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At least 541 records · Page 30
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Large-scale genome sequencing of mycorrhizal fungi provides insights into the early evolution of symbiotic traits

Mycorrhizal fungi are mutualists that play crucial roles in nutrient acquisition in terrestrial ecosystems. Mycorrhizal symbioses arose repeatedly across multiple lineages of Mucoromycotina, Ascomycota, and Basidiomycota. Considerable variation exists in the capacity of mycorrhizal fungi to acquire carbon from soil organic matter. Here, we present a combined analysis of 135 fungal genomes from 73 saprotrophic, endophytic and pathogenic species, and 62 mycorrhizal species, including 29 new mycorrhizal genomes. This study samples ecologically dominant fungal guilds for which there were previously no symbiotic genomes available, including ectomycorrhizal Russulales, Thelephorales and Cantharellales. Our analyses show that transitions from saprotrophy to symbiosis involve (1) widespread losses of degrading enzymes acting on lignin and cellulose, (2) co-option of genes present in saprotrophic ancestors to fulfill new symbiotic functions, (3) diversification of novel, lineage-specific symbiosis-induced genes, (4) proliferation of transposable elements and (5) divergent genetic innovations underlying the convergent origins of the ectomycorrhizal guild.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

A genomic region associated with iteroparous spawning phenology is linked with age‐at‐maturity in female steelhead trout

Abstract Age‐at‐maturity and iteroparity are two life history variations of steelhead trout ( Oncorhynchus mykiss ) that are believed to increase population resilience and stability. While repeat‐spawning individuals are thought to have historically made up a substantial portion of the reproductive population in the Columbia River and the majority of females still attempt outmigration as kelts, return rates of repeat‐spawner are low throughout the basin and below 1% for the furthest migrating stocks. Notably, outmigrating adults exhibit variation in rematuration phenology, displaying either “consecutive” (reproduce immediately the following season) or “skip” (delay spawning for future seasons) spawning patterns. Here, we use low coverage whole genome sequencing of consecutive versus skip spawning female Columbia River steelhead from two populations to test for genomic differences between these two iteroparous phenotypes. We identified genomic regions on several chromosomes which were associated with the phenology of iteroparity, including a region on chromosome 25 containing two genes, estradiol receptor beta ( ER β) and glycoprotein hormone beta‐5 ( GPHB5 ), which, in mammals, are estrogen‐sensitive and expressed in reproductive tissues. Allele frequencies in this ER β/ GPHB5 region differed among female steelhead of different age at maturity, but not males. These genes also shared an island of linkage disequilibrium with the SIX6 gene, 600Kbp away on the same chromosome, a region of known association with age‐at‐maturity. These observations contribute to growing evidence that age‐at‐maturity and the phenology of iteroparity are determined by overlapping physiological processes and genetic pathways.

Willis, Stuart↗
NASA NTRS1974

Correlations and linkages between the sun and the earth's atmosphere: Needed measurements and observations

A summary of needed measurements and observations is reported to identify the sequence of processes leading from change in solar input to change in tropospheric circulation and weather. Changes in the solar electromagnetic radiation have to be carefully monitored since variations over the solar cycle are small (less than one percent). It is suggested that changes in the ionization at the Pfotzer maximum could influence the formation of thunderstorms by changing the electric potential gradient. This could be checked by measuring the global atmospheric electric field. As an example of spacecraft observations, a worldwide distribution plot of nocturnal thunderstorms compiled from OSO-5 data shown; no obvious correlation with solar data had been found, but the time span of the data is rather limited and more sophisticated observation techniques could be used. Continuous and careful monitoring is recommended of the input of electromagnetic and particle radiation into the earth's atmosphere ozone distributions in the region above 30 km, and wind systems in the mesosphere and lower thermosphere. In addition, special phenomena suspected to be important in the causal chain, such as cirrus cloud formation at high latitudes and thunderstorm activity, should be monitored on a global basis.

