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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 613 records · Page 34
All sourcesNASA NTRSDOE OSTI
NASA NTRS2021

Dual Quaternion Visual Servo Control

This paper focuses on a dual quaternion-based estimation and control approach for position-based visual servoing (PBVS). The pose estimation of the camera is achieved using a dual quaternion-based Extended Kalman Filter (EKF), which estimates the position and orientation of the camera based on feature points acquired through a sequence of camera images. Based on the estimation, a dual quaternion control law is developed to regulate the camera to the desired pose. Leveraging the local exponential stability of the EKF and the global exponential stability of the designed controller, a nonlinear separation principle is used to prove the stability of the joint estimation and control for PBVS. The method is distinguished from other PBVS methods in the sense that a compact representation of dual quaternion is used to represent the pose, and a joint stability of estimator and controller for PBVS in dual quaternion space is presented. The proposed dual quaternion PBVS method is validated using a simulation.

Quaternions↗
DOE OSTI2019

Prediction of bacterial E3 ubiquitin ligase effectors using reduced amino acid peptide fingerprinting

Background Although pathogenic Gram-negative bacteria lack their own ubiquitination machinery, they have evolved or acquired virulence effectors that can manipulate the host ubiquitination process through structural and/or functional mimicry of host machinery. Many such effectors have been identified in a wide variety of bacterial pathogens that share little sequence similarity amongst themselves or with eukaryotic ubiquitin E3 ligases. Methods To allow identification of novel bacterial E3 ubiquitin ligase effectors from protein sequences we have developed a machine learning approach, the SVM-based Identification and Evaluation of Virulence Effector Ubiquitin ligases (SIEVE-Ub). We extend the string kernel approach used previously to sequence classification by introducing reduced amino acid (RED) alphabet encoding for protein sequences. Results We found that 14mer peptides with amino acids represented as simply either hydrophobic or hydrophilic provided the best models for discrimination of E3 ligases from other effector proteins with a receiver-operator characteristic area under the curve (AUC) of 0.90. When considering a subset of E3 ubiquitin ligase effectors that do not fall into known sequence based families we found that the AUC was 0.82, demonstrating the effectiveness of our method at identifying novel functional family members. Feature selection was used to identify a parsimonious set of 10 RED peptides that provided good discrimination, and these peptides were found to be located in functionally important regions of the proteins involved in E2 and host target protein binding. Our general approach enables construction of models based on other effector functions. We used SIEVE-Ub to predict nine potential novel E3 ligases from a large set of bacterial genomes. SIEVE-Ub is available for download at https://doi.org/10.6084/m9.figshare.7766984.v1 or https://github.com/biodataganache/SIEVE-Ub for the most current version.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2017

Novel Approach to Quantification of Telomere Length with Direct Nanopore Sequencing and PCR Amplification

The ends of human chromosomes contain telomeres, or tandem arrays of repeating DNA sequences capped by multiple associated proteins that protect chromosomal ends from degradation. Telomeres function to preserve genomic stability by preventing natural chromosomal ends from being recognized as broken DNA double-strand breaks and triggering inappropriate DNA damage responses. Mounting evidence shows telomere length is an inherited trait that decreases with cellular division and normal aging. In addition, telomere length also appears to be influenced by other factors such as cellular oxidative stress, radiation and mechanical unloading of tissues as in microgravity. To measure these potential effects of the space environment on telomere lengths and cellular aging and regenerative potential we developed a novel telomere measurement approach based on nanopore sequencing of PCR amplified bar-coded chromosome termini. Specifically, telomeres can be directly enriched using barcode sequences ligated to the end of a free end- repaired telomere using the WetLab-2 facility SmartCycler on ISS. Prior to the ligation and amplification protocol a proteinase K digestion of capping proteins followed by a single 95-degree C heat denaturation of the protease is included. After digestion and bar-code ligation, PCR amplification will initiate with the ligated barcoded sequence, suppressing amplification of intra-genomic fragments and resulting in long read barcoded telomere amplicons including the nanopore motor protein sequences. Purified PCR amplicons are then used for nanopore sequencing library generation by simple addition of motor proteins and sequencing library is loaded into the MinION nanopore DNA-sequencer. Amplicon sequence reads from the nanopore device can be base-called quickly on ISS due to barcoding ligation and subsequent PCR amplification enhancing the telomere sequence resolution. If successfully implemented on ISS this technique will provide a novel means of measuring regenerative ability of somatic stem cells in astronauts, and of determining whether spaceflight in microgravity alters their telomere lengths and causes premature cellular aging.

