Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “Sequence”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 901 records · Page 50
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Plant sulfate transporter protein sequences for phylogenetic analysis

Sulfur is an essential macronutrient that supports plant growth, development, and responses to environmental stress. Sulfate is the predominant inorganic form of sulfur in soils, and its uptake by roots and translocation to shoots are facilitated by the sulfate transporter (SULTR) family of proteins. Although the first plant SULTR gene was identified nearly three decades ago, several subfamily members, particularly those in the expansive and angiosperm-specific SULTR3 group, remain poorly characterized. To support comprehensive phylogenetic and sequence-based analyses, we compiled a curated dataset of 262 SULTR protein sequences from 22 plant species spanning the evolutionary breadth of land plants. This collection includes representatives from two basal lineages, two early-divergent angiosperms, six monocots, and ten dicots. All sequences were extracted from genome assemblies available in Phytozome v13 (Joint Genome Institute) and manually curated, with cross-referencing to additional databases such as NCBI when needed. This dataset provides a valuable resource for reconstructing the evolutionary history of the SULTR family, with particular emphasis on the diversification of SULTR3 transporters in flowering plants. This resource may also support functional annotation, comparative genomics, and structural modeling of sulfate transport proteins.

CBI↗
DOE OSTI2013

Metagenome Sequence Analysis of Filamentous Microbial Communities Obtained from Geochemically Distinct Geothermal Channels Reveals Specialization of Three Aquificales Lineages

The Aquificales are thermophilic microorganisms that inhabit hydrothermal systems worldwide and are considered one of the earliest lineages of the domain Bacteria. We analyzed metagenome sequence obtained from six thermal “filamentous streamer” communities (~40 Mbp per site), which targeted three different groups of Aquificales found in Yellowstone National Park (YNP). Unassembled metagenome sequence and PCR-amplified 16S rRNA gene libraries revealed that acidic, sulfidic sites were dominated by Hydrogenobaculum (Aquificaceae) populations, whereas the circum-neutral pH (6.5–7.8) sites containing dissolved sulfide were dominated by Sulfurihydrogenibium spp. (Hydrogenothermaceae). Thermocrinis (Aquificaceae) populations were found primarily in the circum-neutral sites with undetectable sulfide, and to a lesser extent in one sulfidic system at pH 8. Phylogenetic analysis of assembled sequence containing 16S rRNA genes as well as conserved protein-encoding genes revealed that the composition and function of these communities varied across geochemical conditions. Each Aquificales lineage contained genes for CO2 fixation by the reverse-TCA cycle, but only the Sulfurihydrogenibium populations perform citrate cleavage using ATP citrate lyase (Acl). The Aquificaceae populations use an alternative pathway catalyzed by two separate enzymes, citryl-CoA synthetase (Ccs), and citryl-CoA lyase (Ccl). All three Aquificales lineages contained evidence of aerobic respiration, albeit due to completely different types of heme Cu oxidases (subunit I) involved in oxygen reduction. The distribution of Aquificales populations and differences among functional genes involved in energy generation and electron transport is consistent with the hypothesis that geochemical parameters (e.g., pH, sulfide, H2, O2) have resulted in niche specialization among members of the Aquificales.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2017

A Multilocus Sequence Analysis Scheme for Phylogeny of Thioclava Bacteria and Proposal of Two Novel Species

A multilfocus sequence analysis (MLSA) was established and performed on the genus Thioclava, including 23 strains isolated from diverse marine environments, with the aim of better differentiation of strains and species within this genus. The study was based on sequences of 16S rRNA gene and five protein-coding housekeeping genes, gyrB, rpoD, dnaK, trpB, and recA. In contrast to 16S rRNA gene-based tree that was unable to separate some species within this genus, each tree based on a single housekeeping gene and MLSA had consistently defined seven clades, corresponding to the five established ones and two novel ones. The digital DNA-DNA hybridization and average nucleotide identity analyses based on genome sequences of the representative strains reconfirmed the validity of the MLSA analysis, and recommended a 97.3% MLSA similarity as the soft species threshold and nine species representing the five known and four putative novel species. Two of the four new species were identified as Thioclava sediminum sp. nov. (type strain TAW-CT134T = MCCC 1A10143T = LMG 29615T ) and Thioclava marinus sp. nov. (type strain 11.10-0-13T = MCCC 1A03502T = LMG 29618T ) by using a polyphasic taxonomic approach. Taken together, the newly established MLSA in this study first described the variability and phylogeny of the genus Thioclava which contributes to better understanding its ecology and evolution.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Genomic-based biosurveillance for avian influenza: whole genome sequencing from wild mallards sampled during autumn migration in 2022–2023 reveals a high co-infection rate on migration stopover site in Georgia

