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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 1,387 records · Page 77
All sourcesNASA NTRSDOE OSTI
DOE OSTI2014

CDvist: A webserver for identification and visualization of conserved domains in protein sequences

Identification of domains in protein sequences allows their assigning to biological functions. Several webservers exist for identification of protein domains using similarity searches against various databases of protein domain models. However, none of them provides comprehensive domain coverage while allowing bulk querying and their visualization schemes can be improved. To address these issues, we developed CDvist (a comprehensive domain visualization tool), which combines the best available search algorithms and databases into a user-friendly framework. First, a given protein sequence is matched to domain models using high-specificity tools and only then unmatched segments are subjected to more sensitive algorithms resulting in a best possible comprehensive coverage. In conclusion, bulk querying and rich visualization and download options provide improved functionality to domain architecture analysis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Rapid Shifts in the Temperature Dependence of Locomotor Performance in an Invasive Frog, Xenopus laevis , Implications for Conservation

Abstract Temperature is a critical abiotic factor impacting all aspects of the biology of organisms, especially in ectotherms. As such, it is an important determinant of the potential invasive ability of organisms and may limit population expansion unless organisms can physiologically respond to changes in temperature either through plasticity or by adapting to their novel environment. Here, we studied the African clawed frog, Xenopus laevis, which has become invasive on a global scale. We compared adults from an invasive population of western France with individuals from two populations in the native range in South Africa. We measured the thermal dependence of locomotor performance in adults given its relevance to dispersal, predator escape, and prey capture. Our results show significant differences in the limits of the 80% performance breadth interval for endurance with the French population showing a left shift in its limits congruent with the colder climate experienced in France. The French invasive population was introduced only about 40 years ago suggesting a rapid shift in the thermal physiology. Given that all individuals were acclimated under laboratory conditions at 23°C for 2 months this suggests that the invasive frogs have adapted to their new environment. These data may allow the refinement of physiologically informed species distribution models permitting better estimates of future ranges at risk of invasion.

Araspin, Laurie↗
DOE OSTI2020

Caveat mutator: alanine substitutions for conserved amino acids in RNA ligase elicit unexpected rearrangements of the active site for lysine adenylylation

Naegleria gruberi RNA ligase (NgrRnl) exemplifies the Rnl5 family of adenosine triphosphate (ATP)-dependent polynucleotide ligases that seal 3'-OH RNA strands in the context of 3'-OH/5'-PO 4 nicked duplexes. Like all classic ligases, NgrRnl forms a covalent lysyl–AMP intermediate. A two-metal mechanism of lysine adenylylation was established via a crystal structure of the NgrRnl•ATP•(Mn 2+ ) 2 Michaelis complex. Here we conducted an alanine scan of active site constituents that engage the ATP phosphates and the metal cofactors. We then determined crystal structures of ligase-defective NgrRnl-Ala mutants in complexes with ATP/Mn 2+ . The unexpected findings were that mutations K170A, E227A, K326A and R149A (none of which impacted overall enzyme structure) triggered adverse secondary changes in the active site entailing dislocations of the ATP phosphates, altered contacts to ATP, and variations in the numbers and positions of the metal ions that perverted the active sites into off-pathway states incompatible with lysine adenylylation. Each alanine mutation elicited a distinctive off-pathway distortion of the ligase active site. Our results illuminate a surprising plasticity of the ligase active site in its interactions with ATP and metals. More broadly, they underscore a valuable caveat when interpreting mutational data in the course of enzyme structure-function studies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

POGO-DB—a database of pairwise-comparisons of genomes and conserved orthologous genes

POGO-DB (http://pogo.ece.drexel.edu/) provides an easy platform for comparative microbial genomics. POGO-DB allows users to compare genomes using pre-computed metrics that were derived from extensive computationally intensive BLAST comparisons of >2000 microbes. These metrics include (i) average protein sequence identity across all orthologs shared by two genomes, (ii) genomic fluidity (a measure of gene content dissimilarity), (iii) number of ‘orthologs’ shared between two genomes, (iv) pairwise identity of the 16S ribosomal RNA genes and (v) pairwise identity of an additional 73 marker genes present in >90% prokaryotes. Users can visualize these metrics against each other in a 2D plot for exploratory analysis of genome similarity and of how different aspects of genome similarity relate to each other. The results of these comparisons are fully downloadable. In addition, users can download raw BLAST results for all or user-selected comparisons. Therefore, we provide users with full flexibility to carry out their own downstream analyses, by creating easy access to data that would normally require heavy computational resources to generate. POGO-DB should prove highly useful for researchers interested in comparative microbiology and benefit the microbiome/metagenomic communities by providing the information needed to select suitable phylogenetic marker genes within particular lineages.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Symmetry-conserving purification of quantum states within the density matrix renormalization group

The density matrix renormalization group (DMRG) algorithm was originally designed to efficiently compute the zero-temperature or ground-state properties of one-dimensional strongly correlated quantum systems. The development of the algorithm at finite temperature has been a topic of much interest, because of the usefulness of thermodynamics quantities in understanding the physics of condensed matter systems, and because of the increased complexity associated with efficiently computing temperature-dependent properties. The ancilla method is a DMRG technique that enables the computation of these thermodynamic quantities. In this paper, we review the ancilla method, and improve its performance by working on reduced Hilbert spaces and using canonical approaches. Furthermore we explore its applicability beyond spins systems to t-J and Hubbard models.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