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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 163 records · Page 9
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Transcriptomic and functional analyses uncover a conserved effector driving genotype-dependent virulence in the Sphaerulina musiva-Populus trichocarpa interaction

The introduction of invasive microbes compromises the structure, biodiversity, and function of naïve ecosystems. Sphaerulina musiva, a hemibiotrophic pathogen that causes leaf spot and stem cankers in Populus species, exemplifies an invasive fungal pathogen spread by human activities. However, the genetic mechanisms of pathogenicity and virulence are poorly understood, impeding mitigation strategies. We utilized RNA sequencing to identify fungal effectors linked to stem canker formation, informing the development of future strategies for effective disease management. Our analysis revealed 70 genes differentially expressed at 2 weeks and 110 genes at 3 weeks between inoculated trees and controls. Notably, the gene with the highest expression at 2 weeks and the second highest at 3 weeks was homologous to Extracellular protein 2 (Ecp2). Complementary genome-wide association studies linked sequence polymorphisms in this locus to phenotypic variation in disease severity. Infiltration of S. musiva Ecp2 into Populus trichocarpa leaves induced necrosis in susceptible genotypes. Gene disruption using a CRISPR-Cas9 RNP system resulted in a genotype-dependent reduction of stem canker and disease severity. Tracing the evolutionary history of this effector across the fungal kingdom, we uncovered clade-specific gene-family expansions and orthologs in new species. These findings raise questions about the function and adaptive significance of these gene families in fungal lifestyles. Our study provides the first tractable target for breeding resistant poplar genotypes, addressing the challenges of managing S. musiva and uncovering mechanisms that drive its virulence, and provides deeper insights into the evolutionary dynamics of a conserved small-secreted protein with a diversity of functions.

Sondreli, Kelsey L [Oregon State University]↗
DOE OSTI2024

Chromosome-level genome assemblies and genetic maps reveal heterochiasmy and macrosynteny in endangered Atlantic Acropora

Abstract Background Over their evolutionary history, corals have adapted to sea level rise and increasing ocean temperatures, however, it is unclear how quickly they may respond to rapid change. Genome structure and genetic diversity contained within may highlight their adaptive potential. Results We present chromosome-scale genome assemblies and linkage maps of the critically endangered Atlantic acroporids,Acropora palmataandA. cervicornis. Both assemblies and linkage maps were resolved into 14 chromosomes with their gene content and colinearity. Repeats and chromosome arrangements were largely preserved between the species. The family Acroporidae and the genusAcroporaexhibited many phylogenetically significant gene family expansions. Macrosynteny decreased with phylogenetic distance. Nevertheless, scleractinians shared six of the 21 cnidarian ancestral linkage groups as well as numerous fission and fusion events compared to other distantly related cnidarians. Genetic linkage maps were constructed from oneA. palmatafamily and 16A. cervicornisfamilies using a genotyping array. The consensus maps span 1,013.42 cM and 927.36 cM forA. palmataandA. cervicornis, respectively. Both species exhibited high genome-wide recombination rates (3.04 to 3.53 cM/Mb) and pronounced sex-based differences, known as heterochiasmy, with 2 to 2.5X higher recombination rates estimated in the female maps. Conclusions Together, the chromosome-scale assemblies and genetic maps we present here are the first detailed look at the genomic landscapes of the critically endangered Atlantic acroporids. These data sets revealed that adaptive capacity of Atlantic acroporids is not limited by their recombination rates. The sister species maintain macrosynteny with few genes with high sequence divergence that may act as reproductive barriers between them. In the AtlanticAcropora, hybridization between the two sister species yields an F1 hybrid with limited fertility despite the high levels of macrosynteny and gene colinearity of their genomes. Together, these resources now enable genome-wide association studies and discovery of quantitative trait loci, two tools that can aid in the conservation of these species.

Biotechnology & Applied Microbiology↗
DOE OSTI2021

Improved node culture methods for rapid vegetative propagation of switchgrass (Panicum virgatum L.)