Ma, Kristin R.↗
NASA NTRS1995

Systematic analysis of coding and noncoding DNA sequences using methods of statistical linguistics

We compare the statistical properties of coding and noncoding regions in eukaryotic and viral DNA sequences by adapting two tests developed for the analysis of natural languages and symbolic sequences. The data set comprises all 30 sequences of length above 50 000 base pairs in GenBank Release No. 81.0, as well as the recently published sequences of C. elegans chromosome III (2.2 Mbp) and yeast chromosome XI (661 Kbp). We find that for the three chromosomes we studied the statistical properties of noncoding regions appear to be closer to those observed in natural languages than those of coding regions. In particular, (i) a n-tuple Zipf analysis of noncoding regions reveals a regime close to power-law behavior while the coding regions show logarithmic behavior over a wide interval, while (ii) an n-gram entropy measurement shows that the noncoding regions have a lower n-gram entropy (and hence a larger "n-gram redundancy") than the coding regions. In contrast to the three chromosomes, we find that for vertebrates such as primates and rodents and for viral DNA, the difference between the statistical properties of coding and noncoding regions is not pronounced and therefore the results of the analyses of the investigated sequences are less conclusive. After noting the intrinsic limitations of the n-gram redundancy analysis, we also briefly discuss the failure of the zeroth- and first-order Markovian models or simple nucleotide repeats to account fully for these "linguistic" features of DNA. Finally, we emphasize that our results by no means prove the existence of a "language" in noncoding DNA.

NASA Discipline Number 14-10↗
DOE OSTI2018

SpaRC: scalable sequence clustering using Apache Spark

MOTIVATION: Whole genome shotgun based next-generation transcriptomics and metagenomics studies often generate 100-1000 GB sequence data derived from tens of thousands of different genes or microbial species. Assembly of these data sets requires tradeoffs between scalability and accuracy. Current assembly methods optimized for scalability often sacrifice accuracy and vice versa. An ideal solution would both scale and produce optimal accuracy for individual genes or genomes. RESULTS: In this work we describe an Apache Spark-based scalable sequence clustering application, SparkReadClust (SpaRC), that partitions reads based on their molecule of origin to enable downstream assembly optimization. SpaRC produces high clustering performance on transcriptomes and metagenomes from both short and long read sequencing technologies. It reaches near-linear scalability with input data size and number of compute nodes. SpaRC can run on both cloud computing and HPC environments without modification while delivering similar performance. Our findings demonstrate that SpaRC provides a scalable solution for clustering billions of reads from next-generation sequencing experiments, and Apache Spark represents a cost-effective solution with rapid development/deployment cycles for similar large-scale sequence data analysis problems. AVAILABILITY AND IMPLEMENTATION: https://bitbucket.org/berkeleylab/jgi-sparc.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2003

Carbonate Platform Development and Stromatolite Morphogenesis: Constraints on Environmental and Biological Evolution

