Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “Reading”

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 1,783 records · Page 99
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

CheckV assesses the quality and completeness of metagenome-assembled viral genomes

Abstract Millions of new viral sequences have been identified from metagenomes, but the quality and completeness of these sequences vary considerably. Here we present CheckV, an automated pipeline for identifying closed viral genomes, estimating the completeness of genome fragments and removing flanking host regions from integrated proviruses. CheckV estimates completeness by comparing sequences with a large database of complete viral genomes, including 76,262 identified from a systematic search of publicly available metagenomes, metatranscriptomes and metaviromes. After validation on mock datasets and comparison to existing methods, we applied CheckV to large and diverse collections of metagenome-assembled viral sequences, including IMG/VR and the Global Ocean Virome. This revealed 44,652 high-quality viral genomes (that is, >90% complete), although the vast majority of sequences were small fragments, which highlights the challenge of assembling viral genomes from short-read metagenomes. Additionally, we found that removal of host contamination substantially improved the accurate identification of auxiliary metabolic genes and interpretation of viral-encoded functions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

A robust benchmark for detection of germline large deletions and insertions

New technologies and analysis methods are enabling genomic structural variants (SVs) to be detected with ever-increasing accuracy, resolution and comprehensiveness. To help translate these methods to routine research and clinical practice, we developed a sequence-resolved benchmark set for identification of both false-negative and false-positive germline large insertions and deletions. To create this benchmark for a broadly consented son in a Personal Genome Project trio with broadly available cells and DNA, the Genome in a Bottle Consortium integrated 19 sequence-resolved variant calling methods from diverse technologies. The final benchmark set contains 12,745 isolated, sequence-resolved insertion (7,281) and deletion (5,464) calls ≥50 base pairs (bp). The Tier 1 benchmark regions, for which any extra calls are putative false positives, cover 2.51 Gbp and 5,262 insertions and 4,095 deletions supported by ≥1 diploid assembly. We demonstrate that the benchmark set reliably identifies false negatives and false positives in high-quality SV callsets from short-, linked- and long-read sequencing and optical mapping.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza

The genus Oryza is a model system for the study of molecular evolution over time scales ranging from a few thousand to 15 million years. Using 13 reference genomes spanning the Oryza species tree, we show that despite few large-scale chromosomal rearrangements rapid species diversification is mirrored by lineage-specific emergence and turnover of many novel elements, including transposons, and potential new coding and noncoding genes. Our study resolves controversial areas of the Oryza phylogeny, showing a complex history of introgression among different chromosomes in the young ‘AA’ subclade containing the two domesticated species. This study highlights the prevalence of functionally coupled disease resistance genes and identifies many new haplotypes of potential use for future crop protection. Finally, this study marks a milestone in modern rice research with the release of a complete long-read assembly of IR 8 ‘Miracle Rice’, which relieved famine and drove the Green Revolution in Asia 50 years ago.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

2'-O-methylation in mRNA disrupts tRNA decoding during translation elongation

Chemical modifications of mRNA may regulate many aspects of mRNA processing and protein synthesis. Recently, 2'-O-methylation of nucleotides was identified as a frequent modification in translated regions of human mRNA, showing enrichment in codons for certain amino acids. Here, using single-molecule, bulk kinetics and structural methods, we show that 2'-O-methylation within coding regions of mRNA disrupts key steps in codon reading during cognate tRNA selection. Our results suggest that 2'-O-methylation sterically perturbs interactions of ribosomal-monitoring bases (G530, A1492 and A1493) with cognate codon–anticodon helices, thereby inhibiting downstream GTP hydrolysis by elongation factor Tu (EF-Tu) and A-site tRNA accommodation, leading to excessive rejection of cognate aminoacylated tRNAs in initial selection and proofreading. In conclusion, our current and prior findings highlight how chemical modifications of mRNA tune the dynamics of protein synthesis at different steps of translation elongation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Structural basis for tRNA decoding and aminoacylation sensing by T-box riboregulators

T-box riboregulators are a class of cis-regulatory RNAs that govern the bacterial response to amino acid starvation by binding, decoding and reading the aminoacylation status of specific transfer RNAs. In this work, we provide a high-resolution crystal structure of a full-length T-box from Mycobacterium tuberculosis that explains tRNA decoding and aminoacylation sensing by this riboregulator. Overall, the T-box consists of decoding and aminoacylation sensing modules bridged by a rigid pseudoknot structure formed by the mid-region domains. Stem-I and the Stem-II S-turn assemble a claw-like decoding module, while the antiterminator, Stem-III, and the adjacent linker form a tightly interwoven aminoacylation sensing module. The uncharged tRNA is selectively recognized by an unexpected set of favorable contacts from the linker region in the aminoacylation sensing module. A complex structure with a charged tRNA mimic shows that the extra moiety dislodges the linker, which is indicative of the possible chain of events that lead to alternative base-pairing and altered expression output.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Longitudinal dataset of human-building interactions in U.S. offices

