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Maren Depke Results Pathogen Gene Expression Profiling purine metabolism glycerol 01276 glpK lactate 00206 ldh1 02922 ldh2 pyruvate 01818 ald1 01452 ald2 alanine asparagine 01497 ahsA aspartate 00899 argG imidazolacetolphosphate 00733 hisC 02607 hutU AICAR 03008 hisF 03010 hisG 03009 hisA alanine aspartate 02916 panD glycolysis / gluconeogenesis glucose 01430 crr (PTSIIA) 00209 (PTSIIBC) 00900 pgi fru-6-P 02822 fbp 01807 pfkA fru-1,6-BP 02366 fba DHAP 00797 tpiA GA-3-P 01794 gap2 00795 gap1 00796 pgk 01833 serA 00798 pgm 01910 pckA PEP pyruvate 01806 pykA 02289 ilvA 01064 pycA 00898 argH malate fumarate 01983 fumC oxalo acetate 01103 sdhC 01104 sdhA 01105 sdhB succinate 01216 sucC 01218 sucD 01802 citZ citrate succinyl- CoA TCA cycle 03013 hisD histidine 02607 hutU 03014 hisG phosphoribosylpyrophosphate pentose phosphate pathway 01394 lysC 01395 asd 01396 dapA 01397 dapB 01398 dapD 01319 thrA 01322 thrB homoserine 01320 dhoM 00013 acetylhomoserine 01321 thrC cystathionine 02286 leuB threonine 02289 ilvA 2-oxobutanoate cysteine 02287 leuC 02288 leuD pyruvate 02282 ilvB acetyl-CoA indole acetaldehyde indole acetate 00153 ipdC indole pyruvate indole serine 01371 trpB tryptophan 01371 trpB 01846 acsA 00132 aldA 02363 (02142 aldA2) 01347 citB 01416 sucB 01418 sucA 01801 citC 00895 gudB NH 3 02606 hutI 02610 hutG glutamate 02869 rocA 00148 arcJ 2-oxoglutarate pyrroline-5- carboxylate 02244 01401 lysA lysine homocysteine methionine isoleucine 02284 ilvC 02281 ilvD valine 02285 leuA 02287 leuC 02288 leuD 02919 panB 02739 panE pantoate 00286 leuB spontaneous 01369 trpC 01370 trpF chorismate prephenate 01364 tyrA 00113 adhE 00608 adhA 00733 hisC phenylalanine tyrosine argininosuccinate carbymoylphosphate citruline 02968 arcB 02969 arcA 00898 argH 00149 argC 00150 urea cycle 00894 proline 02409 arg, rocF urea glutamate semialdehyde leucine acetyl-CoA acetate acetaldehyde ethanol ornithine arginine Fig. R.5.26: Pathway map of amino acid biosyntheses, glycolysis/gluconeogenesis, TCA cycle and urea cycle. Pathway reactions were extracted from KEGG (KEGG: Kyoto Encyclopedia of Genes and Genomes, http://www.genome.jp/kegg/) and arranged according to genes differentially expressed in S9 cell internalized staphylococci in reference to the baseline sample of 1 h serum/CO 2 control. Arrows represent reactions and dots substrates/products when these are not specially named. Numbers next to enzyme reactions will result in the LocusTag of the gene when combined with “SAOUHSC_*” instead of the wildcard character. Colored arrows in combination with colored gene names indicate differential expression, whereas a colored gene name alone (with a black arrow) indicates a trend of regulation when only one criterium, p* < 0.05 or minimal absolute fold change > 2, is fulfilled. Induction of gene expression is marked in red and repression in green color. 160
mean normalized intensity mean normalized intensity mean normalized intensity mean normalized intensity Maren Depke Results Pathogen Gene Expression Profiling A fold change in comparison to baseline 1 h serum/CO 2 control tyrS leuS thrS pheS pheT serS aspS hisS ileS alaS metS asnS gltX trpS valS glyS cysS argS proS lysS S. aureus RN1HG sample conditions and time points exponential growth phase -1.1 -1.0 -1.4 -1.2 -1.3 -1.2 -1.3 -1.2 -1.2 -1.2 -1.1 -1.1 -1.1 1.2 -1.2 3.3 -1.0 -1.1 -1.1 -1.0 2.5 h internalized -2.7 -2.0 -2.1 -2.5 -2.7 -2.2 -1.6 -1.8 -1.5 -1.3 -1.6 -2.0 -1.5 -1.4 -1.1 -1.1 1.5 -1.3 -1.0 -1.2 6.5 h internalized -3.3 -2.3 -2.4 -3.4 -3.5 -2.4 -2.1 -2.3 -1.8 -1.5 -1.4 -1.8 -1.2 -1.3 1.6 1.9 -1.1 -1.2 1.1 -1.0 2.5 h serum/CO 2 control -5.1 -3.0 -2.8 -3.8 -3.9 -2.9 -4.6 -4.5 -3.3 -1.8 -1.2 -1.7 -1.2 1.1 -2.4 2.3 1.2 1.2 -1.6 -1.5 6.5 h serum/CO 2 control -11.2 -5.0 -3.6 -6.2 -4.8 -3.2 -7.5 -8.8 -4.4 -1.8 -1.5 -2.1 -1.3 -1.0 -2.3 1.6 2.0 1.1 -2.0 -1.6 2.5 h anaerobic incubation -3.9 -2.0 -1.5 -2.1 -2.3 -1.9 -3.8 -3.5 -2.9 -1.8 -1.2 -1.5 -1.4 1.0 -2.0 2.1 1.1 1.1 -1.9 -1.9 B C 10.0 10.0 tyrS ileS leuS alaS thrS metS 1.0 pheS pheT serS 1.0 asnS gltX trpS aspS hisS 0.1 0.1 D 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 E 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 10.0 10.0 1.0 valS glyS cysS 1.0 argS proS lysS 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 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 Fig. R.5.27: tRNA synthetase 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. The sample “6.5 h serum/CO 2 control” could not be included in statistical testing because of small group size (n = 2). B-E. 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” (1 h co.). Although not being continuous data, values were depicted as line graphs instead of bar charts for better facility of inspection. Twenty tRNA synthetase genes were assigned to four groups: genes repressed in at least one time point of internalization (B), genes with trend of repression in at least one time point of internalization with p* < 0.05, but an absolute fold change of less than 2 (C), genes with trend of induction in one time point of internalization (D), and genes exhibiting no change in expression (E). (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) After having observed the described changes in metabolic gene expression, the possible differential expression of transporter genes was addressed directly. Here, two groups could be distinguished. The first group consisted of transporter genes with repressed gene expression in at least one analyzed time point of internalized staphylococci. The urea transporter SAOUHSC_02557 belonged to this group. Noticeably, the adjacent urease operon SAOUHSC_02558 to SAOUHSC_02565 (ureABCEFGD) possessed a similar expression pattern, although not all genes were detected as differentially expressed (Fig. R.5.28). 161
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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 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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