Work has been completed on the digital mapping of a terminal Proterozoic reef complex in Namibia. This complex formed an isolated carbonate platform developed downdip on a carbonate ramp of the Nama Group. The stratigraphic evolution of the platform was digitally reconstructed from an extensive dataset that was compiled by using digital surveying technologies. The platform comprises three accommodation cycles in which each subsequent cycle experienced progressively greater influence of a long-term accommodation increase. Aggradation and progradation during the first cycle resulted in a flat, uniform, sheet-like platform. The coarsening and shallowing-upward sequence representing the first cycle is dominated by columnar stromatolitic thrombolites and massive dolostones with interbedded mudstone-grainstone at the base of the sequence grading into cross-bedded dolostones. The second cycle features aggradation, formation of a distinct margin containing thrombolite mounds and domes, and the development of a bucket geometry. Columnar stromatolitic thrombolites dominate the platform interior. The final stage of platform development shows a deepening trend with initial aggradation and formation of well-bedded, thin deposits in the interior and mound development at the margins. While the interior drowned, the platform margin kept up with rising sea level and a complex pinnacle reef formed containing fused and coalesced thrombolite mounds flanked by bioclastic grainstones (containing Cloudina and Namacalathus fossils) and collapse breccias. A set of isolated large thrombolite mounds flanked by shales indicate the final stage of the carbonate platform. During a progressive increase in accommodation, a flat-topped isolated carbonate platform becomes aerially less extensive by either backstepping or formation of smaller pinnacles or a combination of both. The overall geometric evolution of the studied platform from flat-topped to bucket with elevated margins is recorded in many Proterozoic and Phanerozoic isolated carbonate platforms with similar dimensions. The terminal Proterozoic, microbial-dominated, isolated carbonate platform of this study clearly illustrates that the answer to accommodation changes was already familiar among carbonate platforms before the dawn of metazoan-dominated platforms.

Grotzinger, John P.↗
NASA NTRS1994

A DNA enzyme that cleaves RNA

BACKGROUND: Several types of RNA enzymes (ribozymes) have been identified in biological systems and generated in the laboratory. Considering the variety of known RNA enzymes and the similarity of DNA and RNA, it is reasonable to imagine that DNA might be able to function as an enzyme as well. No such DNA enzyme has been found in nature, however. We set out to identify a metal-dependent DNA enzyme using in vitro selection methodology. RESULTS: Beginning with a population of 10(14) DNAs containing 50 random nucleotides, we carried out five successive rounds of selective amplification, enriching for individuals that best promote the Pb(2+)-dependent cleavage of a target ribonucleoside 3'-O-P bond embedded within an otherwise all-DNA sequence. By the fifth round, the population as a whole carried out this reaction at a rate of 0.2 min-1. Based on the sequence of 20 individuals isolated from this population, we designed a simplified version of the catalytic domain that operates in an intermolecular context with a turnover rate of 1 min-1. This rate is about 10(5)-fold increased compared to the uncatalyzed reaction. CONCLUSIONS: Using in vitro selection techniques, we obtained a DNA enzyme that catalyzes the Pb(2+)-dependent cleavage of an RNA phosphoester in a reaction that proceeds with rapid turnover. The catalytic rate compares favorably to that of known RNA enzymes. We expect that other examples of DNA enzymes will soon be forthcoming.

Non-NASA Center↗
NASA NTRS2003

Search-based optimization

The problem of determining the minimum cost hypothetical ancestral sequences for a given cladogram is known to be NP-complete (Wang and Jiang, 1994). Traditionally, point estimations of hypothetical ancestral sequences have been used to gain heuristic, upper bounds on cladogram cost. These include procedures with such diverse approaches as non-additive optimization of multiple sequence alignment, direct optimization (Wheeler, 1996), and fixed-state character optimization (Wheeler, 1999). A method is proposed here which, by extending fixed-state character optimization, replaces the estimation process with a search. This form of optimization examines a diversity of potential state solutions for cost-efficient hypothetical ancestral sequences and can result in greatly more parsimonious cladograms. Additionally, such an approach can be applied to other NP-complete phylogenetic optimization problems such as genomic break-point analysis. c2003 The Willi Hennig Society. Published by Elsevier Science (USA). All rights reserved.