Adaptive interactions between building occupants and their surrounding environments affect both energy use and environmental quality, as demonstrated by a large body of modeling research that quantifies the impacts of occupant behavior on building operations. Yet, available occupant field data are insufficient to explore the mechanisms that drive this interaction. This paper introduces data from a one year study of 24 U.S. office occupants that recorded a comprehensive set of possible exogenous and endogenous drivers of personal comfort and behavior over time. The longitudinal data collection protocol merges individual thermal comfort, preference, and behavior information from online daily surveys with datalogger readings of occupants’ local thermal environments and control states, yielding 2503 survey responses alongside tens of thousands of concurrent behavior and environment measurements. These data have been used to uncover links between the built environment, personal variables, and adaptive actions, and the data contribute to international research collaborations focused on understanding the human-building interaction.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2021

A high-fidelity residential building occupancy detection dataset

Abstract This paper describes development of a data acquisition system used to capture a range of occupancy related modalities from single-family residences, along with the dataset that was generated. The publicly available dataset includes: grayscale images at 32-by-32 pixels, captured every second; audio files, which have undergone processing to remove personally identifiable information; indoor environmental readings, captured every ten seconds; and ground truth binary occupancy status. The data acquisition system, coined the mobile human presence detection (HPDmobile) system, was deployed in six homes for a minimum duration of one month each, and captured all modalities from at least four different locations concurrently inside each home. The environmental modalities are available as captured, but to preserve the privacy and identity of the occupants, images were downsized and audio files went through a series of processing steps, as described in this paper. This dataset adds to a very small body of existing data, with applications to energy efficiency and indoor environmental quality.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2017

Candidatus Mycoplasma girerdii replicates, diversifies, and co-occurs with Trichomonas vaginalis in the oral cavity of a premature infant

Genital mycoplasmas, which can be vertically transmitted, have been implicated in preterm birth, neonatal infections, and chronic lung disease of prematurity. Our prior work uncovered 16S rRNA genes belonging to a novel, as-yet-uncultivated mycoplasma (lineage 'Mnola') in the oral cavity of a premature neonate. Here, we characterize the organism's associated community, growth status, metabolic potential, and population diversity. Sequencing of genomic DNA from the infant's saliva yielded 1.44 Gbp of high-quality, non-human read data, from which we recovered three essentially complete (including 'Mnola') and three partial draft genomes (including Trichomonas vaginalis). The completed 629,409-bp 'Mnola' genome (Candidatus Mycoplasma girerdii str. UC-B3) was distinct at the strain level from its closest relative, vaginally-derived Ca. M. girerdii str. VCU-M1, which is also associated with T. vaginalis. Replication rate measurements indicated growth of str. UC-B3 within the infant. Genes encoding surface-associated proteins and restriction-modification systems were especially diverse within and between strains. In UC-B3, the population genetic underpinnings of phase variable expression were evident in vivo. Unique among mycoplasmas, Ca. M. girerdii encodes pyruvate-ferredoxin oxidoreductase and may be sensitive to metronidazole. This study reveals a metabolically unique mycoplasma colonizing a premature neonate, and establishes the value of genome-resolved metagenomics in tracking phase variation.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2017

Graphene-Insulator-Semiconductor Junction for Hybrid Photodetection Modalities

A sensitive optical detector is presented based on a deeply depleted graphene-insulator-semiconducting (D 2 GIS) junction, which offers the possibility of simultaneously leveraging the advantages of both charge integration and localized amplification. Direct read-out and built-in amplification are accomplished via photogating of a graphene field-effect transistor (GFET) by carriers generated within a deeply depleted low-doped silicon substrate. Analogous to a depleted metal-oxide-semiconducting junction, photo-generated charge collects in the potential well that forms at the semiconductor/insulator interface and induces charges of opposite polarity within the graphene film modifying its conductivity. This device enables simultaneous photo-induced charge integration with continuous “on detector” readout through use of graphene. The resulting devices exhibit responsivities as high as 2,500 A/W (25,000 S/W) for visible wavelengths and a dynamic range of 30 dB. As both the graphene and device principles are transferrable to arbitrary semiconductor absorbers, D2GIS devices offer a high-performance paradigm for imaging across the electromagnetic spectrum

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2018

Effects of timber harvesting on the genetic potential for carbon and nitrogen cycling in five North American forest ecozones

