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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 1,405 records · Page 78
All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

THE K2 M67 STUDY: AN EVOLVED BLUE STRAGGLER IN M67 FROM K2 MISSION ASTEROSEISMOLOGY

Yellow straggler stars (YSSs) fall above the subgiant branch in optical color–magnitude diagrams (CMDs), between the blue stragglers and the red giants. YSSs may represent a population of evolved blue stragglers, but none have the direct and precise mass and radius measurements needed to determine their evolutionary states and formation histories. Here we report the first asteroseismic mass and radius measurements of such a star, the yellow straggler S1237 in the open cluster M67. We apply asteroseismic scaling relations to a frequency analysis of the Kepler K2 light curve and find a mass of 2.9 ± 0.2 M {sub ⊙} and a radius of 9.2 ± 0.2 R{sub ⊙}. This is more than twice the mass of the main-sequence turnoff in M67, suggesting that S1237 is indeed an evolved blue straggler. S1237 is the primary in a spectroscopic binary. We update the binary orbital solution and use spectral energy distribution fitting to constrain the CMD location of the secondary star. We find that the secondary is likely an upper main-sequence star near the turnoff, but a slightly hotter blue straggler companion is also possible. We then compare the asteroseismic mass of the primary to its mass from CMD fitting, finding that the photometry implies a mass and radius more than 2 σ below the asteroseismic measurement. Finally, we consider formation mechanisms for this star and suggest that S1237 may have formed from dynamical encounters resulting in stellar collisions or a binary merger.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2013

Genome analysis and physiological comparison of Alicycliphilus denitrificans strains BC and K601T

The genomes of the Betaproteobacteria Alicycliphilus denitrificans strains BC and K601T have been sequenced to get insight into the physiology of the two strains. Strain BC degrades benzene with chlorate as electron acceptor. The cyclohexanol-degrading denitrifying strain K601T is not able to use chlorate as electron acceptor, while strain BC cannot degrade cyclohexanol. The 16S rRNA sequences of strains BC and K601T are identical and the fatty acid methyl ester patterns of the strains are similar. Basic Local Alignment Search Tool (BLAST) analysis of predicted open reading frames of both strains showed most hits with Acidovorax sp. JS42, a bacterium that degrades nitro-aromatics. The genomes include strain-specific plasmids (pAlide201 in strain K601T and pAlide01 and pAlide02 in strain BC). Key genes of chlorate reduction in strain BC were located on a 120 kb megaplasmid (pAlide01), which was absent in strain K601T. Genes involved in cyclohexanol degradation were only found in strain K601T. Benzene and toluene are degraded via oxygenase-mediated pathways in both strains. Genes involved in the meta-cleavage pathway of catechol are present in the genomes of both strains. Strain BC also contains all genes of the ortho-cleavage pathway. The large number of mono- and dioxygenase genes in the genomes suggests that the two strains have a broader substrate range than known thus far.

Oosterkamp, Margreet J.↗
DOE OSTI2012

Genomic Comparison of Escherichia coli O104:H4 Isolates from 2009 and 2011 Reveals Plasmid, and Prophage Heterogeneity, Including Shiga Toxin Encoding Phage stx2

