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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 397 records · Page 22
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

UAE6 - Wind Tunnel Tests Data - UAE6 - Sequence M - Raw Data

Sequence M: Transition Fixed (P) Test sequence M used an upwind, rigid turbine with a 0° cone angle. The wind speed ranged from 5 m/s to 15 m/s. Yaw angles ranged from 0° to 90°. The blade tip pitch was 3°. The rotor rotated at 72 RPM. Blade pressure measurements were collected. The five-hole probes were removed and the plugs were installed. Plastic tape 0.03-mm-thick was used to smooth the interface between the plugs and the blade. The teeter dampers were replaced with rigid links, and these two channels were flagged as not applicable by setting the measured values in the data file to –99999.99 Nm. The teeter link load cell was pre-tensioned to 40,000 N. During post-processing, the probe channels were set to read –99999.99. Zigzag tape was installed near the leading edge of the instrumented blade on both the upper and lower surfaces as described in Appendix K. In addition to the standard 30-second campaigns, yaw sweeps were done at 7 m/s and 10 m/s. These 90-second campaigns were collected while the yaw drive rotated the turbine 90° at a rate of 1°/s. The file names for these campaigns use the letter designation, followed by two digits for wind speed, followed by YSU, followed by 00.

17 WIND ENERGY↗
DOE OSTI2022

UAE6 - Wind Tunnel Tests Data - UAE6 - Sequence V - Raw Data

Sequence V: Tip Plate (F) This test sequence used an upwind, rigid turbine with a 0° cone angle. The wind speed ranged from 5 m/s to 25 m/s, and the yaw angle was held at 0°. The blade pitch angle was 3°. The rotor rotated at 72 RPM. Blade pressure measurements were collected. The five-hole probes were removed and the plugs were installed. Plastic tape 0.03-mm-thick was used to smooth the interface between the plugs and the blade. The teeter dampers were replaced with rigid links, and these two channels were flagged as not applicable by setting the measured values in the data file to –99999.99 Nm. The teeter link load cell was pre-tensioned to 40,000 N. During post-processing, the probe channels were set to read -99999.99. The standard tip blocks were replaced with a tip plate to simulate the effect of an undeployed tip-mounted aerodynamic brake as shown in Appendix A. Note that the blade radius was not changed during post-processing so the pressure tap locations are at the same radial location, but the reference to 30% represents 30% of 5.029 m, not 4.943 m. Throughout this report, references to the blade span are made for the 5.029- m radius, not the 4.943-m radius.

17 WIND ENERGY↗
DOE OSTI2022

UAE6 - Wind Tunnel Tests Data - UAE6 - Sequence X - Raw Data

Sequence X: Elevated RPM (F) This test sequence used an upwind, rigid turbine with a 0° cone angle. The wind speed ranged from 5 m/s to 12 m/s, and yaw angles of ±30° were obtained. The blade pitch angle was 3°. The rotor rotated at 90 RPM. Blade pressure measurements were collected. The five-hole probes were removed and the plugs were installed. Plastic tape 0.03-mm-thick was used to smooth the interface between the plugs and the blade. The teeter dampers were replaced with rigid links, and these two channels were flagged as not applicable by setting the measured values in the data file to –99999.99 Nm. The teeter link load cell was pre-tensioned to 40,000 N. During post-processing, the probe channels were set to read -99999.99. As described in Appendix F, the hydrostatic correction derived for operation at 72 RPM was applied to these data.

17 WIND ENERGY↗
DOE OSTI2023

KBase Narrative - Complete Genome Sequence of Acidovorax temperans strain LMJ

We have isolated a new strain of Acidovorax temperans strain LMJ (hereafter called strain LMJ) from a contaminated Tris-Acetate-Phosphate (TAP) medium plate of a green micro-alga Chlamydomonas reinhardtii strain LMJ.SG0182 (a Chlamydomonas Library project (CLiP) strain). We sequenced the whole genome of the strain LMJ using the PacBio Sequel II technology and have submitted it to NCBI along with the SRA and PacBio methylation motif data. We present the whole genome sequence of this strain that offer insights into its coding and non-coding genes and its nearest taxonomic neighbors.