Abstract Background Switchgrass ( Panicum virgatum L.) is an important bioenergy and forage crop. The outcrossing nature of switchgrass makes it infeasible to maintain a genotype through sexual propagation. Current asexual propagation protocols in switchgrass have various limitations. An easy and highly-efficient vegetative propagation method is needed to propagate large natural collections of switchgrass genotypes for genome-wide association studies (GWAS). Results Micropropagation by node culture was found to be a rapid method for vegetative propagation of switchgrass. Bacterial and fungal contamination during node culture is a major cause for cultural failure. Adding the biocide, Plant Preservative Mixture (PPM, 0.2%), and the fungicide, Benomyl (5 mg/l), in the incubation solution after surface sterilization and in the culture medium significantly decreased bacterial and fungal contamination. In addition, “shoot trimming” before subculture had a positive effect on shoot multiplication for most genotypes tested. Using the optimized node culture procedure, we successfully propagated 330 genotypes from a switchgrass GWAS panel in three separate experiments. Large variations in shoot induction efficiency and shoot growth were observed among genotypes. Separately, we developed an in planta node culture method by stimulating the growth of aerial axillary buds into shoots directly on the parent plants, through which rooted plants can be generated within 6 weeks. By circumventing the tissue culture step and avoiding application of exterior hormones, the in planta node culture method is labor- and cost-efficient, easy to master, and has a high success rate. Plants generated by the in planta node culture method are similar to seedlings and can be used directly for various experiments. Conclusions In this study, we optimized a switchgrass node culture protocol by minimizing bacterial and fungal contamination and increasing shoot multiplication. With this improved protocol, we successfully propagated three quarters of the genotypes in a diverse switchgrass GWAS panel. Furthermore, we established a novel and high-throughput in planta node culture method. Together, these methods provide better options for researchers to accelerate vegetative propagation of switchgrass.

Wang, Yongqin↗
DOE OSTI2023

Surface Water Disinfection Byproducts and Organic Matter Characterization Data Associated with: “Disinfection byproducts formed during drinking water treatment reveal an export control point for dissolved organic matter in a subalpine headwater stream”

This dataset is associated with the publication “Disinfection byproducts formed during drinking water treatment reveal an export control point for dissolved organic matter in a subalpine headwater stream” published in Water Research X (Leonard et al. 2022; https://doi.org/10.1016/j.wroa.2022.100144). The associated study analyzed temporal trends from the Town of Crested Butte water treatment facility and synoptic sampling at Coal Creek in Crested Butte, Colorado, US. This work demonstrates how drinking water quality archives combined with synoptic sampling and targeted analyses can be used to identify and understand export control points for dissolved organic matter. This dataset is comprised of one main data folder containing (1) file-level metadata; (2) data dictionary; (3) metadata and international geo-sample number (IGSN) mapping file; (4) dissolved organic carbon (DOC), ultraviolet absorbance at 254 nanometers (UV254), total nitrogen (TN), and specific ultraviolet absorbance (SUVA) data; (5) disinfection bioproduct formation potential (DBP-FP) data; (6) readme; (7) methods codes; (8) water collection protocol; (9) folder of high resolution characterization of organic matter via 12 Tesla Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) through the Environmental Molecular Sciences Laboratory (EMSL; https://www.pnnl.gov/environmental-molecular-sciences-laboratory); and (10) folder of excitation emissions matrix (EEM) spectra. The FTICR folder contains a file of DOC (measured as non-purgeable organic carbon; NPOC) used for FTICR sample preparation. The FTICR folder also contains three subfolders: one subfolder containing the raw .xml data files, one containing the processed data, and the other containing instructions for using Formularity (https://omics.pnl.gov/software/formularity) and an R script to process the data based on the user's specific needs. All files are .csv, .pdf, .dat, .R, .ref, or .xml

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Yield, chemistry, and TEA/LCA data for 84 switchgrass (Panicum virgatum L.) variants

