Search NASA⌕ Search

SEARCH · Search NASA

Results for “predictive markers”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 181 records · Page 10
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Chasing ghosts: characterization of artifact generation in coded aperture decoding due to experimental implementation

Coded aperture imaging is a form of lensless aperture imaging that projects multiple overlapping images of the source onto the detector, enhancing signal strength, which is advantageous for low-flux sources or high-resolution imaging. This technique requires decoding of the detector signal to reconstruct the original source, which involves convolving the detector data with the aperture pattern. When the signal is from a centered point source, the reconstructed source image is known as the point spread function (PSF). A clean PSF without artifacts is a Dirac delta function [Appl. Opt. 20, 1858 (1981)]. This paper examines the robustness of the decoding process against variations in experimental tolerances by analyzing artifact growth in the reconstructed PSF. We illustrate the effects of incorrect magnification, rotation, and detector size and find that aperture–detector rotational misalignment about the imaging axis is the most sensitive parameter, with significant artifact generation occurring with angular offsets of less than one degree. We discuss compensation methods for imperfect aperture placement, finding that small detector sizes produce uncompensatable artifact generation, and compare theoretical predictions with experimental PSF measurements of a rank , 6.8 mm thick (less than one mean free path) coded aperture with a 3.5 mm cell size, conducted at the MegaJOuLe Neutron Imaging Radiography dense plasma focus [IEEE Trans. Plasma Sci. 49, 3299 (2021)] using a 2.45 MeV neutron source. Based on our findings, we recommend using magnified coded apertures in the under-sampled regime, which allows for the inclusion of fiducial markers to characterize aperture–detector rotational offsets and the addition of mechanical coupling, where possible, to constrain rotational and magnification offsets.

Selwood, M. P. [Lawrence Livermore National Labora↗
DOE OSTI2023

Strategies to identify and edit improvements in synthetic genome segments episomally

Genome engineering projects often utilize bacterial artificial chromosomes (BACs) to carry multi-kilobase DNA segments at low copy number. However, all stages of whole-genome engineering have the potential to impose mutations on the synthetic genome that can reduce or eliminate the fitness of the final strain. Here, we describe improvements to a multiplex automated genome engineering (MAGE) protocol to improve recombineering frequency and multiplexability. This protocol was applied to recoding an Escherichia coli strain to replace seven codons with synonymous alternatives genome wide. Ten 44 402–47 179 bp de novo synthesized DNA segments contained in a BAC from the recoded strain were unable to complement deletion of the corresponding 33–61 wild-type genes using a single antibiotic resistance marker. Next-generation sequencing (NGS) was used to identify 1–7 non-recoding mutations in essential genes per segment, and MAGE in turn proved a useful strategy to repair these mutations on the recoded segment contained in the BAC when both the recoded and wild-type copies of the mutated genes had to exist by necessity during the repair process. Finally, two web-based tools were used to predict the impact of a subset of non-recoding missense mutations on strain fitness using protein structure and function calls.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2016

Metabolomic and Genomic Markers of Atherosclerosis as Related to Oxidative Stress, Inflammation, and Vascular Function in Twin Astronauts

