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All sourcesNASA NTRSDOE OSTI
DOE OSTI2015

Pathosphere.org: pathogen detection and characterization through a web-based, open source informatics platform

The detection of pathogens in complex sample backgrounds has been revolutionized by wide access to next-generation sequencing (NGS) platforms. However, analytical methods to support NGS platforms are not as uniformly available. Pathosphere (found at Pathosphere.org) is a cloud - based open - sourced community tool that allows for communication, collaboration and sharing of NGS analytical tools and data amongst scientists working in academia, industry and government. The architecture allows for users to upload data and run available bioinformatics pipelines without the need for onsite processing hardware or technical support. The pathogen detection capabilities hosted on Pathosphere were tested by analyzing pathogen-containing samples sequenced by NGS with both spiked human samples as well as human and zoonotic host backgrounds. Pathosphere analytical pipelines developed by Edgewood Chemical Biological Center (ECBC) identified spiked pathogens within a common sample analyzed by 454, Ion Torrent, and Illumina sequencing platforms. ECBC pipelines also correctly identified pathogens in human samples containing arenavirus in addition to animal samples containing flavivirus and coronavirus. These analytical methods were limited in the detection of sequences with limited homology to previous annotations within NCBI databases, such as parvovirus. Utilizing the pipeline-hosting adaptability of Pathosphere, the analytical suite was supplemented by analytical pipelines designed by the United States Army Medical Research Institute of Infectious Diseases and Walter Reed Army Institute of Research (USAMRIID-WRAIR). These pipelines were implemented and detected parvovirus sequence in the sample that the ECBC iterative analysis previously failed to identify. By accurately detecting pathogens in a variety of samples, this work demonstrates the utility of Pathosphere and provides a platform for utilizing, modifying and creating pipelines for a variety of NGS technologies developed to detect pathogens in complex sample backgrounds. These results serve as an exhibition for the existing pipelines and web-based interface of Pathosphere as well as the plug-in adaptability that allows for integration of newer NGS analytical software as it becomes available.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Feature selection and causal analysis for microbiome studies in the presence of confounding using standardization

Abstract Background Microbiome studies have uncovered associations between microbes and human, animal, and plant health outcomes. This has led to an interest in developing microbial interventions for treatment of disease and optimization of crop yields which requires identification of microbiome features that impact the outcome in the population of interest. That task is challenging because of the high dimensionality of microbiome data and the confounding that results from the complex and dynamic interactions among host, environment, and microbiome. In the presence of such confounding, variable selection and estimation procedures may have unsatisfactory performance in identifying microbial features with an effect on the outcome. Results In this manuscript, we aim to estimate population-level effects of individual microbiome features while controlling for confounding by a categorical variable. Due to the high dimensionality and confounding-induced correlation between features, we propose feature screening, selection, and estimation conditional on each stratum of the confounder followed by a standardization approach to estimation of population-level effects of individual features. Comprehensive simulation studies demonstrate the advantages of our approach in recovering relevant features. Utilizing a potential-outcomes framework, we outline assumptions required to ascribe causal, rather than associational, interpretations to the identified microbiome effects. We conducted an agricultural study of the rhizosphere microbiome of sorghum in which nitrogen fertilizer application is a confounding variable. In this study, the proposed approach identified microbial taxa that are consistent with biological understanding of potential plant-microbe interactions. Conclusions Standardization enables more accurate identification of individual microbiome features with an effect on the outcome of interest compared to other variable selection and estimation procedures when there is confounding by a categorical variable.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

