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At least 883 records · Page 49
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Identification of shared viral sequences in peat moss metagenomes reveals elements of a possible Sphagnum core virome

Viruses are an understudied component of plant microbiomes. Identifying viruses that are shared between individual plants, or members of the “core virome”, could reveal stable viral populations with the potential to modulate the composition and function of the microbiome. Here, we examined the virome associated with Sphagnum mosses, a keystone species that has direct influence over the fate of peatland carbon stores. We analyzed bulk metagenomes and metatranscriptomes generated from Sphagnum field samples collected over a ten-month period to identify virus-like sequences shared among plants. Individual Sphagnum samples harbored distinct DNA and RNA viromes where only a small percentage (< 1%) of the total number of identified viral contigs were shared among all samples. Based on taxonomic classification, the shared viral contigs represent bacterial viruses, or phage (Caudoviricetes), as well as viruses of eukaryotes, namely nucleocytoplasmic large DNA viruses (Nucleocytoviricota) and RNA viruses (Riboviria). We linked the shared phage-like contigs to viral regions within sequenced genomes of bacterial taxa that are members of the Sphagnum core microbiome, suggesting that these contigs represent temperate phage or degraded prophage. The putative nucleocytoplasmic large DNA viruses and RNA viruses were phylogenetically diverse and showed sequence similarity to viruses associated with a broad range of hosts and environmental sources. The identification of shared viral contigs suggested that, despite the compositional heterogeneity between samples, Sphagnum mosses may harbor a core virome. Future work validating the presence of the core virome is warranted as it may aid in understanding how persistent viruses impact microbiome ecology and symbiont evolution within this climatically relevant keystone species.

Metagenomics↗
DOE OSTI2020

The crystal structure of a Polerovirus exoribonuclease-resistant RNA shows how diverse sequences are integrated into a conserved fold

Exoribonuclease-resistant RNAs (xrRNAs) are discrete elements that block the progression of 5' to 3' exoribonucleases using specifically folded RNA structures. A recently discovered class of xrRNA is widespread in several genera of plant-infecting viruses, within both noncoding and protein-coding subgenomic RNAs. The structure of one such xrRNA from a dianthovirus revealed three-dimensional details of the resistant fold but did not answer all questions regarding the conservation and diversity of this xrRNA class. Here, we present the crystal structure of a representative polerovirus xrRNA that contains sequence elements that diverge from the previously solved structure. This new structure rationalizes previously unexplained sequence conservation patterns and shows interactions not present in the first structure. Together, the structures of these xrRNAs from dianthovirus and polerovirus genera support the idea that these plant virus xrRNAs fold through a defined pathway that includes a programmed intermediate conformation. This work deepens our knowledge of the structure-function relationship of xrRNAs and shows how evolution can craft similar RNA folds from divergent sequences.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2012

Sequence-Specific Targeting of Dosage Compensation in Drosophila Favors an Active Chromatin Context

The Drosophila MSL complex mediates dosage compensation by increasing transcription of the single X chromosome in males approximately two-fold. This is accomplished through recognition of the X chromosome and subsequent acetylation of histone H4K16 on X-linked genes. Initial binding to the X is thought to occur at ‘‘entry sites’’ that contain a consensus sequence motif (‘‘MSL recognition element’’ or MRE). However, this motif is only ~2 fold enriched on X, and only a fraction of the motifs on X are initially targeted. Here we ask whether chromatin context could distinguish between utilized and non-utilized copies of the motif, by comparing their relative enrichment for histone modifications and chromosomal proteins mapped in the modENCODE project. Through a comparative analysis of the chromatin features in male S2 cells (which contain MSL complex) and female Kc cells (which lack the complex), we find that the presence of active chromatin modifications, together with an elevated local GC content in the surrounding sequences, has strong predictive value for functional MSL entry sites, independent of MSL binding. We tested these sites for function in Kc cells by RNAi knockdown of Sxl, resulting in induction of MSL complex. We show that ectopic MSL expression in Kc cells leads to H4K16 acetylation around these sites and a relative increase in X chromosome transcription. Collectively, our results support a model in which a pre-existing active chromatin environment, coincident with H3K36me3, contributes to MSL entry site selection. The consequences of MSL targeting of the male X chromosome include increase in nucleosome lability, enrichment for H4K16 acetylation and JIL-1 kinase, and depletion of linker histone H1 on active X-linked genes. Our analysis can serve as a model for identifying chromatin and local sequence features that may contribute to selection of functional protein binding sites in the genome.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Genome Sequence and Transcriptome Analyses of Chrysochromulina tobin: Metabolic Tools for Enhanced Algal Fitness in the Prominent Order Prymnesiales (Haptophyceae)

