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NASA NTRS1984

Processes and subdivisions in diogenites, a multivariate statistical analysis

Multivariate statistical techniques used on diogenite orthopyroxene analyses show the relationships that occur within diogenites and the two orthopyroxenite components (class I and II) in the polymict diogenite Garland. Cluster analysis shows that only Peckelsheim is similar to Garland class I (Fe-rich) and the other diogenites resemble Garland class II. The unique diogenite Y 75032 may be related to type I by fractionation. Factor analysis confirms the subdivision and shows that Fe does not correlate with the weakly incompatible elements across the entire pyroxene composition range, indicating that igneous fractionation is not the process controlling total diogenite composition variation. The occurrence of two groups of diogenites is interpreted as the result of sampling or mixing of two main sequences of orthopyroxene cumulates with slightly different compositions.

Harriott, T. A.↗

NASA NTRS1986

The association of chromospheric and coronal phenomena with the evolution of the quiet sun magnetic fields

Using daily full-disk magnetograms and He I 10830 spectroheliograms to study the count and surface distribution of ephemeral regions over the solar cycle, Harvey (1985) concluded that the small dark structures seen in 10830, thought to correspond to X-ray bright points, were more often associated with magnetic bipoles that appeared to result from an encounter of already existing opposite polarity magentic flux than with emerging small magnetic bipoles (ephemeral regions). Such encounters would be more likely to occur in areas of mixed polarity. The fractional area of the sun covered by mixed polarity fields varies anti-correlated with the solar cycle leading to a possible explanation for the 180 degrees out of phase solar cycle variation of X-ray bright points. To establish the validity of this suggestion, a detailed study of time-sequence magnetic field, He I wavelength 10830, Ha, C IV, and Si II observations of selected areas of the quiet sun was initiated about 2 years ago. The preliminary results of this study are reported.

Harvey, Karen L.↗

DOE OSTI2017

Patterns of genomic variation in Coho salmon following reintroduction to the interior Columbia River

Abstract Coho salmon were extirpated in the mid‐20th century from the interior reaches of the Columbia River but were reintroduced with relatively abundant source stocks from the lower Columbia River near the Pacific coast. Reintroduction of Coho salmon to the interior Columbia River (Wenatchee River) using lower river stocks placed selective pressures on the new colonizers due to substantial differences with their original habitat such as migration distance and navigation of six additional hydropower dams. We used restriction site‐associated DNA sequencing ( RAD ‐seq) to genotype 5,392 SNP s in reintroduced Coho salmon in the Wenatchee River over four generations to test for signals of temporal structure and adaptive variation. Temporal genetic structure among the three broodlines of reintroduced fish was evident among the initial return years (2000, 2001, and 2002) and their descendants, which indicated levels of reproductive isolation among broodlines. Signals of adaptive variation were detected from multiple outlier tests and identified candidate genes for further study. This study illustrated that genetic variation and structure of reintroduced populations are likely to reflect source stocks for multiple generations but may shift over time once established in nature.

Campbell, Nathan R.↗

DOE OSTI2021

Unmanned aircraft system (UAS) detection and assessment via temporal intensity aliasing

A method and system for temporal frequency analysis for identification of unmanned aircraft systems. The method includes obtaining a sequence of video image frames and providing a pixel from an output frame of the video; generating a fluctuating pixel value vector; examining the fluctuating pixel value vector over a period of time; obtaining the frequency information present in the pixel fluctuations; summing the frequency coefficients for the vectorized pixel values from the fluctuating pixel value vector; obtaining an image representing a two dimensional space based on the summed center frequency coefficients; generating a series of still frames equal to a summation of the center frequency coefficients for pixel variations; and combining the temporal information into spatial locations in a matrix to provide a single image containing the spatial and temporal information present in the sequence of video image frame.

