Search NASA⌕ Search

SEARCH · Search NASA

Results for “sequence features”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,351 records · Page 75
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Natural transformation as a tool in Acinetobacter baylyi : Streamlined engineering and mutational analysis

Natural transformation and homologous recombination in a soil bacterium, Acinetobacter baylyi ADP1, occur with exceptionally high efficiency. These genetic features can be harnessed to address a wide variety of fundamental and applied scientific topics. Recent advances in synthetic biology and laboratory evolution have led to renewed appreciation for the use of A. baylyi as a model organism. To complement several review articles that highlight new tool sets, this chapter focuses on simple protocols and examples of transformation assays that facilitate genetic analysis and engineering. Whole genome sequencing often reveals extensive genetic variation among closely related isolates that can confound the association of genotypic and phenotypic changes. In A. baylyi, such associations can be deciphered in unique ways by directly transforming cells with linear DNA fragments. The resulting allelic replacement, which occurs at high frequency, rapidly generates desired mutants via targeted chromosomal editing. Diverse screening and selection methods can be used to test hypotheses and streamline experimental strategies to reveal the significance of specific DNA sequences. Moreover, large procedural variations are well tolerated, and techniques can be readily adapted for new purposes. Furthermore, one goal of highlighting natural transformation methodology in A. baylyi is to expand the community of researchers using this versatile bacterial host.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Environmental effects on the UV upturn in local clusters of galaxies

ABSTRACT We explore the dependence of ultraviolet (UV) upturn colours in early-type cluster galaxies on the properties of their parent clusters (such as velocity dispersion and X-ray luminosity) and on the positions and kinematics of galaxies within them. We use a sample of 24 nearby clusters with highly complete spectroscopy and optical/infrared data to select a suitable sample of red-sequence galaxies, whose far-ultraviolet and NUV magnitudes we measure from archival GALEX data. Our results show that the UV upturn colour has no dependence on cluster properties and has the same range in all clusters. There is also no dependence on the projected position within clusters or on line-of-sight velocity. Therefore, our conclusion is that the UV upturn phenomenon is an intrinsic feature of cluster early-type galaxies, irrespective of their cluster environment.

Ali, Sadman S.↗
NASA NTRS1990

Constraints on astronomical silicate dust

Numerical radiative-transfer models are used to discuss the properties of circumstellar dust grains around the premain-sequence star AB Aur (HD 31293). It is assumed that the dust consists of a silicate-graphite mixture with Draine and Lee (1984) optical properties. The modeling technique is to match the observed FUV through FIR energy distribution with the spectral energy distribution predicted for a spherical dust shell around a luminous hot star. Special attention is given to matching the observed 10-micron silicate emission feature and the observed circumstellar absorption curve at UV wavelengths, making it possible to strengthen constraints on dust-grain opacity and chemical composition. It is concluded that, although silicate grains can explain the observed 10-micron emission feature, the Draine and Lee silicate-graphite mixture cannot explain the observed FUV circumstellar absorption at the same time. The dust shell around AB Aur contains an additional population of small particles, the most likely candidate being amorphous carbon grains in a nonhydrogenated form.

Sorrell, Wilfred H.↗
NASA NTRS2001

EUNIS: An Extreme-Ultraviolet Normal-Incidence Spectrometer

GSFC is in the process of assembling an Extreme-Ultraviolet Normal-Incidence Spectrometer called EUNIS, to be flown as a sounding rocket payload. This instrument builds on the many technical innovations pioneered by our highly successful SERTS experiment over its past ten flights. The new design will have somewhat improved spatial and spectral resolutions, as well as 100 times greater sensitivity, permitting EUV spectroscopy with a temporal resolution near 1-second for the first time ever. To achieve such high time cadence, a novel Active-Pixel-Sensor detector is being developed as a key component of our design. The high sensitivity of EUNIS will allow entirely new studies of transient coronal phenomena, such as the rapid loop dynamics seen by TRACE, and searches for non-thermal motions indicative of magnetic reconnection or wave heating. The increased sensitivity will also permit useful EUV spectra at heights of 2-3-R$ \odot$ above the limb, where the transition between the static corona and the solar wind might occur. In addition, the new design features two independent optical systems, more than doubling the spectral bandwidth covered on each flight. Its 300-370\AA\ bandpass includes He-II 304\AA\ and strong lines from Fe-XI-XVI, extending the current SERTS range of 300-355\AA\ to further improve our ongoing series of calibration under-flights for SOHO/CDS and EIT. The second bandpass of 170-230\AA\ has a sequence of very strong Fe-IX-XIV lines, and will allow under-flight support for two more channels on SOHO/EIT, two channels on TRACE, one on Solar-B/EIS, and all four channels on the STEREO/EUVI instrument. First flight of the new EUNIS payload is scheduled for 2002 October.