In May of 2011, an enteroaggregative Escherichia coli O104:H4 strain that had acquired a Shiga toxin 2-converting phage caused a large outbreak of bloody diarrhea in Europe which was notable for its high prevalence of hemolytic uremic syndrome cases. Several studies have described the genomic inventory and phylogenies of strains associated with the outbreak and a collection of historical E. coli O104:H4 isolates using draft genome assemblies. We present the complete, closed genome sequences of an isolate from the 2011 outbreak (2011C–3493) and two isolates from cases of bloody diarrhea that occurred in the Republic of Georgia in 2009 (2009EL–2050 and 2009EL–2071). Comparative genome analysis indicates that, while the Georgian strains are the nearest neighbors to the 2011 outbreak isolates sequenced to date, structural and nucleotide-level differences are evident in the Stx2 phage genomes, the mer/tet antibiotic resistance island, and in the prophage and plasmid profiles of the strains, including a previously undescribed plasmid with homology to the pMT virulence plasmid of Yersinia pestis. In addition, multiphenotype analysis showed that 2009EL–2071 possessed higher resistance to polymyxin and membrane-disrupting agents. Finally, we show evidence by electron microscopy of the presence of a common phage morphotype among the European and Georgian strains and a second phage morphotype among the Georgian strains. The presence of at least two stx2 phage genotypes in host genetic backgrounds that may derive from a recent common ancestor of the 2011 outbreak isolates indicates that the emergence of stx2 phage-containing E. coli O104:H4 strains probably occurred more than once, or that the current outbreak isolates may be the result of a recent transfer of a new stx2 phage element into a pre-existing stx2-positive genetic background.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Cation and Anion Channelrhodopsins: Sequence Motifs and Taxonomic Distribution

Cation and anion channelrhodopsins (CCRs and ACRs, respectively) primarily from two algal species, Chlamydomonas reinhardtii and Guillardia theta, have become widely used as optogenetic tools to control cell membrane potential with light. We mined algal and other protist polynucleotide sequencing projects and metagenomic samples to identify 75 channelrhodopsin homologs from four channelrhodopsin families, including one revealed in dinoflagellates in this study. We carried out electrophysiological analysis of 33 natural channelrhodopsin variants from different phylogenetic lineages and 10 metagenomic homologs in search of sequence determinants of ion selectivity, photocurrent desensitization, and spectral tuning in channelrhodopsins. Our results show that association of a reduced number of glutamates near the conductance path with anion selectivity depends on a wider protein context, because prasinophyte homologs with a glutamate pattern identical to that in cryptophyte ACRs are cation selective. Desensitization is also broadly context dependent, as in one branch of stramenopile ACRs and their metagenomic homologs, its extent roughly correlates with phylogenetic relationship of their sequences. Regarding spectral tuning, we identified two prasinophyte CCRs with red-shifted spectra to 585 nm. They exhibit a third residue pattern in their retinal-binding pockets distinctly different from those of the only two types of red-shifted channelrhodopsins known (i.e., the CCR Chrimson and RubyACRs). In cryptophyte ACRs we identified three specific residue positions in the retinal-binding pocket that define the wavelength of their spectral maxima. Lastly, we found that dinoflagellate rhodopsins with a TCP motif in the third transmembrane helix and a metagenomic homolog exhibit channel activity. Channelrhodopsins are widely used in neuroscience and cardiology as research tools and are considered prospective therapeutics, but their natural diversity and mechanisms remain poorly characterized. Genomic and metagenomic sequencing projects are producing an ever-increasing wealth of data, whereas biophysical characterization of the encoded proteins lags behind. In this study, we used manual and automated patch clamp recording of representative members of four channelrhodopsin families, including a family in dinoflagellates that we report in this study. Our results contribute to a better understanding of molecular determinants of ionic selectivity, photocurrent desensitization, and spectral tuning in channelrhodopsins.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Sequence Diagrams & PFMEA Table - VGI [SWR-25-107]

As part of the VGI work under the National Charging Experience (ChargeX) Consortium, reliability analysis of communication interfaces for multiple SCM/VGI use-cases was performed using a Process Failure Modes and Analysis (PFMEA) style framework. This repository hosts all the relevant files for each of these use-cases which include: *A visual representation of their communication architecture: Image file (.png) *UML sequence diagram: Plant-UML source file (.puml). Visio file (.vsdx) and image file (.png) derived from the UML sourceX` *The PFMEA table: Excel file (.xlsx) These files are meant to serve as a starting point and can be adapted to company / organization specific SCM implementation.

