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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 289 records · Page 16
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Structural basis of tRNA recognition by the widespread OB fold

The widespread oligonucleotide/oligosaccharide-binding (OB)-fold recognizes diverse substrates from sugars to nucleic acids and proteins, and plays key roles in genome maintenance, transcription, translation, and tRNA metabolism. OB-containing bacterial Trbp and yeast Arc1p proteins are thought to recognize the tRNA elbow or anticodon regions. Here we report a 2.6 Å co-crystal structure of Aquifex aeolicus Trbp111 bound to tRNA Ile , which reveals that Trbp recognizes tRNAs solely by capturing their 3' ends. Structural, mutational, and biophysical analyses show that the Trbp/EMAPII-like OB fold precisely recognizes the single-stranded structure, 3' terminal location, and specific sequence of the 3' CA dinucleotide — a universal feature of mature tRNAs. Arc1p supplements its OB – tRNA 3' end interaction with additional contacts that involve an adjacent basic region and the tRNA body. This study uncovers a previously unrecognized mode of tRNA recognition by an ancient protein fold, and provides insights into protein-mediated tRNA aminoacylation, folding, localization, trafficking, and piracy.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earth’s biomes

Bacteriophages from the Inoviridae family (inoviruses) are characterized by their unique morphology, genome content and infection cycle. One of the most striking features of inoviruses is their ability to establish a chronic infection whereby the viral genome resides within the cell in either an exclusively episomal state or integrated into the host chromosome and virions are continuously released without killing the host. To date, a relatively small number of inovirus isolates have been extensively studied, either for biotechnological applications, such as phage display, or because of their effect on the toxicity of known bacterial pathogens including Vibrio cholerae and Neisseria meningitidis. Here, we show that the current 56 members of the Inoviridae family represent a minute fraction of a highly diverse group of inoviruses. Using a machine learning approach leveraging a combination of marker gene and genome features, we identified 10,295 inovirus-like sequences from microbial genomes and metagenomes. Collectively, our results call for reclassification of the current Inoviridae family into a viral order including six distinct proposed families associated with nearly all bacterial phyla across virtually every ecosystem. Putative inoviruses were also detected in several archaeal genomes, suggesting that, collectively, members of this supergroup infect hosts across the domains Bacteria and Archaea. Finally, we identified an expansive diversity of inovirus-encoded toxin–antitoxin and gene expression modulation systems, alongside evidence of both synergistic (CRISPR evasion) and antagonistic (superinfection exclusion) interactions with co-infecting viruses, which we experimentally validated in a Pseudomonas model. Capturing this previously obscured component of the global virosphere may spark new avenues for microbial manipulation approaches and innovative biotechnological applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Machine learning prediction of enzyme optimum pH

The relationship between pH and enzyme catalytic activity, especially the optimal pH (pH opt ) at which enzymes function, is critical for biotechnological applications. Hence, computational methods to predict pH opt will enhance enzyme discovery and design by facilitating accurate identification of enzymes that function optimally at specific pH levels, and by elucidating sequence-function relationships. Here, in this study, we proposed and evaluated various machine learning methods for predicting pH opt , conducting extensive hyperparameter optimization and training over 11,000 model instances. Our results demonstrate that models utilizing language model embeddings markedly outperform other methods in predicting pHopt. We present EpHod, the best-performing model, to predict pHopt, making it publicly available to researchers. From sequence data, EpHod directly learns structural and biophysical features that relate to pH opt , including proximity of residues to the catalytic centre and the accessibility of solvent molecules. Overall, EpHod presents a promising advancement in pH opt prediction and will potentially speed up the development of enzyme technologies.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Sulfurospirillum diekertiae sp. nov., a tetrachloroethene-respiring bacterium isolated from contaminated soil