Non-NASA Center↗
DOE OSTI2018

DNA Conformation Induces Adaptable Binding by Tandem Zinc Finger Proteins

Tandem zinc finger (ZF) proteins are the largest and most rapidly diverging family of DNA-binding transcription regulators in mammals. ZFP568 represses a transcript of placental-specific insulin like growth factor 2 (Igf2-P0) in mice. ZFP568 binds a 24-base pair sequence-specific element upstream of Igf2-P0 via the eleven-ZF array. Both DNA and protein conformations deviate from the conventional one finger-three bases recognition, with individual ZFs contacting 2, 3, or 4 bases and recognizing thymine on the opposite strand. These interactions arise from a shortened minor groove caused by an AT-rich stretch, suggesting adaptability of ZF arrays to sequence variations. Despite conservation in mammals, mutations at Igf2 and ZFP568 reduce their binding affinity in chimpanzee and humans. Furthermore, our studies provide important insights into the evolutionary and structural dynamics of ZF-DNA interactions that play a key role in mammalian development and evolution.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Mapping analysis of scaffold/matrix attachment regions (s/MARs) from two different mammalian cell lines

Scaffold/matrix attachment regions (S/MARs) are potential element that can be integrated into expression vector to increase expression of recombinant protein. Many studies on S/MAR have been done but none has revealed the distribution of S/MAR in a genome. In this study, we have isolated S/MAR sequences from HEK293 and Chinese hamster ovary cell lines (CHO DG44) using two different methods utilizing 2 M NaCl and lithium-3,5-diiodosalicylate (LIS). The isolated S/MARs were sequenced using Next Generation Sequencing (NGS) platform. Based on reference mapping analysis against human genome database, a total of 8,994,856 and 8,412,672 contigs of S/MAR sequences were retrieved from 2M NaCl and LIS extraction of HEK293 respectively. On the other hand, reference mapping analysis of S/MAR derived from CHO DG44 against our own CHO DG44 database have generated a total of 7,204,348 and 4,672,913 contigs from 2 M NaCl and LIS extraction method respectively.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2018

Conservation and Diversification of Circadian Rhythmicity Between a Model Crassulacean Acid Metabolism Plant Kalanchoë fedtschenkoi and a Model C 3 Photosynthesis Plant Arabidopsis thaliana

Crassulacean acid metabolism (CAM) improves photosynthetic efficiency under limited water availability relative to C 3 photosynthesis. It is widely accepted that CAM plants have evolved from C 3 plants and it is hypothesized that CAM is under the control of the internal circadian clock. However, the role that the circadian clock plays in the evolution of CAM is not well understood. To identify the molecular basis of circadian control over CAM evolution, rhythmic gene sets were identified in a CAM model plant species ( Kalanchoë fedtschenkoi ) and a C 3 model plant species ( Arabidopsis thaliana ) through analysis of diel time-course gene expression data using multiple periodicity detection algorithms. Based on protein sequences, ortholog groups were constructed containing genes from each of these two species. The ortholog groups were categorized into five gene sets based on conservation and diversification of rhythmic gene expression. Interestingly, minimal functional overlap was observed when comparing the rhythmic gene sets of each species. Specifcally, metabolic processes were enriched in the gene set under circadian control in K. fedtschenkoi and numerous genes were found to have retained or gained rhythmic expression in K. fedtsechenkoi . Additonally, several rhythmic orthologs, including CAM-related orthologs, displayed phase shifts between species. Results of this analysis point to several mechanisms by which the circadian clock plays a role in the evolution of CAM. These genes provide a set of testable hypotheses for future experiments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Exploring microscopic driving volatility in naturalistic driving environment prior to involvement in safety critical events—Concept of event-based driving volatility