The Caucasus region, including Georgia, is an important intersection for migratory waterbirds, offering potential for avian influenza virus (AIV) transmission between populations from different geographic areas. In 2022 and 2023, wild ducks were sampled during autumn migration events in Georgia to study the genetic relationships and molecular characteristics of influenza strains. Sequencing and phylogenetic analysis were used to compare the sampled strains to reference sequences from Africa, Asia, and Europe, allowing assessment of genetic relationships and virus transmission between migratory birds. Protein language modeling identified potential co-infections. Of 225 duck samples, 128 tested positive for the influenza M gene. 55 influenza-positive samples underwent whole-genome sequencing, revealing significant diversity. Analysis of the hemagglutinin (HA) segment showed notable differences among subtypes. Most samples were H6N1 and H6N6, but co-infections with combinations like H6H3, N8N1, N6H9, N2N6, and H9H6/N1N2 were also identified. These findings demonstrate the high variability of influenza viruses in migratory waterbirds in Georgia, including a notable rate of co-infections. Some samples exhibited uncommon genetic characteristics compared to other strains from the same year, suggesting Georgia’s role as a mixing vessel for influenza viruses. This facilitates reassortment during co-infections and contributes to the genetic diversity observed across flyways.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Deposition, Diagenesis, and Sequence Stratigraphy of the Pennsylvanian Morrowan and Atokan Intervals at Farnsworth Unit

Farnsworth Field Unit (FWU), a mature oilfield currently undergoing CO2-enhanced oil recovery (EOR) in the northeastern Texas panhandle, is the study area for an extensive project undertaken by the Southwest Regional Partnership on Carbon Sequestration (SWP). SWP is characterizing the field and monitoring and modeling injection and fluid flow processes with the intent of verifying storage of CO2 in a timeframe of 100–1000 years. Collection of a large set of data including logs, core, and 3D geophysical data has allowed us to build a detailed reservoir model that is well-grounded in observations from the field. This paper presents a geological description of the rocks comprising the reservoir that is a target for both oil production and CO2 storage, as well as the overlying units that make up the primary and secondary seals. Core descriptions and petrographic analyses were used to determine depositional setting, general lithofacies, and a diagenetic sequence for reservoir and caprock at FWU. The reservoir is in the Pennsylvanian-aged Morrow B sandstone, an incised valley fluvial deposit that is encased within marine shales. The Morrow B exhibits several lithofacies with distinct appearance as well as petrophysical characteristics. The lithofacies are typical of incised valley fluvial sequences and vary from a relatively coarse conglomerate base to an upper fine sandstone that grades into the overlying marine-dominated shales and mudstone/limestone cyclical sequences of the Thirteen Finger limestone. Observations ranging from field scale (seismic surveys, well logs) to microscopic (mercury porosimetry, petrographic microscopy, microprobe and isotope data) provide a rich set of data on which we have built our geological and reservoir models.

04 OIL SHALES AND TAR SANDS↗
DOE OSTI2016

Supermassive black holes and their host spheroids. II. The red and blue sequence in the M{sub BH}–M{sub *,SPH} diagram

In our first paper, we performed a detailed (i.e., bulge, disks, bars, spiral arms, rings, halo, nucleus, etc.) decomposition of 66 galaxies, with directly measured black hole masses, M{sub BH}, imaged at 3.6 μm with Spitzer. Our sample is the largest to date and, for the first time, the decompositions were checked for consistency with the galaxy kinematics. We present correlations between M{sub BH} and the host spheroid (and galaxy) luminosity, L{sub sph} (and L{sub gal}), and also stellar mass, M{sub ∗,sph}. While most previous studies have used galaxy samples that were overwhelmingly dominated by high-mass, early-type galaxies, our sample includes 17 spiral galaxies, half of which have M{sub BH}<10{sup 7} M{sub ⊙}, and allows us to better investigate the poorly studied low-mass end of the M{sub BH}--M{sub ∗,sph} correlation. The bulges of early-type galaxies follow M{sub BH} ∝ M{sub ∗,sph}{sup 1.04±0.10} and define a tight red sequence with intrinsic scatter ϵ{sub (M{sub B{sub H|M{sub ∗{sub ,{sub s{sub p{sub h)}}}}}}}} = 0.43 ± 0.06 dex and a median M{sub BH}/M{sub ∗,sph} ratio of 0.68 ± 0.04%, i.e., a ±2σ range of 0.1%–5%. At the low-mass end, the bulges of late-type galaxies define a much steeper blue sequence, with M{sub BH} ∝ M{sub ∗,sph}{sup 2−3} and M{sub BH}/M{sub ∗,sph} equal to 0.02% at M{sub BH} ≈ 10{sup 6} M{sub ⊙}. We additionally report that (1) our Sérsic galaxy sample follows M{sub BH} ∝ M{sub ∗,sph}{sup 1.48±0.20}, a less steep sequence than previously reported; (2) bulges with Sérsic index n{sub sph}<2, argued by some to be pseudo-bulges, are not offset to lower M{sub BH} from the correlation defined by the current bulge sample with n{sub sph}>2; and (3) L{sub sph} and L{sub gal} correlate equally well with M{sub BH}, in terms of intrinsic scatter, only for early-type galaxies—once reasonable numbers of spiral galaxies are included, the correlation with L{sub sph} is better than that with L{sub gal}.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2016