Kellogg, W. W.↗
NASA NTRS1979

Refractory-element-rich inclusions in CM meteorites

Refractory-element-rich inclusions of a variety of types occur in CM meteorites. Based on detailed study of Murchison and more limited investigations of Murray, Nogoya, Cold Bokkeveld and Mighei, the most common of these inclusions are small spinel-hibonite bodies rimmed with diopside. Bulk chemical compositions are estimated to be approximately 67% Al2O3, 21% MgO, 5.5% CaO, 5.5% TiO2, and 1% SiO2. Although this chemical composition does not agree closely with current theoretically predicted compositions of early condensate assemblages, the inclusions have many features which suggest that they are indeed early condensates. These include texture, mineralogical composition, sequence of minerals and magnesium isotopic composition of hibonite. The CM refractory inclusions exhibit several differences from those observed in Allende and other CV meteorites. These probably record variations in time, place or physical conditions of origin for the two cases.

Macdougall, J. D.↗
NASA NTRS1994

Imaging spectroscopy of the solar CO lines at 4.67 microns

We analyze spatially and temporally resolved spectra of the fundamental vibration-rotation transitions of carbon monoxide (CO) in the solar spectrum at 4.67 micrometers. Our observations imply that, in the quiet Sun, spatial variations in CO intensity are largely dynamical in nature, reinforcing the suggestion that dynamical effects play a key role in the formation of the dark CO cores. Time sequences of resolved spectra exhibit mainly 3 minute power in line-core intensity but mainly a 5 minute period in Doppler shift. The weak 7-6 R68 line shows normal Evershed flow in the penumbra of a sunspot; we find evidence for the onset of inverse Evershed flow in the strong 3-2 R14 line. Spectra at the limb indicate that 3-2 R14 emission extends approximately 360 km beyond the continuum limb.

Uitenbroek, Han↗
NASA NTRS2004

Mesosphere-Stratosphere Coupling: Implications for Climate Variability and Trends

A key aspect of this project is the establishment of a causal link from circulation anomalies in the lower mesosphere and stratopause region downward through the stratosphere to the troposphere. The observational link for stratospheric sudden warmings and surface climate is fairly clear. However, our understanding of the dynamics is incomplete. We have been making significant progress in the area of dynamical mechanisms by which circulation anomalies in the stratosphere affect the troposphere. We are trying to understand the details and sequence of events that occur when a middle atmosphere (wind) anomaly propagates downward to near the tropopause. The wind anomaly could be caused by a warming or solar variations in the low-latitude stratopause region, or could have other causes. The observations show a picture that is consistent with a circulation anomaly that descends to the tropopause region, and can be detected as low as the mid-troposphere. Processes near the stratopause in the tropics appear to be important precursors to the wintertime development of the northern polar vortex. This may affect significantly our understanding of the process by which low-latitude wind anomalies in the low mesosphere and upper stratosphere evolve through the winter and affect the polar vortex.

Baldwin, Mark P.↗
DOE OSTI2023

Energy variation of double K -shell photoionization of Ne

Herein we report on an experimental and theoretical study of double K-shell photoionization of Ne over the 2.3–8.5 keV x-ray energy range. The ratio of double-to-single K-shell photoionization cross sections was determined experimentally by measuring the relative rates of the KK–KL 2,3 L 2,3 ( 2 D) Auger hypersatellite and the K–L 2,3 L 2,3 ( 1 D) diagram Auger transitions. By scaling the hypersatellite-diagram Auger-electron ratios to KK/K cross-section ratios, comparison was made with theoretical cross-section ratios of He-like Ne 8+ determined by the R matrix with pseudostates method. The experimental Ne and theoretical Ne 8+ cross-section ratios show similar variations with energy, but the experimental ratios systematically exceed the calculated ratios and also show a lower threshold energy for double K-shell photoionization onset compared to the computed Ne 8+ threshold. The discrepancy is attributed to effects of L-shell electrons not included in the He-like Ne 8+ calculations. Quantified scaling with nuclear charge Z along the He-like isoelectronic sequence indicates that the measured 10-electron Z = 10 double K-shell photoionization cross section behaves like the computed He-like Z = 8.9 cross section, suggesting an effective nuclear screening parameter of s L =1.1 by the additional eight outer L-shell electrons. Experimental results for the energy variations of Auger electron transitions from other multielectron hole states are also discussed.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2017

