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Maren Depke Results Host Cell Gene Expression Pattern in an in vitro Infection Model repressed (CDH10, −1.9). Increased expression was also observed for adhesion molecules ALCAM (1.8) and CEACAM1 (9.9). ALCAM was one of the genes whose protein abundance change was in accordance with the differential expression (Table R.4.10, Table R.4.3). Table R.4.10: Overview on selected differentially expressed cell adhesion related genes in S9 cells 6.5 h after start of infection with S. aureus RN1HG GFP. gene name description Rosetta Resolver annotation Entrez Gene ID alias fold change a ITGA2 integrin, alpha 2 (CD49B, alpha 2 subunit of VLA-2 receptor) 3673 BR, GPIa, CD49B,VLA-2 2.9 ITGA5 integrin, alpha 5 (fibronectin receptor, alpha polypeptide) 3678 FNRA, CD49e,VLA5A 2.0 ITGA11 integrin, alpha 11 22801 1.6 ITGB8 integrin, beta 8 3696 ITGB8 2.6 ITGB1BP2 integrin beta 1 binding protein (melusin) 2 26548 CHORDC3, ITGB1BP 1.8 CYTH1 cytohesin 1 9267 B2-1,SEC7,PSCD1 2.1 PCDH7 protocadherin 7 5099 BHPCDH 4.1 PCDH17 protocadherin 17 27253 PCH68, PCDH68 2.1 CDH8 cadherin 8, type 2 1006 1.6 CDH10 cadherin 10, type 2 (T2-cadherin) 1008 -1.9 ALCAM activated leukocyte cell adhesion molecule 214 MEMD, CD166 1.8 CEACAM1 carcinoembryonic antigen-related cell adhesion molecule 1 (biliary glycoprotein) 634 BGP, BGP1, BGPI 9.9 a Fold change values were calculated for the comparison of infected GFP + S9 cell with the baseline of medium control samples. 6.5 h 130
Maren Depke Results PATHOGEN GENE EXPRESSION PROFILING Growth Media Comparison Study Reproducibility of replicates and clustering of experimental condition groups Cultivation of S. aureus RN1HG in pMEM medium was performed in triplicate. In the tiling array analysis of the sample points exponential growth, stationary phase t 2 , and stationary phase t 4 , the replicates of each group were arranged together in a cluster. As expected, for the stationary t 4 time point, which is defined as 4 h after entry into stationary phase, a higher similarity to the t 2 samples, which were harvested 2 h earlier, than to the exponential growth samples was detected. This similarity was especially visible for the t 4 biological replicates 2 and 1, whereas the replicate 3 held more distance to the other samples (Fig. R.5.1). exponentialgrowth stationary phase t 2 stationary phase t 4 biological replicate 1 biological replicate 2 biological replicate 3 Fig. R.5.1: Hierarchical clustering of 9 tiling array data sets from growth in pMEM medium. The following clustering algorithms were applied on z-score-transformed data: Agglomerative clustering with average linkage using cosine correlation as similarity measure. All sequences were included in the cluster analysis. Three major classes according to the sample points during growth were discernible: 1) exponential growth, 2) stationary phase t 2, and 3) stationary phase t 4. As expected for the stationary t 4 time point, a higher similarity to the t 2 samples than to the exponential growth samples was detected. This similarity was especially visible for the t 4 biological replicates 2 and 1, whereas the replicate 3 held more distance to the other samples. Comparison of experimental condition groups and assessment of differentially regulated genes The consumption of medium components and the reduction of growth rate after beginning of stationary phase was accompanied by a substantial change of gene expression. This change was visualized by the strong scattering when comparing stationary phase t 2 and stationary phase t 4 samples to the exponential growth in scatter plots (Fig. R.5.2). The comparison of stationary phase samples with exponential growth samples by statistical testing resulted in 2243 and 1399 sequences, which exhibited a significant difference to exponential growth at the t 2 and the t 4 time point, respectively. Of these, 1423 sequences exceeded an absolute fold change of 2 in the t 2 samples, and 1086 sequences passed the cutoff in the 2 h later samples of the t 4 time point (Table R.5.1). 131
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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 2005). SaP
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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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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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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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