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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

Final Report

This report summarizes our research activities. In the award period, we have made significant progress on the first aim, with new discoveries reported in one published paper (1) and in one submitted manuscript (2) currently under review. The published manuscript reports on our discovery of plant ribokinase and the metabolic pathway in which it functions; the submitted manuscript is identification and characterization of the plant fructokinase family of enzymes from expression studies, sequence comparisons, subcellular localizations and enzymatic activities of recombinant proteins. Our study of loss-of-function mutants in the fructokinase family members (2) revealed that there were no phenotypic differences observed for the five genes analyzed, so we have adopted the Crispr/Cas9 system to isolate mutants in the two genes for which there are no currently available insertion mutants, and we are generating higher order mutants (double, triples, etc) to discern the relative roles and significance for each fructokinase. These mutants will be an important resource to understand regulation of carbohydrate movement and catabolism in plants. As studies from others indicate, alteration of fructokinases results in changes in cell walls and vasculatures, which have importance relative to biofuel yield and quality. In the second aim, we have characterized the protein-protein interactions for the pkfB proteins FLN1 and FLN2 that are localized to chloroplast transcriptional complexes and have proposed a new model for how chloroplast transcription is regulated. This work has been submitted for publication, been revised and will be re-submitted in December 2016

09 BIOMASS FUELS↗
DOE OSTI2024

High throughput, accurate gene annotation through AI and HPC-enabled structural analysis

With the advances in next generation sequencing technologies, the number of sequenced genomes is growing exponentially, resulting in a technology bottleneck for the translation of sequence information into usable hypotheses about the function of each gene. We have proposed leveraging our leadership high-performance computing (HPC) resources to help break this annotation bottleneck. Here we design an HPC-based framework to infer gene function from gene sequence by incorporating information about protein structure and interactions predicted by deep learning approaches. Accurate functional prediction and gene annotation using computational methods will facilitate breakthroughs in the genomic sciences essential to understanding and harnessing life processes in bacteria, fungi and plants. The development and applications of the state-of-the-art deep neural networks to protein structural modeling, interaction prediction, sequence comparison, and quality assessment of protein structural models will be made possible by leadership computational resources. These HPC-enabled bioinformatics and molecular modeling tools will provide powerful insights into molecular functions of genes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

A Single Amino Acid Change in Nramp6 from Sedum Alfredii Hance Affects Cadmium Accumulation

SaNramp6 in Sedum alfredii encodes a membrane-localized metal transporter. We isolated the SaNramp6h allele from the hyperaccumulating ecotype (HE) of S. alfredii . When this allele was expressed in transgenic yeast and Arabidopsis thaliana , it enhanced their cadmium (Cd) sensitivity by increased Cd transport and accumulation. We isolated another allele, SaNramp6n , from a nonhyperaccumulating ecotype (NHE) of S. alfredii . Amino acid sequence comparisons revealed three amino acid differences between SaNramp6h and SaNramp6n. We investigated the Cd transport activity of the Nramp6 allele, and determined which residues are essential for the transport activity. We conducted structure-function analyses of SaNramp6 based on site-directed mutagenesis and functional assays of the mutants in yeast and Arabidopsis . The three residues that differed between SaNramp6h and SaNramp6n were mutated. Only the L157P mutation of SaNramp6h impaired Cd transport. The other mutations, S218N and T504A, did not affect the transport activity of SaNramp6h, indicating that these residues are not essential for metal selectivity. Transgenic plants overexpressing SaNramp6h L157P showed altered metal accumulation in shoots and roots. Our results suggest that the conserved site L157 is essential for the high metal transport activity of SaNramp6h. This information may be useful for limiting or increasing Cd transport by other plant natural resistance associated macrophage protein (NRAMP) proteins.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1986

Laser-produced spectra and QED effects for Fe-, Co-, Cu-, and Zn-like ions of Au, Pb, Bi, Th, and U

Spectra of very highly charged ions of Au, Pb, Bi, Th, and U have been observed in laser-produced plasmas generated by the OMEGA laser. Line identifications in the region 9-110 A were made for ions in the Fe, Co, Cu, and Zn isoelectronic sequences. Comparison of the measured wavelengths of the Cu-like ions with values calculated with and without QED corrections shows that the inclusion of QED corrections greatly improves the accuracy of the calculated 4s-4p wavelengths. However, significant differences between the observed and calculated values remain.

