Escherichia coli biofilms vs planktonic culture
Ontology highlight
ABSTRACT:
ORGANISM(S): Escherichia coli Escherichia coli K-12
PROVIDER: GSE24914 | GEO | 2013/12/30
SECONDARY ACCESSION(S): PRJNA133407
REPOSITORIES: GEO
Similar Datasets
Project description:Transcription profile of Escherichia coli cells in biofilms under static batch culture was compared to that of E. coli cells in planktonic cultures. Both E. coli biofilm and planktonic cultures were cultivated for 18 h in 10% Luria-Bertani broth at room temperature (20 degree Celsius). Biofilms were grown in static batch culture in petri dishes. Both planktonic culture and biofilms were homogenized and run through a separated protocol. Two condition experiments: E. coli biofilm vs E. coli planktonic cultures. Two biological replicates with independently grown and harvested biofilms or planktonic cultures. Each biological replicate has two technical replicates of hybridization on microarray slides. Each slide has three built-in replicates for each probe.
2013-12-30 | E-GEOD-24914 | biostudies-arrayexpress
Project description:Biofilm formation by Escherichia coli was significantly inhibited when co-cultured with Stenotrophomonas maltophilia in static systems. Genes of E. coli involved in species interactions with S. maltophilia were identified in order to allow the study of the mechanisms of inhibited E. coli biofilm formation in co-culture. A total of 89 and 108 genes were identified as differentially expressed in mixed species cultures when growing as biofilm and as planktonic cultures, respectively, compared to the counterpart of pure cultured E. coli. Differential expression of certain identified genes was confirmed using E. coli reporter strains combined with single-cell based flow cytometry analysis. Co-culture with S. maltophilia affected genes involved in metabolism, signal transduction, cell wall composition, and biofilm formation of E. coli. Several selected genes were further confirmed as affecting E. coli biofilm formation in mixed species cultures with S. maltophilia. The data suggest that these genes were involved in species interactions between E. coli and S. maltophilia. This SuperSeries is composed of the SubSeries listed below.
2013-12-30 | GSE24915 | GEO
Project description:The role of rpoS gene in the formation of Escherichia coli biofilms were investigated. The gene expression was compared among E. coli MG1655 wild type strain and rpoS knock-out strain in the biofilms, the planktonic exponential phase, and the planktonic stationary phase. The analysis revealed that the wild type bilfilms (WBF) showed similar pattern of gene expression with the WT planktonic stationary phase (WS), whereas the rpoS knock-out biofilms (MBF) showed similar pattern of gene expression with the wild type planktonic exponential phase (WE). Genes involved in the energy metabolism and the flagella synthesis showed higher expression in the rpoS knock-out biofilms (MBF), but not in the wild type biofilms (WBF). Moreover, genes involved in the stress responses showed higher expression in the wild type biofilms (WBF), but not in the rpoS knock-out biofilms (MBF). Keywords: cell type comparison (biofilms vs planktonic cells, wild type vs rpoS knock-out strains)
2008-05-23 | GSE7885 | GEO
Project description:Escherichia coli biofilms vs planktonic culture
| PRJNA133407 | ENA
Project description:The role of rpoS gene in the formation of Escherichia coli biofilms were investigated. The gene expression was compared among E. coli MG1655 wild type strain and rpoS knock-out strain in the biofilms, the planktonic exponential phase, and the planktonic stationary phase. The analysis revealed that the wild type bilfilms (WBF) showed similar pattern of gene expression with the WT planktonic stationary phase (WS), whereas the rpoS knock-out biofilms (MBF) showed similar pattern of gene expression with the wild type planktonic exponential phase (WE). Genes involved in the energy metabolism and the flagella synthesis showed higher expression in the rpoS knock-out biofilms (MBF), but not in the wild type biofilms (WBF). Moreover, genes involved in the stress responses showed higher expression in the wild type biofilms (WBF), but not in the rpoS knock-out biofilms (MBF). Experiment Overall Design: Affymetrix E. coli antisense genome array was used to compare the gene expression among E. coli wild type and rpoS konck-out strains in the biofilms, the planktonic exponential phase, and the planktonic stationary phase. All samples were grown in MOPS minimal media with 0.2% glucose. Biofilms were grown for 72 hours on glass surface in flow cells (1x4x40 mm), and planktonic cells were grown for 8 hours (exponential phase) and 12 hours (stationary phase). Experiments were repeated 3 times, which resulted in 3 replicates of 6 different samples.