Recent galaxy mergers and residual star formation of red sequence galaxies in galaxy clusters

This study explored the Galaxy Evolution Explorer ultraviolet (UV) properties of optical red sequence galaxies in four rich Abell clusters at z⩽0.1. In particular, we tried to find a hint of merger-induced recent star formation (RSF) in red sequence galaxies. Using the NUV − r{sup ′} colors of the galaxies, RSF fractions were derived based on various criteria for post-merger galaxies and normal galaxies. Following k-correction, about 36% of the post-merger galaxies were classified as RSF galaxies with a conservative criterion (NUV − r{sup ′}⩽5), and that number was doubled (∼72%) when using a generous criterion (NUV − r{sup ′}⩽5.4). The trend was the same when we restricted the sample to galaxies within 0.5 × R {sub 200}. Post-merger galaxies with strong UV emission showed more violent, asymmetric features in the deep optical images. The RSF fractions did not show any trend along the clustocentric distance within R {sub 200}. We performed a Dressler–Shectman test to check whether the RSF galaxies had any correlation with the substructures in the galaxy clusters. Within R {sub 200} of each cluster, the RSF galaxies did not appear to be preferentially related to the clusters’ substructures. Our results suggested that only 30% of RSF red sequence galaxies show morphological hints of recent galaxy mergers. This implies that internal processes (e.g., stellar mass loss or hot gas cooling) for the supply of cold gas to early-type galaxies may play a significant role in the residual star formation of early-type galaxies at a recent epoch.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

DESI Survey Validation Data in the COSMOS/Hyper Suprime-Cam Field: Cool Gas Trace Main-sequence Star-forming Galaxies at the Cosmic Noon

We present the first result in exploring the gaseous halo and galaxy correlation using the Dark Energy Spectroscopic Instrument survey validation data in the Cosmic Evolution Survey (COSMOS) and Hyper Suprime-Cam field. We obtain multiphase gaseous halo properties in the circumgalactic medium by using 115 quasar spectra (signal-to-noise ratio > 3). We detect Mg ii absorption at redshift 0.6 < z < 2.5, C iv absorption at 1.6 < z < 3.6, and H i absorption associated with the Mg ii and C iv. By crossmatching the COSMOS2020 catalog, we identify the Mg ii and C iv host galaxies in 10 quasar fields at 0.9< z < 3.1. We find that within the impact parameter of 250 kpc, a tight correlation is seen between the strong Mg ii equivalent width and the host galaxy star formation rate. The covering fraction f c of the strong Mg ii selected galaxies, which is the ratio of the absorbing galaxy in a certain galaxy population, shows significant evolution in the main-sequence galaxies and marginal evolution in all the galaxy populations within 250 kpc at 0.9 < z < 2.2. The f c increase in the main-sequence galaxies likely suggests the coevolution of strong Mg ii absorbing gas and the main-sequence galaxies at the cosmic noon. Furthermore, Mg ii and C iv absorbing gas is detected out of the galaxy virial radius, tentatively indicating the feedback produced by the star formation and/or the environmental effects.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2016

THE RED SEQUENCE AT BIRTH IN THE GALAXY CLUSTER Cl J1449+0856 AT z = 2

We use Hubble Space Telescope /WFC3 imaging to study the red population in the IR-selected, X-ray detected, low-mass cluster Cl J1449+0856 at z = 2, one of the few bona fide established clusters discovered at this redshift, and likely a typical progenitor of an average massive cluster today. This study explores the presence and significance of an early red sequence in the core of this structure, investigating the nature of red-sequence galaxies, highlighting environmental effects on cluster galaxy populations at high redshift, and at the same time underlining similarities and differences with other distant dense environments. Our results suggest that the red population in the core of Cl J1449+0856 is made of a mixture of quiescent and dusty star-forming galaxies, with a seedling of the future red sequence already growing in the very central cluster region, and already characterizing the inner cluster core with respect to lower-density environments. On the other hand, the color–magnitude diagram of this cluster is definitely different from that of lower-redshift z ≲ 1 clusters, as well as of some rare particularly evolved massive clusters at similar redshift, and it is suggestive of a transition phase between active star formation and passive evolution occurring in the protocluster and established lower-redshift cluster regimes.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2011