Seely, J. F.↗
NASA NTRS1989

Stratospheric H2(O-18) distribution from far infrared observations

The stratospheric distribution of H2(O-18) in the 22 to 37 km altitude range has been obtained from balloon-based measurement of far infrared thermal emission spectra with an unapodized spectral resolution of 0.0033/cm. The analysis is based on the observed spectra of 9 isolated spectral lines in the 46 to 72/cm region obtained from four complete limb sequences. Comparison of the results with the statistically expected values indicates enhancement in the H2(O-18) concentrations increasing from 27 + or - 14 percent at 29 km to 40 + or - 23 percent at 37 km. No significant enhancement at lower altitudes was observed.

Guo, J.↗
NASA NTRS1992

Global synchronization algorithms for the Intel iPSC/860

In a distributed memory multicomputer that has no global clock, global processor synchronization can only be achieved through software. Global synchronization algorithms are used in tridiagonal systems solvers, CFD codes, sequence comparison algorithms, and sorting algorithms. They are also useful for event simulation, debugging, and for solving mutual exclusion problems. For the Intel iPSC/860 in particular, global synchronization can be used to ensure the most effective use of the communication network for operations such as the shift, where each processor in a one-dimensional array or ring concurrently sends a message to its right (or left) neighbor. Three global synchronization algorithms are considered for the iPSC/860: the gysnc() primitive provided by Intel, the PICL primitive sync0(), and a new recursive doubling synchronization (RDS) algorithm. The performance of these algorithms is compared to the performance predicted by communication models of both the long and forced message protocols. Measurements of the cost of shift operations preceded by global synchronization show that the RDS algorithm always synchronizes the nodes more precisely and costs only slightly more than the other two algorithms.

Seidel, Steven R.↗
NASA NTRS1995

On the levels of enzymatic substrate specificity: Implications for the early evolution of metabolic pathways

The most frequently invoked explanation for the origin of metabolic pathways is the retrograde evolution hypothesis. In contrast, according to the so-called 'patchwork' theory, metabolism evolved by the recruitment of relatively inefficient small enzymes of broad specificity that could react with a wide range of chemically related substrates. In this paper it is argued that both sequence comparisons and experimental results on enzyme substrate specificity support the patchwork assembly theory. The available evidence supports previous suggestions that gene duplication events followed by a gradual neoDarwinian accumulation of mutations and other minute genetic changes lead to the narrowing and modification of enzyme function in at least some primordial metabolic pathways.

Lazcano, A.↗
NASA NTRS2002

Protein Kinase Classification with 2866 Hidden Markov Models and One Support Vector Machine

The main application considered in this paper is predicting true kinases from randomly permuted kinases that share the same length and amino acid distributions as the true kinases. Numerous methods already exist for this classification task, such as HMMs, motif-matchers, and sequence comparison algorithms. We build on some of these efforts by creating a vector from the output of thousands of structurally based HMMs, created offline with Pfam-A seed alignments using SAM-T99, which then must be combined into an overall classification for the protein. Then we use a Support Vector Machine for classifying this large ensemble Pfam-Vector, with a polynomial and chisquared kernel. In particular, the chi-squared kernel SVM performs better than the HMMs and better than the BLAST pairwise comparisons, when predicting true from false kinases in some respects, but no one algorithm is best for all purposes or in all instances so we consider the particular strengths and weaknesses of each.

Weber, Ryan↗
NASA NTRS2003

Bacterial Actins? An Evolutionary Perspective

According to the conventional wisdom, the existence of a cytoskeleton in eukaryotes and its absence in prokaryotes constitute a fundamental divide between the two domains of life. An integral part of the dogma is that a cytoskeleton enabled an early eukaryote to feed upon prokaryotes, a consequence of which was the occasional endosymbiosis and the eventual evolution of organelles. Two recent papers present compelling evidence that actin, one of the principal components of a cytoskeleton, has a homolog in Bacteria that behaves in many ways like eukaryotic actin. Sequence comparisons reveml that eukaryotic actin and the bacterial homolog (mreB protein), unlike many other proteins common to eukaryotes and Bacteria, have very different and more highly extended evolutionary histories.

