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At least 1,765 records · Page 98
All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

Comparative structural analysis of Bru1 region homeologs in Saccharum spontaneum and S. officinarum

Here, sugarcane is a major sugar and biofuel crop, but genomic research and molecular breeding have lagged behind other major crops due to the complexity of auto-allopolyploid genomes. Sugarcane cultivars are frequently aneuploid with chromosome number ranging from 100 to 130, consisting of 70-80 % S. officinarum , 10-20 % S. spontaneum , and 10 % recombinants between these two species. Analysis of a genomic region in the progenitor autoploid genomes of sugarcane hybrid cultivars will reveal the nature and divergence of homologous chromosomes. As a result, to investigate the origin and evolution of haplotypes in the Bru1 genomic regions in sugarcane cultivars, we identified two BAC clones from S. spontaneum and four from S. officinarum and compared to seven haplotype sequences from sugarcane hybrid R570. The results clarified the origin of seven homologous haplotypes in R570, four haplotypes originated from S. officinarum , two from S. spontaneum and one recombinant.. Retrotransposon insertions and sequences variations among the homologous haplotypes sequence divergence ranged from 18.2 % to 60.5 % with an average of 33. 7 %. Gene content and gene structure were relatively well conserved among the homologous haplotypes. Exon splitting occurred in haplotypes of the hybrid genome but not in its progenitor genomes. Tajima's D analysis revealed that S. spontaneum hapotypes in the Bru1 genomic regions were under strong directional selection. Numerous inversions, deletions, insertions and translocations were found between haplotypes within each genome. In conclusion, this is the first comparison among haplotypes of a modern sugarcane hybrid and its two progenitors. Tajima's D results emphasized the crucial role of this fungal disease resistance gene for enhancing the fitness of this species and indicating that the brown rust resistance gene in R570 is from S. spontaneum . Species-specific InDel, sequences similarity and phylogenetic analysis of homologous genes can be used for identifying the origin of S. spontaneum and S. officinarum haplotype in Saccharum hybrids. Comparison of exon splitting among the homologous haplotypes suggested that the genome rearrangements in Saccharum hybrids S. officinarum would be sufficient for proper genome assembly of this autopolyploid genome. Retrotransposon insertions and sequences variations among the homologous haplotypes sequence divergence may allow sequencing and assembling the autopolyploid Saccharum genomes and the auto-allopolyploid hybrid genomes using whole genome shotgun sequencing.

09 BIOMASS FUELS↗
DOE OSTI2020

Transition Core Analysis for HEU to LEU Fuel Conversion at the University of Missouri Research Reactor

A new type of low-enriched uranium (LEU) fuel based on an alloy of uranium and molybdenum is expected to allow the conversion of U.S. domestic high-performance research and test reactors requiring high density fuel from highly enriched uranium (HEU) to LEU. The University of Missouri Research Reactor (MURR (R)) has undergone design and performance calculations for conversion to this LEU fuel. Presented in this paper is the analysis of a crucial step in the conversion process: the sequence of MURR transition cores from all fresh to equilibrium burnup LEU operations. During the initial conversion from HEU to LEU fuel, MURR will operate atypically due to the lack of burned LEU elements. Given the constraints of MURR operation and experiments, a proposed transition scheme minimizes the time MURR operates atypically compared to the prototypic cycles currently run with HEU fuel and moves quickly to the same sort of equilibrium cycles for the LEU fuel.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2013

Structure-Based Comparative Analysis and Prediction of N-Linked Glycosylation Sites in Evolutionarily Distant Eukaryotes

