wind Energy Facilities."

collision risk↗
DOE OSTI2022

Understanding interactions between biomolecules and two-dimensional nanomaterials using in silico microscopes

We report two-dimensional (2D) nanomaterials such as graphene are increasingly used in research and industry for various biomedical applications. Extensive experimental and theoretical studies have revealed that 2D nanomaterials are promising drug delivery vehicles, yet certain materials exhibit toxicity under biological conditions. So far, it is known that 2D nanomaterials possess strong adsorption propensities for biomolecules. To mitigate potential toxicity and retain favorable physical and chemical properties of 2D nanomaterials, it is necessary to explore the underlying mechanisms of interactions between biomolecules and nanomaterials for the subsequent design of biocompatible 2D nanomaterials for nanomedicine. The purpose of this review is to integrate experimental findings with theoretical observations and facilitate the study of 2D nanomaterial interaction with biomolecules at the molecular level. We discuss the current understanding and progress of 2D nanomaterial interaction with proteins, lipid membranes, and DNA based on molecular dynamics (MD) simulation. In this review, we focus on the 2D graphene nanosheet and briefly discuss other 2D nanomaterials. With the ever-growing computing power, we can image nanoscale processes using MD simulation that are otherwise not observable in experiment. We expect that molecular characterization of the complex behavior between 2D nanomaterials and biomolecules will help fulfill the goal of designing effective 2D nanomaterials as drug delivery platforms.

2D nanomaterials↗
DOE OSTI2025

How do Hydrological Variability and Human Activities Control the Spatiotemporal Changes of Riverine Nitrogen Export in the Upper Mississippi River Basin?

Excessive nitrogen export from agricultural watersheds remains a critical water quality challenge, with the Upper Mississippi River Basin (UMRB) significantly contributing to downstream eutrophication and hypoxia in the Gulf. This study investigates the spatiotemporal dynamics of riverine nitrate plus nitrite (NO 3 − + NO 2 − -N) export across the UMRB at high spatial resolution (12-digit Hydrologic Unit Codes or HUC12 subwatershed scale) during 2001−2020 and quantifies the effects of anthropogenic activities and hydrological variability on riverine NO 3 − + NO 2 − -N export changes in the region between 2001−2005 and 2016−2020. Our results revealed hotspots of substantial increases in NO 3 − + NO 2 − -N yields across the UMRB, with distinct regional patterns in driving factors. Over the entire UMRB, NO 3 − + NO 2 − -N yields increased by 9.7 kg/ha/yr on average from 2001−2005 to 2016−2020, with anthropogenic activities contributing 4.8 kg/ha/yr and hydrological variability contributing 4.9 kg/ha/yr. The northern and western UMRB had combined influences from both anthropogenic activities and hydrological variability, while the east-central regions had predominantly hydrologically driven changes. Agricultural sources, including fertilizer, manure, and biological nitrogen fixation, collectively contributed over 80% of NO 3 − + NO 2 − -N loading throughout the basin. Furthermore, this framework for disentangling human and hydrological impacts provides critical insights for developing effective and targeted watershed management strategies to reduce nutrient losses and improve water quality.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Fragment-based determination of a proteinase K structure from MicroED data using ARCIMBOLDO_SHREDDER

Structure determination of novel biological macromolecules by X-ray crystallography can be facilitated by the use of small structural fragments, some of only a few residues in length, as effective search models for molecular replacement to overcome the phase problem. Independence from the need for a complete pre-existing model with sequence similarity to the crystallized molecule is the primary appeal of ARCIMBOLDO , a suite of programs which employs this ab initio algorithm for phase determination. Here, the use of ARCIMBOLDO is investigated to overcome the phase problem with the electron cryomicroscopy (cryoEM) method known as microcrystal electron diffraction (MicroED). The results support the use of the ARCIMBOLDO_SHREDDER pipeline to provide phasing solutions for a structure of proteinase K from 1.6 Å resolution data using model fragments derived from the structures of proteins sharing a sequence identity of as low as 20%. ARCIMBOLDO_SHREDDER identified the most accurate polyalanine fragments from a set of distantly related sequence homologues. Alternatively, such templates were extracted in spherical volumes and given internal degrees of freedom to refine towards the target structure. Both modes relied on the rotation function in Phaser to identify or refine fragment models and its translation function to place them. Model completion from the placed fragments proceeded through phase combination of partial solutions and/or density modification and main-chain autotracing using SHELXE . The combined set of fragments was sufficient to arrive at a solution that resembled that determined by conventional molecular replacement using the known target structure as a search model. This approach obviates the need for a single, complete and highly accurate search model when phasing MicroED data, and permits the evaluation of large fragment libraries for this purpose.

59 BASIC BIOLOGICAL SCIENCES↗