Two anaerobic, tetrachloroethene- (PCE-) respiring bacterial isolates, designated strain ACS DCE T and strain ACS TCE , were characterized using a polyphasic approach. Cells were Gram-stain-negative, motile, non-spore-forming and shared a vibrioid- to spirillum-shaped morphology. Optimum growth occurred at 30°C and 0.1–0.4% salinity. The pH range for growth was pH 5.5–7.5, with an optimum at pH 7.2. Hydrogen, formate, pyruvate and lactate as electron donors supported respiratory reductive dechlorination of PCE to cis-1,2-dichloroethene (cDCE) in strain ACS DCE T and of PCE to trichloroethene (TCE) in strain ACS TCE . Both strains were able to grow with pyruvate under microaerobic conditions. Nitrate, elemental sulphur, and thiosulphate were alternative electron acceptors. Autotrophic growth was not observed and acetate served as carbon source for both strains. The major cellular fatty acids were C 16:1 ω7c, C 16:0 , C 14:0 and C 18:1 ω7c. Both genomes feature a circular plasmid. Strains ACS DCE T and ACS TCE were previously assigned to the candidate species 'Sulfurospirillum acididehalogenans'. Here, based on key genomic features and pairwise comparisons of whole-genome sequences, including average nucleotide identity, digital DNA–DNA hybridization and average amino acid identity, strains ACS DCE T and ACS TCE , 'Ca. Sulfurospirillum diekertiae' strains SL2-1 and SL2-2, and the unclassified Sulfurospirillum sp. strain SPD-1 are grouped into one distinct species separate from previously described Sulfurospirillum species. Compared to Sulfurospirillum multivorans and Sulfurospirillum halorespirans, which dechlorinate PCE to cDCE without substantial TCE accumulation, these five strains produce TCE or cDCE as the end product. In addition, some cellular fatty acids (e.g., C 16:0 3OH, C 17:0 iso 3OH, C 17:0 2OH) were detected in strains ACS DCE T and ACS TCE but not in other Sulfurospirillum species. On the basis of phylogenetic, physiological and phenotypic characteristics, 'Ca. Sulfurospirillum acididehalogenans' and 'Ca. Sulfurospirillum diekertiae' are proposed to be merged into one novel species within the genus Sulfurospirillum, for which the name Sulfurospirillum diekertiae sp. nov. is proposed. Finally, the type strain is ACS DCE T (=JCM 33349 T = KCTC 15819 T =CGMCC 1.5292 T ).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

ForceGen: End-to-end de novo protein generation based on nonlinear mechanical unfolding responses using a language diffusion model

Through evolution, nature has presented a set of remarkable protein materials, including elastins, silks, keratins and collagens with superior mechanical performances that play crucial roles in mechanobiology. However, going beyond natural designs to discover proteins that meet specified mechanical properties remains challenging. Here, we report a generative model that predicts protein designs to meet complex nonlinear mechanical property-design objectives. Our model leverages deep knowledge on protein sequences from a pretrained protein language model and maps mechanical unfolding responses to create proteins. Via full-atom molecular simulations for direct validation, we demonstrate that the designed proteins are de novo, and fulfill the targeted mechanical properties, including unfolding energy and mechanical strength, as well as the detailed unfolding force-separation curves. Our model offers rapid pathways to explore the enormous mechanobiological protein sequence space unconstrained by biological synthesis, using mechanical features as the target to enable the discovery of protein materials with superior mechanical properties.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

cjohnson-LANL/GRL_Kilauea

The python routines are outlined in detail to perform the methods and results in the manuscript under review in the journal Geophysical Research Letters titled “Seismic features predict ground motions during repeating caldera collapse sequence” with LA-UR-23-33345. All routines are written in open source python and were applied to publicly available data sets. The codes formats the data into the appropriate structure required to train a boosted tree regression model. Other codes produce figure results.