Abstract The asparagine-X-serine/threonine (NXS/T) motif, where X is any amino acid except proline, is the consensus motif for N-linked glycosylation. Significant numbers of high-resolution crystal structures of glycosylated proteins allow us to carry out structural analysis of the N-linked glycosylation sites (NGS). Our analysis shows that there is enough structural information from diverse glycoproteins to allow the development of rules which can be used to predict NGS. A Python-based tool was developed to investigate asparagines implicated in N-glycosylation in five species: Homo sapiens, Mus musculus, Drosophila melanogaster, Arabidopsis thaliana and Saccharomyces cerevisiae. Our analysis shows that 78% of all asparagines of NXS/T motif involved in N-glycosylation are localized in the loop/turn conformation in the human proteome. Similar distribution was revealed for all the other species examined. Comparative analysis of the occurrence of NXS/T motifs not known to be glycosylated and their reverse sequence (S/TXN) shows a similar distribution across the secondary structural elements, indicating that the NXS/T motif in itself is not biologically relevant. Based on our analysis, we have defined rules to determine NGS. Using machine learning methods based on these rules we can predict with 93% accuracy if a particular site will be glycosylated. If structural information is not available the tool uses structural prediction results resulting in 74% accuracy. The tool was used to identify glycosylation sites in 108 human proteins with structures and 2247 proteins without structures that have acquired NXS/T site/s due to non-synonymous variation. The tool, Structure Feature Analysis Tool (SFAT), is freely available to the public at http://hive.biochemistry.gwu.edu/tools/sfat.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2012

Groundtruthing Next-Gen Sequencing for Microbial Ecology–Biases and Errors in Community Structure Estimates from PCR Amplicon Pyrosequencing

Analysis of microbial communities by high-throughput pyrosequencing of SSU rRNA gene PCR amplicons has transformed microbial ecology research and led to the observation that many communities contain a diverse assortment of rare taxa–a phenomenon termed the Rare Biosphere. Multiple studies have investigated the effect of pyrosequencing read quality on operational taxonomic unit (OTU) richness for contrived communities, yet there is limited information on the fidelity of community structure estimates obtained through this approach. Given that PCR biases are widely recognized, and further unknown biases may arise from the sequencing process itself, a priori assumptions about the neutrality of the data generation process are at best unvalidated. Furthermore, post-sequencing quality control algorithms have not been explicitly evaluated for the accuracy of recovered representative sequences and its impact on downstream analyses, reducing useful discussion on pyrosequencing reads to their diversity and abundances. Here we report on community structures and sequences recovered for in vitro-simulated communities consisting of twenty 16S rRNA gene clones tiered at known proportions. PCR amplicon libraries of the V3–V4 and V6 hypervariable regions from the in vitro-simulated communities were sequenced using the Roche 454 GS FLX Titanium platform. Commonly used quality control protocols resulted in the formation of OTUs with >1% abundance composed entirely of erroneous sequences, while over-aggressive clustering approaches obfuscated real, expected OTUs. The pyrosequencing process itself did not appear to impose significant biases on overall community structure estimates, although the detection limit for rare taxa may be affected by PCR amplicon size and quality control approach employed. Meanwhile, PCR biases associated with the initial amplicon generation may impose greater distortions in the observed community structure.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRSDate not supplied

Optimizing a Small RNAseq Analysis Pipeline for NASA GeneLab Using Open-Source Tools and Libraries

