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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 289 records · Page 16
All sourcesNASA NTRSDOE OSTI
DOE OSTI2010

CLaMS: Classifier for Metagenomic Sequences

CLaMS-"Classifer for Metagenonic Sequences" is a Java application for binning assembled metagenomes wings user-specified training sequence sets and other user-specified initial parameters. Since ClAmS analyzes and matches sequence composition-based genomic signatures, it is much faster than binning tools that rely on alignments to homologs; CLaMS can bin ~20,000 sequences in 3 minutes on a laptop with a 2.4 Ghz. Intel Core 2 Duo processor and 2 GB Ram. CLaMS is meant to be desktop application for biologist and can be run on any machine under any operating system on which the Java Runtime Environment is enabled. CLaMS is freely available in both GVI-based and command-line based forms.

Pati, Amrita↗
DOE OSTI2018

VIRULIGN: fast codon-correct alignment and annotation of viral genomes

Abstract Summary Virus sequence data are an essential resource for reconstructing spatiotemporal dynamics of viral spread as well as to inform treatment and prevention strategies. However, the potential benefit of these applications critically depends on accurate and correctly annotated alignments of genetically heterogeneous data. VIRULIGN was built for fast codon-correct alignments of large datasets, with standardized and formalized genome annotation and various alignment export formats. Availability and implementation VIRULIGN is freely available at https://github.com/rega-cev/virulign as an open source software project. Supplementary information Supplementary data is available at Bioinformatics online.

Libin, Pieter J. K. (ORCID:000000033906758X)↗
DOE OSTI2016

acdc – Automated Contamination Detection and Confidence estimation for single-cell genome data

Abstract Background A major obstacle in single-cell sequencing is sample contamination with foreign DNA. To guarantee clean genome assemblies and to prevent the introduction of contamination into public databases, considerable quality control efforts are put into post-sequencing analysis. Contamination screening generally relies on reference-based methods such as database alignment or marker gene search, which limits the set of detectable contaminants to organisms with closely related reference species. As genomic coverage in the tree of life is highly fragmented, there is an urgent need for a reference-free methodology for contaminant identification in sequence data. Results We present acdc, a tool specifically developed to aid the quality control process of genomic sequence data. By combining supervised and unsupervised methods, it reliably detects both known and de novo contaminants. First, 16S rRNA gene prediction and the inclusion of ultrafast exact alignment techniques allow sequence classification using existing knowledge from databases. Second, reference-free inspection is enabled by the use of state-of-the-art machine learning techniques that include fast, non-linear dimensionality reduction of oligonucleotide signatures and subsequent clustering algorithms that automatically estimate the number of clusters. The latter also enables the removal of any contaminant, yielding a clean sample. Furthermore, given the data complexity and the ill-posedness of clustering, acdc employs bootstrapping techniques to provide statistically profound confidence values. Tested on a large number of samples from diverse sequencing projects, our software is able to quickly and accurately identify contamination. Results are displayed in an interactive user interface. Acdc can be run from the web as well as a dedicated command line application, which allows easy integration into large sequencing project analysis workflows. Conclusions Acdc can reliably detect contamination in single-cell genome data. In addition to database-driven detection, it complements existing tools by its unsupervised techniques, which allow for the detection of de novo contaminants. Our contribution has the potential to drastically reduce the amount of resources put into these processes, particularly in the context of limited availability of reference species. As single-cell genome data continues to grow rapidly, acdc adds to the toolkit of crucial quality assurance tools.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Community detection in sequence similarity networks based on attribute clustering

Networks are powerful tools for the presentation and analysis of interactions in multi-component systems. A commonly studied mesoscopic feature of networks is their community structure, which arises from grouping together similar nodes into one community and dissimilar nodes into separate communities. Here in this paper, the community structure of protein sequence similarity networks is determined with a new method: Attribute Clustering Dependent Communities (ACDC). Sequence similarity has hitherto typically been quantified by the alignment score or its expectation value. However, pair alignments with the same score or expectation value cannot thus be differentiated. To overcome this deficiency, the method constructs, for pair alignments, an extended alignment metric, the link attribute vector, which includes the score and other alignment characteristics. Rescaling components of the attribute vectors qualitatively identifies a systematic variation of sequence similarity within protein superfamilies. The problem of community detection is then mapped to clustering the link attribute vectors, selection of an optimal subset of links and community structure refinement based on the partition density of the network. ACDC-predicted communities are found to be in good agreement with gold standard sequence databases for which the "ground truth" community structures (or families) are known. ACDC is therefore a community detection method for sequence similarity networks based entirely on pair similarity information. A serial implementation of ACDC is available from https://cmb.ornl.gov/resources/developments