Haptophytes are recognized as seminal players in aquatic ecosystem function. These algae are important in global carbon sequestration, form destructive harmful blooms, and given their rich fatty acid content, serve as a highly nutritive food source to a broad range of eco-cohorts. Haptophyte dominance in both fresh and marine waters is supported by the mixotrophic nature of many taxa. Despite their importance the nuclear genome sequence of only one haptophyte, Emiliania huxleyi (Isochrysidales), is available. Here we report the draft genome sequence of Chrysochromulina tobin (Prymnesiales), and transcriptome data collected at seven time points over a 24-hour light/dark cycle. The nuclear genome of C. tobin is small (59 Mb), compact (~40% of the genome is protein coding) and encodes approximately 16,777 genes. Genes important to fatty acid synthesis, modification, and catabolism show distinct patterns of expression when monitored over the circadian photoperiod. The C. tobin genome harbors the first hybrid polyketide synthase/non-ribosomal peptide synthase gene complex reported for an algal species, and encodes potential anti-microbial peptides and proteins involved in multidrug and toxic compound extrusion. A new haptophyte xanthorhodopsin was also identified, together with two “red” RuBisCO activases that are shared across many algal lineages. In conclusion, the Chrysochromulina tobin genome sequence provides new information on the evolutionary history, ecology and economic importance of haptophytes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Genetic interaction mapping with microfluidic-based single cell sequencing

Genetic interaction mapping is useful for understanding the molecular basis of cellular decision making, but elucidating interactions genome-wide is challenging due to the massive number of gene combinations that must be tested. Here, we demonstrate a simple approach to thoroughly map genetic interactions in bacteria using microfluidic-based single cell sequencing. Using single cell PCR in droplets, we link distinct genetic information into single DNA sequences that can be decoded by next generation sequencing. Our approach is scalable and theoretically enables the pooling of entire interaction libraries to interrogate multiple pairwise genetic interactions in a single culture. The speed, ease, and low-cost of our approach makes genetic interaction mapping viable for routine characterization, allowing the interaction network to be used as a universal read out for a variety of biology experiments, and for the elucidation of interaction networks in non-model organisms.

Science & Technology - Other Topics↗
DOE OSTI2018

Characterization of the naive murine antibody repertoire using unamplified high-throughput sequencing

Antibody specificity and diversity are generated through the enzymatic splicing of genomic gene segments within each B cell. Antibodies are heterodimers of heavy- and light-chains encoded on separate loci. We studied the antibody repertoire from pooled, splenic tissue of unimmunized, adult female C57BL/6J mice, using high-throughput sequencing (HTS) without amplification of antibody transcripts. We recovered over 90,000 heavy-chain and over 135,000 light-chain immunoglobulin sequences. Individual V-, D-, and J-gene segment usage was uniform among the three mouse pools, particularly in highly abundant gene segments, with low frequency V-gene segments not being detected in all pools. Despite the similar usage of individual gene segments, the repertoire of individual B-cell CDR3 amino acid sequences in each mouse pool was highly varied, affirming the combinatorial diversity in the B-cell pool that has been previously demonstrated. There also was some skewing in the V-gene segments that were detected depending on chromosomal location. This study presents a unique, non-primer biased glimpse of the conventionally housed, unimmunized antibody repertoire of the C57BL6/J mouse.

Science & Technology - Other Topics↗
DOE OSTI2019

GenomeGraphR: A user-friendly open-source web application for foodborne pathogen whole genome sequencing data integration, analysis, and visualization

Food safety risk assessments and large-scale epidemiological investigations have the potential to provide better and new types of information when whole genome sequence (WGS) data are effectively integrated. Today, the NCBI Pathogen Detection database WGS collections have grown significantly through improvements in technology, coordination, and collaboration, such as the GenomeTrakr and PulseNet networks. However, high-quality genomic data is not often coupled with high-quality epidemiological or food chain metadata. We have created a set of tools for cleaning, curation, integration, analysis and visualization of microbial genome sequencing data. It has been tested using Salmonella enterica and Listeria monocytogenes data sets provided by NCBI Pathogen Detection (160,000 sequenced isolates in 2018). GenomeGraphR presents foodborne pathogen WGS data and associated curated metadata in a user-friendly interface that allows a user to query a variety of research questions such as, transmission sources and dynamics, global reach, and persistence of genotypes associated with contamination in the food supply and foodborne illness across time or space. The application is freely available (https://fda-riskmodels.foodrisk.org/ genomegraphr/).

