Abstract
Viruses are integral components of all ecosystems and microbiomes on Earth. Through pervasive infections of their cellular hosts, viruses can reshape microbial community structure and drive ...global nutrient cycling. Over the past decade, viral sequences identified from genomes and metagenomes have provided an unprecedented view of viral genome diversity in nature. Since 2016, the IMG/VR database has provided access to the largest collection of viral sequences obtained from (meta)genomes. Here, we present the third version of IMG/VR, composed of 18 373 cultivated and 2 314 329 uncultivated viral genomes (UViGs), nearly tripling the total number of sequences compared to the previous version. These clustered into 935 362 viral Operational Taxonomic Units (vOTUs), including 188 930 with two or more members. UViGs in IMG/VR are now reported as single viral contigs, integrated proviruses or genome bins, and are annotated with a new standardized pipeline including genome quality estimation using CheckV, taxonomic classification reflecting the latest ICTV update, and expanded host taxonomy prediction. The new IMG/VR interface enables users to efficiently browse, search, and select UViGs based on genome features and/or sequence similarity. IMG/VR v3 is available at https://img.jgi.doe.gov/vr, and the underlying data are available to download at https://genome.jgi.doe.gov/portal/IMG_VR.
Abstract
The Genomes OnLine Database (GOLD) (https://gold.jgi.doe.gov/) is a manually curated, daily updated collection of genome projects and their metadata accumulated from around the world. The ...current version of the database includes over 1.17 million entries organized broadly into Studies (45 770), Organisms (387 382) or Biosamples (101 207), Sequencing Projects (355 364) and Analysis Projects (283 481). These four levels contain over 600 metadata fields, which includes 76 controlled vocabulary (CV) tables containing 3873 terms. GOLD provides an interactive web user interface for browsing and searching by a wide range of project and metadata fields. Users can enter details about their own projects in GOLD, which acts as a gatekeeper to ensure that metadata is accurately documented before submitting sequence information to the Integrated Microbial Genomes (IMG) system for analysis. In order to maintain a reference dataset for use by members of the scientific community, GOLD also imports projects from public repositories such as GenBank and SRA. The current status of the database, along with recent updates and improvements are described in this manuscript.
Viruses represent the most abundant life forms on the planet. Recent experimental and computational improvements have led to a dramatic increase in the number of viral genome sequences identified ...primarily from metagenomic samples. As a result of the expanding catalog of metagenomic viral sequences, there exists a need for a comprehensive computational platform integrating all these sequences with associated metadata and analytical tools. Here we present IMG/VR (https://img.jgi.doe.gov/vr/), the largest publicly available database of 3908 isolate reference DNA viruses with 264 413 computationally identified viral contigs from >6000 ecologically diverse metagenomic samples. Approximately half of the viral contigs are grouped into genetically distinct quasi-species clusters. Microbial hosts are predicted for 20 000 viral sequences, revealing nine microbial phyla previously unreported to be infected by viruses. Viral sequences can be queried using a variety of associated metadata, including habitat type and geographic location of the samples, or taxonomic classification according to hallmark viral genes. IMG/VR has a user-friendly interface that allows users to interrogate all integrated data and interact by comparing with external sequences, thus serving as an essential resource in the viral genomics community.
Abstract
The Integrated Microbial Genome/Virus (IMG/VR) system v.2.0 (https://img.jgi.doe.gov/vr/) is the largest publicly available data management and analysis platform dedicated to viral genomics. ...Since the last report published in the 2016, NAR Database Issue, the data has tripled in size and currently contains genomes of 8389 cultivated reference viruses, 12 498 previously published curated prophages derived from cultivated microbial isolates, and 735 112 viral genomic fragments computationally predicted from assembled shotgun metagenomes. Nearly 60% of the viral genomes and genome fragments are clustered into 110 384 viral Operational Taxonomic Units (vOTUs) with two or more members. To improve data quality and predictions of host specificity, IMG/VR v.2.0 now separates prokaryotic and eukaryotic viruses, utilizes known prophage sequences to improve taxonomic assignments, and provides viral genome quality scores based on the estimated genome completeness. New features also include enhanced BLAST search capabilities for external queries. Finally, geographic map visualization to locate user-selected viral genomes or genome fragments has been implemented and download options have been extended. All of these features make IMG/VR v.2.0 a key resource for the study of viruses.
Harmonic Pulse Testing (HPT) has been developed as a type of well testing applicable during ongoing field operations because a pulsed signal is superimposed on background pressure trend. Its purpose ...is to determine well and formation parameters such as wellbore storage, skin, permeability, and boundaries within the investigated volume. Compared to conventional well testing, HPT requires more time to investigate the same reservoir volume. The advantage is that it does not require the interruption of well and reservoir injection/production before and/or during the test because it allows the extraction of an interpretable periodic signal from measured pressure potentially affected by interference. This makes it an ideal monitoring tool. Interpretation is streamlined through diagnostic plots mimicking conventional well test interpretation methods. To this end, analytical solutions in the frequency domain are available. The methodology was applied to monitor stimulation operations performed at an Enhanced Geothermal System site in Pohang, Korea. The activities were divided into two steps: first, a preliminary sequence of tests, injection/fall‐off, and two HPTs, characterized by low injection rates and dedicated to estimate permeability prior to stimulation operations, and then stimulation sequence characterized by a higher injection rate. During the stimulation operations other HPT were performed to monitor formation properties behavior. The interpretation of HPT data through the derivative approach implemented in the frequency domain provided reliable results in agreement with the injection test. Moreover, it provided an estimation of hydraulic properties without cessation of stimulation operations, thus confirming the effectiveness of HPT application for monitoring purposes.
