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Evaluating Detection Limits of Next-Generation Sequencing for the Surveillance and Monitoring of International Marine Pests

Overview of attention for article published in PLOS ONE, September 2013
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  • In the top 25% of all research outputs scored by Altmetric
  • High Attention Score compared to outputs of the same age (85th percentile)
  • Good Attention Score compared to outputs of the same age and source (79th percentile)

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1 policy source
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10 X users

Citations

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149 Dimensions

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217 Mendeley
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1 CiteULike
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Title
Evaluating Detection Limits of Next-Generation Sequencing for the Surveillance and Monitoring of International Marine Pests
Published in
PLOS ONE, September 2013
DOI 10.1371/journal.pone.0073935
Pubmed ID
Authors

Xavier Pochon, Nathan J. Bott, Kirsty F. Smith, Susanna A. Wood

Abstract

Most surveillance programmes for marine invasive species (MIS) require considerable taxonomic expertise, are laborious, and are unable to identify species at larval or juvenile stages. Therefore, marine pests may go undetected at the initial stages of incursions when population densities are low. In this study, we evaluated the ability of the benchtop GS Junior™ 454 pyrosequencing system to detect the presence of MIS in complex sample matrices. An initial in-silico evaluation of the mitochondrial cytochrome c oxidase subunit I (COI) and the nuclear small subunit ribosomal DNA (SSU) genes, found that multiple primer sets (targeting a ca. 400 base pair region) would be required to obtain species level identification within the COI gene. In contrast a single universal primer set was designed to target the V1-V3 region of SSU, allowing simultaneous PCR amplification of a wide taxonomic range of MIS. To evaluate the limits of detection of this method, artificial contrived communities (10 species from 5 taxonomic groups) were created using varying concentrations of known DNA samples and PCR products. Environmental samples (water and sediment) spiked with one or five 160 hr old Asterias amurensis larvae were also examined. Pyrosequencing was able to recover DNA/PCR products of individual species present at greater than 0.64% abundance from all tested contrived communities. Additionally, single A. amurensis larvae were detected from both water and sediment samples despite the co-occurrence of a large array of environmental eukaryotes, indicating an equivalent sensitivity to quantitative PCR. NGS technology has tremendous potential for the early detection of marine invasive species worldwide.

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Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 217 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United States 5 2%
United Kingdom 3 1%
Australia 2 <1%
Portugal 1 <1%
Israel 1 <1%
Canada 1 <1%
Sweden 1 <1%
Estonia 1 <1%
New Zealand 1 <1%
Other 2 <1%
Unknown 199 92%

Demographic breakdown

Readers by professional status Count As %
Researcher 62 29%
Student > Ph. D. Student 48 22%
Student > Master 27 12%
Student > Bachelor 18 8%
Other 14 6%
Other 18 8%
Unknown 30 14%
Readers by discipline Count As %
Agricultural and Biological Sciences 96 44%
Environmental Science 44 20%
Biochemistry, Genetics and Molecular Biology 18 8%
Earth and Planetary Sciences 4 2%
Economics, Econometrics and Finance 3 1%
Other 14 6%
Unknown 38 18%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 10. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 18 December 2017.
All research outputs
#3,163,451
of 22,719,618 outputs
Outputs from PLOS ONE
#41,625
of 193,931 outputs
Outputs of similar age
#28,950
of 196,871 outputs
Outputs of similar age from PLOS ONE
#1,035
of 5,049 outputs
Altmetric has tracked 22,719,618 research outputs across all sources so far. Compared to these this one has done well and is in the 86th percentile: it's in the top 25% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 193,931 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 15.0. This one has done well, scoring higher than 78% of its peers.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 196,871 tracked outputs that were published within six weeks on either side of this one in any source. This one has done well, scoring higher than 85% of its contemporaries.
We're also able to compare this research output to 5,049 others from the same source and published within six weeks on either side of this one. This one has done well, scoring higher than 79% of its contemporaries.