Background: Future human space travel will consist primarily of long-duration missions onboard the International Space Station (ISS) or exploration-class missions to Mars, its moons, or nearby asteroids. Astronauts participating in long-duration missions may be at an increased risk of oxidative stress and inflammatory damage due to radiation, psychological stress, altered physical activity, nutritional insufficiency, and hyperoxia during extravehicular activity. By studying one identical twin during his 1-year ISS mission and one ground-based twin, this work extends a current NASA-funded investigation to determine whether these spaceflight factors contribute to an accelerated progression of atherosclerosis. This study of twins affords a unique opportunity to examine the spaceflight-related atherosclerosis risk independent of the confounding factors associated with different genotypes. Purpose: The purpose of this investigation is to determine whether biomarkers of oxidative and inflammatory stress are elevated during and after long-duration spaceflight and determine if a relation exists between levels of these biomarkers and structural and functional indices of atherosclerotic risk measured in the carotid and brachial arteries. These physiological and biochemical data will be extended by using an exploratory approach to investigate the relationship between intermediate phenotypes and risk factors for atherosclerosis and the metabolomic signature from plasma and urine samples. Since metabolites are often the indirect products of gene expression, we will simultaneously assess gene expression and DNA methylation in leukocytes. Hypothesis: We predict that the space-flown twin will experience elevated biomarkers of oxidative stress and inflammatory damage, altered arterial structure and function, accelerated telomere shortening, dysregulation of genes associated with oxidative stress and inflammation, and a metabolic profile shift that is associated with elevated atherosclerosis risk factors. Conversely, these will not be observed in the ground-based twin. Methods: We will measure blood and urine biomarkers of oxidative stress and inflammation as well as arterial structure and function (carotid intima-medial thickness and brachial artery flow-mediated dilation) in one twin astronaut before, during, and after long-duration spaceflight and in his twin serving as a ground-based control. Furthermore, we will measure metabolomics (targeted and untargeted approaches) and genomic markers (DNA methylation, mRNA gene expression, telomere length) to elucidate the molecular mechanisms involved. A panel of biomarkers of oxidative and inflammatory stress will be measured in venous blood samples and 24-hour (in-flight) and 48-hour (pre- and post-flight) urine pools twice before flight, early (flight days 15 and 60) and late (2 weeks before landing) during the mission, and early in the post-flight recovery phase (approximately 3-5 days after landing). Arterial structure, assessed from measures of intima-media thickness, will be measured at the same times. Arterial function will be assessed using brachial flow-mediated dilation, a well-validated measure used to assess endothelium-dependent vasodilation and a sensitive predictor of atherosclerotic risk, only before and after spaceflight. Discussion: Pre- and in-flight data collection is in progress for the space-flown twin, and similar data have been obtained from the ground-based twin. Blood and urine samples will be batch processed when received from ISS after the conclusion of the 1-year mission. Results from these individual subjects will be compared to the larger complement of subjects participating in the companion study currently ongoing in ISS astronauts.

Lee, Stuart M. C.↗
DOE OSTI2022

Sporophyte Stage Genes Exhibit Stronger Selection Than Gametophyte Stage Genes in Haplodiplontic Giant Kelp

Macrocystis pyrifera (giant kelp), a haplodiplontic brown macroalga that alternates between a macroscopic diploid (sporophyte) and a microscopic haploid (gametophyte) phase, provides an ideal system to investigate how ploidy background affects the evolutionary history of a gene. In M. pyrifera , the same genome is subjected to different selective pressures and environments as it alternates between haploid and diploid life stages. We assembled M. pyrifera gene models using available expression data and validated 8,292 genes models using the model alga Ectocarpus siliculosus . Differential expression analysis identified gene models expressed in either or both the haploid and diploid life stages while functional annotation identified processes enriched in each stage. Genes expressed preferentially or exclusively in the gametophyte stage were found to have higher nucleotide diversity (π = 2.3 × 10 –3 and 2.8 × 10 –3 , respectively) than those for sporophytes (π = 1.1 × 10 –3 and 1 × 10 –3 , respectively). While gametophyte-biased genes show faster sequence evolution, the sequence evolution exhibits less signatures of adaptations when compared to sporophyte-biased genes. Our findings contrast the standing masking hypothesis, which predicts higher standing genetic variation at the sporophyte stage, and support the strength of expression theory, which posits that genes expressed more strongly are expected to evolve slower. We argue that the sporophyte stage undergoes more stringent selection compared with the gametophyte stage, which carries a heavy genetic load associated with broadcast spawning. Furthermore, using whole-genome sequencing, we confirm the strong population structure in wild M. pyrifera populations previously established using microsatellite markers, and estimate population genetic parameters, such as pairwise genetic diversity and Tajima’s D , important for conservation and domestication of M. pyrifera .