COMPILE: a GWAS computational pipeline for gene discovery in complex genomes

Abstract Background Genome-Wide Association Studies (GWAS) are used to identify genes and alleles that contribute to quantitative traits in large and genetically diverse populations. However, traits with complex genetic architectures create an enormous computational load for discovery of candidate genes with acceptable statistical certainty. We developed a streamlined computational pipeline for GWAS (COMPILE) to accelerate identification and annotation of candidate maize genes associated with a quantitative trait, and then matches maize genes to their closest rice and Arabidopsis homologs by sequence similarity. Results COMPILE executed GWAS using a Mixed Linear Model that incorporated, without compression, recent advancements in population structure control, then linked significant Quantitative Trait Loci (QTL) to candidate genes and RNA regulatory elements contained in any genome. COMPILE was validated using published data to identify QTL associated with the traits of α-tocopherol biosynthesis and flowering time, and identified published candidate genes as well as additional genes and non-coding RNAs. We then applied COMPILE to 274 genotypes of the maize Goodman Association Panel to identify candidate loci contributing to resistance of maize stems to penetration by larvae of the European Corn Borer ( Ostrinia nubilalis ). Candidate genes included those that encode a gene of unknown function, WRKY and MYB-like transcriptional factors, receptor-kinase signaling, riboflavin synthesis, nucleotide-sugar interconversion, and prolyl hydroxylation. Expression of the gene of unknown function has been associated with pathogen stress in maize and in rice homologs closest in sequence identity. Conclusions The relative speed of data analysis using COMPILE allowed comparison of population size and compression. Limitations in population size and diversity are major constraints for a trait and are not overcome by increasing marker density. COMPILE is customizable and is readily adaptable for application to species with robust genomic and proteome databases.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Impact of nutrition and rotavirus infection on the infant gut microbiota in a humanized pig model

Background Human rotavirus (HRV) is a major cause of viral gastroenteritis in infants; particularly in developing countries where malnutrition is prevalent. Malnutrition perturbs the infant gut microbiota leading to sub-optimal functioning of the immune system and further predisposing infants to enteric infections. Therefore, we hypothesized that malnutrition exacerbates rotavirus disease severity in infants. Methods In the present study, we used a neonatal germ free (GF) piglets transplanted with a two-month-old human infant’s fecal microbiota (HIFM) on protein deficient and sufficient diets. We report the effects of malnourishment on the HRV infection and the HIFM pig microbiota in feces, intestinal and systemic tissues, using MiSeq 16S gene sequencing (V 4 -V 5 region). Results Microbiota analysis indicated that the HIFM transplantation resulted in a microbial composition in pigs similar to that of the original infant feces. This model was then used to understand the interconnections between microbiota diversity, diet, and HRV infection. Post HRV infection, HIFM pigs on the deficient diet had lower body weights, developed more severe diarrhea and increased virus shedding compared to HIFM pigs on sufficient diet. However, HRV induced diarrhea and shedding was more pronounced in non-colonized GF pigs compared to HIFM pigs on either sufficient or deficient diet, suggesting that the microbiota alone moderated HRV infection. HRV infected pigs on sufficient diet showed increased microbiota diversity in intestinal tissues; whereas, greater diversity was observed in systemic tissues of HRV infected pigs fed with deficient diet. Conclusions These results suggest that proper nourishment improves the microbiota quality in the intestines, alleviates HRV disease and lower probability of systemic translocation of potential opportunistic pathogens/pathobionts. In conclusion, our findings further support the role for microbiota and proper nutrition in limiting enteric diseases.

Gastroenterology & Hepatology↗
DOE OSTI2015

The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4)

Abstract The DOE-JGI Microbial Genome Annotation Pipeline performs structural and functional annotation of microbial genomes that are further included into the Integrated Microbial Genome comparative analysis system. MGAP is applied to assembled nucleotide sequence datasets that are provided via the IMG submission site. Dataset submission for annotation first requires project and associated metadata description in GOLD. The MGAP sequence data processing consists of feature prediction including identification of protein-coding genes, non-coding RNAs and regulatory RNA features, as well as CRISPR elements. Structural annotation is followed by assignment of protein product names and functions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data