Nearly a decade-long repeatable seasonal diversity patterns of bacterioplankton communities in the eutrophic Lake Donghu (Wuhan, China)

Uncovering which environmental factors have the greatest influence on community diversity patterns and how ecological processes govern community turnover are key questions related to understanding community assembly mechanisms. Although we have good understanding of plant and animal community assembly, the mechanisms regulating diversity patterns of aquatic bacterial communities in lake ecosystems remains poorly understood. Here we present nearly a decade-long time-series study of bacterioplankton communities from the eutrophic Lake Donghu (Wuhan, China) using 16S rRNA gene amplicon sequencing. We found strong repeatable seasonal patterns for the overall community, common (detected in more than 50% samples) and dominant bacterial taxa (relative abundance > 1%). Moreover, community composition tracked the seasonal temperature gradient, indicating that temperature is an important environmental factor controlling observed diversity patterns. Total phosphorus also contributed significantly to the seasonal shifts in bacterioplankton composition. However, any spatial pattern across the main lake areas was overwhelmed by temporal variability in this eutrophic lake system. Phylogenetic analysis further indicated that 75%-82% of community turnover was governed by homogeneous selection, suggesting that the bacterioplankton communities are mainly controlled by niche-based processes. However, dominant niches available within seasons might be occupied by similar combinations of bacterial taxa with modest dispersal rates throughout this lake system. This study gives us important insights into community assembly and seasonal turnover of lake bacterioplankton, it may be also useful to predict temporal patterns of other planktonic communities.

16S rRNA amplicon sequencing↗
DOE OSTI2022

16S and ITS Amplicon Sequencing Fastq files and metadata from PARCHED Panama Tropical Forest soils, 2019-2020,

Model projections predict tropical forests will experience longer periods of drought and more intense precipitation cycles under a changing climate. Such transitions have implications for structure-function relationships within microbial communities. We examine how chronic drying might reshape prokaryotic and fungal communities across four lowland forests in Panama with a wide variation in mean annual precipitation and soil fertility. Four sites were established across a 1000 mm span in mean annual precipitation (2335 to 3300 mm). We expected microbial communities at sites with lower MAP to be less sensitive to chronic drying than sites with higher MAP; while fungal communities to be more resistant to disturbance than prokaryotes. At each location, partial throughfall exclusion structures were established over 10 x 10 m plots to reduce direct precipitation input. Raw demultiplexed sequences (bacteria, archaea, fungal) from soil samples taken from PARCHED Panama Tropical Forest throughfall exclusion experiments. Files that contain 16S are sequences from prokaryotes, ITS indicates sequences from fungi. Compressed fastq files are contained in Field_PARCHED_ITS_fastq_2020.zip, Field_PARCHED_ITS_fastq_2019.zip, Field_PARCHED_16S_fastq_2020.zip, Field_PARCHED_16S_fastq_2019.zip.There are four sites across the isthmus of Panama, each with 4 control and 4 exclusion plots. Throughfall exclusion shelters were built to intercept 50% of throughfall precipitation that hits the soil. Samples were taken on May 2019 and Jan 2020 from 0-10 cm and 10-20 cm depth approximately 9 and 18 months after shelter installation. Metadata and sample IDs for fastq files for 2019 sampling are within Field_PARCHED_Metadata_2019_ITS.csv and Field_PARCHED_Metadata_2019_16S.csv. The metadata for both 16S and ITS fastq files for January 2020 is included in Field_PARCHED_Metadata_2020.csv. No data processing or QA/QC was done on the raw data. Data processing example provided in R notebook file.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

A phase-field diffraction model for thermo-hydro-mechanical propagating fractures