Switchgrass yield, chemistry, technoeconomic assessment (TEA), and life cycle assessment (LCA) data referenced in the manuscript "Economics and Sustainability impacts of yield and composition variation in bioenergy crops: Panicum virgatum L.", Happs, et. al. (manuscript in revision at ACS Sustainable Chemistry & Engineering). These results are based on analysis of yield data generated from a set of switchgrass common garden experiments established by the Center for Bioenergy Innovation (CBI; https://cbi.ornl.gov/). These data include estimates of commercial-scale yields and characterization of biomass chemistry (fermentable carbohydrate fraction) for 84 different switchgrass variants from a genome-wide association study population, as well as estimates of minimum fuel selling price and various life-cycle footprint metrics for cellulosic ethanol produced from that switchgrass biomass.

switchgrass, biofuels↗
DOE OSTI2023

Expanded genetic variation (SNP) and phenomics (image based) dataset for Populus trichocarpa

The image dataset consists of 11,791 images representing 1,219 genotypes of Populus trichocarpa undergoing in planta regeneration. Genotypes were imaged with a median of four weekly timepoints and a median of two replicates each. A representative and diverse subset of 249 images was annotated using the IDEAS annotation interface (ideas.eecs.oregonstate.edu) and these annotated images were used to train a deep semantic segmentation model (PSPNet), which was deployed for inference over the entire dataset. Annotated classes include specific stages of regeneration (callus and shoot) in addition to unregenerated plant material and background. Statistics of relative tissue area were extracted and used for downstream genetic association mapping in a genome-wide association study. The SNP dataset consists of over 40 million single-nucleotide polymorphisms across 1,323 wild accessions of Populus trichocarpa

09 BIOMASS FUELS↗
DOE OSTI2026

Populus_trichocarpa_Breeding_Population_SNPs

These data are from the manuscript “Application of Genomic Prediction in a Populus trichocarpa Breeding Program”, by Brian J. Stanton, David Macaya-Sanz, Chanaka Roshan Abeyratne, David Kainer, Kathy Haiby, Austin Himes, Carlos Gantz, Gerald A. Tuskan, and Stephen P. DiFazio. The data are based on genome resequencing to approximately 10X depth on two collections of Populus trichocarpa trees from Oregon, Washington, California, and British Columbia. The first collection consists of 293 genets collected by Poplar Innovations LLC for a breeding program. The second collection consists of 961 trees collected for the purpose of genome-wide association studies. These genets were sequenced using short, paired-end Illumina sequence reads (Chhetri et al. 2019). Reads were aligned to the P. trichocarpa ′Stettler-14′ reference (Hofmeister et al. 2020), with minor modifications to correct mis-assemblies (Zhou et al. 2020), and variants were called as per methods described in (Abeyratne et al. 2023). Identified variants were filtered using GATK’s VariantFiltration tool (DePristo et al. 2011), with filter expression flag set to “AF < 0.01 || AF > 0.99 || QD < 10.0 || ExcessHet > 20.0 || FS > 10.0 || MQ < 58.0”. SNPs with severe departures from Hardy−Weinberg expectations (exact-test p< 0.01) were also removed using vcftools --hwe flag (Danecek et al. 2011), resulting in 15,627,211 bi-allelic SNPs. The data included here consist of 141,903 high quality bi-allelic genome-wide SNPs obtained by further filtering the original SNP dataset using vcftools with flags --maf 0.05, --max-maf 0.95, --max-missing 0.95, --min-meanDP 10.75, --max-meanDP 43.00, --thin 2000. Collectively, these filtering parameters removed SNPs with 1) a minor allele frequency ≤ 0.05; 2) proportion of missing data for individual loci exceeding 5%; 3) sequencing depth more than 2X mean-depth or less than 0.5X mean-depth; or 4) a distance of

09 BIOMASS FUELS↗
DOE OSTI2023

Few-Shot Learning Enables Population-Scale Analysis of Leaf Traits in Populus trichocarpa

