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Discovery and profiling of small RNAs responsive to stress conditions in the plant pathogen Pectobacterium atrosepticum

Overview of attention for article published in BMC Genomics, January 2016
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About this Attention Score

  • Good Attention Score compared to outputs of the same age (74th percentile)
  • Good Attention Score compared to outputs of the same age and source (76th percentile)

Mentioned by

twitter
4 tweeters
wikipedia
1 Wikipedia page

Citations

dimensions_citation
15 Dimensions

Readers on

mendeley
32 Mendeley
citeulike
2 CiteULike
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Title
Discovery and profiling of small RNAs responsive to stress conditions in the plant pathogen Pectobacterium atrosepticum
Published in
BMC Genomics, January 2016
DOI 10.1186/s12864-016-2376-0
Pubmed ID
Authors

Stanford Kwenda, Vladimir Gorshkov, Aadi Moolam Ramesh, Sanushka Naidoo, Enrico Rubagotti, Paul R. J. Birch, Lucy N. Moleleki

Abstract

Small RNAs (sRNAs) have emerged as important regulatory molecules and have been studied in several bacteria. However, to date, there have been no whole-transcriptome studies on sRNAs in any of the Soft Rot Enterobacteriaceae (SRE) group of pathogens. Although the main ecological niches for these pathogens are plants, a significant part of their life cycle is undertaken outside their host within adverse soil environment. However, the mechanisms of SRE adaptation to this harsh nutrient-deficient environment are poorly understood. In the study reported herein, by using strand-specific RNA-seq analysis and in silico sRNA predictions, we describe the sRNA pool of Pectobacterium atrosepticum and reveal numerous sRNA candidates, including those that are induced during starvation-activated stress responses. Consequently, strand-specific RNA-seq enabled detection of 137 sRNAs and sRNA candidates under starvation conditions; 25 of these sRNAs were predicted for this bacterium in silico. Functional annotations were computationally assigned to 68 sRNAs. The expression of sRNAs in P. atrosepticum was compared under growth-promoting and starvation conditions: 68 sRNAs were differentially expressed with 47 sRNAs up-regulated under nutrient-deficient conditions. Conservation analysis using BLAST showed that most of the identified sRNAs are conserved within the SRE. Subsequently, we identified 9 novel sRNAs within the P. atrosepticum genome. Since many of the identified sRNAs are starvation-induced, the results of our study suggests that sRNAs play key roles in bacterial adaptive response. Finally, this work provides a basis for future experimental characterization and validation of sRNAs in plant pathogens.

Twitter Demographics

The data shown below were collected from the profiles of 4 tweeters who shared this research output. Click here to find out more about how the information was compiled.

Mendeley readers

The data shown below were compiled from readership statistics for 32 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United Kingdom 1 3%
Unknown 31 97%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 7 22%
Student > Bachelor 4 13%
Researcher 4 13%
Student > Master 4 13%
Professor 4 13%
Other 6 19%
Unknown 3 9%
Readers by discipline Count As %
Agricultural and Biological Sciences 14 44%
Biochemistry, Genetics and Molecular Biology 8 25%
Immunology and Microbiology 2 6%
Computer Science 2 6%
Environmental Science 1 3%
Other 0 0%
Unknown 5 16%

Attention Score in Context

This research output has an Altmetric Attention Score of 5. 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 05 April 2017.
All research outputs
#4,431,818
of 16,638,522 outputs
Outputs from BMC Genomics
#2,133
of 9,107 outputs
Outputs of similar age
#93,729
of 374,703 outputs
Outputs of similar age from BMC Genomics
#228
of 1,005 outputs
Altmetric has tracked 16,638,522 research outputs across all sources so far. This one has received more attention than most of these and is in the 73rd percentile.
So far Altmetric has tracked 9,107 research outputs from this source. They receive a mean Attention Score of 4.3. This one has done well, scoring higher than 75% 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 374,703 tracked outputs that were published within six weeks on either side of this one in any source. This one has gotten more attention than average, scoring higher than 74% of its contemporaries.
We're also able to compare this research output to 1,005 others from the same source and published within six weeks on either side of this one. This one has done well, scoring higher than 76% of its contemporaries.