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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 631 records · Page 35
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Sequencing and Analysis of the Sex Determination Region of Populus trichocarpa

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

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

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

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

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Bubble Relaxation Dynamics in Homopolymer DNA Sequences

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

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

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

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

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

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

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

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

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

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

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

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

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

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Deconvolute individual genomes from metagenome sequences through short read clustering

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

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Budding yeasts in the subphylum Saccharomycotina Genome sequencing and assembly

Eukaryotic life depends on the functional elements encoded by both the nuclear genome and organellar genomes, such as those contained within the mitochondria. The content, size, and structure of the mitochondrial genome varies across organisms with potentially large implications for phenotypic variance and resulting evolutionary trajectories. Among yeasts in the subphylum Saccharomycotina, extensive differences have been observed in various species relative to the model yeast Saccharomyces cerevisiae, but mitochondrial genome sampling across many groups has been scarce, even as hundreds of nuclear genomes have become available. By extracting mitochondrial reads from existing short-read genome sequence datasets, we have greatly expanded both the number of available genomes and the coverage across sparsely sampled clades. Comparison of 353 yeast mitochondrial genomes revealed that, while size and GC content were fairly consistent across species, those in the genera Metschnikowia and Saccharomyces trended larger, while several species in the order Saccharomycetales exhibited lower GC content. Extreme examples for both size and GC content were scattered throughout the subphylum. All mitochondrial genomes shared a core set of protein-coding genes for Complexes III, IV, and V, but they varied in the presence or absence of mitochondrially-encoded canonical Complex I genes. We traced the loss of Complex I genes to a major event in the ancestor of the orders Saccharomycetales and Saccharomycodales, but we also observed several independent losses in the orders Phaffomycetales, Pichiales, and Dipodascales. In contrast to prior hypotheses based on smaller-scale datasets, comparison of evolutionary rates in protein-coding genes showed no bias towards elevated rates among aerobically fermenting (Crabtree/Warburg-positive) yeasts. Mitochondrial introns were widely distributed, but highly enriched in some groups. The majority of mitochondrial introns were poorly conserved within groups, but several were shared within groups, between groups, and even across taxonomic orders, which is consistent with horizontal gene transfer, likely involving homing endonucleases acting as selfish elements. As the number of available fungal nuclear genomes continues to expand, the methods described here to retrieve mitochondrial genome sequences from these datasets will prove invaluable to ensuring that studies of fungal mitochondrial genomes keep pace with their nuclear counterparts.

diversity↗
DOE OSTI2024

Pooled whole-genome sequencing in Puccinia novopanici

Sori from switchgrass rust infections of plants in nine locations were sequenced to a high depth using whole-genome sequencing, with the goal of determining genetic diversity and divergence across the pathogen's range.

biofuel↗
NASA NTRS1963

THE ALGEBRA OF PERIODIC SEQUENCES

The set of periodic sequences over a field forms a group-ring algebra in which convolution is the product operation. Decomposition theorems are applied to this ring to aid in finding sequences with an arbitrary, specified autocorrelation function.

Periodic function↗
NASA NTRS1971

Radioactive transitions in the helium isoelectronic sequence

The principles of the atomic spectrum theory are used to quantitatively analyze radiation transitions in two-electron helium-like atomic systems. Quantum theoretical methods, describing absorption and emission of a single photon in a radiative transition between two stationary states of an atomic system, reproduced the energy level diagram for the low lying states of helium. Reliable values are obtained from accurate variationally determined two-electron nonrelativistic wave functions for radiative transition probabilities of 2 3p states in the helium isoelectric sequence, and for the 2 1s and 2 3s1 states of the helium sequence.

Dalgarno, A.↗
NASA NTRS1972

Computer programs for plotting curves with various dashed-line sequences

Two FORTRAN-callable subprograms have been written to draw a smooth curve through a set of input points as a solid line or as a general sequence of long and short dashes. Subroutine LINSEQ draws conventional curves whereas subroutine CONSEQ draws smooth closed curves (contours). The subprograms are based on an approximate calculation of the arc length along the curve and spline interpolation along the arc length. Options are provided for smoothing of the input data and for offsetting the plotted curve from the input data points. The method of calculation of the arc length and the generation of the line sequence are described.Usage descriptions of the main subprograms, sample calling programs illustrating the various features of the subprograms, and sample plots are given. The subroutines should be readily adaptable to almost any computer-driven incremental plotter.

Desmarais, R. N.↗
NASA NTRS1972

Application of optimization techniques to near terminal area sequencing and flow control.

Development of an arrival air-traffic management system for a single runway. Traffic is segregated throughout most of the near terminal area according to performance characteristics. Nominal approach routes for each class of aircraft are determined by an optimization procedure. In this fashion, the nominal approach routes are dependent upon and, hence, determined by the near terminal area operating capabilities of each class of aircraft. The landing order and spacing of aircraft on the common approach path are determined so that a measure of total system deviation from the nominal landing times is minimized and safety standards are met. Delay maneuvers required to satisfy sequencing needs are then carried out in a manner dependent upon the particular class of aircraft being maneuvered. Finally, results are presented to illustrate the effects of the rate of arrivals upon a one-runway system serving three different classes of aircraft employing several different sequencing strategies and measures of total system deviation.

Straeter, T. A.↗
NASA NTRS1972

Recently published protein sequences. I.

Some polypeptide sequences that have been published in the 1972 scientific literature are listed. Only selected sequences are included. The compilation has two objectives. Current information between periods when more comprehensive compilations are published is to be assembled and the use of data that do not include arrangements of unsequenced peptides for 'maximum homology' is to be encouraged.

Jukes, T. H.↗