genomewide characterization of host-pathogen interactions by ...

mean normalized intensity
mean normalized intensity
Maren Depke
Results
Pathogen Gene Expression Profiling
A
B
10.0 10,0
fold change in comparison to
baseline 1 h serum/CO 2 control
S. aureus
RN1HG
sample
conditions
and time
points
dltA dltB dltC dltD lytM ssaA
exponential growth phase 1.0 -1.0 -1.0 -1.2 2.6 1.2
2.5 h internalized -2.5 -2.2 -1.6 -2.2 2.4 3.0
6.5 h internalized -1.5 -1.3 -1.2 -1.3 2.1 2.9
2.5 h serum/CO 2 control 1.0 -1.0 1.1 -1.1 1.4 1.3
6.5 h serum/CO 2 control -2.5 -2.4 -2.5 -2.4 1.5 -1.9
2.5 h anaerobic incubation -2.0 -2.2 -1.9 -2.7 -3.3 -2.5
1.0 1,0
dltA
dltB
dltC
dltD
lytM
ssaA
Fig. R.5.18: Cell wall associated gene expression.
A. Overview on fold change values relative to the baseline sample “1 h serum/CO 2 control” and on significance in statistical group
comparisons. Differentially expressed genes are marked by gray filling for the corresponding sample condition/time point.
Genes which were significant in statistical testing (p* < 0.05) but did not pass the absolute fold change cutoff 2 are indicated in bold
without filling. The sample “6.5 h serum/CO 2 control” could not be included in statistical testing because of small group size (n = 2).
B. Overview on mean normalized gene expression intensity. After the global normalization by inter-chip scaling and detrending, each
individual gene has been normalized to the expression level of the baseline sample “1 h serum/CO 2 control”. Although not being
continuous data, values were depicted as line graphs instead of bar charts for better facility of inspection.
(exp. − exponential growth phase; 1 h co. – 1 h serum/CO 2 control; 2.5 h int. − 2.5 h internalization; 6.5 h int. − 6.5 h internalization;
2.5 h co. − 2.5 h serum/CO 2 control; 6.5 h co. − 6.5 h serum/CO 2 control; 2.5 h anae. − 2.5 h anaerobic incubation)
0.1 0,1
exp.
1 h
co.
2.5 h
int.
6.5 h
int.
2.5 h
co.
6.5 h
co.
2.5 h
anae.
S. aureus RN1HG sample conditions and time points
Biofilm formation is another option for S. aureus to protect the bacterial cells from the
immune system and antimicrobials. Here, bacterial cells are surrounded by a polysaccharide
matrix, composed of poly-N-acetylglucosamine (PNAG). The ica operon encodes the proteins
necessary for PNAG biosynthesis. Of this operon, the icaB gene was repressed in internalized and
control samples of the infection experiment. The icaC and icaD genes behaved similarly, but were
significantly repressed only at the 2.5 h time point of internalization. The fourth gene of the
operon, icaA, and the separately encoded repressor gene, icaR, were not differentially expressed
(Fig. R.5.19 A, B). Furthermore, it was obvious that the expression intensity of icaADBC was low.
A
B
10,0 10.0
fold change in comparison to
baseline 1 h serum/CO 2 control
S. aureus
RN1HG
sample
conditions
and time
points
icaR icaA icaD icaB icaC
exponential growth phase -1.0 2.0 1.6 1.7 1.6
2.5 h internalized -1.2 1.4 -2.2 -3.7 -2.8
6.5 h internalized -1.0 1.0 -1.3 -2.2 -1.5
2.5 h serum/CO 2 control -1.4 1.3 1.1 -2.2 1.1
6.5 h serum/CO 2 control -1.2 1.2 1.5 -1.9 -1.4
2.5 h anaerobic incubation -1.3 1.1 -1.6 -2.4 -1.4
Fig. R.5.19: Biofilm associated gene expression.
A. Overview on fold change values relative to the baseline sample “1 h serum/CO 2 control” and on significance in statistical group
comparisons. Differentially expressed genes are marked by gray filling for the corresponding sample condition/time point.
Genes which were significant in statistical testing (p* < 0.05) but did not pass the absolute fold change cutoff 2 are indicated in bold
without filling. The sample “6.5 h serum/CO 2 control” could not be included in statistical testing because of small group size (n = 2).
B. Overview on mean normalized gene expression intensity. After the global normalization by inter-chip scaling and detrending, each
individual gene has been normalized to the expression level of the baseline sample “1 h serum/CO 2 control”. Although not being
continuous data, values were depicted as line graphs instead of bar charts for better facility of inspection.
(exp. − exponential growth phase; 1 h co. – 1 h serum/CO 2 control; 2.5 h int. − 2.5 h internalization; 6.5 h int. − 6.5 h internalization;
2.5 h co. − 2.5 h serum/CO 2 control; 6.5 h co. − 6.5 h serum/CO 2 control; 2.5 h anae. − 2.5 h anaerobic incubation)
1,0 1.0
0,1 0.1
exp.
1 h
co.
2.5 h
int.
6.5 h
int.
2.5 h
co.
6.5 h
co.
2.5 h
anae.
S. aureus RN1HG sample conditions and time points
icaR
icaA
icaD
icaB
icaC
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