Gadamsetty, Pranav [National Renewable Energy Labo↗
DOE OSTI2021

NASA GeneLab RNA-seq consensus pipeline: Standardized processing of short-read RNA-seq data

With the development of transcriptomic technologies, we are able to quantify precise changes in gene expression profiles from astronauts and other organisms exposed to spaceflight. Members of NASA GeneLab and GeneLab-associated analysis working groups (AWGs) have developed a consensus pipeline for analyzing short-read RNA-sequencing data from spaceflight-associated experiments. The pipeline includes quality control, read trimming, mapping, and gene quantification steps, culminating in the detection of differentially expressed genes. This data analysis pipeline and the results of its execution using data submitted to GeneLab are now all publicly available through the GeneLab database. We present here the full details and rationale for the construction of this pipeline in order to promote transparency, reproducibility, and reusability of pipeline data; to provide a template for data processing of future spaceflight-relevant datasets; and to encourage cross-analysis of data from other databases with the data available in GeneLab.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Functional importance of cardiac enhancer-associated noncoding RNAs in heart development and disease

We report here that the key information processing units within gene regulatory networks are enhancers. Enhancer activity is associated with the production of tissue-specific noncoding RNAs, yet the existence of such transcripts during cardiac development has not been established. Using an integrated genomic approach, we demonstrate that fetal cardiac enhancers generate long noncoding RNAs (lncRNAs) during cardiac differentiation and morphogenesis. Enhancer expression correlates with the emergence of active enhancer chromatin states, the initiation of RNA polymerase II at enhancer loci and expression of target genes. Orthologous human sequences are also transcribed in fetal human hearts and cardiac progenitor cells. Through a systematic bioinformatic analysis, we identified and characterized, for the first time, a catalog of lncRNAs that are expressed during embryonic stem cell differentiation into cardiomyocytes and associated with active cardiac enhancer sequences. RNA-sequencing demonstrates that many of these transcripts are polyadenylated, multi-exonic long noncoding RNAs. Moreover, knockdown of two enhancer-associated lncRNAs resulted in the specific downregulation of their predicted target genes. Interestingly, the reactivation of the fetal gene program, a hallmark of the stress response in the adult heart, is accompanied by increased expression of fetal cardiac enhancer transcripts. Altogether, these findings demonstrate that the activity of cardiac enhancers and expression of their target genes are associated with the production of enhancer-derived lncRNAs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Internal Fragments Generated by Electron Ionization Dissociation Enhance Protein Top-Down Mass Spectrometry

Top-down proteomics by mass spectrometry (MS) involves the mass measurement of an intact protein followed by subsequent activation of the protein to generate product ions. Electron-based fragmentation methods like electron capture dissociation and electron transfer dissociation are widely used for these types of analyses. Recently, electron ionization dissociation (EID), which utilizes higher energy electrons (>20 eV) has been suggested to be more efficient for top-down protein fragmentation compared to other electron-based dissociation methods. In this paper, we demonstrate that the use of EID enhances protein fragmentation and subsequent detection of protein fragments. Protein product ions can form by either single cleavage events, resulting in terminal fragments containing the C-terminus or N-terminus of the protein, or by multiple cleavage events to give rise to internal fragments that include neither the C-terminus nor the N-terminus of the protein. Conventionally, internal fragments have been disregarded, as reliable assignments of these fragments were limited. Here, we demonstrate that internal fragments generated by EID can account for ~20–40% of the mass spectral signals detected by top-down EID-MS experiments. By including internal fragments, the extent of the protein sequence that can be explained from a single tandem mass spectrum increases from ~50 to ~99% for 29 kDa carbonic anhydrase II and 8.6 kDa ubiquitin. When searching for internal fragments during data analysis, previously unassigned peaks can be readily and accurately assigned to confirm a given protein sequence and to enhance the utility of top-down protein sequencing experiments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

A sequence of transformations related to the formation of M{sub 3}X{sub 2}-type superstructures