Small RNA sequencing (small RNAseq) is a powerful tool for studying the regulation of gene expression in various organisms. Small RNAseq has been leveraged in space biology research to study how expression of small RNAs, e.g. micro RNAs (miRNAs), small interfering RNAs (siRNAs), and piwi-interacting RNAs (piRNAs), change upon exposure to the space environment. NASA GeneLab currently hosts small RNAseq raw data derived from space-relevant experiments on the Open Science Data Repository (OSDR). To maximize the accessibility of these data to the scientific community, in addition to hosting raw data, which is only interpretable by bioinformaticians, GeneLab plans to process all small RNAseq datasets and make those processed data available to the scientific community via the OSDR. In this study, we present the development of the GeneLab standardized pipeline for processing small RNAseq datasets. Using human, plant, and synthetic small RNAseq datasets, we interrogate various open-source software and publicly available databases to evaluate their accuracy and reproducibility in each step of the pipeline. For quality control and adapter detection and trimming, we evaluated TrimGalore!, FASTX, SeqKit, and DNApi methods to optimize alignment to reference genomes. We compared BWA, Bowtie, and Bowtie2 to determine the optimal alignment tool. For each alignment tool we also assessed various reference databases, including Ensembl reference genomes and different types of small RNA reference databases, including genome, hairpin, and miRNA references from the miRbase and MirGeneDB databases. To quantify the aligned data, we compared SAMtools, HTSeq, and RSEM for counting alignment events from each alignment tool used. Finally, we evaluated various tools, including DESeq2 and EdgeR, for data normalization and subsequent differential expression analysis. We will present the results from our comparative analyses for each pipeline step and propose a consensus pipeline for processing small RNAseq data derived from various organisms exposed to the space environment.

SmallRNAseq, NASA GeneLab, quality control, adapte↗
DOE OSTI2021

Long-read metagenomics of soil communities reveals phylum-specific secondary metabolite dynamics

Abstract Microbial biosynthetic gene clusters (BGCs) encoding secondary metabolites are thought to impact a plethora of biologically mediated environmental processes, yet their discovery and functional characterization in natural microbiomes remains challenging. Here we describe deep long-read sequencing and assembly of metagenomes from biological soil crusts, a group of soil communities that are rich in BGCs. Taking advantage of the unusually long assemblies produced by this approach, we recovered nearly 3,000 BGCs for analysis, including 712 full-length BGCs. Functional exploration through metatranscriptome analysis of a 3-day wetting experiment uncovered phylum-specific BGC expression upon activation from dormancy, elucidating distinct roles and complex phylogenetic and temporal dynamics in wetting processes. For example, a pronounced increase in BGC transcription occurs at night primarily in cyanobacteria, implicating BGCs in nutrient scavenging roles and niche competition. Taken together, our results demonstrate that long-read metagenomic sequencing combined with metatranscriptomic analysis provides a direct view into the functional dynamics of BGCs in environmental processes and suggests a central role of secondary metabolites in maintaining phylogenetically conserved niches within biocrusts.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Revising the Evolutionary Stage of HD 163899: The Effects of Convective Overshooting and Rotation

We revise the evolutionary status of the B-type supergiant HD 163899 based on the new determinations of the mass–luminosity ratio, effective temperature, and rotational velocity, as well as on the interpretation of the oscillation spectrum of the star. The observed value of the nitrogen-to-carbon abundance fixes the value of the rotation rate of the star. Now, more massive models are strongly preferred than those previously considered, and it is very likely that the star is still in the main-sequence stage. The rotationally induced mixing manifests as the nitrogen overabundance in the atmosphere, which agrees with our analysis of the HARPS spectra. Thus, HD 163899 probably belongs to a group of evolved nitrogen-rich main-sequence stars.

79 ASTRONOMY AND ASTROPHYSICS↗
NASA NTRS1995

Radio-science performance analysis software

The Radio Science Systems Group (RSSG) provides various support functions for several flight project radio-science teams. Among these support functions are uplink and sequence planning, real-time operations monitoring and support, data validation, archiving and distribution functions, and data processing and analysis. This article describes the support functions that encompass radio-science data performance analysis. The primary tool used by the RSSG to fulfill this support function is the STBLTY program set. STBLTY is used to reconstruct observable frequencies and calculate model frequencies, frequency residuals, frequency stability in terms of Allan deviation, reconstructed phase, frequency and phase power spectral density, and frequency drift rates. In the case of one-way data, using an ultrastable oscillator (USO) as a frequency reference, the program set computes the spacecraft transmitted frequency and maintains a database containing the in-flight history of the USO measurements. The program set also produces graphical displays. Some examples and discussions on operating the program set on Galileo and Ulysses data will be presented.