60 APPLIED LIFE SCIENCES↗
DOE OSTI2012

Elucidation of Hepatitis C Virus Transmission and Early Diversification by Single Genome Sequencing

A precise molecular identification of transmitted hepatitis C virus (HCV) genomes could illuminate key aspects of transmission biology, immunopathogenesis and natural history. We used single genome sequencing of 2,922 half or quarter genomes from plasma viral RNA to identify transmitted/founder (T/F) viruses in 17 subjects with acute community-acquired HCV infection. Sequences from 13 of 17 acute subjects, but none of 14 chronic controls, exhibited one or more discrete low diversity viral lineages. Sequences within each lineage generally revealed a star-like phylogeny of mutations that coalesced to unambiguous T/F viral genomes. Numbers of transmitted viruses leading to productive clinical infection were estimated to range from 1 to 37 or more (median = 4). Four acutely infected subjects showed a distinctly different pattern of virus diversity that deviated from a star-like phylogeny. In these cases, empirical analysis and mathematical modeling suggested high multiplicity virus transmission from individuals who themselves were acutely infected or had experienced a virus population bottleneck due to antiviral drug therapy. These results provide new quantitative and qualitative insights into HCV transmission, revealing for the first time virus-host interactions that successful vaccines or treatment interventions will need to overcome. Our findings further suggest a novel experimental strategy for identifying full-length T/F genomes for proteome-wide analyses of HCV biology and adaptation to antiviral drug or immune pressures.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

16S and ITS Amplicon Sequencing Fastq files and metadata from PARCHED Panama Tropical Forest soils, 2019-2020,

Model projections predict tropical forests will experience longer periods of drought and more intense precipitation cycles under a changing climate. Such transitions have implications for structure-function relationships within microbial communities. We examine how chronic drying might reshape prokaryotic and fungal communities across four lowland forests in Panama with a wide variation in mean annual precipitation and soil fertility. Four sites were established across a 1000 mm span in mean annual precipitation (2335 to 3300 mm). We expected microbial communities at sites with lower MAP to be less sensitive to chronic drying than sites with higher MAP; while fungal communities to be more resistant to disturbance than prokaryotes. At each location, partial throughfall exclusion structures were established over 10 x 10 m plots to reduce direct precipitation input. Raw demultiplexed sequences (bacteria, archaea, fungal) from soil samples taken from PARCHED Panama Tropical Forest throughfall exclusion experiments. Files that contain 16S are sequences from prokaryotes, ITS indicates sequences from fungi. Compressed fastq files are contained in Field_PARCHED_ITS_fastq_2020.zip, Field_PARCHED_ITS_fastq_2019.zip, Field_PARCHED_16S_fastq_2020.zip, Field_PARCHED_16S_fastq_2019.zip.There are four sites across the isthmus of Panama, each with 4 control and 4 exclusion plots. Throughfall exclusion shelters were built to intercept 50% of throughfall precipitation that hits the soil. Samples were taken on May 2019 and Jan 2020 from 0-10 cm and 10-20 cm depth approximately 9 and 18 months after shelter installation. Metadata and sample IDs for fastq files for 2019 sampling are within Field_PARCHED_Metadata_2019_ITS.csv and Field_PARCHED_Metadata_2019_16S.csv. The metadata for both 16S and ITS fastq files for January 2020 is included in Field_PARCHED_Metadata_2020.csv. No data processing or QA/QC was done on the raw data. Data processing example provided in R notebook file.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Complete sequences of conjugal helper plasmids pRK2013 and pEVS104

We present the complete sequences of two commonly used conjugal helper plasmids: pRK2013 and pEVS104. These sequences will enable engineering of custom helper plasmids, for example, with different antibiotic markers or origins of replication. We provide both sequence information and plasmid maps to aid future engineering efforts.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2012

Next generation sequencing (NGS) technologies and applications [Slides]