This paper introduces a novel diffraction based thermo-hydraulic–mechanical (THM) model for fracture propagation using a phase-field fracture (PFF) approach. The key innovation of the THM-PFF model lies in its integrated treatment of four solution variables—displacements, phase-field, pressure, and temperature—each governed by a combination of conservation of momentum (mechanics problem), a variational inequality (constrained minimization problem), mass conservation (pressure problem), and energy conservation (temperature problem). This leads to a new formulation of a coupled variational inequality system. A major advancement is the development of an extended fixed-stress algorithm, where displacements, phase-field, pressures, and temperatures are solved in a staggered sequence. An important aspect of this work is the global coupling of pressures and temperatures across the domain using diffraction systems, with diffraction coefficients defined by material parameters weighted by the diffusive phase-field variable. To ensure robust local mass conservation, we employ enriched Galerkin finite elements (EG) for both pressure and temperature diffraction equations. By enriching the continuous Galerkin basis functions with discontinuous piecewise constants, EG accurately represents solution and parameter discontinuities while preserving local mass and energy conservation—crucial aspects for THM problems and realistic behavior. Moreover, the use of a predictor–corrector local mesh adaptivity scheme is employed, allowing the model to handle small phase-field length-scale parameters while maintaining high numerical accuracy and reasonable computational cost. Furthermore, these new model and algorithmic developments represent significant advances in the field and have been substantiated through rigorous numerical tests.

Diffraction systems↗
DOE OSTI2021

Distribution of Bound and Free Water in Anatomical Fractions of Pine Residues and Corn Stover as a Function of Biological Degradation

Biomass quality is influenced by water’s abundance, distribution, and status in relation to other chemical species within the polymer matrix. Water interacts with polymers that make up the cell walls, and these interactions govern the physical and chemical changes that occur during the storage and preprocessing of biomass feedstocks. Time-domain nuclear magnetic resonance (TD-NMR) was employed to explore variations in the physical constraints of water within the lignocellulosic microstructure in distinct anatomical fractions of biomass and as a function of biological degradation. The Carr–Purcell–Meiboom–Gill sequence, when combined with knowledge of the chemical composition and physical structure of pine residues and corn stover anatomical fractions, gives an accurate measurement of the bound and free water. In this work, the impacts of storage and biological degradation were investigated to elucidate changes in the status and distribution of water within distinct plant tissues. We also investigate how degradation during storage affects water interactions in different pine residues (e.g., bark, branch, and needle) and corn stover (e.g., cob, leaf, and stalk) anatomical fractions using transverse relaxation times (T2). As demonstrated herein, TD-NMR provides quantitative data on lignocellulosic biomass–water interactions within anatomical fractions, which can further aid in the investigation of preprocessing effects on feedstock quality. Our findings suggest that biological heating enhances biomass–water interactions at the cellular and macromolecular scale. In addition, analysis of three-dimensional scanning electron microscopy reconstructions indicates that surface roughness wavelengths align with microscale roughness, suggesting that pine forestry residue and corn stover particles have primarily hydrophobic exterior surfaces. Furthermore, this study offers multiscale insights into understanding the microstructure, wettability, and chemical environment that dictate diffusion, enzyme access, and recalcitrance of lignocellulosic biomass.

09 BIOMASS FUELS↗
DOE OSTI2019

Variational quantum state diagonalization

Abstract Variational hybrid quantum-classical algorithms are promising candidates for near-term implementation on quantum computers. In these algorithms, a quantum computer evaluates the cost of a gate sequence (with speedup over classical cost evaluation), and a classical computer uses this information to adjust the parameters of the gate sequence. Here we present such an algorithm for quantum state diagonalization. State diagonalization has applications in condensed matter physics (e.g., entanglement spectroscopy) as well as in machine learning (e.g., principal component analysis). For a quantum state ρ and gate sequence U , our cost function quantifies how far $$U\rho U^\dagger$$ U ρ U † is from being diagonal. We introduce short-depth quantum circuits to quantify our cost. Minimizing this cost returns a gate sequence that approximately diagonalizes ρ . One can then read out approximations of the largest eigenvalues, and the associated eigenvectors, of ρ . As a proof-of-principle, we implement our algorithm on Rigetti’s quantum computer to diagonalize one-qubit states and on a simulator to find the entanglement spectrum of the Heisenberg model ground state.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Assessment of the errors of high-fidelity two-qubit gates in silicon quantum dots

