English (United Kingdom)

https://curated-unify.zendy.io/wp-json/zendy-region/v1/featured_content/oa?rat=en

https://curated-unify.zendy.io/wp-json/zendy-region/v1/highlighted_journal/

Global: Zendy Plus annual

Presents the access of premium content as premium feature

Premium Content

Presents the keyphrase highlighting as premium feature

Keyphrase Highlighting

Presents the summarisation as premium feature

Summarisation

Insights

Presents the pdf analysis as premium feature

PDF Analysis

Presents the zaia usage as premium feature

ZAIA

Global: Zendy Plus monthly

Global: Zendy Tools annual

Global: Zendy Tools monthly

Global: Zendy Free Plan

Background   Pseudomonas aeruginosa  is a common bacterium which is recognized for its association with hospital-acquired infections and its advanced antibiotic resistance mechanisms.  Tuberculosis , one of the major causes of mortality, is initiated by the deposition of  Mycobacterium tuberculosis . Accessory sequences shared by a subset of strains of a species play an important role in a species’ evolution, antibiotic resistance and infectious potential.    Results  Here, with a multiple sequence aligner, we segmented 25  P. aeruginosa  genomes and 28   M. tuberculosis  genomes into core blocks (include sequences shared by all the input genomes) and dispensable blocks (include sequences shared by a subset of the input genomes), respectively. For each input genome, we then constructed a scaffold consisting of its core and dispensable blocks sorted by blocks’ locations on the chromosomes. Consecutive dispensable blocks on these scaffold formed  instable regions . After a comprehensive study of these instable regions, three characteristics of instable regions are summarized: instable regions were short, site specific and varied in different strains. Three DNA elements (directed repeats (DRs), transposons and integrons) were then studied to see whether these DNA elements are associated with the variation of instable regions. A pipeline was developed to search for DR pairs on the flank of every instable sequence. 27 DR pairs in  P. aeruginosa  strains and 6 pairs in  M. tuberculosis  strains were found to exist in the instable regions. On the average, 14% and 12% of instable regions in  P. aeruginosa  strains covered transposase genes and integrase genes, respectively. In  M. tuberculosis  strains, an average of 43% and 8% of instable regions contain transposase genes and integrase genes, respectively.    Conclusions  Instable regions were short, site specific and varied in different strains for both  P. aeruginosa  and  M. tuberculosis . Our experimental results showed that DRs, transposons and integrons may be associated with variation of instable regions.    Electronic supplementary material  The online version of this article (10.1186/s12938-018-0563-8) contains supplementary material, which is available to authorized users.

Comprehensive study of instable regions in Pseudomonas aeruginosa and Mycobacterium tuberculosis