NGS technology overview: (1) NGS library preparation - Nucleic acids extraction, Sample quality control, RNA conversion to cDNA, Addition of sequencing adapters, Quality control of library; (2) Sequencing - Clonal amplification of library fragments, (except PacBio), Sequencing by synthesis, Data output (reads and quality); and (3) Data analysis - Read mapping, Genome assembly, Gene expression, Operon structure, sRNA discovery, and Epigenetic analyses.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Applying Waveform Correlation to Aftershock Sequences Using a Global Sparse Network

Agencies that monitor for underground nuclear tests are interested in techniques that automatically characterize earthquake aftershock sequences to reduce the human analyst effort required to produce high-quality event bulletins. Waveform correlation is effective in detecting similar seismic waveforms from repeating earthquakes, including aftershock sequences. We report the results of an experiment that uses waveform templates recorded by multiple stations of the Comprehensive Nuclear-Test-Ban Treaty International Monitoring System during the first twelve hours after a mainshock to detect and identify aftershocks that occur during the subsequent week. We discuss approaches for station and template selection, threshold setting, and event detection that are specialized for aftershock processing for a sparse, global network. We apply the approaches to three aftershock sequences to evaluate the potential for establishing a set of standards for aftershock waveform correlation processing that can be effective for operational monitoring systems with a sparse network. We compare candidate events detected with our processing methods to the Reviewed Event Bulletin of the International Data Center to develop an intuition about potential reduction in analyst workload.

58 GEOSCIENCES↗
DOE OSTI2026

Lessons from the IEC Durability of Adhesion Accelerated Test Sequence

The IEC 62788-1-1 and IEC 63209-2 standards use aging sequences for durability of adhesion in photovoltaic (PV) modules, which may be evaluated using the single cantilever beam (SCB) test. Because the encapsulant forms critical interfaces with the front glass and solar cells, degradation at those interfaces under ultraviolet (UV) exposure, elevated temperature, and humidity can lead to interfacial delamination - compromising the long-term reliability. In this work, adhesion durability of UV-transmitting poly(ethylene-co-vinyl acetate) (EVA) encapsulant to glass and to silicon solar cells is evaluated after sequenced UV and damp heat aging (85C/85%RH). Laminates were prepared using StarPhire solar front glass with thin glass or PERC cells, and two EVA formulations with different concentrations of siloxane coupling agent. Adhesion was quantified by measuring critical debond energy using the SCB method. Both formulations exhibit similar qualitative trends, while different adhesion is observed at the periphery despite the use of low-shrink manufacturing. The results show that while glass/EVA adhesion remains stable or increases after UV exposure and shows only moderate changes after damp heat, the EVA/cell interface exhibits an irreversible loss of adhesion following UV and then damp heat exposure. Although glass/EVA interfaces generally exhibit lower debond energies, the EVA/cell interface is significantly more vulnerable to UV-driven degradation, identifying it as the dominant reliability risk location through early- and intermediate-module life. These results demonstrate that accelerated aging sequences can expose large, interface-specific losses in adhesion durability and underscore the importance of interface engineering for long-term PV module reliability.

14 SOLAR ENERGY↗
DOE OSTI2019

Single-molecule Real-time (SMRT) Isoform Sequencing (Iso-Seq) in Plants: The Status of the Bioinformatics Tools to Unravel the Transcriptome Complexity

Background: The advent of the Single-Molecule Real-time (SMRT) Isoform Sequencing(Iso-Seq) has paved the way to obtain longer full-length transcripts. This method was found tobe much superior in identifying full-length splice variants and other post-transcriptional events ascompared to the Next Generation Sequencing (NGS)-based short read sequencing (RNA-Seq).Several different bioinformatics tools to analyze the Iso-Seq data have been developed and someof them are still being refined to address different aspects of transcriptome complexity. However, acomprehensive summary of the available tools and their utility is still lacking. Objective: Here, we summarized the existing Iso-Seq analysis tools and presented an integratedbioinformatics pipeline for Iso-Seq analysis, which overcomes the limitations of NGS and generateslong contiguous Full-Length Non-Chimeric (FLNC) reads for the analysis of posttranscriptionalevents. Results: In this review, we summarized recent applications of Iso-Seq in plants, which include improvedgenome annotations, identification of novel genes and lncRNAs, identification of fulllengthsplice isoforms, detection of novel Alternative Splicing (AS) and Alternative Polyadenylation(APA) events. In addition, we also discussed the bioinformatics pipeline for comprehensiveIso-Seq data analysis, including how to reduce the error rate in the reads and how to identify andquantify post-transcriptional events. Furthermore, the visualization approach of Iso-Seq was discussedas well. Finally, we discussed methods to combine Iso-Seq data with RNA-Seq for transcriptomequantification. Conclusion: Overall, this review demonstrates that the Iso-Seq is pivotal for analyzing transcriptomecomplexity and this new method offers unprecedented opportunities to comprehensively understandtranscripts diversity.

