1. Presented by-
Neha Gupta
Priyanka Bhatt

2. Introduction and Background
• About CF
• Previous studies

3. Hypothesis
Transcriptional profiling would identify
potential adaptive expression traits in
P. aeruginosa lineages that evolved in
vivo

4. Methods
• Isolate collection and genetic analyses
• P. aeruginosa annotation
• Expression profiling
• Microarray analyses

5. Isolate collection and genetic analyses
Fig 1
• Genetic typing - RAPD

6. P. aeruginosa annotation
• All analysis were based in PAO1 annotation
• Genes used to develop probe set were selected by
reciprocal best-hit BLAST among strains PAO1, PA14,
PA7 and LESB58
• Probe set selection
• 5,391 coding genes were selected for Microarray

7. Expression profiling
All Isolated from CF individuals + PAO1 & PA14
RNA isolation
cDNA preparation
cDNA added to Affymetrix GeneChip
Washed, Stained and scanned

8. Microarray analyses
• RMA method used for Hierarchical Clustering
• Gene expression analysis
– DE genes between clonal groups
– DE genes over time within clonal groups

9. Results – Hierarchical clustering of Microarray Data

13. Discussion

14. Future Work
• The current therapeutics can be altered based on the
gene expression profiles.
• As the number of traits undergoing parallel evolution
may be underestimated, sampling P.aeruginosa RNA
directly from sputum samples is very challenging
• Many of these 24 genes encode proteins of unknown
function . Understanding the roles of these genes
could provide insight into selective pressures in CF
lung.

15. Thank You!
Questions?