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All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

Physiological and Comparative Genomic Analysis of Arthrobacter sp. SRS-W-1-2016 Provides Insights on Niche Adaptation for Survival in Uraniferous Soils

Arthrobacter sp. strain SRS-W-1-2016 was isolated on high concentrations of uranium (U) from the Savannah River Site (SRS) that remains co-contaminated by radionuclides, heavy metals, and organics. SRS is located on the northeast bank of the Savannah River (South Carolina, USA), which is a U.S. Department of Energy (DOE) managed ecosystem left historically contaminated from decades of nuclear weapons production activities. Predominant contaminants within the impacted SRS environment include U and Nickel (Ni), both of which can be transformed microbially into less toxic forms via metal complexation mechanisms. Strain SRS-W-1-2016 was isolated from the uraniferous SRS soils on high concentrations of U (4200 μM) and Ni (8500 μM), but rapid growth was observed at much lower concentrations of 500 μM U and 1000 μM Ni, respectively. Microcosm studies established with strain SRS-W-1-2016 revealed a rapid decline in the concentration of spiked U such that it was almost undetectable in the supernatant by 72 h of incubation. Conversely, Ni concentrations remained unchanged, suggesting that the strain removed U but not Ni under the tested conditions. To obtain a deeper understanding of the metabolic potential, a draft genome sequence of strain SRS-W-1-2016 was obtained at a coverage of 90×, assembling into 93 contigs with an N50 contig length of 92,788 bases. The genomic size of strain SRS-W-1-2016 was found to be 4,564,701 bases with a total number of 4327 putative genes. An in-depth, genome-wide comparison between strain SRS-W-1-2016 and its four closest taxonomic relatives revealed 1159 distinct genes, representing 26.7% of its total genome; many associating with metal resistance proteins (e.g., for cadmium, cobalt, and zinc), transporter proteins, stress proteins, cytochromes, and drug resistance functions. Additionally, several gene homologues coding for resistance to metals were identified in the strain, such as outer membrane efflux pump proteins, peptide/nickel transport substrate and ATP-binding proteins, a high-affinity nickel-transport protein, and the spoT gene, which was recently implicated in bacterial resistance towards U. Detailed genome mining analysis of strain SRS-W-1-2016 also revealed the presence of a plethora of secondary metabolite biosynthetic gene clusters likely facilitating resistance to antibiotics, biocides, and metals. Additionally, several gene homologous for the well-known oxygenase enzyme system were also identified, potentially functioning to generate energy via the breakdown of organic compounds and thus enabling the successful colonization and natural attenuation of contaminants by Arthrobacter sp. SRS-W-1-2016 at the SRS site.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Hydrodynamic Zone of Influence Due to a Floating Structure in a Fjordal Estuary—Hood Canal Bridge Impact Assessment

Floating structures such as barges and ships affect near-field hydrodynamics and create a zone of influence (ZOI). Extent of the ZOI is of particular interest due to potential obstruction to and impact on out-migrating juvenile fish. Here, we present an assessment of ZOI from Hood Canal (Floating) Bridge, located within the 110-km-long fjord-like Hood Canal sub-basin in the Salish Sea, Washington. A field data collection program allowed near-field validation of a three-dimensional hydrodynamic model of Hood Canal with the floating bridge section embedded. The results confirm that Hood Canal Bridge, with a draft of 4.6 m covering ~85% of the width of Hood Canal, obstructs the brackish outflow surface layer. This induces increased local mixing near the bridge, causes pooling of water (up-current) during ebb and flood, and results in shadow/sheltering of water (down-current). The change in ambient currents, salinity, and temperature is highest at the bridge location and reduces to background levels with distance from the bridge. The ZOI extends ~20 m below the surface and varies from 2–3 km for currents, from 2–4 km for salinity, and from 2–5 km for temperature before the deviations with the bridge drop to <10% relative to simulated background conditions without the bridge present.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Genomic Analysis of Aspergillus Section Terrei Reveals a High Potential in Secondary Metabolite Production and Plant Biomass Degradation

Aspergillus terreus has attracted interest due to its application in industrial biotechnology, particularly for the production of itaconic acid and bioactive secondary metabolites. As related species also seem to possess a prosperous secondary metabolism, they are of high interest for genome mining and exploitation. Here, we present draft genome sequences for six species from Aspergillus section Terrei and one species from Aspergillus section Nidulantes. Whole-genome phylogeny confirmed that section Terrei is monophyletic. Genome analyses identified between 70 and 108 key secondary metabolism genes in each of the genomes of section Terrei, the highest rate found in the genus Aspergillus so far. The respective enzymes fall into 167 distinct families with most of them corresponding to potentially unique compounds or compound families. Moreover, 53% of the families were only found in a single species, which supports the suitability of species from section Terrei for further genome mining. Intriguingly, this analysis, combined with heterologous gene expression and metabolite identification, suggested that species from section Terrei use a strategy for UV protection different to other species from the genus Aspergillus. Section Terrei contains a complete plant polysaccharide degrading potential and an even higher cellulolytic potential than other Aspergilli, possibly facilitating additional applications for these species in biotechnology.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2017

