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log 2 (ratio) log 2 (ratio) log 2 (ratio) log 2 (ratio) log 2 (ratio) log 2 (ratio) log 2 (ratio) log 2 (ratio) log 2 (ratio) log 2 (ratio) log 2 (ratio) log 2 (ratio) Maren Depke Results Pathogen Gene Expression Profiling For the new transcripts included in the 2.5 h internalization signature, 6 cluster groups were defined (Fig. R.5.37 A). Cluster group 1 contained 26 transcripts. Expression was increased in the 2.5 h samples and still slightly stronger in the 6.5 h samples. The serum/CO 2 controls at both time points also exhibited increase of expression. Cluster group 2 harbored 32 transcripts which featured increase in expression at the 2.5 h and to a lesser extent at the 6.5 h internalization time points and in the later 6.5 h serum/CO 2 control whereas the 2.5 h serum/CO 2 control exhibited in average no change. Transcripts with decreased expression in the 2.5 h internalized and less strongly in the 6.5 h sample belonged to cluster group 3 which included 42 transcripts. The 2.5 h serum/CO 2 control exhibited no apparent trend of regulation whereas the 6.5 h control exhibited a decrease in expression. In cluster group 4, 26 transcripts were classified, which exhibited a decrease of expression in both internalization samples, a slight increase in the 2.5 h serum/CO 2 controls and a decline of expression to the reference level in the 6.5 h serum/CO 2 controls. Internalization samples in cluster group 5 showed an increase of expression 2.5 h after start of infection, which again declined in samples after 6.5 h. Contrarily, expression in the serum/CO 2 controls was induced at the 2.5 h time point and further increased at the 6.5 h time point. This cluster contained 49 sequences. Finally, cluster group 6 contained 25 sequences which were increased in both internalized samples, and possessed a variable expression pattern in the 2.5 h serum/CO 2 control with increased, repressed and unchanged values, while the 6.5 h serum/CO 2 control samples exhibited a trend of decreased expression. A B cluster group 1 cluster group 2 cluster group 1 cluster group 2 6 4 2 0 -2 -4 -6 1 h n. ad. 2.5 h int. 6.5 h int. 2.5 h co. 6.5 h co. 6 4 2 0 -2 -4 -6 1 h n. ad. 2.5 h int. 6.5 h int. 2.5 h co. 6.5 h co. 6 4 2 0 -2 -4 -6 1 h n. ad. 2.5 h int. 6.5 h int. 2.5 h co. 6.5 h co. 6 4 2 0 -2 -4 -6 1 h n. ad. 2.5 h int. 6.5 h int. 2.5 h co. 6.5 h co. cluster group 3 cluster group 4 cluster group 3 cluster group 4 6 4 2 0 -2 -4 -6 1 h n. ad. 2.5 h int. 6.5 h int. 2.5 h co. 6.5 h co. 6 4 2 0 -2 -4 -6 1 h n. ad. 2.5 h int. 6.5 h int. 2.5 h co. 6.5 h co. 6 4 2 0 -2 -4 -6 1 h n. ad. 2.5 h int. 6.5 h int. 2.5 h co. 6.5 h co. 6 4 2 0 -2 -4 -6 1 h n. ad. 2.5 h int. 6.5 h int. 2.5 h co. 6.5 h co. cluster group 5 cluster group 6 cluster group 5 cluster group 6 6 4 2 0 -2 -4 -6 1 h n. ad. 2.5 h int. 6.5 h int. 2.5 h co. 6.5 h co. 6 4 2 0 -2 -4 -6 1 h n. ad. 2.5 h int. 6.5 h int. 2.5 h co. 6.5 h co. 6 4 2 0 -2 -4 -6 1 h n. ad. 2.5 h int. 6.5 h int. 2.5 h co. 6.5 h co. 6 4 2 0 -2 -4 -6 1 h n. ad. 2.5 h int. 6.5 h int. 2.5 h co. 6.5 h co. Fig. R.5.37: K-means clustering of gene expression data from newly identified transcripts, which exhibited differential expression in the 2.5 h internalized sample (A) or in the 6.5 h internalized sample (B) in comparison to the 1 h serum/CO 2 control with statistical testing and multiple testing correction (p* < 0.05) and a minimal absolute fold change cutoff of 2. For k-means clustering, the following parameters were applied: Transcripts should be assigned to the user-defined number of 6 groups and sorted by deviation using the metric type cosine correlation. No additional data preparation or statistical cuts were applied. The ratio data set (experimental condition normalized to the 1 h serum/CO 2 control) employed for clustering consisted of the five experimental conditions of non-adherent (1 h), internalized (2.5 h and 6.5 h), and serum/CO 2 control (2.5 h and 6.5 h) staphylococci. Although not being continuous data, values were depicted as line graphs instead of bar charts for better facility of inspection. (1 h n. ad. – non-adherent staphylococci after 1 h of infection; 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) Correspondingly, also for the new transcripts included in the 6.5 h internalization signature, 6 cluster groups were defined (Fig. R.5.37 B). Here, cluster group 1 contained 19 transcripts with 168
Maren Depke Results Pathogen Gene Expression Profiling an increase in expression at both internalization time points and in the later 6.5 h serum/CO 2 control whereas the 2.5 h serum/CO 2 control exhibited in average no change. In cluster group 2, to which 17 sequences were assigned, transcripts exhibited a decrease of expression in both internalization samples, and in general no change in the 2.5 h serum/CO 2 controls. Some of the sequences were slightly decreased and some other slightly increased in the later 6.5 h serum/CO 2 controls. Cluster group 3 included 36 transcripts with increased expression at both internalization and serum/CO 2 control time points. Transcripts with mainly decreased expression in both internalized samples belonged to cluster group 4 which included 34 transcripts. The 2.5 h serum/CO 2 control exhibited a varying trend of regulation with some repressed and some induced sequences, whereas the 6.5 h control exhibited a decrease in expression. The 16 transcripts in cluster group 5 possessed an increase in the 2.5 h and 6.5 h internalization samples. Also in the serum/CO 2 controls at both time points a slight tendency of induction of expression was observed, but less prominent than the internalization samples. The last cluster group 6 comprised the remaining 16 transcripts with similar expression pattern as the transcripts in cluster group 5 with exception of the expression change in the serum/CO 2 controls, where only minor changes in the 2.5 h and slight decrease in expression in the 6.5 h samples were visible. Transcripts in all cluster groups of both 2.5 h and 6.5 h internalization signatures showed only minor variation from the non-changed value of 1 in the sample of non-adherent staphylococci. This finding was expected as the similarity between this sample and the 1 h serum/CO 2 control baseline had been unveiled before. 169