Plant phenotyping is typically a time-consuming and expensive endeavor, requiring large groups of researchers to meticulously measure biologically relevant plant traits, and is the main bottleneck in understanding plant adaptation and the genetic architecture underlying complex traits at population scale. In this work, we address these challenges by leveraging few-shot learning with convolutional neural networks to segment the leaf body and visible venation of 2,906 Populus trichocarpa leaf images obtained in the field. In contrast to previous methods, our approach (a) does not require experimental or image preprocessing, (b) uses the raw RGB images at full resolution, and (c) requires very few samples for training (e.g., just 8 images for vein segmentation). Traits relating to leaf morphology and vein topology are extracted from the resulting segmentations using traditional open-source image-processing tools, validated using real-world physical measurements, and used to conduct a genome-wide association study to identify genes controlling the traits. In this way, the current work is designed to provide the plant phenotyping community with (a) methods for fast and accurate image-based feature extraction that require minimal training data and (b) a new population-scale dataset, including 68 different leaf phenotypes, for domain scientists and machine learning researchers. All of the few-shot learning code, data, and results are made publicly available.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1973

Monthly and annual percentage levels of wind speed differences computed by using FPS-16 radar/Jimsphere wind profile data from Cape Kennedy, Florida

The percentage levels of wind speed differences are presented computed from sequential FPS-16 radar/Jimsphere wind profiles. The results are based on monthly profiles obtained from December 1964 to July 1970 at Cape Kennedy, Florida. The profile sequences contain a series of three to ten Jimspheres released at approximately 1.5-hour intervals. The results given are the persistence analysis of wind speed difference at 1.5-hour intervals to a maximum time interval of 12 hours. The monthly percentage of wind speed differences and the annual percentage of wind speed differences are tabulated. The percentage levels are based on the scalar wind speed changes calculated over an altitude interval of approximately 50 meters and printed out every 25 meters as a function of initial wind speed within each five-kilometer layer from near sea level to 20 km. In addition, analyses were made of the wind speed difference for the 0.2 to 1 km layer as an aid for studies associated with take-off and landing of the space shuttle.

Susko, M.↗
NASA NTRS1974

Determination of left ventricular size and shape

Significant advances have occurred over the past 15 years in the ability to measure ventricular dimensions. Angiocardiography still remains the most reliable method for overall determination of chamber size and shape and serves as a standard for calibration or comparison for newer methods. Improvements in the use of radiographic methods over the next few years are anticipated with more extensive use of multiplane studies associated with repeated injections of improved contrast materials that produce fewer physiological effects or with substances that adhere to the endocardial surfaces. It is also anticipated that existing methods for automatically obtaining dimensional information from X rays will be continued and improved.

Sandler, H.↗
NASA NTRS1978

A study of the IC 5146 dark cloud complex

The IC 5146 dark cloud complex has been studied in the infrared in order to identify and study associated young stellar objects. Most of the objects detected in the survey appear to be field stars, predominantly late-type giants. Three young objects were detected in the survey: the B0 star BD +46 deg 3474, the Ae star BD +46 deg 3471, and a previously unidentified object which appears to be a heavily obscured FU Orionis star. The properties of the last two objects are examined in detail, and an attempt is made to produce reasonable models for them. It is suggested that FU Orionis stars are binaries, and some consequences of this model are described. Photometry of the brighter stars in the IC 5146 cluster has been used to establish a distance to the cluster of 900 + or - 100 pc.

Elias, J. H.↗
NASA NTRS1970

Design problems of small turbomachinery

Advanced design and testing techniques developed at NASA Lewis to achieve high efficiency in small turbomachines are described. Small radial and axial turbines and compressors were built for space power systems and associated studies at the Lewis Research Center. A six stage axial compressor of 3.5 inches diameter and axial turbines of 5 and 8.5 inches diameter were included. Radial turbines and compressors ranged from 3.5 to 6 inches. Topics discussed include maximum efficiency as a function of speed, the effect of compressibility on passage size, the use of quasi-orthogonals to calculate cross-channel velocity gradients, a design point velocity diagram study for axial turbines, and estimating off-design performance. Special turbine instruments and calibration procedures were developed to test compressors and turbines, to determine Reynolds and size number effects clearance, specific speed effects, and compressor performance. Laboratory tests conducted to study system operation and shaft and bearing motions are also reviewed.

Rohlik, H. E.↗
NASA NTRS1980

Severe storms forecast systems

Two research tasks are described: (1) the improvement and enhancement of an existing mesoscale numerical simulation system, and (2) numerical diagnostic studies associated with an individual case of severe storm development (April 10, 1979 in the Red River Valley of Texas and Oklahoma).