Mitra, Mautusi↗
DOE OSTI2024

KBase Narrative - Genome sequences of four bacterial strains isolated from organofluorine enrichment cultures

These genome announcement narratives are associated with the manuscript "Genome sequences of four bacterial strains isolated from organofluorine enrichment cultures" by Jennifer L. Goff, Chris Hahn, Rebecca A. Ingrassia, Chanistha Tiyapun, Gray G. Waldschmidt, Emma R. Smith, Miranda N. Marini, Olga Shevchenko, and Julia A. Maresca Assembeled genome sequences for all four genomes are available on this page and in the individual genome announcement narratives listed below. All methodological details can be found within the individual narratives.

Goff, Jennifer↗
DOE OSTI2024

KBase Narrative - Complete genome sequence of a novel Microbacterium sp. strain Clip185.

We have isolated a new species of Microbacterium, an Actinobacterium. We have temporarily named this bacterium as Microbacterium sp. strain Clip185 (hereafter called strain Clip185) from a contaminated Tris-Acetate-Phosphate (TAP) medium culture plate of a green micro-alga Chlamydomonas reinhardtii strain LMJ.RY0402.185141 (a Chlamydomonas Library project CLiP strain). We sequenced the whole genome of strain Clip185 using the PacBio Sequel II Continuous Long Read technology and have submitted it to NCBI along with the SRA and PacBio methylation motif data. Additionally, we have submitted the PacBio methylome to REBASE, Ref#35996. We present the whole genome sequence of this new Microbacterium species that offers insights into its coding and non-coding genes and its nearest taxonomic neighbors.

Mitra, Mautusi↗
DOE OSTI2025

Complete genome sequence of Sphingobium yanoikuyae strain CC4533

We have isolated a new strain of Sphingobium yanoikuyae , which belongs to the class Alphaproteobacteria, order Sphingomonadales, and family Sphingomonadaceae. This carotenoid-producing strain is capable of degrading xenobiotics and is tolerant to toxic levels of six heavy metals. We have designated the newly isolated strain of S. yanoikuyae as S. yanoikuyae strain CC4533 (hereafter called strain CC4533) because it was isolated from a contaminated Tris-Acetate-Phosphate (TAP) medium culture plate of a green micro-alga Chlamydomonas reinhardtii wild type strain CC4533. We sequenced the whole genome of strain CC4533 using the PacBio Sequel II Continuous Long Read technology and have submitted it to NCBI along with the SRA and PacBio methylation motif data. Additionally, we have submitted the PacBio methylome to REBASE, Ref#35996. We present the whole genome sequence of S. yanoikuyae strain CC4533 that offers insights into its coding and non-coding genes and its nearest taxonomic neighbors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Genome Extraction from Shotgun Metagenome Sequence Data

Uncultivated Bacteria and Archaea comprise the vast majority of species on Earth, but obtaining their genomes directly from the environment, using shotgun sequencing, has only recently become possible. To realize the hope of capturing Earth’s microbial genetic complement, technologies that accelerate recovery of high-quality genomes are necessary. We present a series of analysis steps and data products for the extraction of high quality metagenome-assembled genomes (MAGs) from microbiomes using the U.S. Department of Energy Systems Biology Knowledgebase (KBase) platform (http://www.kbase.us/). In KBase, the process is end-to-end, allowing a user to go from the initial sequencing reads all the way through to MAG genomes, which can then be analyzed with other KBase capabilities such as phylogenetic placement, functional assignment, metabolic modeling, pangenome functional profiling, RNA-Seq, and others. While portions of such capabilities are individually available from other resources, the combination of the intuitive usability, data interoperability, and integration of tools in a freely available compute resource makes KBase a uniquely powerful platform for obtaining MAGs from microbiomes. While this workflow offers tools for each of the key steps in the genome extraction process, it also provides a scaffold that can be easily extended, with additional MAG recovery and analysis tools, via the KBase SDK (Software Development Kit).

