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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 613 records · Page 34
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Platform for Single-Cell Dual RNA Sequencing of Host-Pathogen Interactions

The aim of this project was to advance single-cell RNA-Seq methods toward the establishment of a platform that may be used to simultaneously interrogate the gene expression profiles of mammalian host cells and bacterial pathogens. Existing genetic sequencing methods that measure bulk groups of cells do not account for the heterogeneity of cell-microbe interactions that occur within a complex environment, have limited efficiency, and cannot simultaneously interrogate bacterial sequences. In order to overcome these challenges, separate biochemistry workflows were developed based on a No-So-Random hexamer priming strategy or libraries of targeted molecular probes. Computational tools were developed to facilitate these methods, and feasibility was demonstrated for single-cell RNA-Seq for both bacterial and mammalian transcriptomes. This work supports cross-agency national priorities on addressing the threat of biological pathogens and understanding the role of the microbiome in modulating immunity and susceptibility to infection.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

De Novo Design of Molecular Recognition for Sequence Defined Polymers

The proposed research aims at developing a computational framework that allows the de novo design of sequence defined polymers for molecular recognition. This framework will include the prediction of the 1) accessible backbone conformational space in solution environments for small to medium polymer length and 2) how side chains of different size and functionality can be used to design convergent or divergent receptor configurations. A structural database inspired by the protein database will be build that can be used to construct larger scaffolds based on smaller sequences

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Structural and Dynamical Design Principles for Iron-Sulfur Clusters in Sequence Defined Polymers

This integrated synthetic and computational effort uses sequence defined polymers such as peptoids, and triazines, capable of mimicking a flexible protein environment to control the positioning of side chains around redox cofactors. This strategy will allow modulation of redox properties through both direct and indirect mechanisms. To this end the aim is defined to test the underlying hypothesis: that principles and critical functionalities governing the binding and tuning of naturally occurring electron carrier co-factors can be identified and used to predictably design and synthesize maquettes based on non-natural polymers resulting in new modular biomimetic scaffolds for Electron Transfer Materials. This will be achieved through design and synthesis of ligands that can stabilize iron-sulfur clusters and tune the redox potential based on sequence.

36 MATERIALS SCIENCE↗
DOE OSTI2022

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

Sequence W: Extended Blade (F) This test sequence used an upwind, rigid turbine with a 0° cone angle. The wind speed ranged from 5 m/s to 21 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 pretensioned to 40,000 N. During postprocessing, the probe channels were set to read –99999.99. The standard tip blocks were replaced with blade extensions that created a 5.532-m radius rotor as shown in Appendix A. The extension used the S809 airfoil throughout, and the linear taper of the blade continued along the extension. 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 5.532 m. Throughout this report, references to the blade span are made for the 5.029-m radius, not the 5.532-m radius.

17 WIND ENERGY↗
DOE OSTI2022

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

Sequence E: Yaw Releases (P) This test sequence used a downwind, rigid turbine with a 3.4° cone angle. The wind speeds ranged from 7 m/s to 17 m/s. Initial yaw angles of ±90° were achieved. The blade tip pitch was 3°. The rotor rotated at 72 RPM. Blade and probe pressure measurements were collected. 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. The turbine was positioned at each specified yaw angle. A 30- second data set was collected with the yaw brake engaged. These points used a letter for the last digit beginning with A and proceeding through the alphabet as repeat points were needed. These points were plotted and compared to ascertain the functionality of the instrumentation. The files ending in numbers beginning with 0 and increasing with each repetition represent yaw release points. Once the fixed-position yaw test was complete, the yaw drive was engaged to hold the turbine. The yaw brake was released, and the yaw drive was disabled allowing the turbine to yaw freely. The yaw drive was disabled about 5 seconds into the campaign, and the turbine was allowed to yaw freely for the rest of the 30-second duration. When the yaw drive is disabled, no torque is applied to the motor, and the inertia and yawing force of the nacelle and rotor overcomes the friction and inertia of the yaw gear and motor. The yaw releases were repeated five times at each condition. Four additional campaigns were collected to determine the turbine’s natural yaw error by releasing the brake at 0° yaw error. These file names use the E designation, followed by two digits for wind speed, followed by XXXX, followed by the repetition digit.

17 WIND ENERGY↗
DOE OSTI2022

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

Sequence F: Downwind High Cone (F) This test sequence used a downwind, rigid turbine with an 18° cone angle. The wind speed ranged from 10 m/s to 20 m/s. Excessive inertial loading due to the high cone angle prevented operation at lower wind speeds. Yaw angles of ±20° were achieved. The blade tip pitch was 3°. The rotor rotated at 72 RPM. Blade and probe pressure measurements were collected. 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 was replaced with a shorter bar so the load cell was not installed during this test. However, the teeter link load cell channel was flagged as not applicable by setting the measured values in the data file to -99999.99 N.

17 WIND ENERGY↗
DOE OSTI2022

UAE6 - Wind Tunnel Tests Data - UAE6 - Sequence 7 - Raw Data

Sequence 7: Shroud Operating (P) This test sequence used a downwind, rigid turbine with a 3.4° cone angle. The wind speed ranged from 5 m/s to 25 m/s. Turntable angles from 0° to 30° were achieved, but the yaw error angle was maintained at 0° by adjusting the nacelle yaw. The blade tip pitch was 3°. The rotor rotated at 72 RPM. Blade and probe pressure measurements were collected. 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. An airfoil-shaped aluminum shroud was placed on the tower below the 34% span five-hole probe. It extended below the 91% span five-hole probe. The turntable angle was adjusted to position the shroud at various angles relative to the flow, but the turbine yaw error angle was maintained at 0°. Two additional points were collected where the turntable angle was 0°, and the turbine yaw angle was 20° (71000200) or -20° (710M0200).

17 WIND ENERGY↗
DOE OSTI2022

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

Sequence G: Upwind Teetered (F) Test sequence G used an upwind, teetered turbine with a 0° cone angle. The wind speeds ranged from 5 m/s to 25 m/s. Yaw angles of ±180° were achieved at low wind speeds and angles of ±10° were achieved at the high wind speeds. The blade tip pitch was 3°. The rotor rotated at 72 RPM. Blade and probe pressure measurements were collected.

17 WIND ENERGY↗
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↗