Molano, Gary↗
NASA NTRS2008

Deconvoluting the Friction Stir Weld Process for Optimizing Welds

In the friction stir welding process, the rotating surfaces of the pin and shoulder contact the weld metal and force a rotational flow within the weld metal. Heat, generated by the metal deformation as well as frictional slippage with the contact surface, softens the metal and makes it easier to deform. As in any thermo-mechanical processing of metal, the flow conditions are critical to the quality of the weld. For example, extrusion of metal from under the shoulder of an excessively hot weld may relax local pressure and result in wormhole defects. The trace of the weld joint in the wake of the weld may vary geometrically depending upon the flow streamlines around the tool with some geometry more vulnerable to loss of strength from joint contamination than others. The material flow path around the tool cannot be seen in real time during the weld. By using analytical "tools" based upon the principles of mathematics and physics, a weld model can be created to compute features that can be observed. By comparing the computed observations with actual data, the weld model can be validated or adjusted to get better agreement. Inputs to the model to predict weld structures and properties include: hot working properties ofthe metal, pin tool geometry, travel rate, rotation and plunge force. Since metals record their prior hot working history, the hot working conditions imparted during FSW can be quantified by interpreting the final microstructure. Variations in texture and grain size result from variations in the strain accommodated at a given strain rate and temperature. Microstructural data from a variety of FSWs has been correlated with prior marker studies to contribute to our understanding of the FSW process. Once this stage is reached, the weld modeling process can save significant development costs by reducing costly trial-and-error approaches to obtaining quality welds.

Schneider, Judy↗
NASA NTRS2017

Metabolomic and Genomic Markers of Atherosclerosis as Related to Oxidative Stress, Inflammation, and Vascular Function in Twin Astronauts

BACKGROUND: Future human space travel will consist primarily of long-duration missions onboard the International Space Station (ISS) or exploration-class missions to Mars, its moons, or nearby asteroids. Astronauts participating in long-duration missions may be at an increased risk of oxidative stress and inflammatory damage due to radiation, psychological stress, altered physical activity, nutritional insufficiency, and hyperoxia during extravehicular activity. By studying one identical twin during his 1-year ISS mission and his ground-based twin, this work extends a current NASA-funded investigation to determine whether these spaceflight factors contribute to an accelerated progression of atherosclerosis. This study of twins affords a unique opportunity to examine spaceflight-related atherosclerosis risk that is independent of the confounding factors associated with different genotypes. PURPOSE: The purpose of this investigation was to determine whether biomarkers of oxidative and inflammatory stress are elevated during and after long-duration spaceflight and determine if a relation exists between levels of these biomarkers and structural and functional indices of atherosclerotic risk measured in the carotid and brachial arteries. These physiological and biochemical data will be extended by using an exploratory approach to investigate the relationship between intermediate phenotypes and risk factors for atherosclerosis and the metabolomic signature from plasma and urine samples. Since metabolites are often the indirect products of gene expression, we simultaneously assessed gene expression and DNA methylation in leukocytes. HYPOTHESIS: We predict that, compared to the ground-based twin, the space-flown twin will experience elevated biomarkers of oxidative stress and inflammatory damage, altered arterial structure and function, accelerated telomere shortening, dysregulation of genes associated with oxidative stress and inflammation, and a metabolic profile shift that is associated with elevated atherosclerosis risk factors. METHODS: In the space-flown twin, a panel of biomarkers of oxidative and inflammatory stress were measured in venous blood samples and in 24-h (in-flight) and 48-h (pre- and post-flight) urine pools collected twice before flight, six times during the mission (~FD15, 75, 180, 240, 300, 335), and early in the post-flight recovery phase (3-5 days after landing). We also measured metabolomic (targeted and untargeted approaches) and genomic markers (DNA methylation, mRNA gene expression, telomere length) in these samples. Arterial structure, assessed from measures of intima-media thickness, also were measured using standard clinical ultrasound at the same time points. Arterial function was assessed using brachial flow-mediated dilation, a well-validated measure used to assess endothelium-dependent vasodilation and a sensitive predictor of atherosclerotic risk, only before and after spaceflight. All of the same measures were obtained in the ground-based twin, but less frequently. DISCUSSION: All data collection has been completed for both the space-flown twin and the ground-based twin. Vascular structure and function measures have been analyzed, blood and urine samples have been batch-processed. Results from these individuals will be compared to each other, to data from other Twin Study investigations, and to the larger complement of subjects participating in the companion study currently ongoing in ISS astronauts.

Lee, Stuart M. C.↗
DOE OSTI2025

Machine Learning-Guided Optimization of SABRE Hyperpolarization for α-Ketoglutarate in Acetone–Water

Signal amplification by reversible exchange (SABRE) is a hyperpolarization method that polarizes target nuclei of metabolites quickly and efficiently. Recent SABRE advances, including Ace-SABRE, yield biocompatible, aqueous solutions of hyperpolarized markers for metabolic monitoring. Building on recent advancements, expanding the substrate scope of Ace-SABRE is desirable. However, SABRE polarization is sensitive to many different parameters; therefore, traditional optimization approaches are experimentally time-consuming. In this proof-of-concept application of machine learning (ML), Bayesian optimization (BO) is used for four important input parameters to model the complex SABRE dynamics while saving experimental time. The presented ML model also provides chemical insights that enable predictions of sample compositions for increased polarization levels. In this paper, we transition from an original average free polarization of p = ∼0.90% to a maximum observed free polarization of p = ∼6.6% for 1- 13 C alpha-ketoglutarate (AKG) with 13 C at natural abundance, utilizing both direct outputs as well as chemical insights revealed by the ML model.