The sequence of instantaneous driving decisions and its variations, known as driving volatility, prior to involvement in safety critical events can be a leading indicator of safety. Here, this study focuses on the component of “driving volatility matrix” related to specific normal and safety-critical events, named “event-based volatility.” The research issue is characterizing volatility in instantaneous driving decisions in the longitudinal and lateral directions, and how it varies across drivers involved in normal driving, crash, and/or near-crash events. To explore the issue, a rigorous quasi-experimental study design is adopted to help compare driving behaviors in normal vs unsafe outcomes. Using a unique real-world naturalistic driving database from the 2nd Strategic Highway Research Program (SHRP), a test set of 9593 driving events featuring 2.2 million temporal samples of real-world driving are analyzed. This study features a plethora of kinematic sensors, video, and radar spatiotemporal data about vehicle movement and therefore offers the opportunity to initiate such exploration. By using information related to longitudinal and lateral accelerations and vehicular jerk, 24 different aggregate and segmented measures of driving volatility are proposed that captures variations in extreme instantaneous driving decisions. In doing so, careful attention is given to the issue of intentional vs. unintentional volatility. The volatility indices, as leading indicators of near-crash and crash events, are then linked with safety critical events, crash propensity, and other event specific explanatory variables. Owing to the presence of unobserved heterogeneity and omitted variable bias, fixed- and random-parameter discrete choice models are developed that relate crash propensity to unintentional driving volatility and other factors. Statistically significant evidence is found that driver volatilities in near-crash and crash events are significantly greater than volatility in normal driving events. After controlling for traffic, roadway, and unobserved factors, the results suggest that greater intentional volatility increases the likelihood of both crash and near-crash events. A one-unit increase in intentional volatility is associated with positive vehicular jerk in longitudinal direction increases the chance of crash and near-crash outcome by 15.79 and 12.52 percentage points, respectively. Importantly, intentional volatility in positive vehicular jerk in lateral direction has more negative consequences than intentional volatility in positive vehicular jerk in longitudinal direction. Compared to acceleration/deceleration, vehicular jerk can better characterize the volatility in microscopic instantaneous driving decisions prior to involvement in safety critical events. Finally, the magnitudes of correlations exhibit significant heterogeneity, and that accounting for the heterogeneous effects in the modeling framework can provide more reliable and accurate results. The study demonstrates the value of quasi-experimental study design and big data analytics for understanding extreme driving behaviors in safe vs. unsafe driving outcomes.

33 ADVANCED PROPULSION SYSTEMS↗
DOE OSTI2022

Parameterization of generic positive sequence models to represent behavior of inverter based resources in low short circuit scenarios

The connection of large inverter based resources (IBR) in transmission systems is often located geographically and electrically far away from load centers. This, coupled with the displacement of synchronous machine plants, results in a reduction of the network short circuit strength at the point of connection. Under these conditions, state-of-the-art positive sequence simulation platforms and models can have difficulties maintaining numerical stability and/or providing an accurate representation of IBR plant dynamic behavior. As a result, computationally heavy time domain electromagnetic transient (EMT) simulations may be required to evaluate these systems. In this paper, a recently developed improved generic positive sequence model is parameterized to provide a representation of IBR behavior in low short circuit networks. Further, comparisons against generic and detailed EMT models demonstrate the suitability of the improved positive sequence model to study practical stability issues experienced with presently in-service plants. Such a model can provide some of the accuracy of an EMT representation with a much lower computational burden. The performance of the positive sequence model is validated against the behavior shown by both open white box and closed black box EMT domain models from around the world.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2015

A topological approach for protein classification

Here, protein function and dynamics are closely related to its sequence and structure. However, prediction of protein function and dynamics from its sequence and structure is still a fundamental challenge in molecular biology. Protein classification, which is typically done through measuring the similarity between proteins based on protein sequence or physical information, serves as a crucial step toward the understanding of protein function and dynamics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Differential sensitivity of Chironomus and human hemoglobin to gamma radiation

Chironomus ramosus is known to tolerate high doses of gamma radiation exposure. Larvae of this insect possess more than 95% of hemoglobin (Hb) in its circulatory hemolymph. This is a comparative study to see effect of gamma radiation on Hb of Chironomus and humans, two evolutionarily diverse organisms one having extracellular and the other intracellular Hb respectively. Stability and integrity of Chironomus and human Hb to gamma radiation was compared using biophysical techniques like Dynamic Light Scattering (DLS), UV-visible spectroscopy, fluorescence spectrometry and CD spectroscopy after exposure of whole larvae, larval hemolymph, human peripheral blood, purified Chironomus and human Hb. Sequence- and structure-based bioinformatics methods were used to analyze the sequence and structural similarities or differences in the heme pockets of respective Hbs. Resistivity of Chironomus Hb to gamma radiation is remarkably higher than human Hb. Human Hb exhibited loss of heme iron at a relatively low dose of gamma radiation exposure as compared to Chironomus Hb. Unlike human Hb, the heme pocket of Chironomus Hb is rich in aromatic amino acids. Higher hydophobicity around heme pocket confers stability of Chironomus Hb compared to human Hb. Previously reported gamma radiation tolerance of Chironomus can be largely attributed to its evolutionarily ancient form of extracellular Hb as evident from the present study. -- Highlights: •Comparison of radiation tolerant Chironomus Hb and radiation sensitive Human Hb. •Amino acid composition of midge and human heme confer differential hydrophobicity. •Heme pocket of evolutionarily ancient midge Hb provide gamma radiation resistivity.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