Morabito, D. D.↗
DOE OSTI2012

Genometa - A Fast and Accurate Classifier for Short Metagenomic Shotgun Reads

Metagenomic studies use high-throughput sequence data to investigate microbial communities in situ. However, considerable challenges remain in the analysis of these data, particularly with regard to speed and reliable analysis of microbial species as opposed to higher level taxa such as phyla. We here present Genometa, a computationally undemanding graphical user interface program that enables identification of bacterial species and gene content from datasets generated by inexpensive high-throughput short read sequencing technologies. Our approach was first verified on two simulated metagenomic short read datasets, detecting 100% and 94% of the bacterial species included with few false positives or false negatives. Subsequent comparative benchmarking analysis against three popular metagenomic algorithms on an Illumina human gut dataset revealed Genometa to attribute the most reads to bacteria at species level (i.e. including all strains of that species) and demonstrate similar or better accuracy than the other programs. Lastly, speed was demonstrated to be many times that of BLAST due to the use of modern short read aligners. Our method is highly accurate if bacteria in the sample are represented by genomes in the reference sequence but cannot find species absent from the reference. This method is one of the most user-friendly and resource efficient approaches and is thus feasible for rapidly analysing millions of short reads on a personal computer.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Bayesian Characterization of Main-sequence Binaries in the Old Open Cluster NGC 188

The binary fractions of open and globular clusters yield powerful constraints on their dynamical state and evolutionary history. We apply publicly available Bayesian analysis tools to a UBV RIJHK {sub S} photometric catalog of the open cluster NGC 188 to detect and characterize photometric binaries along the cluster main sequence. This technique has the advantage of self-consistently handling photometric errors, missing data in various bandpasses, and star-by-star prior constraints on cluster membership. Simulations are used to verify uncertainties and quantify selection biases in our analysis, illustrating that among binaries with mass ratios >0.5, we recover the binary fraction to better than 7% in the mean, with no significant dependence on binary fraction and a mild dependence on assumed mass-ratio distribution. Using our photometric catalog, we recover the majority (65% ± 11%) of spectroscopically identified main-sequence binaries, including eight of the nine with spectroscopically measured mass ratios. Accounting for incompleteness and systematics, we derive a mass-ratio distribution that rises toward lower mass ratios (within our q > 0.5 analysis domain). We observe a raw binary fraction for solar-type main-sequence stars with mass ratios q > 0.5 of 42% ± 4%, independent of the assumed mass-ratio distribution to within its uncertainties, consistent with literature values for old open clusters but significantly higher than the field solar-type binary fraction. We confirm that the binaries identified by our method are more concentrated than single stars, in agreement with previous studies, and we demonstrate that the binary nature of those candidates that remain unidentified spectroscopically is strongly supported by photometry from Gaia DR2.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2014

PS1-10jh: The disruption of a main-sequence star of near-solar composition

When a star comes within a critical distance to a supermassive black hole (SMBH), immense tidal forces disrupt the star, resulting in a stream of debris that falls back onto the SMBH and powers a luminous flare. In this paper, we perform hydrodynamical simulations of the disruption of a main-sequence star by an SMBH to characterize the evolution of the debris stream after a tidal disruption. We demonstrate that this debris stream is confined by self-gravity in the two directions perpendicular to the original direction of the star's travel and as a consequence has a negligible surface area and makes almost no contribution to either the continuum or line emission. We therefore propose that any observed emission lines are not the result of photoionization in this unbound debris, but are produced in the region above and below the forming elliptical accretion disk, analogous to the broad-line region (BLR) in steadily accreting active galactic nuclei. As each line within a BLR is observationally linked to a particular location in the accretion disk, we suggest that the absence of a line indicates that the accretion disk does not yet extend to the distance required to produce that line. This model can be used to understand the spectral properties of the tidal disruption event PS1-10jh, for which He II lines are observed, but the Balmer series and He I are not. Using a maximum likelihood analysis, we show that the disruption of a main-sequence star of near-solar composition can reproduce this event.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2014