Doolittle, Russell F.↗
NASA NTRS2002

A provisional regulatory gene network for specification of endomesoderm in the sea urchin embryo

We present the current form of a provisional DNA sequence-based regulatory gene network that explains in outline how endomesodermal specification in the sea urchin embryo is controlled. The model of the network is in a continuous process of revision and growth as new genes are added and new experimental results become available; see http://www.its.caltech.edu/~mirsky/endomeso.htm (End-mes Gene Network Update) for the latest version. The network contains over 40 genes at present, many newly uncovered in the course of this work, and most encoding DNA-binding transcriptional regulatory factors. The architecture of the network was approached initially by construction of a logic model that integrated the extensive experimental evidence now available on endomesoderm specification. The internal linkages between genes in the network have been determined functionally, by measurement of the effects of regulatory perturbations on the expression of all relevant genes in the network. Five kinds of perturbation have been applied: (1) use of morpholino antisense oligonucleotides targeted to many of the key regulatory genes in the network; (2) transformation of other regulatory factors into dominant repressors by construction of Engrailed repressor domain fusions; (3) ectopic expression of given regulatory factors, from genetic expression constructs and from injected mRNAs; (4) blockade of the beta-catenin/Tcf pathway by introduction of mRNA encoding the intracellular domain of cadherin; and (5) blockade of the Notch signaling pathway by introduction of mRNA encoding the extracellular domain of the Notch receptor. The network model predicts the cis-regulatory inputs that link each gene into the network. Therefore, its architecture is testable by cis-regulatory analysis. Strongylocentrotus purpuratus and Lytechinus variegatus genomic BAC recombinants that include a large number of the genes in the network have been sequenced and annotated. Tests of the cis-regulatory predictions of the model are greatly facilitated by interspecific computational sequence comparison, which affords a rapid identification of likely cis-regulatory elements in advance of experimental analysis. The network specifies genomically encoded regulatory processes between early cleavage and gastrula stages. These control the specification of the micromere lineage and of the initial veg(2) endomesodermal domain; the blastula-stage separation of the central veg(2) mesodermal domain (i.e., the secondary mesenchyme progenitor field) from the peripheral veg(2) endodermal domain; the stabilization of specification state within these domains; and activation of some downstream differentiation genes. Each of the temporal-spatial phases of specification is represented in a subelement of the network model, that treats regulatory events within the relevant embryonic nuclei at particular stages. (c) 2002 Elsevier Science (USA).

Non-NASA Center↗
NASA NTRS2000

The chimeric eukaryote: origin of the nucleus from the karyomastigont in amitochondriate protists

We present a testable model for the origin of the nucleus, the membrane-bounded organelle that defines eukaryotes. A chimeric cell evolved via symbiogenesis by syntrophic merger between an archaebacterium and a eubacterium. The archaebacterium, a thermoacidophil resembling extant Thermoplasma, generated hydrogen sulfide to protect the eubacterium, a heterotrophic swimmer comparable to Spirochaeta or Hollandina that oxidized sulfide to sulfur. Selection pressure for speed swimming and oxygen avoidance led to an ancient analogue of the extant cosmopolitan bacterial consortium "Thiodendron latens." By eubacterial-archaebacterial genetic integration, the chimera, an amitochondriate heterotroph, evolved. This "earliest branching protist" that formed by permanent DNA recombination generated the nucleus as a component of the karyomastigont, an intracellular complex that assured genetic continuity of the former symbionts. The karyomastigont organellar system, common in extant amitochondriate protists as well as in presumed mitochondriate ancestors, minimally consists of a single nucleus, a single kinetosome and their protein connector. As predecessor of standard mitosis, the karyomastigont preceded free (unattached) nuclei. The nucleus evolved in karyomastigont ancestors by detachment at least five times (archamoebae, calonymphids, chlorophyte green algae, ciliates, foraminifera). This specific model of syntrophic chimeric fusion can be proved by sequence comparison of functional domains of motility proteins isolated from candidate taxa.