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Alignment-free Visualization of Metagenomic Data by Nonlinear Dimension Reduction

The visualization of metagenomic data, especially without prior taxonomic identification of reconstructed genomic fragments, is a challenging problem in computational biology. An ideal visualization method should, among others, enable clear distinction of congruent groups of sequences of closely related taxa, be applicable to fragments of lengths typically achievable following assembly, and allow the efficient analysis of the growing amounts of community genomic sequence data. Here, we report a scalable approach for the visualization of metagenomic data that is based on nonlinear dimension reduction via Barnes-Hut Stochastic Neighbor Embedding of centered log-ratio transformed oligonucleotide signatures extracted from assembled genomic sequence fragments. The approach allows for alignment-free assessment of the data-inherent taxonomic structure, and it can potentially facilitate the downstream binning of genomic fragments into uniform clusters reflecting organismal origin. We demonstrate the performance of our approach by visualizing community genomic sequence data from simulated as well as groundwater, human-derived and marine microbial communities.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Feasibility of Multimodal Deformable Registration for Head and Neck Tumor Treatment Planning

Purpose: To investigate the feasibility of using deformable registration in clinical practice to fuse MR and CT images of the head and neck for treatment planning. Method and Materials: A state-of-the-art deformable registration algorithm was optimized, evaluated, and compared with rigid registration. The evaluation was based on manually annotated anatomic landmarks and regions of interest in both modalities. We also developed a multiparametric registration approach, which simultaneously aligns T1- and T2-weighted MR sequences to CT. This was evaluated and compared with single-parametric approaches. Results: Our results show that deformable registration yielded a better accuracy than rigid registration, without introducing unrealistic deformations. For deformable registration, an average landmark alignment of approximatively 1.7 mm was obtained. For all the regions of interest excluding the cerebellum and the parotids, deformable registration provided a median modified Hausdorff distance of approximatively 1 mm. Similar accuracies were obtained for the single-parameter and multiparameter approaches. Conclusions: This study demonstrates that deformable registration of head-and-neck CT and MR images is feasible, with overall a significanlty higher accuracy than for rigid registration.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2019

Structure of odd- A Pt isotopes along the line of stability

The structure of the odd-A isotopes 193,195,197 Pt, which lie along the line of stability, has been studied up to high spin through multinucleon transfer reactions. Positive- and negative-parity sequences in Pt- 193,195 Pt have been considerably extended and multiple band crossings established. An isomer with T 1/2 = 5.0(5) ns and I π = 25/2 - is present in 195 Pt. Additionally, the isotopes 193,195 Pt are characterized by moderate oblate deformation, and angular momentum generation at high spin in the yrast, positive-parity sequences is attributed to the rotation alignment of i 13/2 neutrons and h 11/2 protons. Lastly, a detailed understanding of the observed features is presented using calculations based on tilted axis cranking covariant density functional theory as well as others with the ULTIMATE CRANKER code.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2021

Expanding the Scope of Genomic Security: Targeted Genome Editing within Microbiomes through Designer Bacteriophage Vectors

The ability to engineer the genome of a bacterial strain, not as an isolate, but while present among other microbes in a microbiome, would open new technological possibilities in the areas of medicine, energy and biomanufacturing. Our approach is to develop sets of phages (bacterial viruses) active on the target strain and themselves engineered to act not as killers but as vectors for gene delivery. This approach is rooted in our bioinformatic tools that map prophages accurately within bacterial genomes. We present new bioinformatic results in cross-contig search, design of phage genome assemblies, satellites that embed within prophages, alignment of large numbers of biological sequences, and improvement of reference databases for prophage discovery. We targeted a Pseudomonas putida strain within a lignin-degrading microbiome, but were unable to obtain active phages, and turned toward a defined microbiome of the mouse gut.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Microbial and viral-like rhodopsins present in coastal marine sediments from four polar and subpolar regions