Key Points
An advanced methodology for well performance monitoring without production interruption is presented
Diagnostic plots analogous to oil industry conventional well testing for flow geometry and regime identification were adopted
A field case validation shows the successful application of the methodology to monitor the stimulation of a well of an enhanced geothermal system
Abstract Aims Although studies have suggested that vitamin A is associated with cardiovascular events and mortality, it remains unclear whether low doses or high doses of vitamin A have harmful ...effects on the cardiovascular system. This study investigated whether serum vitamin A levels are associated with all-cause and cause-specific mortality in US older adults. Data synthesis We analyzed the mortality information for 6069 participants aged 50 years or older who had serum vitamin A data available from the baseline examination. The participants were categorized as having deficient (<30 μg/dL), normal (30–80 μg/dL), or excessive (>80 μg/dL) levels of serum vitamin A, and a multivariate Cox proportional hazards regression analysis was performed on mortality. We found a U-shaped association between serum vitamin A levels and death from all-cause and cause-specific mortality among US adults. Comparing the normal range of serum vitamin A, the hazard ratio with deficient serum vitamin A was 2.9 (95% CI 2.0–4.3) for all-cause mortality, 2.1 (95% CI 1.1–4.1) for cardiovascular-related mortality and 2.5 (95% CI 1.2–5.3) for coronary artery disease-related mortality. Excessive serum vitamin A was associated with a 1.2-fold (95% CI 1.1–1.4) increased risk of all-cause mortality, a 1.4-fold (95% CI 1.2–1.8) increased risk of cardiovascular-related mortality, and a 1.5-fold (95% CI 1.2–2.0) increased risk of coronary artery disease-related mortality compared with the reference group. Conclusion The finding suggests that serum vitamin A levels less than 30 μg/dL or greater than 80 μg/dL levels may indicate a high risk of subsequent mortality.
The Integrated Microbial Genomes & Microbiomes system (IMG/M: https://img.jgi.doe.gov/m/) at the Department of Energy (DOE) Joint Genome Institute (JGI) continues to provide support for users to ...perform comparative analysis of isolate and single cell genomes, metagenomes, and metatranscriptomes. In addition to datasets produced by the JGI, IMG v.7 also includes datasets imported from public sources such as NCBI Genbank, SRA, and the DOE National Microbiome Data Collaborative (NMDC), or submitted by external users. In the past couple years, we have continued our effort to help the user community by improving the annotation pipeline, upgrading the contents with new reference database versions, and adding new analysis functionalities such as advanced scaffold search, Average Nucleotide Identity (ANI) for high-quality metagenome bins, new cassette search, improved gene neighborhood display, and improvements to metatranscriptome data display and analysis. We also extended the collaboration and integration efforts with other DOE-funded projects such as NMDC and DOE Biology Knowledgebase (KBase).
Viruses are widely recognized as critical members of all microbiomes. Metagenomics enables large-scale exploration of the global virosphere, progressively revealing the extensive genomic diversity of ...viruses on Earth and highlighting the myriad of ways by which viruses impact biological processes. IMG/VR provides access to the largest collection of viral sequences obtained from (meta)genomes, along with functional annotation and rich metadata. A web interface enables users to efficiently browse and search viruses based on genome features and/or sequence similarity. Here, we present the fourth version of IMG/VR, composed of >15 million virus genomes and genome fragments, a ≈6-fold increase in size compared to the previous version. These clustered into 8.7 million viral operational taxonomic units, including 231 408 with at least one high-quality representative. Viral sequences in IMG/VR are now systematically identified from genomes, metagenomes, and metatranscriptomes using a new detection approach (geNomad), and IMG standard annotation are complemented with genome quality estimation using CheckV, taxonomic classification reflecting the latest taxonomic standards, and microbial host taxonomy prediction. IMG/VR v4 is available at https://img.jgi.doe.gov/vr, and the underlying data are available to download at https://genome.jgi.doe.gov/portal/IMG_VR.
This study reports a biogenic approach to the synthesis of Au@CeO2 nanocomposite using electrochemically active biofilms (EABs) in water under normal pressure and 30 °C. This work presents the ...results of extensive morphological, structural, optical, visible light photoelectrochemical and photocatalytic studies of Au@CeO2 nanocomposite. The presence of a large number of interfaces between Au nanoparticles and CeO2 for charge transfer is believed to play a key role in enhancing the optical and visible light photoelectrochemical and photocatalytic performance of Au@CeO2 nanocomposite. The enhanced visible light degradation of methyl orange and methylene blue by Au@CeO2 nanocomposite was much higher than that by pure CeO2. The reusability, stability, and other results suggests that the Au@CeO2 nanocomposite could be exploited as potential candidates for visible light photocatalysis, photovoltaic, and photoelectrochemical devices.
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