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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 991 records · Page 55
All sourcesNASA NTRSDOE OSTI
NASA NTRS2017

Analysis of in Vitro Evolution Reveals the Underlying Distribution of Catalytic Activity Among Random Sequences

The emergence of catalytic RNA is believed to have been a key event during the origin of life. Understanding how catalytic activity is distributed across random sequences is fundamental to estimating the probability that catalytic sequences would emerge. Here, we analyze the in vitro evolution of triphosphorylating ribozymes and translate their fitnesses into absolute estimates of catalytic activity for hundreds of ribozyme families. The analysis efficiently identified highly active ribozymes and estimated catalytic activity with good accuracy. The evolutionary dynamics follow Fisher’s Fundamental Theorem of Natural Selection and a corollary, permitting retrospective inference of the distribution of fitness and activity in the random sequence pool for the first time. The frequency distribution of rate constants appears to be log-normal, with a surprisingly steep dropoff at higher activity, consistent with a mechanism for the emergence of activity as the product of many independent contributions.

Abe Pressman↗
DOE OSTI2012

Complete genome sequence of Thauera aminoaromatica strain MZ1T

Thauera aminoaromatica strain MZ1T, an isolate belonging to genus Thauera, of the family Rhodocyclaceae and the class the Betaproteobacteria, has been characterized for its ability to produce abundant exopolysaccharide and degrade various aromatic compounds with nitrate as an electron acceptor. These properties, if fully understood at the genome-sequence level, can aid in environmental processing of organic matter in anaerobic cycles by short-circuiting a central anaerobic metabolite, acetate, from microbiological conversion to methane, a criti-cal greenhouse gas. Strain MZ1T is the first strain from the genus Thauera with a completely sequenced genome. The 4,496,212 bp chromosome and 78,374 bp plasmid contain 4,071 protein-coding and 71 RNA genes, and were sequenced as part of the DOE Community Se-quencing Program CSP{_}776774.

03 NATURAL GAS↗
DOE OSTI2013

Next Generation Sequencing at the University of Chicago Genomics Core

The University of Chicago Genomics Core provides University of Chicago investigators (and external clients) access to State-of-the-Art genomics capabilities: next generation sequencing, Sanger sequencing / genotyping and micro-arrays (gene expression, genotyping, and methylation). The current presentation will highlight our capabilities in the area of ultra-high throughput sequencing analysis.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2014

Microbial species delineation using whole genome sequences

Species assignments in prokaryotes use a manual, poly-phasic approach utilizing both phenotypic traits and sequence information of phylogenetic marker genes. With thousands of genomes being sequenced every year, an automated, uniform and scalable approach exploiting the rich genomic information in whole genome sequences is desired, at least for the initial assignment of species to an organism. We have evaluated pairwise genome-wide Average Nucleotide Identity (gANI) values and alignment fractions (AFs) for nearly 13,000 genomes using our fast implementation of the computation, identifying robust and widely applicable hard cut-offs for species assignments based on AF and gANI. Using these cutoffs, we generated stable species-level clusters of organisms, which enabled the identification of several species mis-assignments and facilitated the assignment of species for organisms without species definitions.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2018

SNMR pulse sequencing methods and apparatus

Technologies applicable to SNMR pulse sequencing are disclosed, including SNMR acquisition apparatus and methods, SNMR processing apparatus and methods, and combinations thereof. SNMR acquisition may include transmitting SNMR pulse sequences according to any of a variety of techniques. SNMR processing may include combining SNMR from a plurality of pulse sequences.

47 OTHER INSTRUMENTATION↗
DOE OSTI2021

Sequence Impedance Modeling of Grid-Forming Converters: Preprint

Grid-forming control of inverter-based resources (IBRs) has been identified as a critical technology for operating power systems with high levels of inverter-based resources. This paper presents sequence impedance modeling of grid-forming inverters to evaluate its small-signal stability properties. Droop based grid-forming control with full consideration of the multiloop structure is studied, and the impact of individual controller on the inverter impedance characteristics is discussed. The developed sequence impedance model is compared with that of the grid-following inverter. It is found from the developed sequence impedance models that grid-forming inverters are less prone to harmonic resonance problems during operation with weaker grids. The developed models are validated using PSCAD simulations.