Catalysts↗
DOE OSTI2021

DNA Viral Diversity, Abundance, and Functional Potential Vary across Grassland Soils with a Range of Historical Moisture Regimes

Soil viruses are abundant, but the influence of the environment and climate on soil viruses remains poorly understood. Here, we addressed this gap by comparing the diversity, abundance, lifestyle, and metabolic potential of DNA viruses in three grassland soils with historical differences in average annual precipitation, low in eastern Washington (WA), high in Iowa (IA), and intermediate in Kansas (KS). Bioinformatics analyses were applied to identify a total of 2,631 viral contigs, including 14 complete viral genomes from three deep metagenomes (1 terabase [Tb] each) that were sequenced from bulk soil DNA. An additional three replicate metagenomes (~0.5 Tb each) were obtained from each location for statistical comparisons. Identified viruses were primarily bacteriophages targeting dominant bacterial taxa. Both viral and host diversity were higher in soil with lower precipitation. Viral abundance was also significantly higher in the arid WA location than in IA and KS. More lysogenic markers and fewer clustered regularly interspaced short palindromic repeats (CRISPR) spacer hits were found in WA, reflecting more lysogeny in historically drier soil. More putative auxiliary metabolic genes (AMGs) were also detected in WA than in the historically wetter locations. The AMGs occurring in 18 pathways could potentially contribute to carbon metabolism and energy acquisition in their hosts. Structural equation modeling (SEM) suggested that historical precipitation influenced viral life cycle and selection of AMGs. The observed and predicted relationships between soil viruses and various biotic and abiotic variables have value for predicting viral responses to environmental change.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1997

Impact Crises, Mass Extinctions, and Galactic Dynamics: A Unified Theory

A general hypothesis linking mass extinctions of life with impacts of large asteroids and comets is based on astronomical data, impact dynamics, and geological information. The waiting times of large-body impacts on the Earth, derived from the flux of Earth-crossing asteroids and comets, and the estimated size of impacts capable of causing large-scale environmental disasters predict that impacts of objects (sup 3)5 km in diameter ((sup 3)10(exp 7) Mt TNT equivalent) could be sufficient to explain the record of about 25 extinction pulses in the last 540 m.y., with the five recorded major mass extinctions related to the impacts of the largest objects of (sup 3)10 km in diameter ( (sup 3)10(exp 8) Mt events). Smaller impacts (about 10(exp 6)-10(exp 7) Mt), with significant regional and even global environmental effects, could be responsible for the lesser boundaries in the geologic record. Tests of the "kill curve" relationship for impact-induced extinctions based on new data on extinction intensities and several well-dated large impact craters suggest that major mass extinctions require large impacts, and that a step in the kill curve may exist at impacts that produce craters of -100 km diameter, with smaller impacts capable of only relatively weak extinction pulses. Single impact craters < about 60 km in diameter should not be associated with global extinction pulses detectable in the Sepkoski database (although they may explain stage and zone boundaries marked by lesser faunal turnover), but multiple impacts in that size range may produce significant stepped extinction pulses. Statistical tests of the last occurrences of species at mass-extinction boundaries are generally consistent with predictions for abrupt or stepped extinctions, and several boundaries are known to show "catastrophic" signatures of environmental disasters and biomass crash, impoverished postextinction fauna and flora dominated by stress-tolerant and opportunistic species, and gradual ecological recovery and radiation of new taxa. Isotopic and other geochemical signatures are also generally consistent with the expected after-effects of catastrophic impacts. Seven of the recognized extinction pulses are associated with concurrent (in some cases multiple) stratigraphic impact markers (e.g., layers with high Ir, shocked minerals, microtektites), and/or large, dated impact craters. Other less-well-studied crisis intervals show elevated Ir, still well below that of the K/T spike, which might be explained by low-Ir impactors, ejecta blowoff, or the sedimentary reworking and dilution of impact signatures. The best explanation for a possible periodic component of about 30 m.y. in mass extinctions and clusters of impacts is the modulation of the comet flux associated with the solar system's periodic passage through the plane of the Milky Way Galaxy. The quantitative agreement among paleontological, geological, and astronomical data suggests an important underlying unification of the processes involved.