Thomas, Roger J.↗
NASA NTRS2001

Chromospheric Structure and Wind Acceleration in Zeta Aur Stars

This NASA grant supported an analysis of the variability of the wind of the supergiant primary star (K4 Ib) in the eclipsing binary Zeta Aurigae (Zeta Aur). In the ultraviolet, the main-sequence companion star (B5 V) dominates the observed flux, and therefore serves as a convenient probe of the cool supergiant's wind. This study utilized the extensive set of (100+) ultraviolet spectroscopic observations obtained with the International Ultraviolet Explorer (IUE) satellite over its operational lifetime of 1978-1995. Although the resolution of IUE is limited (about 25 km/s), it is adequate to resolve variability in the wind features in Zeta Aur's ultraviolet spectrum, which are blueshifted 70 km/s from line center. Our analysis used the tau-v technique of Cardelli and Savage, which makes full use of the available line profile information. We find that the wind column densities vary by up to an order of magnitude over time. These results are being written up for submission to the Astrophysical Journal as the third paper of a series on the chromosphere and wind of Zeta Aurigae. The first two papers report on the construction of mean chromosphere and wind models respectively, based on HST/GHRS observations and funded by STScI. The third paper - this research - reports on variability of the Zeta Aur wind as determined from our analysis of the long IUE time series. This paper will be completed within the next three months; the delay in publication was to allow the completion of Papers 1 and 2, which logically precede the present work. Therefore, an additional no-cost extension was requested in order to ensure budgeted funds remain available for publication of this work. Unfortunately, this request was denied, and so I am forced to write this final report before publication of Paper 3. Regardless, this paper will be submitted for publication within the next three months.

Bennett, Philip D.↗
DOE OSTI2015

Statistical tests on clustered global earthquake synthetic data sets

Abstract We study the ability of statistical tests to identify nonrandom features of earthquake catalogs, with a focus on the global earthquake record since 1900. We construct four types of synthetic data sets containing varying strengths of clustering, with each data set containing on average 10,000 events over 100 years with magnitudes above M = 6. We apply a suite of statistical tests to each synthetic realization in order to evaluate the ability of each test to identify the sequences of events as nonrandom. Our results show that detection ability is dependent on the quantity of data, the nature of the type of clustering, and the specific signal used in the statistical test. Data sets that exhibit a stronger variation in the seismicity rate are generally easier to identify as nonrandom for a given background rate. We also show that we can address this problem in a Bayesian framework, with the clustered data sets as prior distributions. Using this new Bayesian approach, we can place quantitative bounds on the range of possible clustering strengths that are consistent with the global earthquake data. At M = 7, we can estimate 99th percentile confidence bounds on the number of triggered events, with an upper bound of 20% of the catalog for global aftershock sequences, with a stronger upper bound on the fraction of triggered events of 10% for long‐term event clusters. At M = 8, the bounds are less strict due to the reduced number of events. However, our analysis shows that other types of clustering could be present in the data that we are unable to detect. Our results aid in the interpretation of the results of statistical tests on earthquake catalogs, both worldwide and regionally.

Daub, Eric G.↗
DOE OSTI2020

Horizontal gene transfer in Fungi

Horizontal gene transfer (HGT), the sharing of genes between species outside of inheritance, is a common feature among prokaryotes, but a growing body of evidence supports HGT in eukaryotic genomes. The driving forces behind horizontal gene transfer occur within a shared environment, and are selective—meaning they improve survivability of stress, increase nutrient access, or provide an evolutionary advantage. The development of toxic and pathogenic properties was one of the first indications of phenotypic transfer among fungal species. An growing species diversity of genome sequences has brought a new set of tools to tracking HGT. The detection of HGT based on sequence similarity utilizes species tree phylogenies, which compare similarity of core conserved genes to determine lineage. Divergence of an HGT candidate gene from a phylogenetic background tree can show inter-species DNA transfer. It is by following phenotypes and analysis of DNA sequence context and content that we can uncover previous transfer events, and track lab fostered and recorded HGT. Evidence of HGT is found heavily in parasitic and pathogenic fungi; both of these lifestyles rely on phagocytosis and assimilation of host parts and pieces, suggesting phagocytosis is implicated in DNA uptake mechanisms. Our understanding of the molecular mechanisms of DNA uptake and incorporation of foreign DNA into fungal genomes, i.e. natural competence, remain based on a set of laboratory conditions used in molecular transformation. The mechanism of DNA uptake in the natural world and new DNA incorporation remain under investigation.