2008-06-18 | E-GEOD-7885 | biostudies-arrayexpress
Project description:Transcription profile of Escherichia coli cells in mono-species pure planktonic cultures was compared to that of E. coli cells in E. coli-Stenotrophomonas maltophilia dual-species planktonic cultures E. coli cells were separated from dual-species planktonic cultures before total RNA extraction to eliminate possible cross hybridization from S. maltophilia transcripts. The separation method was developed by combining the use of reagent RNAlater and immuno-magnetic separation. Pure E. coli planktonic cultures were processed with the same separation protocol before RNA extraction. Two condition experiments: E. coli mono-species pure planktonic culture vs E. coli in mixed-species planktonic cultures. Two biological replicates with independently grown and harvested planktonic cultures. Each biological replicate has two technical replicates of hybridization on microarray slides. Each slide has three built-in replicates for each probe.
2013-12-30 | E-GEOD-24913 | biostudies-arrayexpress
Project description:Transcription profile of Escherichia coli cells in mono-species pure planktonic cultures was compared to that of E. coli cells in E. coli-Stenotrophomonas maltophilia dual-species planktonic cultures E. coli cells were separated from dual-species planktonic cultures before total RNA extraction to eliminate possible cross hybridization from S. maltophilia transcripts. The separation method was developed by combining the use of reagent RNAlater and immuno-magnetic separation. Pure E. coli planktonic cultures were processed with the same separation protocol before RNA extraction.
2013-12-30 | GSE24913 | GEO
Project description:In this work we have demonstrated increased mutability of Staphylococcus aureus and S. epidermidis in biofilms and have explored the mechanisms underlying the enhanced mutability. A novel static biofilm model, utilising cellulose filter disks, was developed to support the formation of mature biofilms with sufficiently high cell densities to permit determination of mutation frequencies. The mutability of biofilm cultures increased up to 60 fold and 4 fold for S. aureus and S. epidermidis, respectively, compared with planktonic cultures. Incorporation of antioxidants into S. aureus biofilms reduced mutation frequencies, indicating that increased oxidative stress underlies increased mutability in the biofilm. Transcriptional profiling revealed upregulation of the superoxide dismutase gene, sodA, in early biofilm cultures, also suggesting enhanced oxidative stress in these cultures. However, loss of the genes encoding superoxide dismutases or peroxidases did not specifically exacerabate biofilm mutability. In S. aureus SH1000, hydrogen peroxide was found to contribute to biofilm mutability.
2012-03-01 | GSE35837 | GEO
Project description:In this work we have demonstrated increased mutability of Staphylococcus aureus and S. epidermidis in biofilms and have explored the mechanisms underlying the enhanced mutability. A novel static biofilm model, utilising cellulose filter disks, was developed to support the formation of mature biofilms with sufficiently high cell densities to permit determination of mutation frequencies. The mutability of biofilm cultures increased up to 60 fold and 4 fold for S. aureus and S. epidermidis, respectively, compared with planktonic cultures. Incorporation of antioxidants into S. aureus biofilms reduced mutation frequencies, indicating that increased oxidative stress underlies increased mutability in the biofilm. Transcriptional profiling revealed upregulation of the superoxide dismutase gene, sodA, in early biofilm cultures, also suggesting enhanced oxidative stress in these cultures. However, loss of the genes encoding superoxide dismutases or peroxidases did not specifically exacerabate biofilm mutability. In S. aureus SH1000, hydrogen peroxide was found to contribute to biofilm mutability. Three growth conditions (18 hr planktonic growth, 48 hr biofilm growth and 144 biofilm growth) of which there are three biological replicates of each
2012-03-01 | E-GEOD-35837 | biostudies-arrayexpress
Project description:Biofilm formation by Escherichia coli was significantly inhibited when co-cultured with Stenotrophomonas maltophilia in static systems. Genes of E. coli involved in species interactions with S. maltophilia were identified in order to allow the study of the mechanisms of inhibited E. coli biofilm formation in co-culture. A total of 89 and 108 genes were identified as differentially expressed in mixed species cultures when growing as biofilm and as planktonic cultures, respectively, compared to the counterpart of pure cultured E. coli. Differential expression of certain identified genes was confirmed using E. coli reporter strains combined with single-cell based flow cytometry analysis. Co-culture with S. maltophilia affected genes involved in metabolism, signal transduction, cell wall composition, and biofilm formation of E. coli. Several selected genes were further confirmed as affecting E. coli biofilm formation in mixed species cultures with S. maltophilia. The data suggest that these genes were involved in species interactions between E. coli and S. maltophilia. This SuperSeries is composed of the SubSeries listed below. Refer to individual Series.
2013-12-30 | E-GEOD-24915 | biostudies-arrayexpress