Rhodopsins are broadly distributed. In this work, we analyzed 23 metagenomes corresponding to marine sediment samples from four regions that share cold climate conditions (Norway; Sweden; Argentina and Antarctica). In order to investigate the genes evolution of viral rhodopsins, an initial set of 6224 bacterial rhodopsin sequences according to COG5524 were retrieved from the 23 metagenomes. After selection by the presence of transmembrane domains and alignment, 123 viral (51) and non-viral (72) sequences (>50 amino acids) were finally included in further analysis. Viral rhodopsin genes were homologs of Phaeocystis globosa virus and Organic lake Phycodnavirus. Non-viral microbial rhodopsin genes were ascribed to Bacteroidetes, Planctomycetes, Firmicutes, Actinobacteria, Cyanobacteria, Proteobacteria, Deinococcus-Thermus and Cryptophyta and Fungi. A rescreening using Blastp, using as queries the viral sequences previously described, retrieved 30 sequences (>100 amino acids). Phylogeographic analysis revealed a geographical clustering of the sequences affiliated to the viral group. This clustering was not observed for the microbial non-viral sequences. The phylogenetic reconstruction allowed us to propose the existence of a putative ancestor of viral rhodopsin genes related to Actinobacteria and Chloroflexi. This is the first report about the existence of a phylogeographic association of the viral rhodopsin sequences from marine sediments.

marine sediment↗
DOE OSTI2014

The Hunt for Green Every April: Factors Affecting Fitness in Switchgrass

This grant funded work was undertaken to develop fundamental biological knowledge of the factors affecting the complex plant trait “fitness” in switchgrass (Panicum virgatum L.), a plant being developed as a biomass crop. Using a diverse range of latitudinally-adapted switchgrass plants, genomic, molecular and physiological studies were performed to track a number of different aspects of plant genetics and physiology over the course of the growing season. Work was performed on both genetically unrelated and genetically related plants. Plants were established in the field from seedlings raised in a greenhouse, or from clones present in other field nurseries. Field grown plants were used as the source of all tissues. The three objectives of this proposal were:(1) Transcript Profiling, Metabolomics, and C and N Partitioning and Recycling in Crowns and Rhizomes of Switchgrass over two growing seasons; (2) Gene Profiling During Regreening and Dormancy of Bulked Segregants; (3) Extent of Linkage Disequilibrium in Populations for Adaptation and Fitness Traits Being Developed for Central and Northern USA, that Show Significant Heterosis. Objective 1 results: Plants were labeled using 13 CO2 (a stable isotope) using an acrylic chamber constructed specifically for this purpose. Plants became labeled with 13 C and label decayed in aerial tissues over the course of the growing season. Varying amounts of 13 C were recovered in the rhizomes. These data are being analyzed. Plants were also labeled with 15 N-urea. Plants absorbed significant amounts of label that was remobilized to the growing shoots. N-dynamics would suggest that a portion of the 15 N absorbed into the crowns and rhizomes is sequestered below ground. Variable amounts of 15 N were translocated from the shoots to the roots over the course of the growing season. Polar metabolites extracted from a diverse array of rhizomes were analyzed using GCMS. Data indicated that there was a significant shift in metabolite pools over the course of the growing season, and differences in the levels of specific metabolites could be linked to the progression of dormancy. Several metabolites that accumulate in dormant rhizomes were identified. Some of these metabolites could be potentially linked to winter-survival of switchgrass. Extensive high-throughput sequencing was conducted on crown and rhizome samples collected from field grown plants. Initial work was performed on a Roche 454 system. All later work was performed on an Illumina sequencing-by-synthesis system. Some of these datasets have been published as peer-reviewed papers, other data are currently being analyzed and being readied for publication. Objective 2 results: Genetically related but phenotypically divergent plants from an octaploid switchgrass population were grown in a replicated field nursery. Rhizomes were harvested at four different times over the course of the growing season from plants with high winter survival and those with lower winter survival. RNA-Seq was performed on harvested materials. Initial analysis suggests that plants with lowered winter survival experience a greater level of cellular stress in dormant tissues. This aspect of plant function is being probed in greater depth. Objective 3 results: A total of 592 individual clones with three clonal replications in a randomized complete block design from each of five populations used in Objective 1 studies were rated for heading date in 2012 and 2014, green-up day of year in 2013, anthesis date in 2012, and yield in 2012, they were also subjected to NIR spectroscopy to derive cell wall composition estimates based on prior NIR calibrations. Plants were genotyped via a genotyping by sequencing (GBS) approach from reduced representation libraries constructed with adaptors that identified each individual. Libraries generated with the restriction enzyme PstI and called SNPs using Samtools after alignment to version 1.1 of the switchgrass genome sequence. A total of approximately 40,000 SNPs were found. These were then further filtered to eliminate markers with a minor allele frequency of < 0.05. The results of population analysis using STRUCTURE with expected population sizes or cluster numbers (K), clearly shows the hybrid composition of the KxS population and discriminated easily between upland (Summer) and lowland (Kanlow) populations. Under an assumption of 5 distinct populations there were detectable differences in allele frequencies between subpopulations within the three Kanlow populations particularly with respect to Kanlow EM and Kanlow base. We detected 110 SNPs with an allele frequency difference of ≥ 0.2 between Kanlow EM and Kanlow base populations, while 120 SNPs showed an allele frequency difference of ≥ 0.15 between Kanlow N1 and Kanlow base populations. These data are being readied for publication.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