Non-contiguous finished genome sequence of the opportunistic oral pathogen Prevotella multisaccharivorax type strain (PPPA20 T )

Prevotella multisaccharivorax Sakamoto et al. 2005 is a species of the large genus Prevotella, which belongs to the family Prevotellaceae. The species is of medical interest because its members are able to cause diseases in the human oral cavity such as periodontitis, root caries and others. Although 77 Prevotella genomes have already been sequenced or are targeted for sequencing, this is only the second completed genome sequence of a type strain of a species within the genus Prevotella to be published. The 3,388,644 bp long genome is assembled in three non-contiguous contigs, harbors 2,876 protein-coding and 75 RNA genes and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2012

Complete genome sequence of Halopiger xanaduensis type strain (SH6T)

Halopiger xanaduensis is the type species of the genus Halopiger and belongs to the euryarchaeal family Halobacteriaceae. H. xanaduensis strain SH-6, which is designated as the type strain, was isolated from the sediment of a salt lake in Inner Mongolia, Lake Shangmatala. Like other members of the family Halobacteriaceae, it is an extreme halophile requiring at least 2.5 M salt for growth. We report here the sequencing and annotation of the 4,355,268 bp genome, which includes one chromosome and three plasmids. This genome is part of a Joint Genome Institute (JGI) Community Sequencing Program (CSP) project to sequence diverse haloarchaeal genomes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Genome sequence of the Thermotoga thermarum type strain (LA 3 T ) from an African solfataric spring

Thermotoga thermarum Windberger et al. 1989 is a member to the genomically well characterized genus Thermotoga in the phylum ' Thermotogae '. T. thermarum is of interest for its origin from a continental solfataric spring vs. predominantly marine oil reservoirs of other members of the genus. The genome of strain LA3T also provides fresh data for the phylogenomic positioning of the (hyper-)thermophilic bacteria. T. thermarum strain LA3 T is the fourth sequenced genome of a type strain from the genus Thermotoga , and the sixth in the family Thermotogaceae to be formally described in a publication. Phylogenetic analyses do not reveal significant discrepancies between the current classification of the group, 16S rRNA gene data and whole-genome sequences. Nevertheless, T. thermarum significantly differs from other Thermotoga species regarding its iron-sulfur cluster synthesis, as it contains only a minimal set of the necessary proteins. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,039,943 bp long chromosome with its 2,015 protein-coding and 51 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

Genome sequence of the moderately thermophilic sulfur-reducing bacterium Thermanaerovibrio velox type strain (Z-9701 T ) and emended description of the genus Thermanaerovibrio

Thermanaerovibrio velox Zavarzina et al. 2000 is a member of the Synergistaceae, a family in the phylum Synergistetes that is already well-characterized at the genome level. Members of this phylum were described as Gram-negative staining anaerobic bacteria with a rod/vibrioid cell shape and possessing an atypical outer cell envelope. They inhabit a large variety of anaerobic environments including soil, oil wells, wastewater treatment plants and animal gastrointestinal tracts. They are also found to be linked to sites of human diseases such as cysts, abscesses, and areas of periodontal disease. The moderately thermophilic and organotrophic T. velox shares most of its morphologic and physiologic features with the closely related species, T. acidaminovorans. In addition to Su883 T , the type strain of T. acidaminovorans, stain Z-9701 T is the second type strain in the genus Thermanaerovibrio to have its genome sequence published. Here we describe the features of this organism, together with the non-contiguous genome sequence and annotation. The 1,880,838 bp long chromosome (non-contiguous finished sequence) with its 1,751 protein-coding and 59 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

Genome sequence of Phaeobacter inhibens type strain (T5 T ), a secondary metabolite producing representative of the marine Roseobacter clade, and emendation of the species description of Phaeobacter inhibens