Bredeweg, Erin L.↗
DOE OSTI2019

Microstructural and Mechanical Characterization of Directionally Solidified Conventional and Nb-Modified Mar-M247 Superalloy

This study analyzes the effects of replacing Ta by Nb (at.% basis) in the phase transformation temperatures, Scheil solidification behavior, and microstructural mechanical features of a Nb-modified as well as conventional Mar-M247 superalloys. Both alloys were directionally solidified at a withdrawal rate of 18 cm/h under a thermal gradient of about 80 °C/cm. DSC results were compared to thermodynamic simulations of phase transformation temperatures and showed a good correlation. The replacement of Ta by Nb has not altered the solidification path of Mar-M247, keeping the sequence L → L + γ → L + γ + MC → L + γ + MC + γ/γ′ eutectic. Due to the segregation of Hf and Zr to the very last liquid to solidify, a low melting point γ/Ni{sub 5}(Hf,Zr) constituent was observed. The as-solidified microstructures of both Mar-M247(Nb) and Mar-M247 were constituted of columnar dendrites of gamma matrix (γ) phase with cuboidal gamma-prime (γ′) precipitates. In addition, γ/γ′-eutectic was observed in the interdendritic region along with MC carbides in blocky, script (blocky dendritic), needle-like and fine nodular morphologies. Both alloys contained about 1.5 vol.% of MC carbides. The MC carbides in Mar-M247(Nb) and Mar-M247 are, respectively, Nb-rich and Ta-rich, with only a limited amount of Hf being detected in the MC phase. The yield stress of Nb-modified Mar-M247 showed higher values up to 750 °C. For higher temperatures, above 800 °C, a conventional Mar-M247 presented a higher value of yield stress.

36 MATERIALS SCIENCE↗
DOE OSTI2017

Molecular-Level Insights into Oxygen Reduction Catalysis by Graphite-Conjugated Active Sites

With a combination of experimental and computational investigations, we design a consistent mechanistic model for the oxygen reduction reaction (ORR) at molecularly well-defined graphite-conjugated catalyst ( GCC ) active sites featuring aryl-pyridinium moieties ( N+-GCC ). ORR catalysis at glassy carbon surfaces modified with N+-GCC fragments displays near-first-order dependence in O 2 partial pressure and near-zero-order dependence on electrolyte pH. Tafel analysis suggests an equilibrium one-electron transfer process followed by a rate-limiting chemical step at modest overpotentials that transitions to a rate-limiting electron transfer sequence at higher overpotentials. Finite-cluster computational modeling of the N+-GCC active site reveals preferential O 2 adsorption at electrophilic carbons alpha to the pyridinium moiety. Together, the experimental and computational data indicate that ORR proceeds via a proton-decoupled O 2 activation sequence involving either concerted or stepwise electron transfer and adsorption of O 2 , which is then followed by a series of electron/proton transfer steps to generate water and turn over the catalytic cycle. The introduced mechanistic model serves as a roadmap for the bottom-up synthesis of highly active N-doped carbon ORR catalysts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

A Deep State Space Model for Rainfall‐Runoff Simulations

The classical way of studying the rainfall‐runoff processes in the water cycle relies on conceptual or physically‐based hydrologic models. Deep learning (DL) has recently emerged as an alternative and blossomed in the hydrology community for rainfall‐runoff simulations. However, the decades‐old Long Short‐Term Memory (LSTM) network remains the benchmark for this task, outperforming newer architectures like Transformers. In this work, we propose a State Space Model (SSM), specifically the Frequency Tuned Diagonal State Space Sequence (S4D‐FT) model, for rainfall‐runoff simulations. The proposed S4D‐FT is benchmarked against the established LSTM and a physically‐based Sacramento Soil Moisture Accounting model under in‐sample and out‐of‐sample simulation setups across 531 watersheds in the contiguous United States (CONUS). Results show that S4D‐FT is able to outperform the LSTM model across diverse regions under both simulation setups, especially for regions that feature snowmelt‐driven or intermittent flow regimes. In contrast, S4D‐FT tends to underperform in flashier, high‐magnitude flow regimes, likely due to its global state‐space convolution computation that emphasizes slow, storage‐driven dynamics, which makes it less effective at picking up short bursts and noisy spikes in the data. In summary, our pioneering introduction of the S4D‐FT for rainfall‐runoff simulations challenges the dominance of LSTM in the hydrology community and expands the arsenal of DL tools available for hydrological modeling.