41 EE - Solar Energy Technologies Office (EE-4S)↗
DOE OSTI2021

Athena: High-Performance Sparse Tensor Contraction Sequence on Heterogeneous Memory

Sparse tensor contraction sequence has been widely employed in many fields, such as chemistry and physics. However, how to efficiently implement the sequence faces multiple challenges, such as redundant computations and memory operations, massive memory consumption, and inefficient utilization of hardware. To address the above challenges, we introduce Athena, a high-performance framework for SpTC sequences. Athena introduces new data structures, leverages emerging Optane-based heterogeneous memory (HM) architecture, and stage parallelism. In particular, Athena introduces shared hash table-represented sparse accumulator to eliminate unnecessary input processing and data migration; Athena uses a novel data-semantic guided dynamic migration solution to make the best use of the Optane-based HM for high performance; Athena also co-runs execution phases with different characteristics to enable high hardware utilization. Evaluating with 12 datasets, we show that Athena brings 327-7362× speedup over the state-of-the-art SpTC algorithm. With the dynamic data placement guided by data semantics, Athena brings performance improvement on Optane-based HM over a state-of-the-art software-based data management solution, a hardware-based data management solution, and PMM-only by 1.58×, 1.82×, and 2.34× respectively.

Liu, Jiawen↗
DOE OSTI2021

Sequence Impedance Modeling of Grid-Forming Inverters

Grid-forming control of inverter-based resources has been identified as a critical technology for operating power systems with high levels of inverter-based resources. This paper presents the sequence impedance modeling of a grid-forming inverter to evaluate its small-signal stability properties. Droop control structure is implemented to control the inverter in grid-forming mode, and the impact of individual controller on the inverter impedance characteristics is discussed. The developed sequence impedance model is compared with that of the grid-following inverter. It is found from the developed sequence impedance models that grid-forming inverters are less prone to harmonic resonance problems during operation with weaker grids. The developed models are validated using PSCAD simulations.

grid-following inverter↗
DOE OSTI2022

Programmable pseudo-random sequence generator for use with universal lidar and its associated method of operation

A pseudo-random sequence generator for use within a universal lidar system and its corresponding method of operation. The pseudo-random sequence generator uses synchronized shift registers that are in series Binary adders are provided. The signal output of each of the shift registers is tapped and directed to the binary adders. High-speed switches are provided between the shift registers and the binary adders. The switches are programmed to connect only two of the shift registers to the binary adders for each of the pseudo-random patterns being generated. The binary adders generate an output signal that is received by the first shift register. The signal propagates through all the shift registers to the last shift register. The last shift register outputs a pseudo-random sequence.

Datta, Shubhashish↗
DOE OSTI2022

Sorghum Association Panel whole‐genome sequencing establishes cornerstone resource for dissecting genomic diversity

SUMMARY Association mapping panels represent foundational resources for understanding the genetic basis of phenotypic diversity and serve to advance plant breeding by exploring genetic variation across diverse accessions. We report the whole‐genome sequencing (WGS) of 400 sorghum ( Sorghum bicolor (L.) Moench) accessions from the Sorghum Association Panel (SAP) at an average coverage of 38× (25–72×), enabling the development of a high‐density genomic marker set of 43 983 694 variants including single‐nucleotide polymorphisms (approximately 38 million), insertions/deletions (indels) (approximately 5 million), and copy number variants (CNVs) (approximately 170 000). We observe slightly more deletions among indels and a much higher prevalence of deletions among CNVs compared to insertions. This new marker set enabled the identification of several novel putative genomic associations for plant height and tannin content, which were not identified when using previous lower‐density marker sets. WGS identified and scored variants in 5‐kb bins where available genotyping‐by‐sequencing (GBS) data captured no variants, with half of all bins in the genome falling into this category. The predictive ability of genomic best unbiased linear predictor (GBLUP) models was increased by an average of 30% by using WGS markers rather than GBS markers. We identified 18 selection peaks across subpopulations that formed due to evolutionary divergence during domestication, and we found six F st peaks resulting from comparisons between converted lines and breeding lines within the SAP that were distinct from the peaks associated with historic selection. This population has served and continues to serve as a significant public resource for sorghum research and demonstrates the value of improving upon existing genomic resources.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2000

Co-conservation of rRNA tetraloop sequences and helix length suggests involvement of the tetraloops in higher-order interactions

Terminal loops containing four nucleotides (tetraloops) are common in structural RNAs, and they frequently conform to one of three sequence motifs, GNRA, UNCG, or CUUG. Here we compare available sequences and secondary structures for rRNAs from bacteria, and we show that helices capped by phylogenetically conserved GNRA loops display a strong tendency to be of conserved length. The simplest interpretation of this correlation is that the conserved GNRA loops are involved in higher-order interactions, intramolecular or intermolecular, resulting in a selective pressure for maintaining the lengths of these helices. A small number of conserved UNCG loops were also found to be associated with conserved length helices, consistent with the possibility that this type of tetraloop also takes part in higher-order interactions.