Woo, Bryana Lynn↗

DOE OSTI2023

Unmanned aircraft system (UAS) detection and assessment via temporal intensity aliasing

Woo, Bryana Lynn↗

DOE OSTI2018

Signatures of host specialization and a recent transposable element burst in the dynamic one-speed genome of the fungal barley powdery mildew pathogen

BACKGROUND: Powdery mildews are biotrophic pathogenic fungi infecting a number of economically important plants. The grass powdery mildew, Blumeria graminis , has become a model organism to study host specialization of obligate biotrophic fungal pathogens. We resolved the large-scale genomic architecture of B. graminis forma specialis hordei (Bgh) to explore the potential influence of its genome organization on the co-evolutionary process with its host plant, barley ( Hordeum vulgare ). RESULTS: The near-chromosome level assemblies of the Bgh reference isolate DH14 and one of the most diversified isolates, RACE1, enabled a comparative analysis of these haploid genomes, which are highly enriched with transposable elements (TEs). We found largely retained genome synteny and gene repertoires, yet detected copy number variation (CNV) of secretion signal peptide-containing protein-coding genes ( SPs ) and locally disrupted synteny blocks. Genes coding for sequence-related SPs are often locally clustered, but neither the SPs nor the TEs reside preferentially in genomic regions with unique features. Extended comparative analysis with different host-specific B. graminis formae speciales revealed the existence of a core suite of SPs , but also isolate-specific SP sets as well as congruence of SP CNV and phylogenetic relationship. We further detected evidence for a recent, lineage-specific expansion of TEs in the Bgh genome. CONCLUSIONS: The characteristics of the Bgh genome (largely retained synteny, CNV of SP genes, recently proliferated TEs and a lack of significant compartmentalization) are consistent with a "one-speed" genome that differs in its architecture and (co-)evolutionary pattern from the "two-speed" genomes reported for several other filamentous phytopathogens.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Sodium azide mutagenesis induces a unique pattern of mutations

The nature and effect of mutations are of fundamental importance to the evolutionary process. The generation of mutations with mutagens has also played important roles in genetics. Applications of mutagens include dissecting the genetic basis of trait variation, inducing desirable traits in crops, and understanding the nature of genetic load. Previous studies of sodium azide-induced mutations have reported single nucleotide variants (SNVs) found in individual genes. To characterize the nature of mutations induced by sodium azide, we analyze whole-genome sequencing (WGS) of 11 barley lines derived from sodium azide mutagenesis, where all lines were selected for diminution of plant fitness owing to induced mutations. We contrast observed mutagen-induced variants with those found in standing variation in WGS of 13 barley landraces. Here, we report indels that are two orders of magnitude more abundant than expected based on nominal mutation rates. We found induced SNVs are very specific, with C → T changes occurring in a context followed by another C on the same strand (or the reverse complement). The codons most affected by the mutagen include the sodium azide-specific CC motif (or the reverse complement), resulting in a handful of amino acid changes and few stop codons. The specific nature of induced mutations suggests that mutagens could be chosen based on experimental goals. Sodium azide would not be ideal for gene knockouts but will create many missense mutations with more subtle effects on protein function.

Genetics & Heredity↗

DOE OSTI2026

Sampling Microbial Dynamics in the Salish Sea Estuary: Evaluating Methods to Capture Cyanobacteria and Cyanophage

Introduction: Picocyanobacteria from the genera Prochlorococcus and Synechococcus thrive across the globe in aquatic environments, have relatively small genomes, and have growth dynamics regulated by both viral interactions and abiotic conditions, making them excellent model organisms for exploring host-pathogencoevolution. Methods: We developed and refined methods to sample and sequence cyanobacteria, cyanophages, and measured features of their abiotic environment. Results: The protocol described herein can successfully discriminate large-cell eukaryotic organisms, but size fractionation of picocyanobacteria appears to be affected by the presence of free DNA, multicellular structures, and abundant tycheposons. Our preferred final protocol from this exploratory effort included a combination of in-line and single vacuum flask filtrations, which reduced filtration processing time by over threefold in some cases compared to other tested methods, such as a fully in-line sequence or in-site filtrations. We successfully extracted an average of approximately 400–1200 ng for all filter fractions, with some variations between kits. Discussion: The protocol described herein can successfully discriminate large-cell eukaryotic organisms, but size fractionation of picocyanobacteria appears to be affected by the presence of free DNA, multicellular structures, and abundant tycheposons.