Johnson, Christopher W↗
DOE OSTI2020

Draft genome of Rosenbergiella nectarea strain 8N4 T provides insights into the potential role of this species in its plant host

Background: Rosenbergiella nectarea strain 8N4 T , the type species of the genus Rosenbergiella, was isolated from Amygdalus communis (almond) floral nectar. Other strains of this species were isolated from the floral nectar of Citrus paradisi (grapefruit), Nicotiana glauca (tobacco tree) and from Asphodelus aestivus. R. nectarea strain 8N4 T is a Gram-negative, oxidase-negative, facultatively anaerobic bacterium in the family Enterobacteriaceae. Results: Here we describe features of this organism, together with its genome sequence and annotation. The DNA GC content is 47.38%, the assembly size is 3,294,717 bp, and the total number of genes are 3,346. The genome discloses the possible role that this species may play in the plant. The genome contains both virulence genes, like pectin lyase and hemolysin, that may harm plant cells and genes that are predicted to produce volatile compounds that may impact the visitation rates by nectar consumers, such as pollinators and nectar thieves. Conclusions: The genome of R. nectarea strain 8N4T reveals a mutualistic interaction with the plant host and a possible effect on plant pollination and fitness.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1975

The ultraviolet spectrum of B-type supergiants

OAO-2 spectral scans of several early-type main-sequence stars and the shell star zeta Tau are analyzed to derive a representative UV spectrum for B-type supergiants. The absorption lines in the spectra of the B-type supergiants are shown to be stronger than those in main-sequence stars and to have a broad pointed feature at 1720 A that is constant in all such stars. The UV resonance lines of C IV, N V, Si III, and Si IV are found to be displaced toward the shorter wavelengths by velocities of up to 1800 km/s, indicating an escaping atmosphere. For B5 stars, the atmosphere is estimated to be expanding at about 120 km/s. The spectrum of eta CMa (B5Ia) is found to be well represented by the LTE theory of line formation, the presence of a stationary circumstellar shell, and a slowly expanding model atmosphere.

Underhill, A. B.↗
NASA NTRS1985

The 3.5 b.y. old Onverwacht Group: A remnant of ancient oceanic crust

The interaction between seawater and submarine volcanic rock has had important consequences for the chemistry of the ocean during the Phanerozoic. Most extant terranes have been regionally metamorphosed to the amphibolite and granulite facies, so that their precursor lithologies and structures are not readily determinable. However, the 3.5 b.y. old supracrustal rocks of the Barberton Mountain Land, South Africa, have not been subjected to high grade regional metamorphism, and therefore there was reason to hope that a laboratory investigation might reveal the extent to which these rocks had been exposed to subseafloor hydrothermal activity. Hart and de Wit describe bulk geochemical evidence from the entire suite as well as field evidence which support the concept of hydrothermal activity in the Barberton Mountain Land. Mineralogical and textural features which unequivocally mark it as a submarine sequence emplaced in a midocean ridge/fracture zone or back arc/fracture zone environment are briefly discussed.

Hoffman, S.↗
NASA NTRS1990

Beam Stop For High-Power Lasers

Graphite/aluminum plate absorbs most of light. Beam stop fits on standard optical mounting fixture. Graphite plate thick enough to absorb incident laser beam but thin enough to transfer heat quickly to heat sink. Device used for variety of blocking purposes. For example, blocks laser beam after it passes through experimental setup, or at each stage of setup so stages checked and tested in sequence. Negligible reflectance of device is valuable safety feature, protecting both users and equipment from reflections.

Mcdermid, Iain S.↗
NASA NTRS1993

The dependence on morphology of the gas content in galactic disks

The classification S0 was introduced by Hubble to serve as a description of galaxies whose morphological characteristics seemed to lie between the disk-dominated spirals and the spheroidal elliptical systems. Since then there has been extensive discussion as to whether this classification sequence is also an evolutionary sequence. Many studies have focussed on a particular feature such as the luminosity profile, the bulge-to-disk ratio, or the nature of the interstellar matter, but the question of the evolution remains contentious. Equally contentious is the question of the classification itself. For systems with well-developed disks there usually is no problem. Many spheroidal systems also are unambiguously classified as ellipticals in most catalogs. However, there are a number of early systems which have been reclassified following review using improved optical material. For example, Eder et al. (AJ, 102, 572, 1991) found that many of the S0 galaxies which are rich in neutral hydrogen have faint spiral features. The confusion about classification propagates into the discussion of the properties of early-type systems. Attempts to put the classification system on a quantitative basis have in general been unsuccessful. Recently Sandage (private communication) has reviewed the classification of early systems and has defined a set of sub-classes for these objects. The S0 galaxies are divided into three groups, depending on the prominence of the disk. There are six subdivisions of Sa galaxies, depending upon the relative prominence of knots and other arm-like characteristics. We have explored the total gas content in these objects to see if there is a dependence on the galaxy morphology, as denoted by these new subclasses.