Achieving high-fidelity entangling operations between qubits consistently is essential for the performance of multi-qubit systems. Solid-state platforms are particularly exposed to errors arising from materials-induced variability between qubits, which leads to performance inconsistencies. Here we study the errors in a spin qubit processor, tying them to their physical origins. We use this knowledge to demonstrate consistent and repeatable operation with above 99% fidelity of two-qubit gates in the technologically important silicon metal-oxide-semiconductor quantum dot platform. Analysis of the physical errors and fidelities in multiple devices over extended periods allows us to ensure that we capture the variation and the most common error types. Physical error sources include the slow nuclear and electrical noise on single qubits and contextual noise that depends on the applied control sequence. Furthermore, we investigate the impact of qubit design, feedback systems and robust gate design to inform the design of future scalable, high-fidelity control strategies. Our results highlight both the capabilities and challenges for the scaling-up of silicon spin-based qubits into full-scale quantum processors.

Quantum dots↗
DOE OSTI2024

Comprehensive SNP Data for 1,323 GWAS Population in Populus trichocarpa and Combined Annotation Files for P. trichocarpa v3.0 and v3.1

The VCF dataset includes genetic variations found in 1,323 Populus trichocarpa genotypes, providing valuable information for scientists studying plant genetics. Researchers have generated this dataset using whole-genome DNA short-read sequencing on the Illumina Genome Analyzer, HiSeq 2000, and HiSeq 2500 platforms. This sequencing effort ensured a minimum expected sequencing depth of 15×. The dataset comprises more than 9.7 million single nucleotide polymorphisms (SNPs) and indel variants. The combined annotation files are derived from P. trichocarpa v3.0 and v3.1. We merged these files to create a comprehensive annotation file used for GWAS analysis. In total, 38,830 genes overlapped between the two versions. For overlapping genes, we defined the start as the smaller and the end as the larger among the two versions to increase the likelihood of locating candidate genetic loci. Additionally, we included 2,505 unique genes from v3.0 and 4,120 unique genes from v3.1, resulting in a total of 45,455 genes in the updated annotation file.

09 BIOMASS FUELS↗
NASA NTRS1988

Petrology and physical conditions of metamorphism of calcsilicate rocks from low- to high-grade transition area, Dharmapuri District, Tamil Nadu

Calc-silicate rocks comprising quartz, plagioclase, diopside, sphene, scapolite, grossularite-andradite and wollastonite occur as lensoid enclaves within the greasy migmatitic and charnockitic gneisses of the Archaean amphibolite- to granulite-facies transition zone in Dharmapuri district, Tamil Nadu. The calc-silicate rocks are characterized by the absence of K-feldspar and primary calcite, presence of large modal quartz and plagioclase and formation of secondary garnet and zoisite rims around scapolite and wollastonite. The mineral distributions suggest compositional layering. The chemical composition and mineralogy of the calc-silicate rocks indicate that they were derived from impure silica-rich calcareous sediments whose composition is similar to that of pelite-limestone mixtures. From the mineral assemblages the temperature, pressure and fluid composition during metamorphism were estimated. The observed mineral reaction sequences require a range of X sub CO2 values demonstrating that an initially CO2-rich metamorphic fluid evolved with time towards considerably more H2O-rich compositions. These variations in fluid composition suggest that there were sources of water-rich fluids external to the calc-silicate rocks and that mixing of these fluids with those of calc-silicate rocks was important in controlling fluid composition in calc-silicate rocks and some adjacent rock types as well.