Resistance Determinants and Mobile Genetic Elements of an NDM-1-Encoding Klebsiella pneumoniae Strain

Multidrug-resistant Enterobacteriaceae are emerging as a serious infectious disease challenge. These strains can accumulate many antibiotic resistance genes though horizontal transfer of genetic elements, those for b-lactamases being of particular concern. Some b-lactamases are active on a broad spectrum of b-lactams including the last-resort carbapenems. The gene for the broad-spectrum and carbapenem-active metallo-b-lactamase NDM-1 is rapidly spreading. We present the complete genome of Klebsiella pneumoniae ATCC BAA-2146, the first U.S. isolate found to encode NDM-1, and describe its repertoire of antibiotic-resistance genes and mutations, including genes for eight b-lactamases and 15 additional antibiotic-resistance enzymes. To elucidate the evolution of this rich repertoire, the mobile elements of the genome were characterized, including four plasmids with varying degrees of conservation and mosaicism and eleven chromosomal genomic islands. One island was identified by a novel phylogenomic approach, that further indicated the cps-lps polysaccharide synthesis locus, where operon translocation and fusion was noted. Unique plasmid segments and mosaic junctions were identified. Plasmid-borne blaCTX-M-15 was transposed recently to the chromosome by ISEcp1. None of the eleven full copies of IS26, the most frequent IS element in the genome, had the expected 8-bp direct repeat of the integration target sequence, suggesting that each copy underwent homologous recombination subsequent to its last transposition event. Comparative analysis likewise indicates IS26 as a frequent recombinational junction between plasmid ancestors, and also indicates a resolvase site. In one novel use of high-throughput sequencing, homologously recombinant subpopulations of the bacterial culture were detected. In a second novel use, circular transposition intermediates were detected for the novel insertion sequence ISKpn21 of the ISNCY family, suggesting that it uses the two-step transposition mechanism of IS3. Robust genome-based phylogeny showed that a unified Klebsiella cluster contains Enterobacter aerogenes and Raoultella, suggesting the latter genus should be abandoned.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Pebble Tanker Model for Nuclear Criticality Safety Needs

This report documents a study performed to investigate the requirements for criticality safety benchmark experiments for high-assay, low-enriched uranium (HALEU) fuel in transportation applications. In this work, an exploratory application model, the “Pebble Tanker,” was developed to represent TRISO fuel in a transportation scenario for an analysis of the validation basis in industrial quantities. An aspect of the criticality validation process involves assessing the “similarity” between application and experimental benchmark systems through an integral index parameter evaluation. Here, this includes propagating nuclear data uncertainties and calculating a correlation coefficient (hereinafter referred to as “c k ”) to evaluate the similarity of benchmark experiments compared with the application Pebble Tanker model. Finding sufficient critical benchmark experiments allows for the evaluation of bias and bias uncertainty, thus determining the upper subcritical limit (USL) of the transportation package. A target k eff of ~0.94 was used in this work to establish appropriate modeling conditions, reflecting a reasonable estimate for a USL. Two container models were investigated: one with the Hermes-type pebble and one with the Pebble Bed Modular Reactor (PBMR)–type pebble. The models were simplified, considering only fuel, containment structure, and either water or air. This allows a focus on the underlying physics of applications involving TRISO fuel pebbles using the Pebble Tanker model. A crucial consideration is the transport package's ability to safely hold pebbles while flooded, maintaining subcritical conditions. Tools available in the SCALE 6.3.1 suite—the CSAS6-Shift, TSUNAMI-3D-Shift, and TSUNAMI-IP sequences—were employed for neutronics and sensitivity and uncertainty (S/U) analysis of the Pebble Tanker. Findings demonstrated sufficient available critical experiment benchmarks to perform a validation of the Pebble Tanker in the most reactive state, i.e., when the Tanker is flooded.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2024