Chivian, Dylan↗
DOE OSTI2025

Next-generation sequencing dataset of genome-scale CRISPRi in Synechococcus sp. PCC 7002 across seven conditions

A 33,298-member sgRNA library developed for Synechococus sp. PCC 7002 was screened with two replicates across seven growth conditions and sequenced with Illumina NextSeq (paired end, 2x150 bp) for a total of ~700M reads. The original plasmid library and the library after transformation into a dCas9-containing and dCas9-absent strain were also sequenced as a reference for initial sgRNA abundance.

genome- wide screens environmental acclimation spe↗
DOE OSTI2025

Section-level genome sequencing and comparative genomics of Aspergillus sections Cavernicolus and Usti.

The genus Aspergillus is diverse, including species of industrial importance, human pathogens, plant pests, and model organisms. Aspergillus includes species from sections Usti and Cavernicolus, which until recently were joined in section Usti, but have now been proposed to be non-monophyletic and were split by section Nidulantes, Aenei and Raperi. To learn more about these sections, we have sequenced the genomes of 13 Aspergillus species from section Cavernicolus (A. cavernicola, A. californicus, and A. egyptiacus), section Usti (A. carlsbadensis, A. germanicus, A. granulosus, A. heterothallicus, A. insuetus, A. keveii, A. lucknowensis, A. pseudodeflectus and A. pseudoustus), and section Nidulantes (A. quadrilineatus, previously A. tetrazonus). We compared these genomes with 16 additional species from Aspergillus to explore their genetic diversity, based on their genome content, repeat-induced point mutations (RIPs), transposable elements, carbohydrate-active enzyme (CAZyme) profile, growth on plant polysaccharides, and secondary metabolite gene clusters (SMGCs). All analyses support the split of section Usti and provide additional insights: Analyses of genes found only in single species show that these constitute genes which appear to be involved in adaptation to new carbon sources, regulation to fit new niches, and bioactive compounds for competitive advantages, suggesting that these support species differentiation in Aspergillus species. Sections Usti and Cavernicolus have mainly unique SMGCs. Section Usti contains very large and information-rich genomes, an expansion partially driven by CAZymes, as section Usti contains the most CAZyme-rich species seen in genus Aspergillus. Section Usti is clearly an underutilized source of plant biomass degraders and shows great potential as industrial enzyme producers. Citation: Nybo JL, Vesth TC, Theobald S, Frisvad JC, Larsen TO, Kjaerboelling I, Rothschild-Mancinelli K, Lyhne EK, Barry K, Clum A, Yoshinaga Y, Ledsgaard L, Daum C, Lipzen A, Kuo A, Riley R, Mondo S, LaButti K, Haridas S, Pangalinan J, Salamov AA, Simmons BA, Magnuson JK, Chen J, Drula E, Henrissat B, Wiebenga A, Lubbers RJM, Müller A, dos Santos Gomes AC, Mäkelä MR, Stajich JE, Grigoriev IV, Mortensen UH, de Vries RP, Baker SE, Andersen MR (2025). Section-level genome sequencing and comparative genomics of Aspergillus sections Cavernicolus and Usti. Studies in Mycology 111: 101-114. doi: 10.3114/sim.2025.111.03.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Sequencing and Analysis of the Sex Determination Region of Populus trichocarpa

The ages and sizes of a sex-determination region (SDR) are difficult to determine in non-model species. Due to the lack of recombination and enrichment of repetitive elements in SDRs, the quality of assembly with short sequencing reads is universally low. Unique features present in the SDRs help provide clues about how SDRs are established and how they evolve in the absence of recombination. Several Populus species have been reported with a male heterogametic configuration of sex (XX/XY system) mapped on chromosome 19, but the exact location of the SDR has been inconsistent among species, and thus far, none of these SDRs has been fully assembled in a genomic context. Here we identify the Y-SDR from a Y-linked contig directly from a long-read PacBio assembly of a Populus trichocarpa male individual. We also identified homologous gene sequences in the SDR of P. trichocarpa and the SDR of the W chromosome in Salix purpurea. We show that inverted repeats (IRs) found in the Y-SDR and the W-SDR are lineage-specific. We hypothesize that, although the two IRs are derived from the same orthologous gene within each species, they likely have independent evolutionary histories. Furthermore, the truncated inverted repeats in P. trichocarpa may code for small RNAs that target the homologous gene for RNA-directed DNA methylation. These findings support the hypothesis that diverse sex-determining systems may be achieved through similar evolutionary pathways, thereby providing a possible mechanism to explain the lability of sex-determination systems in plants in general.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Genome Sequence and Analysis of the Flavinogenic Yeast Candida membranifaciens IST 626