Review, Tutorial↗
DOE OSTI2015

Large Scale Sequencing of Dothideomycetes Provides Insights into Genome Evolution and Adaptation

Dothideomycetes is the largest and most diverse class of ascomycete fungi with 23 orders 110 families, 1300 genera and over 19,000 known species. We present comparative analysis of 70 Dothideomycete genomes including over 50 that we sequenced and are as yet unpublished. This extensive sampling has almost quadrupled the previous study of 18 species and uncovered a 10 fold range of genome sizes. We were able to clarify the phylogenetic positions of several species whose origins were unclear in previous morphological and sequence comparison studies. We analyzed selected gene families including proteases, transporters and small secreted proteins and show that major differences in gene content is influenced by speciation.

Haridas, Sajeet↗
DOE OSTI2012

Pool scrubbing under jet injection regime: An enhancement of the SPARC90 code

The SPARC90 code was developed to calculate the aerosol pool trapping during vent discharge processes, at low gas velocities. However, there are accident sequences, like SGTR core meltdown sequences, at which particle laden gases reach the aqueous ponds at very high velocities and new particle removal mechanisms become effective right at the inlet. As a result of the shearing off of roll wave water crests, water droplets are entrained in the gas core and sweep out aerosol particles, mainly by inertial impaction and interception. This paper summarizes the update of the SPARC90 code based on state-of-the-art equations for jet hydrodynamics and aerosol removal. Equations for variables like droplets population, size and velocity have been implemented. Based on the anticipated conditions in case of an SGTR severe accident sequence, comparisons of estimates from this new version (SPAR90-Jet) and the original one are set in terms of decontamination factor. Even though further work is still ahead, this work highlights how substantial particle retention at the pool inlet can reach under jet regime and how different aerosol removal mechanisms are with respect to the globule injection regime. (authors)

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2022

Legacy surface change analyses of the 1993 Rock Valley earthquake sequence for direct comparison to planned NA-22 underground conventional high-explosive experiments (Source Physics Experiment 3 (SPE3) - RV/DC Task 1.3 FY22 Final Report)

Recent work under two previous phases of the NNSA NA-22 Source Physics Experiment (SPE) have shown that underground chemical high-explosive experiments can produce detectable surface changes that differ in spatial extent and vertical magnitude depending on the geologic media at the site (Schultz-Fellenz et al., 2018; 2020; Crawford et al., 2021). Neither of these two prior phases of SPE identified natural earthquake-related surface effects in the same region that occurred at a similar depth as the explosive experiments for direct comparison. While earthquakes can also produce surface changes that are detectable using remote sensing data analyses, it is expected that the pattern and spatial extent of surface changes would vary between earthquakes and explosions. However, no direct-observed surface-change signature comparison between earthquakes and explosions has ever been performed. The SPE Phase 3 Rock Valley/Direct Comparison (RV/DC) program presents a unique opportunity to investigate and characterize co-occurrence of both earthquakes and explosions. In this project, we worked to address five tasks in a workflow, as follows: 1. Identify and obtain existing high-resolution legacy satellite and aerial imagery as close in time before and after the 1993 Rock Valley earthquake sequence to temporally constrain the analyses. 2. Transform these pre-earthquake and post-earthquake datasets into digital elevation models (DEMs) using geospatial analysis software packages (e.g., ArcGIS, Agisoft Metashape, and Google Earth Engine). 3. Perform DEM differencing analyses to assess and quantify earthquake-related changes from the 1993 sequence, and develop map products that visualize these analyses. 4. Use the analyses from (3) to: (a) assess spatial distribution and magnitude of surface changes due to the 1993 Rock Valley earthquake sequence, and (b) determine parameters of forthcoming, planned explosion-related surface change data collection from sensors mounted on unmanned aerial vehicles (UAVs) (e.g., spatial extent of collection, design and density of survey control, sensors to deploy, forward speed and line spacing of UAV flight lines, flight altitude). 5. Develop a summary report on the analyses, including how the analyses define parameters and identify focus areas for any future surface change analytical field campaigns related to the explosive experiment. Analyzing these legacy data and identifying whether they can detect any surface changes related to the earthquake sequence facilitates opportunities for direct signature comparison of surface change from explosions at one location, which has never previously been performed. Comparing the surface change signatures from a co-located and depth-equivalent earthquake and an explosion could help to advance remote sensing event discrimination techniques. This report summarizes the work completed toward this ambitious goal.