Rampino, M.R.↗
DOE OSTI2021

Serum MicroRNAs as Xerostomia Biomarkers in Patients With Oropharyngeal Cancer Undergoing Radiation Therapy

Severe xerostomia is noted in the majority of patients irradiated for oropharyngeal cancer. Extracellular microRNAs (miRNAs) may serve as effective tools allowing prediction of radiation-related toxicity. The aim of this study was to create an efficient prognostic miRNA-based test for severe, patient-rated xerostomia 3 months after primary treatment.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2023

Co-located temperature and electrical resistivity measurements for permafrost mapping, Teller 27, Teller 47 and Kougarok 64, Seward Peninsula, Alaska, late summers of 2018, 2019, 2021, and 2022

This data set contains co-located shallow soil (0.8m below ground level) and electrical resistivity at various depth extracted from Electrical Resistivity Tomography (ERT) measurements. Data were acquired at three watersheds on the southern Seward Peninsula during the late summers of 2018, 2019, 2021, and 2022. The three watersheds are located along the Nome-Teller Highway at mile markers 27 and 47, and along Kougarok Road mile marker 64. The co-located temperature and electrical resistivity data were used to (1) map the spatial extend of near surface permafrost, and (2) for supervised classification of permafrost bodies. This dataset contains .csv, .txt, .srv files and flmd reporting format with data dictionary. Find information about the .srv files at "https://e4d-userguide.pnnl.gov/e4d_guide/elec/e4d_e4d-survey.html". The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research. The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska. Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗
NASA NTRSDate not supplied

Use of the SPoRT Stoplight Product to Support NWS Decision Support Services

The National Weather Service Forecast Offices (NWSFOs) use many weather tools and observational datasets to provide support for critical decision-making by core partners such as public safety officials, emergency managers, and first responders. These core partners who need weather decision support services (DSS) for outdoor events require up-to-the-minute weather information to ensure the safety and protection of attendees and workers. Storms and lightning, potentially deadly, pose a significant threat during outdoor events and are among the weather phenomena frequently cited as a DSS requirement. According to the National Lightning Safety Council, from 2014 up to August 2024, lightning resulted in 222 fatalities in the U.S. For outdoor events with hundreds to thousands of attendees, having the right tools to detect and monitor lightning activity is of utmost importance to protect lives. Common guidelines for lightning safety include moving inside a substantial structure at the first sight of threatening skies or the first sound of thunder, and waiting 30 minutes after the last lightning flash or thunder before returning outside. Using this guidance as a framework, scientists at the NASA Short-term Prediction Research and Transition (SPoRT) center have developed the Geostationary Lightning Mapper (GLM) Stoplight tool. This experimental tool uses the GLM Flash Extent Density imagery to display the location and recency of lightning flashes. To simplify interpretation, these lightning pixels are color-coded in 10-minute bins, ranging from red (lightning detected 0 to 10 minutes ago) to yellow (10 to 20 minutes ago) to green (20 to 30 minutes ago). The Stoplight tool also allows users to place markers at the location of outdoor events with range rings around the location to help in assessing the location and relative age of lightning flashes near and upstream of the event. The goal is to help NWS forecasters provide core partners with the necessary information to make the best decisions possible. While the Stoplight tool is experimental, forecasters at NWSFO Raleigh, NC, have periodically used the Stoplight guidance to evaluate its utility within NWS DSS. This presentation will discuss how the Stoplight tool was successfully used for DSS for four outdoor events in central NC in 2023 and 2024. Future improvements to this tool, including the addition of AI applications and the merging of ground-based lightning data with GLM data, will be reviewed.