The ascomycetous yeast Candida membranifaciens has been isolated from diverse habitats, including humans, insects, and environmental sources, exhibiting a remarkable ability to use different carbon sources that include pentoses, melibiose, and inulin. In this study, we isolated four C. membranifaciens strains from soil and investigated their potential to overproduce riboflavin. C. membranifaciens IST 626 was found to produce the highest concentrations of riboflavin. The volumetric production of this vitamin was higher when C. membranifaciens IST 626 cells were cultured in a commercial medium without iron and when xylose was the available carbon source compared to the same basal medium with glucose. Supplementation of the growth medium with 2 g/L glycine favored the metabolization of xylose, leading to biomass increase and consequent enhancement of riboflavin volumetric production that reached 120 mg/L after 216 h of cultivation. To gain new insights into the molecular basis of riboflavin production and carbon source utilization in this species, the first annotated genome sequence of C. membranifaciens is reported in this article, as well as the result of a comparative genomic analysis with other relevant yeast species. A total of 5619 genes were predicted to be present in C. membranifaciens IST 626 genome sequence (11.5 Mbp). Among them are genes involved in riboflavin biosynthesis, iron homeostasis, and sugar uptake and metabolism. This work put forward C. membranifaciens IST 626 as a riboflavin overproducer and provides valuable molecular data for future development of superior producing strains capable of using the wide range of carbon sources, which is a characteristic trait of the species.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Bubble Relaxation Dynamics in Homopolymer DNA Sequences

Understanding the inherent timescales of large bubbles in DNA is critical to a thorough comprehension of its physicochemical characteristics, as well as their potential role on helix opening and biological function. In this work, we employ the coarse-grained Peyrard–Bishop–Dauxois model of DNA to study relaxation dynamics of large bubbles in homopolymer DNA, using simulations up to the microsecond time scale. By studying energy autocorrelation functions of relatively large bubbles inserted into thermalised DNA molecules, we extract characteristic relaxation times from the equilibration process for both adenine–thymine (AT) and guanine–cytosine (GC) homopolymers. Bubbles of different amplitudes and widths are investigated through extensive statistics and appropriate fittings of their relaxation. Characteristic relaxation times increase with bubble amplitude and width. We show that, within the model, relaxation times are two orders of magnitude longer in GC sequences than in AT sequences. Overall, our results confirm that large bubbles leave a lasting impact on the molecule’s dynamics, for times between 0.5–500 ns depending on the homopolymer type and bubble shape, thus clearly affecting long-time evolutions of the molecule.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Time-sequence Spectroscopy of Epsilon CrA: The 518 nm Mg i Triplet Region Analyzed with Broadening Functions

High-resolution spectroscopic observations of the W UMa-type binary ϵ CrA obtained as a time-monitoring sequence on four full and four partial nights within two weeks have been used to derive orbital elements of the system and discuss the validity of the Lucy model for description of the radial-velocity data. The observations had more extensive temporal coverage and better quality than similar time-sequence observations of the contact binary AW UMa. The two binaries share several physical properties and show very similar deviations from the Lucy model: the primary component is a rapidly rotating star almost unaffected by the presence of the secondary component, while the latter is embedded in a complex gas flow and appears to have its own rotation-velocity field, in contradiction to the model. The spectroscopic mass ratio is found to be larger than the one derived from the light-curve analysis, as in many other W UMa-type binaries, but the discrepancy for ϵ CrA is relatively minor, much smaller than for AW UMa. The presence of the complex velocity flows contradicting the assumption of solid-body rotation suggests a necessity of modification to the Lucy model, possibly along the lines outlined by Stȩpień in his concept of energy transfer between the binary components.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Tidal Circularization of Binaries by Resonance Locking. I. The Importance of the Pre-main Sequence