42 ENGINEERING↗
NASA NTRS1999

Thermal adaptation analyzed by comparison of protein sequences from mesophilic and extremely thermophilic Methanococcus species

The genome sequence of the extremely thermophilic archaeon Methanococcus jannaschii provides a wealth of data on proteins from a thermophile. In this paper, sequences of 115 proteins from M. jannaschii are compared with their homologs from mesophilic Methanococcus species. Although the growth temperatures of the mesophiles are about 50 degrees C below that of M. jannaschii, their genomic G+C contents are nearly identical. The properties most correlated with the proteins of the thermophile include higher residue volume, higher residue hydrophobicity, more charged amino acids (especially Glu, Arg, and Lys), and fewer uncharged polar residues (Ser, Thr, Asn, and Gln). These are recurring themes, with all trends applying to 83-92% of the proteins for which complete sequences were available. Nearly all of the amino acid replacements most significantly correlated with the temperature change are the same relatively conservative changes observed in all proteins, but in the case of the mesophile/thermophile comparison there is a directional bias. We identify 26 specific pairs of amino acids with a statistically significant (P < 0.01) preferred direction of replacement.

NASA Discipline Exobiology↗
NASA NTRS1985

Insights into the phylogenetic positions of photosynthetic bacteria obtained from 5S rRNA and 16S rRNA sequence data

Comparisons of complete 16S ribosomal ribonucleic acid (rRNA) sequences established that the secondary structure of these molecules is highly conserved. Earlier work with 5S rRNA secondary structure revealed that when structural conservation exists the alignment of sequences is straightforward. The constancy of structure implies minimal functional change. Under these conditions a uniform evolutionary rate can be expected so that conditions are favorable for phylogenetic tree construction.

Fox, G. E.↗
DOE OSTI2014

Comparison of Direct Sequence Spread Spectrum Rake Receiver with a Maximum Ratio Combining Multicarrier Spread Spectrum Receiver

This paper presents a theoretical analysis of the performance of a filter bank-based multicarrier spread spectrum (FB-MC-SS) system. We consider an FB-MC-SS setup where each data symbol is spread across multiple subcarriers, but there is no spreading in time. The results are then compared with those of the well-known direct sequence spread spectrum (DS-SS) system with a rake receiver for its best performance. We compare the two systems when the channel noise is white. We prove that as the processing gains of the two systems tend to infinity both approach the same performance. However, numerical simulations show that, in practice, where processing gain is limited, FB-MC-SS outperforms DS-SS.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2015

Disease insights through cross-species phenotype comparisons

New sequencing technologies have ushered in a new era for diagnosis and discovery of new causative mutations for rare diseases. However, the sheer numbers of candidate variants that require interpretation in an exome or genomic analysis are still a challenging prospect. A powerful approach is the comparison of the patient’s set of phenotypes (phenotypic profile) to known phenotypic profiles caused by mutations in orthologous genes associated with these variants. The most abundant source of relevant data for this task is available through the efforts of the Mouse Genome Informatics group and the International Mouse Phenotyping Consortium. In this review, we highlight the challenges in comparing human clinical phenotypes with mouse phenotypes and some of the solutions that have been developed by members of the Monarch Initiative. These tools allow the identification of mouse models for known disease-gene associations that may otherwise have been overlooked as well as candidate genes may be prioritized for novel associations. The culmination of these efforts is the Exomiser software package that allows clinical researchers to analyse patient exomes in the context of variant frequency and predicted pathogenicity as well the phenotypic similarity of the patient to any given candidate orthologous gene.

59 BASIC BIOLOGICAL SCIENCES↗