Wang, Yihan [Univ. of Oklahoma, Norman, OK (United↗
DOE OSTI2020

Analysis of a preQ1-I riboswitch in effector-free and bound states reveals a metabolite-programmed nucleobase-stacking spine that controls gene regulation

Abstract Riboswitches are structured RNA motifs that recognize metabolites to alter the conformations of downstream sequences, leading to gene regulation. To investigate this molecular framework, we determined crystal structures of a preQ1-I riboswitch in effector-free and bound states at 2.00 Å and 2.65 Å-resolution. Both pseudoknots exhibited the elusive L2 loop, which displayed distinct conformations. Conversely, the Shine-Dalgarno sequence (SDS) in the S2 helix of each structure remained unbroken. The expectation that the effector-free state should expose the SDS prompted us to conduct solution experiments to delineate environmental changes to specific nucleobases in response to preQ1. We then used nudged elastic band computational methods to derive conformational-change pathways linking the crystallographically-determined effector-free and bound-state structures. Pathways featured: (i) unstacking and unpairing of L2 and S2 nucleobases without preQ1—exposing the SDS for translation and (ii) stacking and pairing L2 and S2 nucleobases with preQ1—sequestering the SDS. Our results reveal how preQ1 binding reorganizes L2 into a nucleobase-stacking spine that sequesters the SDS, linking effector recognition to biological function. The generality of stacking spines as conduits for effector-dependent, interdomain communication is discussed in light of their existence in adenine riboswitches, as well as the turnip yellow mosaic virus ribosome sensor.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Crystal structure of MbnF: an NADPH-dependent flavin monooxygenase from Methylocystis strain SB2

Methanobactins (MBs) are ribosomally produced and post-translationally modified peptides (RiPPs) that are used by methanotrophs for copper acquisition. The signature post-translational modification of MBs is the formation of two heterocyclic groups, either an oxazolone, pyrazinedione or imidazolone group, with an associated thioamide from an X -Cys dipeptide. The precursor peptide (MbnA) for MB formation is found in a gene cluster of MB-associated genes. The exact biosynthetic pathway of MB formation is not yet fully understood, and there are still uncharacterized proteins in some MB gene clusters, particularly those that produce pyrazinedione or imidazolone rings. One such protein is MbnF, which is proposed to be a flavin monooxygenase (FMO) based on homology. To help to elucidate its possible function, MbnF from Methylocystis sp. strain SB2 was recombinantly produced in Escherichia coli and its X-ray crystal structure was resolved to 2.6 Å resolution. Based on its structural features, MbnF appears to be a type A FMO, most of which catalyze hydroxylation reactions. Preliminary functional characterization shows that MbnF preferentially oxidizes NADPH over NADH, supporting NAD(P)H-mediated flavin reduction, which is the initial step in the reaction cycle of several type A FMO enzymes. It is also shown that MbnF binds the precursor peptide for MB, with subsequent loss of the leader peptide sequence as well as the last three C-terminal amino acids, suggesting that MbnF might be needed for this process to occur. Finally, molecular-dynamics simulations revealed a channel in MbnF that is capable of accommodating the core MbnA fragment minus the three C-terminal amino acids.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

The complete genome sequence of the yogurt isolate Streptococcus thermophilus ACA-DC 2

Streptococcus thermophilus ACA-DC 2 is a newly sequenced strain isolated from traditional Greek yogurt. Among the 14 fully sequenced strains of S. thermophilus currently deposited in the NCBI database, the ACA-DC 2 strain has the smallest chromosome, containing 1,731,838 bp. The annotation of its genome revealed the presence of 1,850 genes, including 1,556 protein-coding genes, 70 RNA genes and 224 potential pseudogenes. A large number of pseudogenes were identified. This was also accompanied by the absence of pathogenic features suggesting evolution of strain ACA-DC 2 through genome decay processes, most probably due to adaptation to the milk ecosystem. Analysis revealed the existence of one complete lactose-galactose operon, several proteolytic enzymes, one exopolysaccharide cluster, stress response genes and four putative antimicrobial peptides. Interestingly, one CRISPR-cas system and one orphan CRISPR, both carrying only one spacer, were predicted indicating low activity or inactivation of the cas proteins. Nevertheless, four putative restriction-modification systems were determined that may compensate any deficiencies of the CRISPR-cas system. Furthermore, whole genome phylogeny indicated three distinct clades within S. thermophilus. Comparative analysis among selected strains representative for each clade, including strain ACA-DC 2, revealed a high degree of conservation at the genomic scale, but also strain specific regions. Unique genes and genomic islands of strain ACA-DC 2 contained a number of genes potentially acquired through horizontal gene transfer events, that could be related to important technological properties for dairy starters. Our study suggests genomic traits in strain ACA-DC 2 compatible to the production of dairy fermented foods.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1988