Biochemistry & Molecular Biology↗
DOE OSTI2022

UAE6 - Wind Tunnel Tests Data - UAE6 - Sequence Q - Raw Data

Sequence Q: Dynamic Inflow (P) This sequence was designed to characterize the dynamic inflow variation using the five-hole probes that extend upwind of the leading edge of the blade. This test sequence used an upwind, rigid turbine with a 0° cone angle. The wind speeds ranged from 5 m/s to 15 m/s, and data were collected at a 0° yaw angle. The rotor rotated at 72 RPM. Blade and probe pressure measurements were collected. The teeter dampers were replaced with rigid links, and these two channels were flagged as not applicable by setting the measured values in the data file to -99999.99 Nm. The teeter link load cell was pretensioned to 40,000 N. The blade pitch angle was changed from the initial tip pitch angle to the final tip pitch angle at the maximum rate of 67°/s. This angle was maintained for the specified delay time duration. Then the blade was pitched back to the initial pitch angle and held for the specified hold time. This was repeated 20 times. The campaign at 15 m/s was aborted early due to excessive low-speed shaft torque loads. The file length varied depending on the time required to obtain 20 pitch cycles for the specified range of angles. The name convention was the standard format, except for the short campaigns collected to ascertain the functionality of the instrumentation. These points were collected at a 3° pitch angle and use the characters REF in the four digits that normally represent yaw angle.

17 WIND ENERGY↗
DOE OSTI2022

UAE6 - Wind Tunnel Tests Data - UAE6 - Sequence 3 - Raw Data

Sequence 3: Tower Wake Measure (P) Sequence 3 used a downwind, rigid turbine with a 3.4° cone angle. The wind speeds for this sequence corresponded to subcritical [7 m/s], transitional [15 m/s], and supercritical [20 m/s] Reynolds number regimes for the circular cross-section tower. The yaw angle and blade tip pitch angles were selected to traverse the probe tip across the tower wake, while keeping the probe axis approximately parallel to the tunnel centerline. The rotor was parked with the instrumented blade at 180° azimuth. Blade and probe pressure measurements were collected.

17 WIND ENERGY↗
DOE OSTI2022

UAE6 - Wind Tunnel Tests Data - UAE6 - Sequence 4 - Raw Data

Sequence 4: Static Pressure Calibration (P) This test sequence used a downwind, teetered turbine with a 3.4° cone angle. The wind speed ranged from 5 m/s to 25 m/s. Yaw angles of 0° to 30° were achieved. The blade tip pitch was 3°. The rotor rotated at 72 RPM. Blade and probe pressure measurements were collected. A static pitot probe was installed on a boom 2.3 m upwind of the nacelle at hub height and connected to the reference side of the Mensor digital differential pressure transducer through the pneumatic rotary coupling. This provided the reference pressure for all blade-mounted pressure transducers, as opposed to the NASA atmospheric pressure reference that was used for all other test sequences. This simulates the pressure system connections used in field measurements where the static pressure was unknown.

17 WIND ENERGY↗
DOE OSTI2022

UAE6 - Wind Tunnel Tests Data - UAE6 - Sequence 6 - Raw Data

Sequence 6: Shroud Wake Measure (P) This test sequence used a downwind, rigid turbine with a 3.4° cone angle. The wind speeds for this sequence corresponded to subcritical [7 m/s], transitional [15 m/s], and supercritical [20 m/s] Reynolds number regimes for the circular cross-section tower. The yaw angle and blade tip pitch angles were selected to traverse the probe tip across the tower wake while keeping the probe axis approximately parallel to the tunnel centerline. The rotor was parked with the instrumented blade at 180° azimuth. Blade and probe pressure measurements were collected. An airfoil-shaped aluminum shroud was placed on the tower below the 34% span five-hole probe. It extended below the 91% span five-hole probe. The turntable angle was adjusted to position the shroud at various angles relative to the flow.

17 WIND ENERGY↗