A symmetry analysis of monoclinic, orthorhombic, and trigonal M{sub 3}X{sub 2}-type superstructures that can be formed in strongly stoichiometric MX{sub y} compounds with B1 structure is carried out. Channels of order-disorder transitions MX{sub y} → M{sub 3}X{sub 2} are determined. It is shown that, as temperature decreases, two physically admissible sequences of transformations associated with the formation of M{sub 3}X{sub 2} superstructures are possible in nonstoichiometric MX{sub y} compounds of group IV transition metals. By an example of vanadium carbide VC{sub y}, it is demonstrated that orthorhombic or monoclinic V{sub 3}C{sub 2} superstructures can be obtained with the formation of a nanostructure.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2019

Xavier: High-Performance X-Drop Adaptive Banded Pairwise Alignment (Xavier) v1.0

Pairwise sequence alignment is one of the most compute-intense challenges for the analysis of genomics data and it can account for more than 90% of the runtime depending on the application. Despite the effort to reduce the computational cost introducing heuristics such as banded and x-drop alignment, the performance of state-of-the-art software is often unsatisfactory for long sequences. Recent advances in single-molecule sequencing technologies keep increasing the length of the sequences to align at the cost of higher error rates b ranging from 5% to 15% b, emphasizing the need for fast and accurate software. Our long-read alignment software, named Xavier, computes high-performance x-drop adaptive banded pairwise alignment exploiting instruction-level parallelism via Single-Instruction-Multiple-Data (SIMD) operations. Xavier uses a narrow bandwidth that appreciably improves performance reducing the search space for the optimal alignment. In our experiment, the adaptive mechanism enables Xavier to find the optimal alignment between related sequences even when the error rate is as high as 50%. Xavier achieves speed-up up to 5X over competitor software when enabling the x-drop termination and up to 415X when disabling it, with negligible accuracy loss.

Guidi, Giulia↗
DOE OSTI2020

Persistent minimal sequences of SARS-CoV-2

Abstract Motivation Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused more than 14 million cases and more than half million deaths. Given the absence of implemented therapies, new analysis, diagnosis and therapeutics are of great importance. Results Analysis of SARS-CoV-2 genomes from the current outbreak reveals the presence of short persistent DNA/RNA sequences that are absent from the human genome and transcriptome (PmRAWs). For the PmRAWs with length 12, only four exist at the same location in all SARS-CoV-2. At the gene level, we found one PmRAW of size 13 at the Spike glycoprotein coding sequence. This protein is fundamental for binding in human ACE2 and further use as an entry receptor to invade target cells. Applying protein structural prediction, we localized this PmRAW at the surface of the Spike protein, providing a potential targeted vector for diagnostics and therapeutics. In addition, we show a new pattern of relative absent words (RAWs), characterized by the progressive increase of GC content (Guanine and Cytosine) according to the decrease of RAWs length, contrarily to the virus and host genome distributions. New analysis shows the same property during the Ebola virus outbreak. At a computational level, we improved the alignment-free method to identify pathogen-specific signatures in balance with GC measures and removed previous size limitations. Availability and implementation https://github.com/cobilab/eagle. Supplementary information Supplementary data are available at Bioinformatics online.