Strain T5 T is the type strain of the species Phaeobacter inhibens Martens et al. 2006, a secondary metabolite producing bacterium affiliated to the Roseobacter clade. Strain T5 T was isolated from a water sample taken at the German Wadden Sea, southern North Sea. Here we describe the complete genome sequence and annotation of this bacterium with a special focus on the secondary metabolism and compare it with the genomes of the Phaeobacter inhibens strains DSM 17395 and DSM 24588 (2.10), selected because of the close phylogenetic relationship based on the 16S rRNA gene sequences of these three strains. The genome of strain T5 T comprises 4,130,897 bp with 3.923 protein-coding genes and shows high similarities in genetic and genomic characteristics compared to P. inhibens DSM 17395 and DSM 24588 (2.10). Besides the chromosome, strain T5 T possesses four plasmids, three of which show a high similarity to the plasmids of the strains DSM 17395 and DSM 24588 (2.10). Analysis of the fourth plasmid suggested horizontal gene transfer. Most of the genes on this plasmid are not present in the strains DSM 17395 and DSM 24588 (2.10) including a nitrous oxide reductase, which allows strain T5 T a facultative anaerobic lifestyle. The G+C content was calculated from the genome sequence and differs significantly from the previously published value, thus warranting an emendation of the species description.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

Genome sequence of the clover-nodulating Rhizobium leguminosarum bv. trifolii strain TA1

Rhizobium leguminosarum bv. trifolii strain TA1 is an aerobic, motile, Gram-negative, nonspore-forming rod that is an effective nitrogen fixing microsymbiont on the perennial clovers originating from Europe and the Mediterranean basin. TA1 however is ineffective with many annual and perennial clovers originating from Africa and America. Here we describe the features of R. leguminosarum bv. trifolii strain TA1, together with genome sequence information and annotation. The 8,618,824 bp high-quality-draft genome is arranged in a 6 scaffold of 32 contigs, contains 8,493 protein-coding genes and 83 RNA-only encoding genes, and is one of 20 rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Community Sequencing Program.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

Genome sequence of the Ornithopus/Lupinus-nodulating Bradyrhizobium sp. strain WSM471

Bradyrhizobium sp. strain WSM471 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective nitrogen- (N2) fixing root nodule formed on the annual legume Ornithopus pinnatus (Miller) Druce growing at Oyster Harbour, Albany district, Western Australia in 1982. This strain is in commercial production as an inoculant for Lupinus and Ornithopus. Here we describe the features of Bradyrhizobium sp. strain WSM471, together with genome sequence information and annotation. The 7,784,016 bp high-quality-draft genome is arranged in 1 scaffold of 2 contigs, contains 7,372 proteincoding genes and 58 RNA-only encoding genes, and is one of 20 rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Community Sequencing Program.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

Genome sequence of the South American clover-nodulating Rhizobium leguminosarum bv. trifolii strain WSM597

Rhizobium leguminosarum bv. trifolii strain WSM597 is an aerobic, motile, Gram-negative, nonspore-forming rod isolated from a root nodule of the annual clover Trifolium pallidum L. growing at Glencoe Research Station near Tacuarembó, Uruguay. This strain is generally ineffective for nitrogen (N2 ) fixation with clovers of Mediterranean, North American and African origin, but is effective on the South American perennial clover T. polymorphum Poir. Here we describe the features of R. leguminosarum bv. trifolii strain WSM597, together with genome sequence information and annotation. The 7,634,384 bp high-quality-draft genome is arranged in 2 scaffolds of 53 contigs, contains 7,394 protein-coding genes and 87 RNA-only encoding genes, and is one of 20 rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Community Sequencing Program.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

Genome sequence of the lupin-nodulating Bradyrhizobium sp. strain WSM1417

Bradyrhizobium sp. strain WSM1417 is an aerobic, motile, Gram-negative, non-sporeforming rod that was isolated from an effective nitrogen (N2) fixing root nodule of Lupinus sp. collected in Papudo, Chile, in 1995. However, this microsymbiont is a poorly effective N2 fixer with the legume host Lupinus angustifolius L.; a lupin species of considerable economic importance in both Chile and Australia. The symbiosis formed with L. angustifolius produces less than half of the dry matter achieved by the symbioses with commercial inoculant strains such as Bradyrhizobium sp. strain WSM471. Therefore, WSM1417 is an important candidate strain with which to investigate the genetics of effective N2 fixation in the lupin-bradyrhizobia symbioses. Here we describe the features of Bradyrhizobium sp. strain WSM1417, together with genome sequence information and annotation. The 8,048,963 bp high-quality-draft genome is arranged in a single scaffold of 2 contigs, contains 7,695 protein-coding genes and 77 RNA-only encoding genes, and is one of 20 rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Community Sequencing Program.

59 BASIC BIOLOGICAL SCIENCES↗