In many disciplines, data are highly decentralized across thousands of online databases (repositories, registries, and knowledgebases). Wringing value from such databases depends on the discipline of data science and on the humble bricks and mortar that make integration possible; identifiers are a core component of this integration infrastructure. Drawing on our experience and on work by other groups, we outline 10 lessons we have learned about the identifier qualities and best practices that facilitate large-scale data integration. Specifically, we propose actions that identifier practitioners (database providers) should take in the design, provision and reuse of identifiers. We also outline the important considerations for those referencing identifiers in various circumstances, including by authors and data generators. While the importance and relevance of each lesson will vary by context, there is a need for increased awareness about how to avoid and manage common identifier problems, especially those related to persistence and web-accessibility/resolvability. We focus strongly on web-based identifiers in the life sciences; however, the principles are broadly relevant to other disciplines.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Low-Probability High-Consequence (LPHC) Failure Events in Geologic Carbon Sequestration Pipelines and Wells: Framework for LPHC Risk Assessment Incorporating Spatial Variability of Risk

If Carbon dioxide Capture and Storage (CCS) is to be effective in mitigating climate change, it will need to be carried out on a very large scale. This will involve many thousands of miles of dedicated high-pressure pipelines in order to transport many millions of tonnes of CO 2 annually, with the CO 2 delivered to many thousands of wells that will inject the CO 2 underground. The new CCS infrastructure could rival in size the current U.S. upstream natural gas pipeline and well infrastructure. This new infrastructure entails hazards for life, health, animals, the environment, and natural resources. Pipelines are known to rupture due to corrosion, from external forces such as impacts by vehicles or digging equipment, by defects in construction, or from the failure of valves and seals. Similarly, wells are vulnerable to catastrophic failure due to corrosion, cement degradation, or operational mistakes. While most accidents involving pipelines and wells will be minor, there is the inevitable possibility of accidents with very high consequences, especially to public health. The most important consequence of concern is CO 2 release to the environment in concentrations sufficient to cause death by asphyxiation to nearby populations. Such accidents are thought to be very unlikely, but of course they cannot be excluded, even if major engineering effort is devoted (as it will be) to keeping their probability low and their consequences minimized. This project has developed a methodology for analyzing the risks of these rare but high-consequence accidents, using a step-by-step probabilistic methodology. A key difference between risks for pipelines and wells is that the former are spatially distributed along the pipe whereas the latter are confined to the vicinity of the well. Otherwise, the methodology we develop for risk assessment of pipeline and well failures is similar and provides an analysis both of the annual probabilities of accident sequences of concern and of their consequences, and crucially the methodology provides insights into what measures might be taken to mitigate those accident sequences identified as of concern. Mitigating strategies could address reducing the likelihood of an accident sequence of concern, or reducing the consequences, or some combination. The methodology elucidates both local and integrated risks along the pipeline or at the well providing information useful to decision makers at various levels including local (e.g., property owners and town councils), regional (e.g., county and state representatives), and national levels (federal regulators and corporate proponents).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Real-time PCR assays that detect genes for botulinum neurotoxin A–G subtypes

The role of Real-Time PCR assays for surveillance and rapid screening for pathogens is garnering more and more attention because of its versatility and ease of adoption. The goal of this study was to design, test, and evaluate Real-Time TaqMan PCR assays for the detection of botulinum neurotoxin (bont/A-G) genes from currently recognized BoNT subtypes. Assays were computationally designed and then laboratory tested for sensitivity and specificity using DNA preparations containing bont genes from 82 target toxin subtypes, including nine bivalent toxin types; 31 strains representing other clostridial species; and an extensive panel that consisted of DNA from a diverse set of prokaryotic (bacterial) and eukaryotic (fungal, protozoan, plant, and animal) species. In addition to laboratory testing, the assays were computationally evaluated using in silico analysis for their ability to detect bont gene sequences from recently identified toxin subtypes. Seventeen specific assays (two for each of the bont/C, bont/D, bont/E, and bont/G subtypes and three for each of the bont/A, bont/B, and bont/F subtypes) were designed and evaluated for their ability to detect bont genes encoding multiple subtypes from all seven serotypes. These assays could provide an additional tool for the detection of botulinum neurotoxins in clinical, environmental and food samples that can complement other existing methods used in clinical diagnostics, regulatory, public health, and research laboratories.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Enhancement on selenium volatilization for phytoremediation: role of plant and soil microbe interaction