Pratas, Diogo↗
DOE OSTI2018

Chicago Area Waterway System Microbiome Research

This report summarizes the research conducted by Argonne National Laboratory (Argonne) for the Metropolitan Water Reclamation District of Greater Chicago (MWRD) for the first five years (2013-2017) of a seven-year study with emphasis on the impact of disinfection (2016-2017) on the microbial community of the Chicago Area Waterway System (CAWS). The study examines microbial communities following disinfection of secondary treated effluents at the T.J. O’Brien (UV) and Calumet (chlorine and dechlorination) Water Reclamation Plants (WRPs) and the phased implementation of the Tunnel and Reservoir Plan (TARP). The Thornton Composite Reservoir (TCR) was completed in 2015. It provides 7.9 billion gallons of storage and since its completion has captured more than 11.0 billion gallons of combined stormwater and sewage from Calumet WRP that would otherwise overflow into CAWS in rainy weather. In addition to the effects of TARP and disinfection, we present an analysis of potential sources of the microbes found in the CAWS and the results of 16S rRNA amplicon gene sequencing which was used to characterize microbial community variability as a function of location, season, and environmental conditions. A total of 2,077 samples were collected from 2013 to 2017 from WRPs and CAWS and analyzed using high-throughput sequencing. The whole microbial community composition using all the genetic material in the environmental sample was characterized using 16S rRNA gene-based analysis, while functional subsystem attributes of these microbial communities were characterized using shotgun metagenomics. We used a Bayesian statistical tool, SourceTracker 2.0 to determine the likely sources of microbes found in CAWS by sampling location and sampling period.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Complementary Metagenomic Approaches Improve Reconstruction of Microbial Diversity in a Forest Soil

ABSTRACT Soil ecosystems harbor diverse microorganisms and yet remain only partially characterized as neither single-cell sequencing nor whole-community sequencing offers a complete picture of these complex communities. Thus, the genetic and metabolic potential of this “uncultivated majority” remains underexplored. To address these challenges, we applied a pooled-cell-sorting-based mini-metagenomics approach and compared the results to bulk metagenomics. Informatic binning of these data produced 200 mini-metagenome assembled genomes (sorted-MAGs) and 29 bulk metagenome assembled genomes (MAGs). The sorted and bulk MAGs increased the known phylogenetic diversity of soil taxa by 7.2% with respect to the Joint Genome Institute IMG/M database and showed clade-specific sequence recruitment patterns across diverse terrestrial soil metagenomes. Additionally, sorted-MAGs expanded the rare biosphere not captured through MAGs from bulk sequences, exemplified through phylogenetic and functional analyses of members of the phylum Bacteroidetes . Analysis of 67 Bacteroidetes sorted-MAGs showed conserved patterns of carbon metabolism across four clades. These results indicate that mini-metagenomics enables genome-resolved investigation of predicted metabolism and demonstrates the utility of combining metagenomics methods to tap into the diversity of heterogeneous microbial assemblages. IMPORTANCE Microbial ecologists have historically used cultivation-based approaches as well as amplicon sequencing and shotgun metagenomics to characterize microbial diversity in soil. However, challenges persist in the study of microbial diversity, including the recalcitrance of the majority of microorganisms to laboratory cultivation and limited sequence assembly from highly complex samples. The uncultivated majority thus remains a reservoir of untapped genetic diversity. To address some of the challenges associated with bulk metagenomics as well as low throughput of single-cell genomics, we applied flow cytometry-enabled mini-metagenomics to capture expanded microbial diversity from forest soil and compare it to soil bulk metagenomics. Our resulting data from this pooled-cell sorting approach combined with bulk metagenomics revealed increased phylogenetic diversity through novel soil taxa and rare biosphere members. In-depth analysis of genomes within the highly represented Bacteroidetes phylum provided insights into conserved and clade-specific patterns of carbon metabolism.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Differential DNA methylation profile of key genes in malignant prostate epithelial cells transformed by inorganic arsenic or cadmium