Gail Hartfield↗
DOE OSTI2021

Screening and Validation of Molecular Targeted Radiosensitizers

The development of molecular targeted drugs with radiation and chemotherapy is critically important for improving the outcomes of patients with hard-to-treat, potentially curable cancers. However, too many preclinical studies have not translated into successful radiation oncology trials. Major contributing factors to this insufficiency include poor reproducibility of preclinical data, inadequate preclinical modeling of intertumoral genomic heterogeneity that influences treatment sensitivity in the clinic, and a reliance on tumor growth delay instead of local control (TCD50) endpoints. There exists an urgent need to overcome these barriers to facilitate successful clinical translation of targeted radiosensitizers. To this end, we have used 3-dimensional (3D) cell culture assays to better model tumor behavior in vivo. Examples of successful prediction of in vivo effects with these 3D assays include radiosensitization of head and neck cancers by inhibiting epidermal growth factor receptor or focal adhesion kinase signaling, and radioresistance associated with oncogenic mutation of KRAS. To address the issue of tumor heterogeneity, we leveraged institutional resources that allow high-throughput 3D screening of radiation combinations with small-molecule inhibitors across genomically characterized cell lines from lung, head and neck, and pancreatic cancers. This high-throughput screen is expected to uncover genomic biomarkers that will inform the successful clinical translation of targeted agents from the National Cancer Institute Cancer Therapy Evaluation Program portfolio and other sources. Screening “hits” need to be subjected to refinement studies that include clonogenic assays, addition of disease-specific chemotherapeutics, target/biomarker validation, and integration of patient-derived tumor models. The chemoradiosensitizing activities of the most promising drugs should be confirmed in TCD50 assays in xenograft models with or without relevant biomarker and using clinically relevant radiation fractionation. We predict that appropriately validated and biomarker-directed targeted therapies will have a higher likelihood than past efforts of being successfully incorporated into the standard management of hard-to-treat tumors.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
NASA NTRS1994

Predictive isotopic biogeochemistry: hydrocarbons from anoxic marine basins

Carbon isotopic compositions were determined for individual hydrocarbons in water column and sediment samples from the Cariaco Trench and Black Sea. In order to identify hydrocarbons derived from phytoplankton, the isotopic compositions expected for biomass of autotrophic organisms living in surface waters of both localities were calculated based on the concentrations of CO2(aq) and the isotopic compositions of dissolved inorganic carbon. These calculated values are compared to measured delta values for particulate organic carbon and for individual hydrocarbon compounds. Specifically, we find that lycopane is probably derived from phytoplankton and that diploptene is derived from the lipids of chemoautotrophs living above the oxic/anoxic boundary. Three acyclic isoprenoids that have been considered markers for methanogens, pentamethyleicosane and two hydrogenated squalenes, have different delta values and apparently do not derive from a common source. Based on the concentration profiles and isotopic compositions, the C31 and C33 n-alkanes and n-alkenes have a similar source, and both may have a planktonic origin. If so, previously assigned terrestrial origins of organic matter in some Black Sea sediments may be erroneous.

Non-NASA Center↗
DOE OSTI2025

Plant Characteristics, Porewater, Gas Flux, and Soil Biogeochemistry at Council Road Site Mile Marker 71, Seward Peninsula, Alaska, 2023

Data collected at Council, AK (64°51’35.0”N 163°41’59.1”W) during a summer campaign in 2023. Water data consists of soil porewater collected by centrifuging soil cores and also by field collection with porewater samplers (rhizons). Gas data consists of CO2, CH4 and N2O surface soil fluxes measured with a portable FTIR analyzer. Plant and root data consists of biomass, root length, diameter and mass. Soil data consists of total C and N. Air, water and soil samples span two main locations: a thermokarst wetland and an upland tussock. The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research.The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska. Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).This dataset was generated to broadly address the following research question: how will climate change (i.e., thawing permafrost, landscape change) alter the ecosystem flux (sink versus source) of important greenhouse gases such as CO2, CH4 and N2O?Description of the contents of this data package: This dataset contains 5 different individual .csv files containing plant, soil, water and gas data. No software is needed to utilize them. PFTCover: Plant functional type ground cover in 1x1 meter plots. SoilCores: Solidphase and porewater phase soil biogeochemical variablesPlantData: Above and belowground plant traits. GasFlux: Surface plant-soil gas measurementsFieldPorewater: Field collected porewater biogeochemical variables

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

VirION2: a short- and long-read sequencing and informatics workflow to study the genomic diversity of viruses in nature

