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Clustering of Pseudomonas aeruginosa transcriptomes from planktonic cultures, developing and mature biofilms reveals distinct expression profiles

BACKGROUND: Pseudomonas aeruginosa is a genetically complex bacterium which can adopt and switch between a free-living or biofilm lifestyle, a versatility that enables it to thrive in many different environments and contributes to its success as a human pathogen. RESULTS: Transcriptomes derived from...

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Autores principales: Waite, Richard D, Paccanaro, Alberto, Papakonstantinopoulou, Anastasia, Hurst, Jacob M, Saqi, Mansoor, Littler, Eddie, Curtis, Michael A
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2006
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1525188/
https://www.ncbi.nlm.nih.gov/pubmed/16800888
http://dx.doi.org/10.1186/1471-2164-7-162
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author Waite, Richard D
Paccanaro, Alberto
Papakonstantinopoulou, Anastasia
Hurst, Jacob M
Saqi, Mansoor
Littler, Eddie
Curtis, Michael A
author_facet Waite, Richard D
Paccanaro, Alberto
Papakonstantinopoulou, Anastasia
Hurst, Jacob M
Saqi, Mansoor
Littler, Eddie
Curtis, Michael A
author_sort Waite, Richard D
collection PubMed
description BACKGROUND: Pseudomonas aeruginosa is a genetically complex bacterium which can adopt and switch between a free-living or biofilm lifestyle, a versatility that enables it to thrive in many different environments and contributes to its success as a human pathogen. RESULTS: Transcriptomes derived from growth states relevant to the lifestyle of P. aeruginosa were clustered using three different methods (K-means, K-means spectral and hierarchical clustering). The culture conditions used for this study were; biofilms incubated for 8, 14, 24 and 48 hrs, and planktonic culture (logarithmic and stationary phase). This cluster analysis revealed the existence and provided a clear illustration of distinct expression profiles present in the dataset. Moreover, it gave an insight into which genes are up-regulated in planktonic, developing biofilm and confluent biofilm states. In addition, this analysis confirmed the contribution of quorum sensing (QS) and RpoS regulated genes to the biofilm mode of growth, and enabled the identification of a 60.69 Kbp region of the genome associated with stationary phase growth (stationary phase planktonic culture and confluent biofilms). CONCLUSION: This is the first study to use clustering to separate a large P. aeruginosa microarray dataset consisting of transcriptomes obtained from diverse conditions relevant to its growth, into different expression profiles. These distinct expression profiles not only reveal novel aspects of P. aeruginosa gene expression but also provide a growth specific transcriptomic reference dataset for the research community.
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spelling pubmed-15251882006-08-07 Clustering of Pseudomonas aeruginosa transcriptomes from planktonic cultures, developing and mature biofilms reveals distinct expression profiles Waite, Richard D Paccanaro, Alberto Papakonstantinopoulou, Anastasia Hurst, Jacob M Saqi, Mansoor Littler, Eddie Curtis, Michael A BMC Genomics Research Article BACKGROUND: Pseudomonas aeruginosa is a genetically complex bacterium which can adopt and switch between a free-living or biofilm lifestyle, a versatility that enables it to thrive in many different environments and contributes to its success as a human pathogen. RESULTS: Transcriptomes derived from growth states relevant to the lifestyle of P. aeruginosa were clustered using three different methods (K-means, K-means spectral and hierarchical clustering). The culture conditions used for this study were; biofilms incubated for 8, 14, 24 and 48 hrs, and planktonic culture (logarithmic and stationary phase). This cluster analysis revealed the existence and provided a clear illustration of distinct expression profiles present in the dataset. Moreover, it gave an insight into which genes are up-regulated in planktonic, developing biofilm and confluent biofilm states. In addition, this analysis confirmed the contribution of quorum sensing (QS) and RpoS regulated genes to the biofilm mode of growth, and enabled the identification of a 60.69 Kbp region of the genome associated with stationary phase growth (stationary phase planktonic culture and confluent biofilms). CONCLUSION: This is the first study to use clustering to separate a large P. aeruginosa microarray dataset consisting of transcriptomes obtained from diverse conditions relevant to its growth, into different expression profiles. These distinct expression profiles not only reveal novel aspects of P. aeruginosa gene expression but also provide a growth specific transcriptomic reference dataset for the research community. BioMed Central 2006-06-26 /pmc/articles/PMC1525188/ /pubmed/16800888 http://dx.doi.org/10.1186/1471-2164-7-162 Text en Copyright © 2006 Waite et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Waite, Richard D
Paccanaro, Alberto
Papakonstantinopoulou, Anastasia
Hurst, Jacob M
Saqi, Mansoor
Littler, Eddie
Curtis, Michael A
Clustering of Pseudomonas aeruginosa transcriptomes from planktonic cultures, developing and mature biofilms reveals distinct expression profiles
title Clustering of Pseudomonas aeruginosa transcriptomes from planktonic cultures, developing and mature biofilms reveals distinct expression profiles
title_full Clustering of Pseudomonas aeruginosa transcriptomes from planktonic cultures, developing and mature biofilms reveals distinct expression profiles
title_fullStr Clustering of Pseudomonas aeruginosa transcriptomes from planktonic cultures, developing and mature biofilms reveals distinct expression profiles
title_full_unstemmed Clustering of Pseudomonas aeruginosa transcriptomes from planktonic cultures, developing and mature biofilms reveals distinct expression profiles
title_short Clustering of Pseudomonas aeruginosa transcriptomes from planktonic cultures, developing and mature biofilms reveals distinct expression profiles
title_sort clustering of pseudomonas aeruginosa transcriptomes from planktonic cultures, developing and mature biofilms reveals distinct expression profiles
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1525188/
https://www.ncbi.nlm.nih.gov/pubmed/16800888
http://dx.doi.org/10.1186/1471-2164-7-162
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