Genome-scale model development and genomic sequencing of the oleaginous clade Lipomyces

The Lipomyces clade contains oleaginous yeast species with advantageous metabolic features for biochemical and biofuel production. Limited knowledge about the metabolic networks of the species and limited tools for genetic engineering have led to a relatively small amount of research on the microbes. Here, a genome-scale metabolic model (GSM) of Lipomyces starkeyi NRRL Y-11557 was built using orthologous protein mappings to model yeast species. Phenotypic growth assays were used to validate the GSM (66% accuracy) and indicated that NRRL Y-11557 utilized diverse carbohydrates but had more limited catabolism of organic acids. The final GSM contained 2,193 reactions, 1,909 metabolites, and 996 genes and was thus named iLst996. The model contained 96 of the annotated carbohydrate-active enzymes. iLst996 predicted a flux distribution in line with oleaginous yeast measurements and was utilized to predict theoretical lipid yields. Twenty-five other yeasts in the Lipomyces clade were then genome sequenced and annotated. Sixteen of the Lipomyces species had orthologs for more than 97% of the iLst996 genes, demonstrating the usefulness of iLst996 as a broad GSM for Lipomyces metabolism. Pathways that diverged from iLst996 mainly revolved around alternate carbon metabolism, with ortholog groups excluding NRRL Y-11557 annotated to be involved in transport, glycerolipid, and starch metabolism, among others. Overall, this study provides a useful modeling tool and data for analyzing and understanding Lipomyces species metabolism and will assist further engineering efforts in Lipomyces .

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1989

Analysis of the flight dynamics of the Solar Maximum Mission (SMM) off-sun scientific pointing

Algorithms are presented which were created and implemented by the Goddard Space Flight Center's (GSFC's) Solar Maximum Mission (SMM) attitude operations team to support large-angle spacecraft pointing at scientific objectives. The mission objective of the post-repair SMM satellite was to study solar phenomena. However, because the scientific instruments, such as the Coronagraph/Polarimeter (CP) and the Hard X ray Burst Spectrometer (HXRBS), were able to view objects other than the Sun, attitude operations support for attitude pointing at large angles from the nominal solar-pointing attitudes was required. Subsequently, attitude support for SMM was provided for scientific objectives such as Comet Halley, Supernova 1987A, Cygnus X-1, and the Crab Nebula. In addition, the analysis was extended to include the reverse problem, computing the right ascension and declination of a body given the off-Sun angles. This analysis led to the computation of the orbits of seven new solar comets seen in the field-of-view (FOV) of the CP. The activities necessary to meet these large-angle attitude-pointing sequences, such as slew sequence planning, viewing-period prediction, and tracking-bias computation are described. Analysis is presented for the computation of maneuvers and pointing parameters relative to the SMM-unique, Sun-centered reference frame. Finally, science data and independent attitude solutions are used to evaluate the large-angle pointing performance.

Pitone, D. S.↗
NASA NTRS1990

Analysis of the flight dynamics of the Solar Maximum Mission (SMM) off-sun scientific pointing

Algorithms are presented which were created and implemented by the Goddard Space Flight Center's (GSFC's) Solar Maximum Mission (SMM) attitude operations team to support large-angle spacecraft pointing at scientific objectives. The mission objective of the post-repair SMM satellite was to study solar phenomena. However, because the scientific instruments, such as the Coronagraph/Polarimeter (CP) and the Hard X-ray Burst Spectrometer (HXRBS), were able to view objects other than the Sun, attitude operations support for attitude pointing at large angles from the nominal solar-pointing attitudes was required. Subsequently, attitude support for SMM was provided for scientific objectives such as Comet Halley, Supernova 1987A, Cygnus X-1, and the Crab Nebula. In addition, the analysis was extended to include the reverse problem, computing the right ascension and declination of a body given the off-Sun angles. This analysis led to the computation of the orbits of seven new solar comets seen in the field-of-view (FOV) of the CP. The activities necessary to meet these large-angle attitude-pointing sequences, such as slew sequence planning, viewing-period prediction, and tracking-bias computation are described. Analysis is presented for the computation of maneuvers and pointing parameters relative to the SMM-unique, Sun-centered reference frame. Finally, science data and independent attitude solutions are used to evaluate the larg-angle pointing performance.