Phylogeny of Bacterial and Archaeal Genomes Using Conserved Genes: Supertrees and Supermatrices

Over 3000 microbial (bacterial and archaeal) genomes have been made publically available to date, providing an unprecedented opportunity to examine evolutionary genomic trends and offering valuable reference data for a variety of other studies such as metagenomics. The utility of these genome sequences is greatly enhanced when we have an understanding of how they are phylogenetically related to each other. Therefore, we here describe our efforts to reconstruct the phylogeny of all available bacterial and archaeal genomes. We identified 24, single-copy, ubiquitous genes suitable for this phylogenetic analysis. We used two approaches to combine the data for the 24 genes. First, we concatenated alignments of all genes into a single alignment from which a Maximum Likelihood (ML) tree was inferred using RAxML. Second, we used a relatively new approach to combining gene data, Bayesian Concordance Analysis (BCA), as implemented in the BUCKy software, in which the results of 24 single-gene phylogenetic analyses are used to generate a ‘‘primary concordance’’ tree. A comparison of the concatenated ML tree and the primary concordance (BUCKy) tree reveals that the two approaches give similar results, relative to a phylogenetic tree inferred from the 16S rRNA gene. After comparing the results and the methods used, we conclude that the current best approach for generating a single phylogenetic tree, suitable for use as a reference phylogeny for comparative analyses, is to perform a maximum likelihood analysis of a concatenated alignment of conserved, single-copy genes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Sub genome anchored physical frameworks of the allotetraploid Upland cotton (Gossypium hirsutum L.) genome, and an approach toward reference-grade assemblies of polyploids

Like those of many agricultural crops, the cultivated cotton is an allotetraploid and has a large genome (~2.5 gigabase pairs). The two sub genomes, A and D, are highly similar but unequally sized and repeat-rich, which pose significant challenges for accurate genome reconstruction using standard approaches. Here we report the development of BAC libraries, sub genome specific physical maps, and a new-generation sequencing approach that will lead to a reference-grade genome assembly for Upland cotton. Three BAC libraries were constructed, fingerprinted, and integrated with BAC-end sequences (BES) to produce a de novo whole-genome physical map. The BAC map was partitioned by sub genomes through alignment to the diploid progenitor D-genome reference sequence with densely spaced BES anchor points and computational filtering. The physical maps were validated with FISH and genetic mapping of SNP markers derived from BES. Two pairs of homeologous chromosomes, A11/D11 and A12/D12, were used to assess multiplex sequencing approaches for completeness and scalability. The results represent the first sub genome anchored physical maps of Upland cotton, and a new-generation approach to the whole-genome sequencing, which will lead to the reference-grade assembly of allopolyploid cotton and serve as a general strategy for sequencing other polyploid species.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

SSGUI v1.0

SSGUI is a web-based application that integrates the integrative genomics browser (IGV) with upstream alignment pipelines enabling rapid analysis of a batch of next-generation sequencing (NGS) samples. The input to SSGUI is an NGS file system directory that is organized by experiment and reference sequence. The output is an online dashboard containing various sequencing statistics for each sample and an integrated IGV plugin enabling rapid analysis of aligned NGS reads.