Previous work shows altered methylation patterns in inorganic arsenic (iAs)- or cadmium (Cd)-transformed epithelial cells. Here, the methylation status near the transcriptional start site was assessed in the normal human prostate epithelial cell line (RWPE-1) that was malignantly transformed by 10 μM Cd for 11 weeks (CTPE) or 5 μM iAs for 29 weeks (CAsE-PE), at which time cells showed multiple markers of acquired cancer phenotype. Next generation sequencing of the transcriptome of CAsE-PE cells identified multiple dysregulated genes. Of the most highly dysregulated genes, five genes that can be relevant to the carcinogenic process (S100P, HYAL1, NTM, NES, ALDH1A1) were chosen for an in-depth analysis of the DNA methylation profile. DNA was isolated, bisulfite converted, and combined bisulfite restriction analysis was used to identify differentially methylated CpG sites, which was confirmed with bisulfite sequencing. Four of the five genes showed differential methylation in transformants relative to control cells that was inversely related to altered gene expression. Increased expression of HYAL1 (> 25-fold) and S100P (> 40-fold) in transformants was correlated with hypomethylation near the transcriptional start site. Decreased expression of NES (> 15-fold) and NTM (> 1000-fold) in transformants was correlated with hypermethylation near the transcriptional start site. ALDH1A1 expression was differentially expressed in transformed cells but was not differentially methylated relative to control. In conclusion, altered gene expression observed in Cd and iAs transformed cells may result from altered DNA methylation status. - Highlights: • Cd and iAs are known human carcinogens, yet neither appears directly mutagenic. • Prior data suggest epigenetic modification plays a role in Cd or iAs induced cancer. • Altered methylation of four misregulated genes was found in Cd or iAs transformants. • The resulting altered gene expression may be relevant to cellular transformation.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2026

MATEY: multiscale adaptive transformer models for spatiotemporal physical systems

Accurate representation of the multiscale features in spatiotemporal physical systems using vision transformer architectures requires extremely long, computationally prohibitive token sequences. To address this issue, we propose two novel adaptive tokenization schemes that dynamically adjust patch sizes based on local features: one ensures convergent behavior to uniform patch refinement, while the other offers better computational efficiency. Moreover, we present a set of spatiotemporal attention schemes, where the temporal or axial spatial dimensions are decoupled, to evaluate their baseline computational and data efficiencies and to determine whether adaptive tokenization can improve this performance. We assess the performance of the proposed multiscale adaptive model, MATEY, in a sequence of experiments. Compared to a full spatiotemporal attention scheme or a scheme that decouples only the temporal dimension, we find that fully decoupled axial attention is less efficient and expressive, requiring more training time and model parameters to achieve the same accuracy. The experiments on the adaptive tokenization schemes show that, compared to a uniformly refined model, the proposed schemes achieve comparable or improved accuracy at a much lower cost in the tested two-dimensional settings. While the asymptotic analysis suggests the potential for favorable scaling, empirical validation at substantially longer sequence lengths remains to be performed in future work. Finally, we demonstrate in two fine-tuning tasks featuring different physics that models pretrained on PDEBench data outperform the ones trained from scratch, especially in the low data regime with frozen attention.

adaptive tokenization↗
DOE OSTI2014

Spectral energy distribution analysis of class I and class II FU Orionis stars

FU Orionis stars (FUors) are eruptive pre-main sequence objects thought to represent quasi-periodic or recurring stages of enhanced accretion during the low-mass star-forming process. We characterize the sample of known and candidate FUors in a homogeneous and consistent way, deriving stellar and circumstellar parameters for each object. We emphasize the analysis in those parameters that are supposed to vary during the FUor stage. We modeled the spectral energy distributions of 24 of the 26 currently known FUors, using the radiative transfer code of Whitney et al. We compare our models with those obtained by Robitaille et al. for Taurus class II and I sources in quiescence periods by calculating the cumulative distribution of the different parameters. FUors have more massive disks: we find that ∼80% of the disks in FUors are more massive than any Taurus class II and I sources in the sample. Median values for the disk mass accretion rates are ∼10{sup –7} M {sub ☉} yr{sup –1} versus ∼10{sup –5} M {sub ☉} yr{sup –1} for standard young stellar objects (YSOs) and FUors, respectively. While the distributions of envelope mass accretion rates for class I FUors and standard class I objects are similar, FUors, on average, have higher envelope mass accretion rates than standard class II and class I sources. Most FUors (∼70%) have envelope mass accretion rates above 10{sup –7} M {sub ☉} yr{sup –1}. In contrast, 60% of the classical YSO sample has an accretion rate below this value. Our results support the current scenario in which changes experimented by the circumstellar disk explain the observed properties of these stars. However, the increase in the disk mass accretion rate is smaller than theoretically predicted, although in good agreement with previous determinations.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2011