Pitone, D. S.↗
DOE OSTI2018

Proteogenomic Analysis of Burkholderia Species Strains 25 and 46 Isolated from Uraniferous Soils Reveals Multiple Mechanisms to Cope with Uranium Stress

Two Burkholderia spp. (strains SRS-25 and SRS-46) were isolated from high concentrations of uranium (U) from the U.S. Department of Energy (DOE)-managed Savannah River Site (SRS). SRS contains soil gradients that remain co-contaminated by heavy metals from previous nuclear weapons production activities. Uranium (U) is one of the dominant contaminants within the SRS impacted soils, which can be microbially transformed into less toxic forms. We established microcosms containing strains SRS-25 and SRS-46 spiked with U and evaluated the microbially-mediated depletion with concomitant genomic and proteomic analysis. Both strains showed a rapid depletion of U; draft genome sequences revealed SRS-25 genome to be of approximately 8,152,324 bp, a G + C content of 66.5, containing a total 7604 coding sequences with 77 total RNA genes. Similarly, strain SRS-46 contained a genome size of 8,587,429 bp with a G + C content of 67.1, 7895 coding sequences, with 73 total RNA genes, respectively. An in-depth, genome-wide comparisons between strains 25, 46 and a previously isolated strain from our research (Burkholderia sp. strain SRS-W-2-2016), revealed a common pool of 3128 genes; many were found to be homologues to previously characterized metal resistance genes (e.g., for cadmium, cobalt, and zinc), as well as for transporter, stress/detoxification, cytochromes, and drug resistance functions. Furthermore, proteomic analysis of strains with or without U stress, revealed the increased expression of 34 proteins from strain SRS-25 and 52 proteins from strain SRS-46; similar to the genomic analyses, many of these proteins have previously been shown to function in stress response, DNA repair, protein biosynthesis and metabolism. Overall, this comparative proteogenomics study confirms the repertoire of metabolic and stress response functions likely rendering the ecological competitiveness to the isolated strains for colonization and survival in the heavy metals contaminated SRS soil habitat.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2020

Adaptive Stress Testing: Finding Likely Failure Events with Reinforcement Learning

Finding the most likely path to a set of failure states is important to the analysis of safety-critical systems that operate over a sequence of time steps, such as aircraft collision avoidance systems and autonomous cars. In many applications such as autonomous driving, failures cannot be completely eliminated due to the complex stochastic environment in which the system operates.As a result, safety validation is not only concerned about whether a failure can occur, but also discovering which failures are most likely to occur. This article presents adaptive stress testing (AST), a framework for finding the most likely path to a failure event in simulation. We consider a general black box setting for partially observable and continuous-valued systems operating in an environment with stochastic disturbances. We formulate the problem as a Markov decision process and use reinforcement learning to optimize it. The approach is simulation-based and does not require internal knowledge of the system, making it suitable for black-box testing of large systems. We present different formulations depending on whether the state is fully observable or partially observable. In the latter case, we present a modified Monte Carlo tree search algorithm that only requires access to the pseudorandom number generator of the simulator to overcome partial observability. We also present an extension of the framework, called differential adaptive stress testing (DAST), that can find failures that occur in one system but not in another. This type of differential analysis is useful in applications such as regression testing, where we are concerned with finding areas of relative weakness compared to a baseline. We demonstrate the effectiveness of the approach on an aircraft collision avoidance application, where a prototype aircraft collision avoidance system is stress tested to find the most likely scenarios of near mid-air collision.

Verification and Validation↗