Hogg, D. E.↗
NASA NTRS1998

Trellises and Trellis-Based Decoding Algorithms for Linear Block Codes: An Iterative Decoding Algorithm for Linear Block Codes Based on a Low-Weight Trellis Search - Part 3

For long linear block codes, maximum likelihood decoding based on full code trellises would be very hard to implement if not impossible. In this case, we may wish to trade error performance for the reduction in decoding complexity. Sub-optimum soft-decision decoding of a linear block code based on a low-weight sub-trellis can be devised to provide an effective trade-off between error performance and decoding complexity. This chapter presents such a suboptimal decoding algorithm for linear block codes. This decoding algorithm is iterative in nature and based on an optimality test. It has the following important features: (1) a simple method to generate a sequence of candidate code-words, one at a time, for test; (2) a sufficient condition for testing a candidate code-word for optimality; and (3) a low-weight sub-trellis search for finding the most likely (ML) code-word.

Lin, Shu↗
DOE OSTI2021

Machine learning reveals sequence-function relationships in family 7 glycoside hydrolases

Family 7 glycoside hydrolases (GH7) are among the principal enzymes for cellulose degradation in nature and industrially. These important enzymes are often bimodular, including a catalytic domain and carbohydrate binding module (CBM) attached via a flexible linker, and exhibit an active site that binds cello-oligomers of up to ten glucosyl moieties. GH7 cellulases consist of two major subtypes: cellobiohydrolases (CBH) and endoglucanases (EG). Despite the critical importance of GH7 enzymes, there remain gaps in our understanding of how GH7 sequence and structure relate to function. Here, we employed machine learning to gain data-driven insights into relationships between sequence, structure, and function across the GH7 family. Machine-learning models, trained only on the number of residues in the active-site loops as features, were able discriminate GH7 CBHs and EGs with up to 99% accuracy, demonstrating that the lengths of loops A4, B2, B3, and B4 strongly correlate with functional subtype across the GH7 family. Classification rules were derived such that specific residues at 42 different sequence positions each predicted the functional subtype with accuracies surpassing 87%. A random forest model trained on residues at 19 positions in the catalytic domain predicted the presence of a CBM with 89.5% accuracy. Our ML results recapitulate, as top-performing features, a substantial number of the sequence positions determined by previous experimental studies to play vital roles in GH7 activity. We surmise that the yet-to-be-explored sequence positions among the top-performing features also contribute to GH7 functional variation and may be exploited to understand and manipulate function.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS2017

Lava Eruption and Emplacement: Using Clues from Hawaii and Iceland to Probe the Lunar Past

Investigating recent eruptions on Earth is crucial to improving understanding of relationships between eruption dynamics and final lava flow morphologies. In this study, we investigated eruptions in Holuhraun, Iceland, and Kilauea, Hawaii to gain insight into the lava dynamics near the source vent, the initiation of lava channels, and the origin of down-channel features. Insights are applied to Rima Bode on the lunar nearside to deduce the sequence of events that formed this lunar sinuous rille system.These insights are crucial to correctly interpreting whether the volcanic features associated with Rima Bode directly relate to eruption conditions at the vent and, thus, can help us understand those eruption dynamics, or, alternatively, whether the features formed as a result of more localized influences on lava flow dynamics. For example, if the lava channel developed early in the eruption and was linked to pulses in vent activity, its morphology can be analyzed to interpret the flux and duration of the eruption. Conversely, if the lava channel initiated late in the eruption as the result of a catastrophic breaching of lava that had previously pooled within the vent [e.g., 1], then the final channel morphology will not indicate eruption dynamics but rather local dynamics associated with that breach event. Distinguishing between these two scenarios is crucial for correctly interpreting the intensity and duration of volcanic history on the Moon.

sinuous rille↗
NASA NTRS1988

Parallel algorithm for determining motion vectors in ice floe images by matching edge features