Inactivation of Mandelate Racemase by 3-Hydroxypyruvate Reveals a Potential Mechanistic Link between Enzyme Superfamilies

Mandelate racemase (MR), a member of the enolase superfamily, catalyzes the Mg 2+ -dependent interconversion of the enantiomers of mandelate. Several α-keto acids are modest competitive inhibitors of MR [e.g., mesoxalate (K i = 1.8 ± 0.3 mM) and 3-fluoropyruvate (K i = 1.3 ± 0.1 mM)], but, surprisingly, 3-hydroxypyruvate (3-HP) is an irreversible, time-dependent inhibitor (k inact /K I = 83 ± 8 M –1 s –1 ). Protection from inactivation by the competitive inhibitor benzohydroxamate, trypsinolysis and electrospray ionization tandem mass spectrometry analyses, and X-ray crystallographic studies reveal that 3-HP undergoes Schiff-base formation with Lys 166 at the active site, followed by formation of an aldehyde/enol(ate) adduct. Such a reaction is unprecedented in the enolase superfamily and may be a relic of an activity possessed by a promiscuous progenitor enzyme. The ability of MR to form and deprotonate a Schiff-base intermediate furnishes a previously unrecognized mechanistic link to other α/β-barrel enzymes utilizing Schiff-base chemistry and is in accord with the sequence- and structure-based hypothesis that members of the metal-dependent enolase superfamily and the Schiff-base-forming N-acetylneuraminate lyase superfamily and aldolases share a common ancestor.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

A high-throughput skim-sequencing approach for genotyping, dosage estimation and identifying translocations

The development of next-generation sequencing (NGS) enabled a shift from array-based genotyping to directly sequencing genomic libraries for high-throughput genotyping. Even though whole-genome sequencing was initially too costly for routine analysis in large populations such as breeding or genetic studies, continued advancements in genome sequencing and bioinformatics have provided the opportunity to capitalize on whole-genome information. As new sequencing platforms can routinely provide high-quality sequencing data for sufficient genome coverage to genotype various breeding populations, a limitation comes in the time and cost of library construction when multiplexing a large number of samples. Here we describe a high-throughput whole-genome skim-sequencing (skim-seq) approach that can be utilized for a broad range of genotyping and genomic characterization. Using optimized low-volume Illumina Nextera chemistry, we developed a skim-seq method and combined up to 960 samples in one multiplex library using dual index barcoding. With the dual-index barcoding, the number of samples for multiplexing can be adjusted depending on the amount of data required, and could be extended to 3,072 samples or more. Panels of doubled haploid wheat lines ( Triticum aestivum , CDC Stanley x CDC Landmark), wheat-barley ( T . aestivum x Hordeum vulgare ) and wheat-wheatgrass ( Triticum durum x Thinopyrum intermedium ) introgression lines as well as known monosomic wheat stocks were genotyped using the skim-seq approach. Bioinformatics pipelines were developed for various applications where sequencing coverage ranged from 1 × down to 0.01 × per sample. Using reference genomes, we detected chromosome dosage, identified aneuploidy, and karyotyped introgression lines from the skim-seq data. Leveraging the recent advancements in genome sequencing, skim-seq provides an effective and low-cost tool for routine genotyping and genetic analysis, which can track and identify introgressions and genomic regions of interest in genetics research and applied breeding programs.

60 APPLIED LIFE SCIENCES↗