ArticleApplied and environmental microbiology2010
Use of cellular CRISPR (clusters of regularly interspaced short palindromic repeats) spacer-based microarrays for detection of viruses in environmental samples.
Article in Applied and environmental microbiology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
28 citing papers in PubMed.
- Using metagenomic data to boost protein structure prediction and discovery.Computational and structural biotechnology journal · 2022Review
- Comprehensive discovery of CRISPR-targeted terminally redundant sequences in the human gut metagenome: Viruses, plasmids, and more.PLoS computational biology · 2021Article
- CRISPR: A new paradigm of theranostics.Nanomedicine : nanotechnology, biology, and medicine · 2021Review
- New virus isolates from Italian hydrothermal environments underscore the biogeographic pattern in archaeal virus communities.The ISME journal · 2020Article
- Diversity and Distribution of a Novel Genus of HyperthermophilicFrontiers in microbiology · 2020Article
- Natural diversity of CRISPR spacers of Thermus: evidence of local spacer acquisition and global spacer exchange.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2019Article
- Using CAPTURE to detect spacer acquisition in native CRISPR arrays.Nature protocols · 2019Article
- CRISPR/dCas9-mediated biosensor for detection of tick-borne diseases.Sensors and actuators. B, Chemical · 2018Article
- A virus or more in (nearly) every cell: ubiquitous networks of virus-host interactions in extreme environments.The ISME journal · 2018Article
- Active Crossfire Between Cyanobacteria and Cyanophages in Phototrophic Mat Communities Within Hot Springs.Frontiers in microbiology · 2018Article
- Metagenomic reconstructions of bacterial CRISPR loci constrain population histories.The ISME journal · 2016Article
- Nanoarchaeota, Their Sulfolobales Host, and Nanoarchaeota Virus Distribution across Yellowstone National Park Hot Springs.Applied and environmental microbiology · 2015Article
- Article
- CRISPR-Cas systems preferentially target the leading regions of MOBF conjugative plasmids.RNA biology · 2013Article
- Evidence for the widespread distribution of CRISPR-Cas system in the Phylum Cyanobacteria.RNA biology · 2013Article
- Holding a grudge: persisting anti-phage CRISPR immunity in multiple human gut microbiomes.RNA biology · 2013Article
- Hot spring metagenomics.Life (Basel, Switzerland) · 2013Review
- The population and evolutionary dynamics of phage and bacteria with CRISPR-mediated immunity.PLoS genetics · 2013Article
- CRISPR targeting reveals a reservoir of common phages associated with the human gut microbiome.Genome research · 2012Article
- Small RNAs for defence and regulation in archaea.Extremophiles : life under extreme conditions · 2012Review
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
It is currently difficult to detect unknown viruses in any given environment. The recent discovery of CRISPR (clusters of regularly interspaced short palindromic repeats) loci within bacterial and archaeal cellular genomes may provide an alternative approach to detect new viruses. It has been shown that the spacer sequences between the direct repeat units of the CRISPR loci are often derived from viruses and likely function as guide sequences to protect the cell from viral infection. The spacer sequences within the CRISPR loci may therefore serve as a record of the viruses that have replicated within the cell. We have cataloged the CRISPR spacer sequences from cellular metagenomic data from high-temperature (>80°C), acidic (pH < 4) hot spring environments located in Yellowstone National Park (YNP). We designed a microarray platform utilizing these CRISPR spacer sequences as potential probes to detect viruses present in YNP hot spring environments. We show that this microarray approach can detect viral sequences directly from virus-enriched environmental samples, detecting new viruses which have not been previously characterized. We further demonstrated that this microarray approach can be used to examine temporal changes in viral populations within the environment. Our results demonstrate that CRISPR spacer sequence-based microarrays will be useful tools for detecting and monitoring viruses from diverse environmental samples.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.