Comparative Evaluation of U.S. Brand and Generic Intravenous Sodium Ferric Gluconate Complex in Sucrose Injection: In Vitro Cellular Uptake

Iron deficiency anemia is a common clinical consequence for people who suffer from chronic kidney disease, especially those requiring dialysis. Intravenous (IV) iron therapy is a widely accepted safe and efficacious treatment for iron deficiency anemia. Numerous IV iron drugs have been approved by U.S. Food and Drug Administration (FDA), including a single generic product, sodium ferric gluconate complex in sucrose. In this study, we compared the cellular iron uptake profiles of the brand (Ferrlecit®) and generic sodium ferric gluconate (SFG) products. We used a colorimetric assay to examine the amount of iron uptake by three human macrophage cell lines. This is the first published study to provide a parallel evaluation of the cellular uptake of a brand and a generic IV iron drug in a mononuclear phagocyte system. The results showed no difference in iron uptake across all cell lines, tested doses, and time points. The matching iron uptake profiles of Ferrlecit® and its generic product support the FDA’s present position detailed in the draft guidance on development of SFG complex products that bioequivalence can be based on qualitative (Q1) and quantitative (Q2) formulation sameness, similar physiochemical characterization, and pharmacokinetic bioequivalence studies.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

Polymorphic SSR markers for Plasmopara obducens (Peronosporaceae), the newly emergent downy mildew pathogen of Impatiens (Balsaminaceae)

Premise of the study: Simple sequence repeat (SSR) markers were developed for Plasmopara obducens , the causal agent of the newly emergent downy mildew disease of Impatiens walleriana . Methods and Results: A 202‐Mb draft genome assembly was generated from P. obducens using Illumina technology and mined to identify 13,483 SSR motifs. Primers were synthesized for 62 marker candidates, of which 37 generated reliable PCR products. Testing of the 37 markers using 96 P. obducens samples showed 96% of the markers were polymorphic, with 2−6 alleles observed. Observed and expected heterozygosity ranged from 0.000−0.892 and 0.023−0.746, respectively. Just 17 markers were sufficient to identify all multilocus genotypes. Conclusions: These are the first SSR markers available for this pathogen, and one of the first molecular resources. These markers will be useful in assessing variation in pathogen populations and determining the factors contributing to the emergence of destructive impatiens downy mildew disease.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Biomass conversion to produce hydrocarbon liquid fuel via hot-vapor filtered fast pyrolysis and catalytic hydrotreating

Lignocellulosic biomass conversion to produce biofuels has received significant attention because of the quest for a replacement for fossil fuels. Among the various thermochemical and biochemical routes, fast pyrolysis followed by catalytic hydrotreating is considered to be a promising near-term opportunity. This paper reports on experimental methods used 1) at the National Renewable Energy Laboratory (NREL) for fast pyrolysis of lignocellulosic biomass to produce bio-oils in a fluidized-bed reactor and 2) at Pacific Northwest National Laboratory (PNNL) for catalytic hydrotreating of bio-oils in a two-stage, fixed-bed, continuous-flow catalytic reactor. The configurations of the reactor systems, the operating procedures, and the processing and analysis of feedstocks, bio-oils, and biofuels are described in detail in this paper. We also demonstrate hot-vapor filtration during fast pyrolysis to remove fine char particles and inorganic contaminants from bio-oil. Representative results showed successful conversion of biomass feedstocks to fuel-range hydrocarbon biofuels and, specifically, the effect of hot-vapor filtration on bio-oil production and upgrading. As a result, the protocols provided in this report could help to generate rigorous and reliable data for biomass pyrolysis and bio-oil hydrotreating research.