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G E N O M E W I D E C H A R A C T E
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Maren Depke C O N T E N T S GENOMEW
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Maren Depke Z U S A M M E N F A S S
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Maren Depke Zusammenfassung der Dis
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Maren Depke S U M M A R Y O F D I S
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Maren Depke Summary of Dissertation
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Maren Depke I N T R O D U C T I O N
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Maren Depke Introduction Besides op
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Maren Depke Introduction Extracellu
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Maren Depke Introduction with heigh
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Maren Depke Introduction 2005). SaP
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Maren Depke Introduction contains a
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Maren Depke Introduction via fibron
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Maren Depke Introduction cathelicid
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Maren Depke Introduction shock are
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Maren Depke Introduction STUDIES OF
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Maren Depke Introduction are effect
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Maren Depke Introduction cell stimu
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Maren Depke Introduction channel CF
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Maren Depke M A T E R I A L A N D M
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Maren Depke Material and Methods Li
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Maren Depke Material and Methods Ki
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Maren Depke Material and Methods GE
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Maren Depke Material and Methods Ge
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Maren Depke Material and Methods Ho
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Maren Depke Material and Methods Ho
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Maren Depke Material and Methods Pa
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corticosterone [pg/ml plasma] corti
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Maren Depke Results Liver Gene Expr
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lood glucose levels [nmol/l] resist
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LBP [ng/ml] CPR [ng/ml] Maren Depke
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Maren Depke Results Liver Gene Expr
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liver weight [g] Maren Depke Result
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infection rate cfu / 10 mg tissue c
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Maren Depke Results Kidney Gene Exp
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Table R.2.1: Genes displaying stati
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Maren Depke BR1 sign DsigB vs wt BR
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Maren Depke Results GENE EXPRESSION
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Maren Depke Results Gene Expression
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log2(ratio C57BL/6 / BALB/c) at IFN
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Maren Depke Results Host Cell Gene
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Page 171 and 172: Maren Depke D I S C U S S I O N A N
Page 173 and 174: Maren Depke Discussion and Conclusi
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Page 208 and 209: Maren Depke References Athanasopoul
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Maren Depke References Jin T, Bokar
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Maren Depke References Kwan T, Liu
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Maren Depke References Luster AD, U
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Maren Depke References Namiki S, Na
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Maren Depke References Puccetti P.
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Maren Depke References Siewert E, B
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Maren Depke References van den Akke
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Maren Depke References Yang XL, Sch
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Maren Depke A F F I D A V I T / E R
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Maren Depke Acknowledgments Kidney
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