This study aimed at quantifying the potential effects of plant and soil microbial interaction on selenium (Se) volatilization, with the specific objectives of identifying soil bacteria associated with rabbitfoot grass (Polypogon monspeliensis) and demonstrating the enhancement of Se volatilization in the soil-Indian mustard (Brassica juncea) system through inoculation of the soil with the identified best Se-volatilizing bacterial strain. Soil bacteria were isolated from topsoil and rhizosphere soils of rabbitfoot grass, and the bacterial colonies were characterized via PCR-DGGE and DGGE band analysis prior to their identification using 16S rDNA sequencing technique.Bacillus cereusproduced over 500-fold more volatile Se in a culture medium treated with 15 µg Se/mL (equal mixture of SeO 4 2- , SeO 3 2- and selenomethionine) than any of the other eight identified bacterial strains. Inoculation of Indian mustard vegetated soil with the best Se volatilizing bacterial strainB. cereusresulted in a significant (p<0.05) increase in Se volatilization during a 7-day time period, compared to the soil-plant system without inoculation ofB. cereus. Thus, inoculation of the soil withB. cereussubstantially enhanced Se removal via biogenic volatilization in the soil-Indian mustard system. This study evaluated the role ofB. cereusin enhancing Se volatilization in soil-plant systems, and demonstrated the importance of plant and soil microbial interaction for Se phytoremediation.

Plant Sciences↗
DOE OSTI2016

Globular clusters, ultracompact dwarfs, and dwarf galaxies in Abell 2744 at a redshift of 0.308

We report a photometric study of globular clusters (GCs), ultracompact dwarfs (UCDs), and dwarf galaxies in the giant merging galaxy cluster Abell 2744 at z = 0.308. Color–magnitude diagrams of the point sources derived from deep F814W (rest frame r′) and F105W (rest frame I) images of Abell 2744 in the Hubble Space Telescope Frontier Field show a rich population of point sources, which have colors that are similar to those of typical GCs. These sources are as bright as −14.9<M{sub r{sup ′}}⩽−11.4 (26.0 < F814W(Vega) ≤ 29.5) mag, being mostly UCDs and bright GCs in Abell 2744. The luminosity function (LF) of these sources shows a break at M{sub r{sup ′}}≈−12.9 (F814W ≈ 28.0) mag, indicating a boundary between UCDs and bright GCs. The numbers of GCs and UCDs are estimated to be 1,711,640{sup +589,760} {sub −430,500} and 147 ± 26, respectively. The clustercentric radial number density profiles of the UCDs and bright GCs show similar slopes, but these profiles are much steeper than those of the dwarf galaxies and the mass density profile based on gravitational lensing analysis. We derive an LF of the red sequence galaxies for −22.9<M{sub r{sup ′}}⩽−13.9 mag. The faint end of this LF is fit well by a flat power law with α=−1.14±0.08, showing no faint upturn. These results support the galaxy-origin scenario for bright UCDs: they are the nuclei of dwarf galaxies that are stripped when they pass close to the center of massive galaxies or a galaxy cluster, while some of the faint UCDs are at the bright end of the GCs.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2017

Lessons from the Onset of a Common Envelope Episode: the Remarkable M31 2015 Luminous Red Nova Outburst