Forest ecosystems are critical to global biogeochemical cycles but under pressure from harvesting and climate change. We investigated the efects of organic matter (OM) removal during forest harvesting on the genetic potential of soil communities for biomass decomposition and nitrogen cycling in fve ecozones across North America. We analyzed 107 samples, representing four treatments with varied levels of OM removal, at Long-Term Soil Productivity Study sites. Samples were collected more than ten years after harvesting and replanting and were analyzed via shotgun metagenomics. High-quality short reads totaling 1.2 Tbp were compared to the Carbohydrate Active Enzyme (CAZy) database and a custom database of nitrogen cycle genes. Gene profle variation was mostly explained by ecozone and soil layer. Eleven CAZy and nine nitrogen cycle gene families were associated with particular soil layers across all ecozones. Treatment efects on gene profles were mainly due to harvesting, and only rarely to the extent of OM removal. Harvesting generally decreased the relative abundance of CAZy genes while increasing that of nitrogen cycle genes, although these efects varied among ecozones. Our results suggest that ecozone-specifc nutrient availability modulates the sensitivity of the carbon and nitrogen cycles to harvesting with possible consequences for long-term forest sustainability.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2018

A traditional evolutionary history of foot-and-mouth disease viruses in Southeast Asia challenged by analyses of non-structural protein coding sequences

Recombination of rapidly evolving RNA-viruses provides an important mechanism for diversifcation, spread, and emergence of new variants with enhanced ftness. Foot-and-mouth disease virus (FMDV) causes an important transboundary disease of livestock that is endemic to most countries in Asia and Africa. Maintenance and spread of FMDV are driven by periods of dominance of specifc viral lineages. Current understanding of the molecular epidemiology of FMDV lineages is generally based on the phylogenetic relationship of the capsid-encoding genes, with less attention to the process of recombination and evolution of non-structural proteins. In this study, the putative recombination breakpoints of FMDVs endemic to Southeast Asia were determined using full-open reading frame sequences. Subsequently, the lineages’ divergence times of recombination-free genome regions were estimated. These analyses revealed a close relationship between two of the earliest endemic viral lineages that appear unrelated when only considering the phylogeny of their capsid proteins. Contrastingly, one lineage, named O/CATHAY, known for having a particular host predilection (pigs) has evolved independently. Additionally, intra-lineage recombination occurred at diferent breakpoints compared to the inter-lineage process. These results provide new insights about FMDV recombination patterns and the evolutionary interdependence of FMDV serotypes and lineages.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

MEMS terahertz-to-infrared band converter using frequency selective planar metamaterial

A MEMS terahertz-to-infrared converter has been developed based on the unique properties of metamaterials that allow for selective control of the absorptivity and emissivity of the sensors. The converter consists of a sensing element structurally made of planar metamaterial membranes, connected to a substrate frame by four symmetrically-located thermal insulators. Upon THz absorption, the temperature of the sensing element increases and the outward infrared flux from the backside of the element is read by a commercial long-wave infrared camera. Two configurations were designed and fabricated with metamaterial absorptivity optimized for 3.8THz and 4.75THz quantum cascade lasers. The first sensor, fabricated with an oxidized aluminum backside, exhibits higher responsivity, but lower conversion efficiency than the second sensor, fabricated with a metamaterial backside. The spectral characteristics of the metamaterial on the two sides can be optimized to improve both responsivity and sensitivity, while keeping the sensors’ thermal time constant sufficiently small for real time imaging. No dedicated electronics or optics are required for readout making metamaterial-based MEMS THz-to-IR converters very attractive for THz imaging as means of a simple attachment to commercial IR cameras.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2018

The 27 kDa Trypanosoma brucei Pentatricopeptide Repeat Protein is a G-tract Specific RNA Binding Protein

Pentatricopeptide repeat (PPR) proteins, a helical repeat family of organellar RNA binding proteins, play essential roles in post-transcriptional RNA processing. In Trypanosoma brucei, an expanded family of PPR proteins localize to the parasite’s single mitochondrion, where they are believed to perform important roles in both RNA processing and translation. We studied the RNA binding specificity of the simplest T. brucei PPR protein (KRIPP11) using electrophoretic mobility shift assays, fluorescence anisotropy, circular dichroism spectroscopy, and in vitro selection. We found KRIPP11 to be an RNA binding protein with specificity for sequences of four or more consecutive guanosine residues (G-tracts). Such G-tracts are dramatically enriched in T. brucei mitochondrial transcripts that are destined for extensive uridine insertion/deletion editing but are not present in mRNAs following editing. We further found that the quadruplex oligoguanosine RNA conformation is preferentially recognized by KRIPP11 over other conformational forms, and is bound without disruption of the quadruplex structure. In combination with prior data demonstrating association of KRIPP11 with the small ribosomal subunit, these results suggest possible roles for KRIPP11 in bridging mRNA maturation and translation or in facilitating translation of unusual dual-coded open reading frames.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Differences in resource use lead to coexistence of seed-transmitted microbial populations