09 BIOMASS FUELS↗
DOE OSTI2015

High-Density Single Nucleotide Polymorphism Linkage Maps of Lowland Switchgrass using Genotyping-by-Sequencing

Switchgrass (Panicum virgatum L.) is a warm-season perennial grass with promising potential as a bioenergy crop in the United States. However, the lack of genomic resources has slowed the development of plant lines with optimal characteristics for sustainable feedstock production. We generated high-density single nucleotide polymorphism (SNP) linkage maps using a reduced-representation sequencing approach by genotyping 231 F 1 progeny of a cross between two parents of lowland ecotype from the cultivars Kanlow and Alamo. Over 350 million reads were generated and aligned, which enabled identification and ordering of 4611 high-quality SNPs. The total lengths of the resulting framework maps were 1770 cM for the Kanlow parent and 2059 cM for the Alamo parent. These maps show collinearity with maps generated with polymerase chain reaction (PCR)-based simple-sequence repeat (SSR) markers, and new SNP markers were identified in previously unpopulated regions of the genome. Transmission segregation distortion affected all linkage groups (LGs) to differing degrees, and ordering of distorted markers highlighted several regions of unequal inheritance. Framework maps were adversely affected by the addition of distorted markers with varying severity, but distorted maps were of higher marker density and provided additional information for analysis. Alignment of these linkage maps with a draft version of the switchgrass genome assembly demonstrated high levels of collinearity and provides greater confidence in the validity of both resources. This methodology has proven to be a rapid and cost-effective way to generate high-quality linkage maps of an outcrossing species.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Multiple Maize Reference Genomes Impact the Identification of Variants by Genome-Wide Association Study in a Diverse Inbred Panel

Use of a single reference genome for genome-wide association studies (GWAS) limits the gene space represented to that of a single accession. This limitation can complicate identification and characterization of genes located within presence–absence variations (PAVs). In this study, we present the draft de novo genome assembly of ‘PHJ89’, an ‘Oh43’-type inbred line of maize (Zea mays L.). From three separate reference genome assemblies (‘B73’, ‘PH207’, and PHJ89) that represent the predominant germplasm groups of maize, we generated three separate whole-seedling gene expression profiles and single nucleotide polymorphism (SNP) matrices from a panel of 942 diverse inbred lines. We identified 34,447 (B73), 39,672 (PH207), and 37,436 (PHJ89) transcripts that are not present in the respective reference genome assemblies. Genome-wide association studies were conducted in the 942 inbred panel with both the SNP and expression data values to map Sugarcane mosaic virus (SCMV) resistance. Highlighting the impact of alternative reference genomes in gene discovery, the GWAS results for SCMV resistance with expression values as a surrogate measure of PAV resulted in robust detection of the physical location of a known resistance gene when the B73 reference that contains the gene was used, but not the PH207 reference. This study provides the valuable resource of the Oh43-type PHJ89 genome assembly as well as SNP and expression data for 942 individuals generated from three different reference genomes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Neutrino Scattering: Connections Across Theory and Experiment

In this document drafted by the Neutrino Scattering Theory Experiment Collaboration (NuSTEC), we provide input on the synergies between theoretical and experimental efforts that can provide critical input to the prediction accuracy needed for the forthcoming high-precision neutrino measurements. These efforts involve a wide range of energies and interaction processes, as well as target nuclei and interaction probes. The challenges discussed will be overcome only through the active support of integrated collaboration across strong and electroweak physics from both the nuclear and high energy physics communities.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2019

Data from: Multiple maize reference genomes impact the identification of variants by GWAS in a diverse inbred panel

Use of a single reference genome for genome-wide association studies (GWAS) limits the gene space represented to that of a single accession. This limitation can complicate identification and characterization of genes located within presence/absence variations (PAVs). In this study, we present the draft de novo genome assembly of PHJ89, an Oh43-type inbred line. Using three separate reference genome assemblies (B73, PH207, and PHJ89) that represent the predominant germplasm groups of maize, we generated three separate whole-seedling gene expression profile and single nucleotide polymorphism (SNP) matrices from a panel of 942 diverse inbred lines. We identified 34,447 (B73), 39,672 (PH207), and 37,436 (PHJ89) transcripts that are not present in the respective reference genome assembly. GWAS was conducted in the 942 inbred panel using both the SNP and expression data values to map sugarcane mosaic virus (SCMV) resistance. Highlighting the impact of alternative reference genomes in gene discovery, GWAS results for SCMV resistance using expression values as a surrogate measure of PAV resulted in robust detection of the physical location of a known resistance gene when using the B73 reference that contains the gene, but not when using the PH207 reference. This study provides the valuable resource of the Oh43-type PHJ89 genome assembly as well as SNP and expression data for 942 individuals generated using three different reference genomes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Fourth Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE4)

This article summarizes motivations, organization, and activities of the Fourth Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE4). The WSSSPE series promotes sustainable research software by positively impacting principles and best practices, careers, learning, and credit. This article discusses the code of conduct; the mission and vision statements that were drafted at the workshop and finalized shortly after it; the keynote and idea papers, position papers, experience papers, demos, and lightning talks presented during the workshop; and a panel discussion on best practices. The main part of the article discusses the set of working groups that formed during the meeting, along with contact information for readers who may want to join a group. Lastly, it discusses a survey of the workshop attendees.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2017