Narayana, B. L.↗
NASA NTRS2006

A Numerical and Experimental Study of Compression-Loaded Composite Panels With Cutouts

Results from a numerical and experimental study on the effects of laminate orthotropy and circular cutout size on the response of compression-loaded composite curved panels are presented. Several 60-in-radius composite panels with four different laminate configurations were tested with cutout diameters that range from 10% to 60% of the panel width. Finite-element analyses were performed for each panel in order to identify the effects boundary conditions, measured initial geometric imperfections and thickness variations had on the nonlinear and buckling behavior of the panels. The compression-loaded panels considered herein exhibited two separate types of behavior depending on the laminate stacking sequence and cutout size. More specifically, some of the panels exhibited the classical snap-through type buckling response; however, some of the panels exhibited a monotonically increasing stable response and achieved compressive loads in excess of twice the predicted linear bifurcation buckling load. In general, the finite-element analyses were able to predict accurately the nonlinear response and buckling loads of the panels and the prebuckling and postbuckling out-of-plane deformations and strains.

Thornburgh, Robert P.↗
NASA NTRS2016

LO Peg: Surface Differential Rotation, Flares, and Spot-Topographic Evolution

Using the wealth of ∼24 yr multiband data, we present an in-depth study of the star-spot cycles, surface differential rotations (SDR), optical flares, evolution of star-spot distributions, and coronal activities on the surface of young, single, main-sequence, ultrafast rotator LO Peg. From the long-term V-band photometry, we derive rotational period of LO Peg to be 0.4231 +/- 0.0001 d. Using the seasonal variations on the rotational period, the SDR pattern is investigated, and shows a solar-like pattern of SDR. A cyclic pattern with period of ∼2.7 yr appears to be present in rotational period variation. During the observations, 20 optical flares are detected with a flare frequency of ∼1 flare per two days and with flare energy of ∼10(exp 31-34) erg. The surface coverage of cool spots is found to be in the range of ∼9-26 per cent. It appears that the high- and low-latitude spots are interchanging their positions. Quasi-simultaneous observations in X-ray, UV, and optical photometric bands show a signature of an excess of X-ray and UV activities in spotted regions.

Karmakar, Subhajeet↗
DOE OSTI2023

Application of prophage sequence analysis to investigate a disease outbreak involving Salmonella Adjame, a rare serovar and implications for the population structure

Introduction Outbreak investigation of foodborne salmonellosis is hindered when the food source is contaminated by multiple strains of Salmonella , creating difficulties matching an incriminated organism recovered from patients with the specific strain in the suspect food. An outbreak of the rare Salmonella Adjame was caused by multiple strains of the organism as revealed by single-nucleotide polymorphism (SNP) variation. The use of highly discriminatory prophage analysis to characterize strains of Salmonella should enable a more precise strain characterization and aid the investigation of foodborne salmonellosis. Methods We have carried out genomic analysis of S. Adjame strains recovered during the course of a recent outbreak and compared them with other strains of the organism ( n = 38 strains), using SNPs to evaluate strain differences present in the core genome, and prophage sequence typing (PST) to evaluate the accessory genome. Phylogenetic analyses were performed using both total prophage content and conserved prophages. Results The PST analysis of the S. Adjame isolates showed a high degree of strain heterogeneity. We observed small clusters made up of 2-6 isolates ( n = 27) and singletons ( n = 11) in stark contrast with the three clusters observed by SNP analysis. In total, we detected 24 prophages of which only four were highly prevalent, namely: Entero_p88 (36/38 strains), Salmon_SEN34 (35/38 strains), Burkho_phiE255 (33/38 strains) and Edward_GF (28/38 strains). Despite the marked strain diversity seen with prophage analysis, the distribution of the four most common prophages matched the clustering observed using core genome. Discussion Mutations in the core and accessory genomes of S. Adjame have shed light on the evolutionary relationships among the Adjame strains and demonstrated a convergence of the variations observed in both fractions of the genome. We conclude that core and accessory genomes analyses should be adopted in foodborne bacteria outbreak investigations to provide a more accurate strain description and facilitate reliable matching of isolates from patients and incriminated food sources. The outcomes should translate to a better understanding of the microbial population structure and an 46 improved source attribution in foodborne illnesses.

Gao, Ruimin↗