Microbes play fundamental roles in shaping natural ecosystem properties and functions, but do so under constraints imposed by their viral predators. However, studying viruses in nature can be challenging due to low biomass and the lack of universal gene markers. Though metagenomic short-read sequencing has greatly improved our virus ecology toolkit—and revealed many critical ecosystem roles for viruses—microdiverse populations and fine-scale genomic traits are missed. Some of these microdiverse populations are abundant and the missed regions may be of interest for identifying selection pressures that underpin evolutionary constraints associated with hosts and environments. Though long-read sequencing promises complete virus genomes on single reads, it currently suffers from high DNA requirements and sequencing errors that limit accurate gene prediction. Here we introduce VirION2, an integrated short- and long-read metagenomic wet-lab and informatics pipeline that updates our previous method (VirION) to further enhance the utility of long-read viral metagenomics. Using a viral mock community, we first optimized laboratory protocols (polymerase choice, DNA shearing size, PCR cycling) to enable 76% longer reads (now median length of 6,965 bp) from 100-fold less input DNA (now 1 nanogram). Using a virome from a natural seawater sample, we compared viromes generated with VirION2 against other library preparation options (unamplified, original VirION, and short-read), and optimized downstream informatics for improved long-read error correction and assembly. VirION2 assemblies combined with short-read based data (‘enhanced’ viromes), provided significant improvements over VirION libraries in the recovery of longer and more complete viral genomes, and our optimized error-correction strategy using long- and short-read data achieved 99.97% accuracy. In the seawater virome, VirION2 assemblies captured 5,161 viral populations (including all of the virus populations observed in the other assemblies), 30% of which were uniquely assembled through inclusion of long-reads, and 22% of the top 10% most abundant virus populations derived from assembly of long-reads. Viral populations unique to VirION2 assemblies had significantly higher microdiversity means, which may explain why short-read virome approaches failed to capture them. These findings suggest the VirION2 sample prep and workflow can help researchers better investigate the virosphere, even from challenging low-biomass samples. Our new protocols are available to the research community on protocols.io as a ‘living document’ to facilitate dissemination of updates to keep pace with the rapid evolution of long-read sequencing technology.

Long-reads↗
DOE OSTI2022

Spatially calibrating polycyclic aromatic hydrocarbons (PAHs) as proxies of area burned by vegetation fires: Insights from comparisons of historical data and sedimentary PAH fluxes

Many regions worldwide have experienced increasing wildfire activity in recent years and climate changes are predicted to result in more frequent and severe fires. Reconstruction of past fire activity offers paleoenvironmental context for modern and future burning. Pyrogenic polycyclic aromatic hydrocarbons (PAHs) have been increasingly used as a molecular biomarker for fire occurrence in the paleorecord and offer opportunity for nuanced reconstructions of fire characteristics. A suite of PAHs are produced during combustion, and the emission amount and assemblage is influenced by many variables including fuel type, fire temperature, and oxygen availability. Despite recent advances in understanding the controls and taphonomy of these biomass burning markers, the spatial scale of this proxy is unknown. In this paper, measurements of PAH fluxes preserved in a lake sediment archive from the Sierra Nevada, California were compared with a historical geographic information system dataset of area burned up to 150 km distance from the lake to determine the spatial scales for which these biomarkers are reliable proxies of burning. Comparisons of PAH fluxes with charcoal accumulation rates in the same sediments suggest that pyrogenic particulate transport modulates low to mid-molecular weight PAHs via adsorption. Overall, the results indicate that PAH records integrate a combination of spatial signals of area burned and measurement of individual PAHs may enable cross-scale paleofire reconstructions.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Greenhouse Gas Production and Soil Chemistry in Anaerobic Soil Microcosm Incubations after Nitrogen Addition, Teller Road Site, Seward Peninsula, 2018-2019

This dataset provides the results of laboratory soil microcosm incubation experiments conducted under anaerobic conditions with and without the addition of ammonium chloride (NH4Cl). The microcosms contained soil collected in April 2017 from the NGEE Arctic Teller Road Site at mile marker 27 (TL_MM27) near Intensive Site 9 (Toeslope) and Intensive Site 5 (Plateau). Incubations were conducted at 8°C for 55 days, with repeated measurements of headspace greenhouse gas concentrations. Microcosms were destructively harvested and extracted using ultrapure water and 0.1 M KCl for analysis of the porewater geochemistry. This dataset contains two csv files, a pdf user guide. and the raw data in a zip file.The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research.The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska.Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