Although tidal dissipation in binary stars has been studied for over a century, theoretical predictions have yet to match the observed properties of binary populations. This work quantitatively examines the recent proposal of tidal circularization by resonance locking, where tidal dissipation arises from resonances between the star’s natural oscillation frequencies and harmonics of the orbital frequency, and where resonances are “locked” for an extended period of time due to concurrent stellar evolution. We focus on tidal resonances with axi-symmetric gravity modes, and examine binaries with primary masses from one to two solar masses. We find that orbital evolution via resonance locking occurs primarily during the star’s pre-main-sequence phase, with the main-sequence phase contributing negligibly. Resonance locking, ignoring nonlinearity, can circularize binaries with peri-center distances out to ∼10 stellar radii, corresponding to circular periods of ∼4–6 days. However, we find resonantly excited gravity modes will become nonlinear in stellar cores, which prevents them from reaching their full, linear amplitudes. We estimate that such a “saturated resonance lock” reduces the circularization period by about a third, but resonance locking remains much more effective than the cumulative actions of equilibrium tides. In a companion paper, we examine recent binary data to compare against theory.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

A Blueprint for the Milky Way’s Stellar Populations. IV. A String of Pearls—the Galactic Starburst Sequence

We continue our series of papers on phase-space distributions of stars in the Milky Way based on photometrically derived metallicities and Gaia astrometry, with a focus on the halo-disk interface in the local volume. To exploit various photometric databases, we develop a method of empirically calibrating synthetic stellar spectra based on a comparison with observations of stellar sequences and individual stars in the Sloan Digital Sky Survey, the SkyMapper Sky Survey, and the Pan-STARRS1 surveys, overcoming band-specific corrections employed in our previous work. In addition, photometric zero-point corrections are derived to provide an internally consistent photometric system with a spatially uniform metallicity zero-point. Using our phase-space diagrams, we find a remarkably narrow sequence in the rotational velocity (v $\phi$ ) versus metallicity ([Fe/H]) space for a sample of high proper-motion stars (>25 mas yr -1 ), which runs along Gaia Sausage/Enceladus (GSE) and the Splash substructures and is linked to the disk, spanning nearly 2 dex in [Fe/H]. Notably, a rapid increase of v $\phi$ from a nearly zero net rotation to ~180 km s -1 in a narrow metallicity interval (-0.6 ≲ [Fe/H] ≲ -0.4) suggests that some of these stars emerged quickly on a short gas-depletion timescale. Through measurements of a scale height and length, we argue that these stars are distinct from those heated dynamically by mergers. This chain of high proper-motion stars provides additional support for recent discoveries suggesting that a starburst took place when the young Milky Way encountered the gas-rich GSE progenitor, which eventually led to the settling of metal-enriched gas onto the disk.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

Draft genome sequencing and assembly of Favolaschia claudopus CIRM-BRFM 2984 isolated from oak limbs

Favolaschia claudopus, a wood-inhabiting basidiomycete of the Mycenaceae family, is considered an invasive species that has recently spread from Oceania to Europe. The CIRM-BRFM 2984 strain of this fungus was originally isolated from a basidiome collected from the fallen limb of a decayed oak tree in Southwest France. The genome sequence of this strain shared characteristics with other Mycenaceae species, including a large genome size and enriched content of protein-coding genes. The genome sequence provided here will facilitate further investigation on the factors that contribute to the successful global dissemination of F. claudopus.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Deconvolute individual genomes from metagenome sequences through short read clustering

Metagenome assembly from short next-generation sequencing data is a challenging process due to its large scale and computational complexity. Clustering short reads by species before assembly offers a unique opportunity for parallel downstream assembly of genomes with individualized optimization. However, current read clustering methods suffer either false negative (under-clustering) or false positive (over-clustering) problems. Here we extended our previous read clustering software, SpaRC, by exploiting statistics derived from multiple samples in a dataset to reduce the under-clustering problem. Using synthetic and real-world datasets we demonstrated that this method has the potential to cluster almost all of the short reads from genomes with sufficient sequencing coverage. The improved read clustering in turn leads to improved downstream genome assembly quality.

59 BASIC BIOLOGICAL SCIENCES↗