Milky Way Tomography IV: Dissecting Dust

We use SDSS photometry of 73 million stars to simultaneously obtain best-fit main-sequence stellar energy distribution (SED) and amount of dust extinction along the line of sight towards each star. Using a subsample of 23 million stars with 2MASS photometry, whose addition enables more robust results, we show that SDSS photometry alone is sufficient to break degeneracies between intrinsic stellar color and dust amount when the shape of extinction curve is fixed. When using both SDSS and 2MASS photometry, the ratio of the total to selective absorption, R{sub V}, can be determined with an uncertainty of about 0.1 for most stars in high-extinction regions. These fits enable detailed studies of the dust properties and its spatial distribution, and of the stellar spatial distribution at low Galactic latitudes (|b| < 30{sup o}). Our results are in good agreement with the extinction normalization given by the Schlegel et al. (1998, SFD) dust maps at high northern Galactic latitudes, but indicate that the SFD extinction map appears to be consistently overestimated by about 20% in the southern sky, in agreement with recent study by Schlafly et al. (2010). The constraints on the shape of the dust extinction curve across the SDSS and 2MASS bandpasses disfavor the reddening law of O'Donnell (1994), but support the models by Fitzpatrick (1999) and Cardelli et al. (1989). For the latter, we find a ratio of the total to selective absorption to be R{sub V} = 3.0 {+-} 0.1(random) {+-} 0.1 (systematic) over most of the high-latitude sky. At low Galactic latitudes (|b| < 5{sup o}), we demonstrate that the SFD map cannot be reliably used to correct for extinction because most stars are embedded in dust, rather than behind it, as is the case at high Galactic latitudes. We analyze three-dimensional maps of the best-fit R{sub V} and find that R{sub V} = 3.1 cannot be ruled out in any of the ten SEGUE stripes at a precision level of {approx} 0.1 - 0.2. Our best estimate for the intrinsic scatter of R{sub V} in the regions probed by SEGUE stripes is {approx} 0.2. We introduce a method for efficient selection of candidate red giant stars in the disk, dubbed 'dusty parallax relation', which utilizes a correlation between distance and the extinction along the line of sight. We make these best-fit parameters, as well as all the input SDSS and 2MASS data, publicly available in a user-friendly format. These data can be used for studies of stellar number density distribution, the distribution of dust properties, for selecting sources whose SED differs from SEDs for high-latitude main sequence stars, and for estimating distances to dust clouds and, in turn, to molecular gas clouds.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2015

Multidimensional metrics for estimating phage abundance, distribution, gene density, and sequence coverage in metagenomes

Phages are the most abundant biological entities on Earth and play major ecological roles, yet the current sequenced phage genomes do not adequately represent their diversity, and little is known about the abundance and distribution of these sequenced genomes in nature. Although the study of phage ecology has benefited tremendously from the emergence of metagenomic sequencing, a systematic survey of phage genes and genomes in various ecosystems is still lacking, and fundamental questions about phage biology, lifestyle, and ecology remain unanswered. To address these questions and improve comparative analysis of phages in different metagenomes, we screened a core set of publicly available metagenomic samples for sequences related to completely sequenced phages using the web tool, Phage Eco-Locator. We then adopted and deployed an array of mathematical and statistical metrics for a multidimensional estimation of the abundance and distribution of phage genes and genomes in various ecosystems. Experiments using those metrics individually showed their usefulness in emphasizing the pervasive, yet uneven, distribution of known phage sequences in environmental metagenomes. Using these metrics in combination allowed us to resolve phage genomes into clusters that correlated with their genotypes and taxonomic classes as well as their ecological properties. By adding this set of metrics to current metaviromic analysis pipelines, where they can provide insight regarding phage mosaicism, habitat specificity, and evolution.

59 BASIC BIOLOGICAL SCIENCES↗