Salish Sea↗

DOE OSTI2026

The biogeography of soil and airborne fungi in the Southwestern USA in relation to climate and vegetation

To assess how fungal dispersal might respond to climate change, we examined how climate and geography influence the regional distribution of fungi in soil and air. Specifically, we hypothesized that neighboring fungal communities should be more similar than distant communities (i.e. spatially autocorrelated) and that fungal dispersal should be more limited in soil than in air. We collected soil and air samples from 60 sites across five states in the Southwestern USA. Then, we sequenced the ITS2 region to identify fungal taxa in each sample. Next, we used distance-based redundancy analysis to partition variation in fungal community composition between climate variables and spatial structure. Fungi were indeed spatially autocorrelated. Moreover, precipitation, maximum vapor pressure deficit, and soil moisture were significantly related to fungal community composition in soils. In comparison, only precipitation was significantly related to community composition in the air. After accounting for climate, the strength of spatial autocorrelation did not differ significantly in soilborne versus airborne fungi. Dispersal limitation was evident in soilborne fungi at short distances (<100 km) and was not observed at any distance in airborne fungi. Altogether, climate may influence which fungal taxa are present in soil and air, and fungi could feasibly wind disperse over regional scales.

54 ENVIRONMENTAL SCIENCES↗

NASA NTRS1980

A 5.57 hr modulation in the optical counterpart of 2S 1822-371

A periodic 5.57 hr modulation has been observed in the optical counterpart of the X-ray source 2S 1822-371. Two alternative periods are consistent with the data: P = 0.232114d and P = 0.232191d, with statistical uncertainties of 0.000015d in each case. Minimum light occurred at JD 2,444,105.668 + or - 0.005. The amplitude of the modulation is about 1 mag, independent of UBV color, and no variability exceeding the 2% level other than the 5.57 hr effect is found on time scales down to a few seconds. The light curve of the star can be understood in terms of a highly inclined close binary system which contains a relatively large, luminous accretion disk that is periodically occulted by a companion star and an associated gas stream. On the assumption that the companion is a main-sequence star, the distance of the system is found to be more than 600 pc, based on the absence of color variations commensurate with the 5.57 hr intensity cycle.

Mason, K. O.↗

NASA NTRS1985

The Pongola structure of southeastern Africa - The world's oldest preserved rift?

Rocks of the Pongola Supergroup form an elongate belt in the Archean Kaapvaal Craton of southern Africa. Because these rocks exhibit many features that are characteristic of rocks deposited in continental rifts, including rapid lateral variations in thickness and character of sediments, volcanic rocks that are bimodal in silica content, coarse, basement derived conglomerates and thick sequences of shallow water sedimentary facies associations, it is suggested that the Pongola Supergroup was deposited in such a rift. The age of these rocks (approximately 3.0 Ga) makes the Pongola structure the world's oldest well-preserved rift so far recognized, and comparison of the Pongola Rift with other rifts formed more recently in earth history reveals striking similarities, suggesting that the processes that formed this rift were not significantly different from those that form continental rifts today.