Kaplan, M.↗
NASA NTRS1990

Intraocular pressure, retinal vascular, and visual acuity changes during 48 hours of 10-deg head-down tilt

Intraocular pressures, retinal vascular diameters, and visual acuities of nine men, were repeatedly measured while the subjects were tilted 10 deg head-down for 48 h and while they were seated before (baseline), and after the tilt. An immediate increase in intraocular pressure, measured by pneumatonometer was recorded when subjects assumed the head-down position, and diurnal variations in intraocular pressures were observed for the 48 h. The initial and final head-down intraocular pressures were not significantly different. However, when subjects resumed the sitting position, intraocular pressures fell below the initial sitting values. Computer image analysis of the retinal vasculature detected a 6 percent and 2 percent reduction in the caliber of arteries and veins, respectively, as compared with sitting baseline values. No changes in visual acuity were documented during the 48 h of head-down tilt. The data suggest that the choroidal blood reservoir increases in volume over 48 h at continuous head-down position with a compensatory decrease in aqueous volume. These findings may explain intraocular pressure changes noted in astronauts during previous space missions and in studies associated with change in body position.

Mader, Thomas H.↗
NASA NTRS1991

An initial investigation into methods of computing transonic aerodynamic sensitivity coefficients

Continuing studies associated with the development of the quasi-analytical (QA) sensitivity method for three dimensional transonic flow about wings are presented. Furthermore, initial results using the quasi-analytical approach were obtained and compared to those computed using the finite difference (FD) approach. The basic goals achieved were: (1) carrying out various debugging operations pertaining to the quasi-analytical method; (2) addition of section design variables to the sensitivity equation in the form of multiple right hand sides; (3) reconfiguring the analysis/sensitivity package in order to facilitate the execution of analysis/FD/QA test cases; and (4) enhancing the display of output data to allow careful examination of the results and to permit various comparisons of sensitivity derivatives obtained using the FC/QA methods to be conducted easily and quickly. In addition to discussing the above goals, the results of executing subcritical and supercritical test cases are presented.

Carlson, Leland A.↗
NASA NTRS1996

Protoplanetary Formation and the FU Orionis Outburst

The following three publications which reference the above grant from the NASA Origins of Solar Systems program are attached and form the final technical report for this project. The research involved comparisons of the spectral energy distributions of FU Orionis objects with theoretical models and associated studies of the structure of the outbursting accretion disks, as well as related studies on the effects of magnetic fields in disks, which will lead in the future to models of FU Orionis outbursts which include the effects of magnetic fields. The project was renewed under a new grant NAGW-4456, entitled 'Effects of FU Orionis Outbursts on Protoplanetary Disks'. Work now being prepared for publication deals more specifically with the issue of the effects of the outbursts on protoplanetary formation. Models of the spectral energy distribution of FU Orionis stars. A simple model of a buoyant magnetic dynamo in accretion disks and a numerical study of magnetic buoyancy in an accretion disk have been submitted.

Bodenheimer, P. H.↗
NASA NTRS2005

GLOBAL REFERENCE ATMOSPHERIC MODELS FOR AEROASSIST APPLICATIONS

Aeroassist is a broad category of advanced transportation technology encompassing aerocapture, aerobraking, aeroentry, precision landing, hazard detection and avoidance, and aerogravity assist. The eight destinations in the Solar System with sufficient atmosphere to enable aeroassist technology are Venus, Earth, Mars, Jupiter, Saturn, Uranus, Neptune, and Saturn's moon Titan. Engineering-level atmospheric models for five of these targets - Earth, Mars, Titan, Neptune, and Venus - have been developed at NASA's Marshall Space Flight Center. These models are useful as tools in mission planning and systems analysis studies associated with aeroassist applications. The series of models is collectively named the Global Reference Atmospheric Model or GRAM series. An important capability of all the models in the GRAM series is their ability to simulate quasi-random perturbations for Monte Carlo analysis in developing guidance, navigation and control algorithms, for aerothermal design, and for other applications sensitive to atmospheric variability. Recent example applications are discussed.

Duvall, Aleta↗