Integrating Scientific Argumentation to Improve Undergraduate Writing and Learning in a Global Environmental Change Course

We present a strategy for using scientific argumentation in an early undergraduate laboratory course to teach disciplinary writing practices and to promote critical thinking, knowledge transformation, and understanding of the scientific method. The approach combines targeted writing instruction; data analysis and interpretation; formulation of a hypothesis; and construction of an argument. Students submit and receive feedback on two drafts of two different argumentation essays, providing the opportunity for guided practice. Each written argument is intended to draw on several weeks' course material, including short lectures, discussions, readings, and problem sets. Thus our aim with these writing assignments is to help students synthesize content and concepts, deepening their learning. We have found that this inquiry-based approach to writing engages students in course material, and significantly improves both writing and learning. We observed the greatest improvement among students with the lowest initial scores, suggesting that lower-achieving students benefitted disproportionately from this approach. Students have responded positively to the use of writing in the course, many stating on course evaluations that this is the first time they have received instruction in scientific writing. They have also pointed to a greater 'big-picture' understanding of the course gained through writing. We describe the course and our curriculum, and provide suggestions for implementation as well as rubrics used to evaluate problem sets and student argumentation essays.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2021

Surface and Active Layer Water Chemistry, Teller Road Mile Marker 27, Seward Peninsula, Alaska, 2016-2018

This dataset provides the results of spatial surveys of aqueous geochemistry conducted at Teller Road Site, Seward Peninsula, Alaska. Surface water and soil pore water samples were collected from multiple depth within the active layer at designated Intensive Stations 2 through 9 at the Teller Road MM 27 Site (TL_MM27). Reported analytes include dissolved methane and carbon dioxide, dissolved organic and inorganic carbon, major inorganic anions, and major and minor cations. Samples and measurements were collected from 2016-2018. Specifically, samples were collected in September of 2016, August and September of 2017, and August of 2018. Most of the samples were collected from piezometers installed at various depths within the active layer (70 cm max). A few are surface water grab samples. Data are provided in a single comma separated (.xlsx / .csv) file. One supplemental file is also included. It provides the results of a limited set of analyses (dissolved methane and carbon dioxide and Fe(II)) on surface and soil pore water samples collected at Teller (TL_MM27) and Council (CN_MM71) locations in September 2019. The metadata and data are draft with outstanding clarifications and additions to come. The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a 10-year research effort (2012-2022) 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↗
DOE OSTI2023

CONDENSATION-EVAPORATION MODELING OF DRIFT FROM A MECHANICAL COOLING TOWER

Numerical studyfor investigatingthe phase change behavior of a drift from a mechanical draft cooling tower is presented. A k-ε turbulence model, discrete phase model, species transport equations, and a heat-mass exchange model are solved simultaneouslyto capture the heat and mass transfer effects of a drift condensing and evaporatingeffects. The simulation result is compared to an available real scale test data and its limitation is also discussed. A parametric study is carried out by varying the ambient dry bulb temperature, ambient relative humidity, wind speed, liquid droplet diameter, and the drift amount. It is found that by combining the evaporation and condensation models, a drift phase change phenomena is accurately depicted. A parametric study reveals that wind speed impact is affected by the ambient temperature and the number of liquid droplets and their size play a critical role in the phase change phen

Han, Kai↗
NASA NTRS1966

Slide rule-type color chart predicts reproduced photo tones

Slide rule-type color chart determines the final reproduced gray tones in the production of briefing charts that are photographed in black and white. The chart shows both the color by drafting paint manufacturers name and mixture number, and the gray tone resulting from black and white photographic reproduction.

Griffin, J. D.↗
NASA NTRS1971

Space shuttle propulsion systems on-board checkout and monitoring system development study

Investigations on the fundamental space shuttle propulsion systems program are reported, with emphasis on in-depth reviews of preliminary drafts of the guidelines. The guidelines will be used to incorporate the onboard checkout and monitoring function into the basic design of the propulsion systems and associated interfacing systems. The analysis of checkout and monitoring requirements of the Titan 3 L expandable booster propulsion systems was completed, and the techniques for accomplishing the checkout and monitoring functions were determined. Updating results of the basic study of propulsion system checkout and monitoring is continuing.

Source record↗
NASA NTRS1972

Rotor systems research aircraft predesign study. Volume 3: Predesign report

The features of two aircraft designs were selected to be included in the single RSRA configuration. A study was conducted for further preliminary design and a more detailed analysis of development plans and costs. An analysis was also made of foreseeable technical problems and risks, identification of parallel research which would reduce risks and/or add to the basic capability of the aircraft, and a draft aircraft specification.

Schmidt, S. A.↗