Mars: Volcanism in the Valles Marineris overlooked

Do volcanic rocks exist in the Valles Marineris. This question is pertinent because the Valles Marineris are gigantic grabens, rivaling rift valleys on earth in size and depth. The Valles Marineris were interpreted as extensional tectonic structures, perhaps incipient rifts. On earth, rift valleys commonly contain volcanic deposits. On Mars, deposits inside the Valles Marineris grabens do not have the morphologic signature of such easily identified volcanic features as shield volcanoes or lava flows. Therefore, many researchers have not recognized the deposits inside the Valles Marineris as volcanic. Is Mars, then, different from earth in having formed riftlike grabens unaccompanied by volcanism. Overall, results from the study suggest that volcanism was present in the Valles Marineris; the volcanism was explosive in places; some volcanism was more felsic than that generally assumed elsewhere; and the younger sequence of interior beds was emplaced so late in Martian history that the planet may be considered to be still volcanically active.

Lucchitta, B. K.↗
NASA NTRS1989

The browse file of NASA/JPL quick-look radar images from the Loch Linnhe 1989 experiment

The Jet Propulsion Laboratory (JPL) Aircraft Synthetic Aperture Radar (AIRSAR) was deployed to Scotland to obtain radar imagery of ship wakes generated in Loch Linnhe. These observations were part of a joint US and UK experiment to study the internal waves generated by ships under partially controlled conditions. The AIRSAR was mounted on the NASA-Ames DC-8 aircraft. The data acquisition sequence consisted of 8 flights, each about 6 hours in duration, wherein 24 observations of the instrumented site were made on each flight. This Browse File provides the experimenters with a reference of the real time imagery (approximately 100 images) obtained on the 38-deg track. These radar images are copies of those obtained at the time of observation and show the general geometry of the ship wake features. To speed up processing during this flight, the images were all processed around zero Doppler, and thus azimuth ambiguities often occur when the drift angel (yaw) exceeded a few degrees. However, even with the various shortcomings, it is believed that the experimenter will find the Browse File useful in establishing a basis for further investigations.

Brown, Walter E., Jr.↗
NASA NTRS1986

Multistep modeling of protein structure: application to bungarotoxin

Modelling of bungarotoxin in atomic details is presented in this article. The model-building procedure utilizes the low-resolution crystal coordinates of the c-alpha atoms of bungarotoxin, sequence homology within the neurotoxin family, as well as high-resolution x-ray diffraction data of cobratoxin and erabutoxin. Our model-building procedure involves: (a) principles of comparative modelling, (b) embedding procedures of distance geometry, and (c) use of molecular mechanics for optimizing packing. The model is not only consistent with the c-alpha coordinates of crystal structure, but also agrees with solution conformational features of the triple-stranded beta sheet as observed by NOE measurements.

NASA Discipline Exobiology↗
NASA NTRS2006

Using Dissimilarity Metrics to Identify Interesting Designs

A computer program helps to blend the power of automated-search software, which is able to generate large numbers of design solutions, with the insight of expert designers, who are able to identify preferred designs but do not have time to examine all the solutions. From among the many automated solutions to a given design problem, the program selects a smaller number of solutions that are worthy of scrutiny by the experts in the sense that they are sufficiently dissimilar from each other. The program makes the selection in an interactive process that involves a sequence of data-mining steps interspersed with visual displays of results of these steps to the experts. At crucial points between steps, the experts provide directives to guide the process. The program uses heuristic search techniques to identify nearly optimal design solutions and uses dissimilarity metrics defined by the experts to characterize the degree to which solutions are interestingly different. The search, data-mining, and visualization features of the program were derived from previously developed risk-management software used to support a risk-centric design methodology

Feather, Martin↗