Burke, K.↗

NASA NTRSDate not supplied

Simulating a Low-Weight Encoding of the Fermi-Hubbard Model Feedback and Support with QAOA

Recent work [1] has proposed a compact fermion-to-qubit mapping for the Fermi-Hubbard model (FHM), potentially lowering the overhead needed to simulate such a system on quantum hardware. In prior work [2], we numerically investigated how well a quantum annealer could prepare ground states of the FHM encoded using the resource-efficient mapping. In order to compare these results to gate-model systems, we turn to a QAOA-style approach and replace the annealing schedule with both Trotterizations thereof and also more general Hamiltonian-variational ansatze based on the terms of the mapped FH Hamiltonian. We investigate the achievable ground state fidelities of these gate sequences, consider various optimizations of the ansatze structure, and offer resource estimations of the optimized QAOA protocols for near-term hardware.

quantum computing↗

DOE OSTI2024

Exon disruptive variants in Populus trichocarpa associated with wood properties exhibit distinct gene expression patterns

Abstract Forest trees may harbor naturally occurring exon disruptive variants (DVs) in their gene sequences, which potentially impact important ecological and economic phenotypic traits. However, the abundance and molecular regulation of these variants remain largely unexplored. Here, 24,420 DVs were identified by screening 1014Populus trichocarpafull genomes. The identified DVs were predominantly heterozygous with allelic frequencies below 5% (only 26% of DVs had frequencies greater than 5%). Using common garden‐grown trees, DVs were assessed for gene expression variation in the developing xylem, revealing that their gene expression can be significantly altered, particularly for homozygous DVs (in the range of 27%–38% of cases depending on the studied common garden). DVs were further investigated for their correlations with 13 wood quality traits, revealing that, among the 148 discovered DV associations, 15 correlated with more than one wood property and six genes had more than one DV in their coding sequences associated with wood traits. Approximately one‐third of DVs correlated with wood property variation also showed significant gene expression variation, confirming their non‐spurious impact. These findings offer potential avenues for targeted introduction of homozygous mutations using tree biotechnology, and while the exact mechanisms by which DVs may directly influence wood formation remain to be unraveled, this study lays the groundwork for further investigation.

Genetics & Heredity↗

DOE OSTI2024

Genome-scale analysis of interactions between genetic perturbations and natural variation

Interactions between genetic perturbations and segregating loci can cause perturbations to show different phenotypic effects across genetically distinct individuals. To study these interactions on a genome scale in many individuals, we used combinatorial DNA barcode sequencing to measure the fitness effects of 8046 CRISPRi perturbations targeting 1721 distinct genes in 169 yeast cross progeny (or segregants). We identified 460 genes whose perturbation has different effects across segregants. Several factors caused perturbations to show variable effects, including baseline segregant fitness, the mean effect of a perturbation across segregants, and interacting loci. We mapped 234 interacting loci and found four hub loci that interact with many different perturbations. Perturbations that interact with a given hub exhibit similar epistatic relationships with the hub and show enrichment for cellular processes that may mediate these interactions. These results suggest that an individual’s response to perturbations is shaped by a network of perturbation-locus interactions that cannot be measured by approaches that examine perturbations or natural variation alone.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2017

Toward understanding the B[e] phenomenon. VI. Nature and spectral variations of HD 85567

We report the results of high-resolution (R ∼ 80,000) spectroscopic observations of the emission-line object HD 85567, which has been classified as an FS CMa type object or a pre-main-sequence star. The main goal is to put more constraints on the object’s fundamental parameters, as well as on its nature and evolutionary state. Absorption lines in the spectrum of HD 85567 were found to be similar to those of mid-B-type dwarfs and correspond to the following fundamental parameters: T{sub eff} = 15,000 ± 500 K, vsin i=31±3 km s{sup −1}, and log g∼4.0. The interstellar extinction, A{sub V} = 0.50 ± 0.02 mag, was measured using the strengths of some diffuse interstellar bands. We also obtained UBV(RI){sub c} images of a 10′ × 10′ region around the object. Photometry of projectionally close stars was used to derive an interstellar extinction law in this direction and resulted in a distance of 1300 ± 100 pc to the object and a luminosity of log L/L{sub ⊙} = 3.3 ± 0.2. We found no significant radial velocity variations of the absorption lines in the spectra of HD 85567 obtained during two-month-long periods of time in 2012 and 2015. Our analysis of the spectroscopic and photometric data available for the star led us to a conclusion that it cannot be a pre-main-sequence Herbig Ae/Be star. We argue that the circumstellar gas and dust were produced during the object’s evolution as most likely a binary system, which contains an undetected secondary component and is unlikely to be a merger product.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2016