Seeds are involved in the vertical transmission of microorganisms in plants and act as reservoirs for the plant microbiome. They could serve as carriers of pathogens, making the study of microbial interactions on seeds important in the emergence of plant diseases. We studied the influence of biological disturbances caused by seed transmission of two phytopathogenic agents, Alternaria brassicicola Abra43 (Abra43) and Xanthomonas campestris pv. campestris 8004 (Xcc8004), on the structure and function of radish seed microbial assemblages, as well as the nutritional overlap between Xcc8004 and the seed microbiome, to find seed microbial residents capable of outcompeting this pathogen. According to taxonomic and functional inference performed on metagenomics reads, no shift in structure and function of the seed microbiome was observed following Abra43 and Xcc8004 transmission. This lack of impact derives from a limited overlap in nutritional resources between Xcc8004 and the major bacterial populations of radish seeds. However, two native seed-associated bacterial strains belonging to Stenotrophomonas rhizophila displayed a high overlap with Xcc8004 regarding the use of resources; they might therefore limit its transmission. The strategy we used may serve as a foundation for the selection of seed indigenous bacterial strains that could limit seed transmission of pathogens.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

High Density Genetic Maps of Seashore Paspalum Using Genotyping-By-Sequencing and Their Relationship to The Sorghum Bicolor Genome

As a step towards trait mapping in the halophyte seashore paspalum (Paspalum vaginatum Sw.), we developed an F 1 mapping population from a cross between two genetically diverse and heterozygous accessions, 509022 and HI33. Progeny were genotyped using a genotyping-by-sequencing (GBS) approach and sequence reads were analyzed for single nucleotide polymorphisms (SNPs) using the UGbS-Flex pipeline. More markers were identified that segregated in the maternal parent (HA maps) compared to the paternal parent (AH maps), suggesting that 509022 had overall higher levels of heterozygosity than HI33. We also generated maps that consisted of markers that were heterozygous in both parents (HH maps). The AH, HA and HH maps each comprised more than 1000 markers. Markers formed 10 linkage groups, corresponding to the ten seashore paspalum chromosomes. Comparative analyses showed that each seashore paspalum chromosome was syntenic to and highly colinear with a single sorghum chromosome. Four inversions were identified, two of which were sorghum-specific while the other two were likely specific to seashore paspalum. These high-density maps are the first available genetic maps for seashore paspalum. The maps will provide a valuable tool for plant breeders and others in the Paspalum community to identify traits of interest, including salt tolerance.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Standardized phylogenetic and molecular evolutionary analysis applied to species across the microbial tree of life

There is growing interest in reconstructing phylogenies from the copious amounts of genome sequencing projects that target related viral, bacterial or eukaryotic organisms. To facilitate the construction of standardized and robust phylogenies for disparate types of projects, we have developed a complete bioinformatic workflow, with a web-based component to perform phylogenetic and molecular evolutionary (PhaME) analysis from sequencing reads, draft assemblies or completed genomes of closely related organisms. Furthermore, the ability to incorporate raw data, including some metagenomic samples containing a target organism (e.g. from clinical samples with suspected infectious agents), shows promise for the rapid phylogenetic characterization of organisms within complex samples without the need for prior assembly.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Electron-ion coincidence measurements of molecular dynamics with intense X-ray pulses

Molecules can sequentially absorb multiple photons when irradiated by an intense X-ray pulse from a free-electron laser. If the time delay between two photoabsorption events can be determined, this enables pump-probe experiments with a single X-ray pulse, where the absorption of the first photon induces electronic and nuclear dynamics that are probed by the absorption of the second photon. Here we show a realization of such a single-pulse X-ray pump-probe scheme on N 2 molecules, using the X-ray induced dissociation process as an internal clock that is read out via coincident detection of photoelectrons and fragment ions. By coincidence analysis of the kinetic energies of the ionic fragments and photoelectrons, the transition from a bound molecular dication to two isolated atomic ions is observed through the energy shift of the inner-shell electrons. Via ab-initio simulations, we are able to map characteristic features in the kinetic energy release and photoelectron spectrum to specific delay times between photoabsorptions. In contrast to previous studies where nuclear motions were typically revealed by measuring ion kinetics, our work shows that inner-shell photoelectron energies can also be sensitive probes of nuclear dynamics, which adds one more dimension to the study of light-matter interactions with X-ray pulses.

74 ATOMIC AND MOLECULAR PHYSICS↗