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S. aureus RN1HG sample conditions and time points mean intensity of 2 or 3 biological replicates S. aureus RN1HG sample conditions and time points mean intensity of 2 or 3 biological replicates * * * * S. aureus RN1HG sample conditions and time points mean intensity of 2 or 3 biological replicates * * * Maren Depke * p
S. aureus RN1HG sample conditions and time points mean intensity of 2 or 3 biological replicates Maren Depke Results Pathogen Gene Expression Profiling Similarly, tRNA synthetase genes are repressed in stringent response (Anderson KL et al. 2006). Here, repression of these genes was detectable in internalized staphylococci (2.5 h), late serum/CO 2 controls (2.5 h and 6.5 h) and in samples after 2.5 h anaerobic incubation (Fig. R.5.6 B). An exception is the isoleucin tRNA synthetase (ileS), which is induced in stringent response (Anderson KL et al. 2006). But in the 2.5 h and 6.5 h serum/CO 2 controls, this gene shows a trend of repression similar to the other tRNA synthetases with a fold change of −1.5 and −1.8, respectively. Furthermore, translation elongation factor gene expression is known to be suppressed in stringent response (Anderson KL et al. 2006). Such repression physiologically acts in concert with repressed ribosomal protein and tRNA synthetase genes and leads to diminished protein synthesis. In this study, 4 genes for translation elongation factors revealed a trend of repressed expression in late serum/CO 2 controls (2.5 h and 6.5 h). With p = 0.06, statistical significance was only slightly missed in the comparison between these two controls and exponential growth samples (Fig. R.5.6 C). Stringent response is mediated by the regulator RelA whose transcript lateron is increased in stringent response conditions (Anderson KL et al. 2006). A strong trend of induction for relA was observed for the 2.5 h and 6.5 h serum/CO 2 controls. Although relA exhibited significantly different expression (p* < 0.01) in the comparison of all sequences between the 2.5 h serum/CO 2 control and exponential growth phase samples, the 1.8-fold change did not pass the cutoff level of 2. On the other hand, in the comparison between the later 6.5 h serum/CO 2 control and exponential growth phase samples, the fold change amounted to 2.1, but in this comparison statistical testing was not possible because of limited number of replicates relA at the 6.5 h time point (n = 2). Nevertheless, relA could be regarded as induced in the late serum/CO 2 controls, because both time points showed the same trend and all six other experimental samples possessed almost the same, lower gene expression intensity, which proved relA highly reliable measurement of the relA expression by the tiling array approach (Fig. R.5.7). Fig. R.5.7: Comparison of mean expression intensities for the stringent response regulatory gene relA. A strong trend of relA induction was visible for the late serum/CO 2 controls (2.5 h and 6.5 h). Although relA exhibited significantly different expression (one-way textbook ANOVA with Benjamini- Hochberg False Discovery Rate multiple testing correction and p* < 0.01) in the comparison between the 2.5 h serum/CO 2 control and exponential growth phase samples, the 1.8-fold change did not pass the cutoff level of 2. On the other hand, in the comparison between the later 6.5 h serum/CO 2 control and exponential growth phase samples, the fold change amounted to 2.1, but in this comparison statistical testing was not possible because of limited number of replicates at the 6.5 h time point (n = 2). exponential growthOD phase 0.4 1 h serum/CO 2 control 1h CO2 1 non-adh. h non-adherent MOI 25 2.5 h internal. internalized 2.5h 6.5 h internal. internalized 6.5h 2.5 h serum/COCO2 2 control 2.5h 6.5 h serum/COCO2 2 control 6.5h 2.5 h anaerobic anaerobic incubation 2.5h 1.0E+04 10000 2.0E+04 20000 mean intensitySamples of biological replicates 3.0E+04 30000 From repressed or in trend repressed ribosomal protein, tRNA synthetase, and translation elongation factor genes and from the strong tendency of relA infection induction experiments it was reasoned medium comparison that the gene expression signature of late serum/CO 2 controls (2.5 h and 6.5 h) in fact resembled the stationary phase/stringent response. As internalized staphylococci and the early control samples did not possess this similarity, it was concluded that the 1 h serum/CO 2 control sample, although not time-matched, was the most appropriate baseline sample for this infection experiment study. 139
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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 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 Discussion and Conclusi
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Maren Depke References Athanasopoul
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Maren Depke References Byrne GI, Le
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Maren Depke References Demling R. T
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Maren Depke References Foss GS, Pry
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Maren Depke References Hagopian K,
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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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