Draft Assembly of Elite Inbred Line PH207 Provides Insights into Genomic and Transcriptome Diversity in Maize

Intense artificial selection over the last 100 years has produced elite maize (Zea mays) inbred lines that combine to produce high-yielding hybrids. To further our understanding of how genome and transcriptome variation contribute to the production of high-yielding hybrids, we generated a draft genome assembly of the inbred line PH207 to complement and compare with the existing B73 reference sequence. B73 is a founder of the Stiff Stalk germplasm pool, while PH207 is a founder of Iodent germplasm, both of which have contributed substantially to the production of temperate commercial maize and are combined to make heterotic hybrids. Comparison of these two assemblies revealed over 2500 genes present in only one of the two genotypes and 136 gene families that have undergone extensive expansion or contraction. Transcriptome profiling revealed extensive expression variation, with as many as 10,564 differentially expressed transcripts and 7128 transcripts expressed in only one of the two genotypes in a single tissue. Genotype-specific genes were more likely to have tissue/condition-specific expression and lower transcript abundance. The availability of a high-quality genome assembly for the elite maize inbred PH207 expands our knowledge of the breadth of natural genome and transcriptome variation in elite maize inbred lines across heterotic pools.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2017

Data from: Draft assembly of elite inbred line PH207 provides insights into genomic and transcriptome diversity in maize

Intense artificial selection over the last 100 years has produced elite maize (Zea mays) inbred lines that combine to produce high-yielding hybrids. To further our understanding of how genome and transcriptome variation contribute to the production of high-yielding hybrids, we generated a draft genome assembly of the inbred line PH207 to complement and compare with the existing B73 reference sequence. B73 is a founder of the Stiff Stalk germplasm pool, while PH207 is a founder of Iodent germplasm, both of which have contributed substantially to the production of temperate commercial maize and are combined to make heterotic hybrids. Comparison of these two assemblies revealed over 2,500 genes present in only one of the two genotypes and 136 gene families that have undergone extensive expansion or contraction. Transcriptome profiling revealed extensive expression variation, with as many as 10,564 differentially expressed transcripts and 7,128 transcripts expressed in only one of the two genotypes in a single tissue. Genotype-specific genes were more likely to have tissue/condition-specific expression and lower transcript abundance. The availability of a high-quality genome assembly for the elite maize inbred PH207 expands our knowledge of the breadth of natural genome and transcriptome variation in elite maize inbred lines across heterotic pools.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1987

Crystallization behavior of a melt-spun Fe-Ni based steel

Whether Fe-Ni-based alloys solidify with a bcc or fcc structure has been observed by many investigators to be a stronger function of kinetics and undercooling than strictly free-energy minimization. Such behavior has been observed in an Fe(52.8)Ni(28.7)Al(3.4)Ti(6.1)B(9.0) alloy. The alloy was cast as ribbons about 45 microns thick using a dual free-jet variation of chillbock melt spinning against a Cu wheel. Optical, X-ray, and electron analyses of the as-cast and annealed ribbons were performed. A microstructure of at least four layers containing combinations of ecc, bcc, and amorphous phases in differing proportions was observed in the as-cast ribbon. The midthickness layer had the most unusual features, containing fcc grains about 75 nm in size encompassing spherulitic regions as large as 15 microns comprised of fcc grains about 25 nm in size. The crystallization sequence responsible for the as-cast microstructure is discussed in terms of the competition between the formation of bcc and fcc phases as influenced by undercooling, recalescence, and variations in cooling rate experienced by the as-cast ribbon.

Michal, G. M.↗