Kulawik, Mark↗
DOE OSTI2019

diBELLA: Distributed Long Read to Long Read Alignment

© 2019 ACM. We present a parallel algorithm and scalable implementation for genome analysis, specifically the problem of finding overlaps and alignments for data from "third generation" long read sequencers [29]. While long sequences of DNA offer enormous advantages for biological analysis and insight, current long read sequencing instruments have high error rates and therefore require different approaches to analysis than their short read counterparts. Our work focuses on an efficient distributed-memory parallelization of an accurate single-node algorithm for overlapping and aligning long reads. We achieve scalability of this irregular algorithm by addressing the competing issues of increasing parallelism, minimizing communication, constraining the memory footprint, and ensuring good load balance. The resulting application, diBELLA, is the first distributed memory overlapper and aligner specifically designed for long reads and parallel scalability. We describe and present analyses for high level design trade-offs and conduct an extensive empirical analysis that compares performance characteristics across state-of-the-art HPC systems as well as a commercial cloud architectures, highlighting the advantages of state-of-the-art network technologies.

Ellis, Marquita↗
DOE OSTI2020

Distributed Berkeley Efficient Long-Read to Long-Read Aligner and Overlapper (DiBELLA) v1.0.0

We present a parallel algorithm and scalable implementation for genome analysis, specifically the problem of finding overlaps and alignments for data from "third generation" long read sequencers. While long sequences of DNA offer enormous advantages for biological analysis and insight, current long read sequencing instruments have high error rates and therefore require different approaches to analysis than their short read counterparts. Our work focuses on an efficient distributed-memory parallelization of an accurate single-node algorithm for overlapping and aligning long reads. We achieve scalability of this irregular algorithm by addressing the competing issues of increasing parallelism, minimizing communication, constraining the memory footprint, and ensuring good load balance. The resulting application, DiBELLA, is the first distributed memory overlapper and aligner specifically designed for long reads and parallel scalability.

Ellis, Marquita↗
DOE OSTI2022

Galaxy Alignments with Surrounding Structure in the Sloan Digital Sky Survey

Using data from the Sloan Digital Sky Survey Legacy Survey, we study the alignment of luminous galaxies with spectroscopic data with the surrounding larger-scale structure as defined by galaxies with only photometric data. We find that galaxies from the red sequence have a statistically significant tendency for their apparent long axes to align parallel to the projected surrounding structure. Red galaxies more luminous than the median of our sample (M r < –21.78) have a mean alignment angle $\langle$Φ$\rangle$ < 45°, indicating preferred parallel alignment, at a significance level >4.5σ on projected scales 0.1 Mpc < r p ≤ 7.5 Mpc. Fainter red galaxies have $\langle$Φ$\rangle$ < 45° at a significance level >4.3σ at scales 1 Mpc < r p < 3 Mpc. At a projected scale r p = 3.0 Mpc, the mean alignment angle decreases steadily with increasing luminosity for red galaxies with M r ≲ –22.5, reaching $\langle$Φ$\rangle$ = 40$^{°}_{.}$49 ± 0$^{°}_{.}$56 for the most luminous 1% (M r ~ –23.57). Galaxies from the blue sequence show no statistically significant tendency for their axes to align with larger-scale structure, regardless of galaxy luminosity. Galaxies in higher-density regions do not show a statistically significant difference in the mean alignment angle from galaxies in lower-density regions; this holds true for the faint blue, luminous blue, faint red, and luminous red subsets.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2012

Highly similar structural frames link the template tunnel and NTP entry tunnel to the exterior surface in RNA-dependent RNA polymerases

RNA-dependent RNA polymerase (RdRp) is essential to viral replication and is therefore one of the primary targets of countermeasures against these dangerous infectious agents. Development of broad-spectrum therapeutics targeting polymerases has been hampered by the extreme sequence variability of these sequences. RdRps range in length from 400–800 residues, yet contain only 20 residues that are conserved in most species. In this study, we made structure-based comparisons that are independent of sequence composition using a recently developed algorithm. We identified residue-to-residue correspondences of multiple protein structures and created (two-dimensional) structure-based alignment maps of 37 polymerase structures that provide both sequence and structure details. Using these maps, we determined that 75% of each polymerase species consists of seven protein segments, each of which has high structural similarity to segments in other species, though they are widely divergent in sequence composition and order. We define each of these segments as a ‘homomorph’, and each includes (though most are much larger than) the well-known conserved polymerase motifs. All homomorphs contact the template tunnel or nucleoside triphosphate (NTP) entry tunnel and the exterior of the protein, suggesting they constitute a structural and functional skeleton common among the polymerases.

59 BASIC BIOLOGICAL SCIENCES↗