A parallel algorithm is described to determine motion vectors of ice floes using time sequences of images of the Arctic ocean obtained from the Synthetic Aperture Radar (SAR) instrument flown on-board the SEASAT spacecraft. Researchers describe a parallel algorithm which is implemented on the MPP for locating corresponding objects based on their translationally and rotationally invariant features. The algorithm first approximates the edges in the images by polygons or sets of connected straight-line segments. Each such edge structure is then reduced to a seed point. Associated with each seed point are the descriptions (lengths, orientations and sequence numbers) of the lines constituting the corresponding edge structure. A parallel matching algorithm is used to match packed arrays of such descriptions to identify corresponding seed points in the two images. The matching algorithm is designed such that fragmentation and merging of ice floes are taken into account by accepting partial matches. The technique has been demonstrated to work on synthetic test patterns and real image pairs from SEASAT in times ranging from .5 to 0.7 seconds for 128 x 128 images.

Manohar, M.↗
NASA NTRS1976

Mineralogy of the Ibitira eucrite and comparison with other eucrites and lunar samples

The mineralogy of the Ibitira meteorite is studied using single-crystal X-ray and energy-dispersive electron-probe techniques. It is shown that this strongly metamorphosed unbrecciated vesicular eucrite has a primary variolitic and secondary hornfelsic texture dominated by equant grains of pale-brown pyroxene (60%) set in an irregular matrix of plagioclase (30%). Minor phases are detected which indicate igneous crystallization, a prolonged metamorphic history, and vapor deposition. The following sequence of events is suggested as the simplest explanation for the mineralogical features observed: (1) crystallization of the meteorite in a lava flow; (2) prolonged annealing, reduction of primary spinel, and vapor deposition; (3) strong shock sufficient to modify the texture of the plagioclase grains; and (4) sufficient annealing to allow crystallization of the plagioclase as a subparallel mosaic and partial conversion to the low structural state. Evidence for this sequence is examined in detail, particularly in relation to the general features of eucrites, howardites, and mesosiderites

Steele, I. M.↗
DOE OSTI2025

Interface magnetism and anomalous Hall effect in La 0.7 ⁢Sr 0.3⁢ Mn⁢O 3 /SrIr⁢O 3 bilayers

Epitaxial interfaces combining 3d and 5d transition metal oxides are a fertile playground to examine the interplay between topology and electron correlations. In this work, we explore magnetism and transport of bilayers combining ferromagnetic La 0.7⁢ Sr 0.3⁢ Mn⁢O 3 and the strong spin-orbit coupling material SrIr⁢O 3 . We have found an interfacial magnetic proximity effect driving an intrinsic contribution to the anomalous Hall effect of topological origin. The interfacial proximity interaction is enabled by the Mn-O-Ir bonding reconstruction and depends on layer sequence. While bilayers with the La 0.7⁢ Sr 0.3 ⁢Mn⁢O 3 on top featuring a robust Mn magnetism at the interface show the intrinsic AHE contribution, it is absent in bilayers with the inverted layer sequence (SrIr⁢O 3 layer on top) showing strongly suppressed magnetism at the interface. These results illustrate the leading role of interfacial atomic reconstructions on the interplay between topology and correlations at 3d/5d oxide interfaces. This finding may be of interest in future oxide topological spintronics and spin-orbitronics.

36 MATERIALS SCIENCE↗
NASA NTRS1997

Registration of video sequences from multiple sensors

In this paper, we describe an approach for registration of video sequences from a suite of multiple sensors including television, infrared and radar. Video sequences generated by these sensors may contain abrupt changes in local contrast and inconsistent image features, which pose additional difficulties for registration. Our approach to registration addresses the difficulties caused by using multiple sensors. We use a representation for registration that is invariant to local contrast changes, followed by smoothing of the resulting error measure used for registration, for robust estimation of registration parameters. We use an iterative procedure to reduce the effect of inconsistent features. Finally, we describe a method that uses same-sensor registration to aide in performing registration of sequences of video frames across multiple sensors.

Sharma, Ravi K.↗