This paper investigates the recent stellar-merger transient M31LRN 2015 in the Andromeda galaxy. We analyze published optical photometry and spectroscopy along with a Hubble Space Telescope detection of the color and magnitude of the pre-outburst source. The transient outburst is consistent with dynamically driven ejecta at the onset of a common envelope episode, which eventually leads to the complete merger of a binary system. The light curve appears to contain two components: first ∼10{sup −2} M{sub ⊙} of fast ejecta driven by shocks at the onset of common envelope, and later, ∼0.3 M {sub ⊙} of further ejecta as the secondary becomes more deeply engulfed within the primary. Just prior to merger, we find that the primary star is a 3–5.5 M {sub ⊙} subgiant-branch primary star with a radius of 30–40 R {sub ⊙}. Its position in the color–magnitude diagram shows that it is growing in radius, consistent with a picture where it engulfs its companion. By matching the properties of the primary star to the transient outburst, we show that the optical transient lasts less than 10 orbits of the original binary, which had a pre-merger period of ∼10 days. We consider the possible orbital dynamics leading up to the merger, and argue that if the system merged due to the Darwin tidal instability it implies a lower mass main-sequence companion of 0.1–0.6 M {sub ⊙}. This analysis represents a promising step toward a more detailed understanding of flows in common envelope episodes through direct observational constraints.

79 ASTRONOMY AND ASTROPHYSICS↗
NASA NTRS1972

Data acquisition and processing history for the Explorer 33 (AIMP-D) satellite

The quality control monitoring system, using accounting and quality control data bases, made it possible to perform an in-depth analysis. Results show that the percentage of useable data files for experimenter analysis was 97.7%; only 0.4% of the data sequences supplied to the experimenter exhibited missing data. The 50 percentile probability delay values (referenced to station record data) indicate that the analog tapes arrived within 11 days, the data were digitized within 4.2 weeks, and the experimenter tapes were delivered in 8.95 weeks or less.

Karras, T. J.↗
NASA NTRS1982

Estimating the temperature and height of overshooting thunderstorm tops from geostationary satellite infrared data

Information is presented on the extent to which the brightness temperature is overestimated. A revised version of the technique proposed by Adler and Markus (1982) for overcoming this problem is discussed, together with aspects of its application. GOES IR thunderstorm top observations are compared with high-resolution data. The technique described here to estimate the small-scale cloud top temperature from the GOES data corrects for most of the field-of-view effect but requires additional analysis and testing. When applied to a time sequence of a growing thunderstorm, the calculated cloud top temperature time profile is found to agree very well with a similar profile derived from stereo measurements.

Adler, R. F.↗
NASA NTRS1986

Space Station ground processing

The architecture of the Station, the system requirements, and the operational capabilities for ground and flight operations are described. The proposed Space Station design is dual keel and the components of the Station are listed. The initial ground processing activities are to reflect the on-orbit assembly sequence; the four phases of the assembly are examined. The planning and analysis for the ground processing of the Station with an emphasis on cost are discussed. The logistics resupply elements aspect of the ground processing sequence is considered. An example testing the capabilities of the ground processing sequence is presented. Diagrams of the Shuttle, its modules, and ground facilities and equipment are provided.

Scully, E. J.↗
NASA NTRS1988

The stellar composition of X-ray surveys from the Einstein Observatory

A new class of X-ray-luminous 'yellow' stellar objects which contributes significantly to the stellar log N-log S distribution, but which cannot be reconciled with normal G and K main-sequence stars. This identification results from a new analysis of the stellar content of three samples of X-ray-selected X-ray sources observed with the Einstein Observatory, namely the 'Medium Sensitivity Survey', the 'High Sensitivity Survey', and the 'Hyades Region Survey'. In this paper, both X-ray and optical properties of the stellar samples in these surveys are reported. The actual stellar content of the surveys is compared with predictions based on current knowledge of stellar X-ray luminosity functions and the stellar composition and spatial distribution in the Galaxy. It is shown that a plausible identification for the excess population of 'yellow' stars is with the active, RS CVn-like binaries.

Favata, F.↗
NASA NTRS1990

Mars Observer remote science operations

The objectives and the background of the Mars Observer mission are briefly reviewed with emphasis on the remote science operations portion of the mission. In particular, the discussion covers observational planning and instrument sequences, data retrieval, instrument health monitoring, and science analysis. Attention is also given to workstation technology utilization, science team, project data base, common data formats, and security.

Kahn, Peter B.↗