Non-NASA Center↗
DOE OSTI2021

Revisiting the unique structure of autonomously replicating sequences in Yarrowia lipolytica and its role in pathway engineering

Production of industrially relevant compounds in microbial cell factories can employ either genomes or plasmids as an expression platform. Selection of plasmids as pathway carriers is advantageous for rapid demonstration but poses a challenge of stability. Yarrowia lipolytica has attracted great attention in the past decade for the biosynthesis of chemicals related to fatty acids at titers attractive to industry, and many genetic tools have been developed to explore its oleaginous potential. Here, our recent studies on the autonomously replicating sequences (ARSs) of nonconventional yeasts revealed that the ARSs from Y. lipolytica showcase a unique structure that includes a previously unannotated sequence (spacer) linking the origin of replication (ORI) and the centromeric (CEN) element and plays a critical role in modulating plasmid behavior. Maintaining a native 645-bp spacer yielded a 2.2-fold increase in gene expression and 1.7-fold higher plasmid stability compared to a more universally employed minimized ARS. Testing the modularity of the ARS sub-elements indicated that plasmid stability exhibits a pronounced cargo dependency. Instability caused both plasmid loss and intramolecular rearrangements. Altogether, our work clarifies the appropriate application of various ARSs for the scientific community and sheds light on a previously unexplored DNA element as a potential target for engineering Y. lipolytica.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

Characterization of bud emergence 46 (BEM46) protein: Sequence, structural, phylogenetic and subcellular localization analyses

Highlights: •All eukaryotes have at least a single copy of a bem46 ortholog. •The catalytic triad of BEM46 is illustrated using sequence and structural analysis. •We identified indels in the conserved domain of BEM46 protein. •Localization studies of BEM46 protein were carried out using GFP-fusion tagging. -- Abstract: The bud emergence 46 (BEM46) protein from Neurospora crassa belongs to the α/β-hydrolase superfamily. Recently, we have reported that the BEM46 protein is localized in the perinuclear ER and also forms spots close by the plasma membrane. The protein appears to be required for cell type-specific polarity formation in N. crassa. Furthermore, initial studies suggested that the BEM46 amino acid sequence is conserved in eukaryotes and is considered to be one of the widespread conserved “known unknown” eukaryotic genes. This warrants for a comprehensive phylogenetic analysis of this superfamily to unravel origin and molecular evolution of these genes in different eukaryotes. Herein, we observe that all eukaryotes have at least a single copy of a bem46 ortholog. Upon scanning of these proteins in various genomes, we find that there are expansions leading into several paralogs in vertebrates. Usingcomparative genomic analyses, we identified insertion/deletions (indels) in the conserved domain of BEM46 protein, which allow to differentiate fungal classes such as ascomycetes from basidiomycetes. We also find that exonic indels are able to differentiate BEM46 homologs of different eukaryotic lineage. Furthermore, we unravel that BEM46 protein from N. crassa possess a novel endoplasmic-retention signal (PEKK) using GFP-fusion tagging experiments. We propose that three residues namely a serine 188S, a histidine 292H and an aspartic acid 262D are most critical residues, forming a catalytic triad in BEM46 protein from N. crassa. We carried out a comprehensive study on bem46 genes from a molecular evolution perspective with combination of functional analyses. The evolutionary history of BEM46 proteins is characterized by exonic indels in lineage specific manner.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Sequences of seismic and aseismic slip on bimaterial faults show dominant rupture asymmetry and potential for elevated seismic hazard

Here we perform numerical simulations of sequences of earthquake and aseismic slip on planar rate and state faults separating dissimilar material within the 2-D plane strain approximation. We resolve all stages of the earthquake cycle from aseismic slip to fast ruptures while incorporating full inertia effects during seismic event propagation. We show that bimaterial coupling results in favorable nucleation site and subsequent asymmetric rupture propagation. We demonstrate that increasing the material contrast enhances this asymmetry leading to higher slip rates and normal stress drops in the preferred rupture propagation direction. The normal stress drop, induced by the bimaterial effect, leads to strong dynamic weakening of the fault and may destabilize the creeping region on a heterogeneous rate and state fault, resulting in extended rupture propagation. Such rupture penetration into creeping patches may lead to more frequent opening of earthquake gates, causing increased seismic hazard. Furthermore, bimaterial coupling may lead to irregular seismicity pattern in terms of event length, peak slip rates, and hypocenter location, depending on the properties of the creeping patches bordering the seismogenically active part of the fault. Our results highlight robust characteristics of bimaterial interfaces that persist over long sequence of events and suggest the need for further exploration of the role of material contrast in earthquake physics and models of seismic hazard.

58 GEOSCIENCES↗