genomewide characterization of host-pathogen interactions by ...

More documents

Recommendations

Info

Maren Depke Results Gene Expression Pattern of Bone-Marrow Derived Macrophages after Interferon-gamma Treatment higher expression in BALB/c BMM. The same direction of difference was observed for arginase type II (Arg2). Tissue factor pathway inhibitor (Tfpi), coding for a protease inhibitor with anticoagulant function, was higher expressed in C57BL/6 BMM. Genes of lysosomal, matrix degrading, and detoxification enzymes were differentially expressed between BMM of the two mouse strains. Lysosomal enzyme genes showed a mixed pattern with higher expression in BALB/c BMM for cathepsin E (Ctse) and hyaluronidas (Hyal1) and higher expression in C57BL/6 BMM for cathepsins C and H (Ctsc, Ctsh). Matrix metallopeptidase 14 (Mmp14), which is involved in degradation of extracellular matrix, and glutathione S-transferases mu 1 and pi 1 (Gstm1, Gstp1) which are associated with detoxification processes, were detected with higher expression in C57BL/6 BMM (Table R.3.16). Strain-specific difference in expression of IFN-γ related genes BMM of BALB/c and C57BL/6 differ in their ability to eliminate infecting bacteria, especially after IFN-γ treatment (Breitbach et al. 2006). In this study, the primary reaction of BMM to IFN-γ in comparison between both strains was analyzed. Therefore, a network centered around the starting node IFN-γ was created using Ingenuity Pathway Analysis (IPA, www.ingenuity.com). This network contained 181 genes (Fig. R.3.5 A, B) additionally to the starting node IFN-γ. Genes were grouped manually into four categories: 1) difference existed between BALB/c BMM and C57BL/6 BMM at both treatment levels, control and after IFN-γ treatment; 2) difference between BMM of the two strains occurred only at control level; 3) difference between BMM of the two strains occurred only after IFN-γ treatment; 4) no strain difference was observed, but the gene expression was influenced at least in BMM of one mouse strain. A second categorization divided each group exhibiting strain differences into genes higher expressed in BALB/c BMM and into genes higher expressed in C57BL/6 BMM. After restricting the network to genes described to be linked to IFN-γ in macrophages or RAW cells in the Ingenuity Pathway Knowledge Base (IPKB), a list of 132 new macrophage-related genes out of 181 IFN-γ linked genes could be obtained. Correspondingly, a list of 49 of 181 genes that are already included in the IPKB as IFN-γ related in macrophages or RAW cells were exported. Fig. R.3.5: Ingenuity Pathway Analysis (IPA, www.ingenuity.com) of IFN-γ related genes. A, B. Network resulting from application of the grow-tool on transcriptome data To create a network centered around the starting node IFN-γ the grow-tool of IPA‘s pathway function was applied. The addition of further nodes according to information stored in the so-called Ingenuity Pathway Knowledge Base (IPKB) was restricted to a list of genes that are differentially expressed in at least 1 of 4 comparisons 1) IFN-γ effects in BALB/c BMM, 2) IFN-γ effects in C57BL/6 BMM, 3) strain difference at non-treated control level and 4) strain difference after IFN-γ treatment. Further restrictions were not included. Networks are colored according to strain difference at control level (A) or at IFN-γ treated level (B). Green represents a higher expression in BALB/c BMM than in C57BL/6 BMM whereas red indicates higher expression in C57BL/6 BMM than in BALB/c BMM. The intensity of color correlates with the magnitude of difference: The shade of color becomes darker with increasing absolute fold change. 108
Maren Depke Results Gene Expression Pattern of Bone-Marrow Derived Macrophages after Interferon-gamma Treatment A regulation by IFN-γ at least in BMM of one strain; no significant difference in expression between BMM of both strains difference between BMM of the two mouse strains only after IFN-γ treatment B higher expression in BALB/c BMM higher expression in C57BL/6 BMM difference between BMM of the two mouse strains only at control level difference between BMM of the two mouse strains at both control and IFN-γ treated level regulation by IFN-γ at least in BMM of one strain; no significant difference in expression between BMM of both strains difference between BMM of the two mouse strains only after IFN-γ treatment higher expression in BALB/c BMM higher expression in C57BL/6 BMM difference between BMM of the two mouse strains only at control level difference between BMM of the two mouse strains at both control and IFN-γ treated level 109
Page 1 and 2:
G E N O M E W I D E C H A R A C T E
Page 3 and 4:
Maren Depke C O N T E N T S GENOMEW
Page 5 and 6:
Maren Depke Z U S A M M E N F A S S
Page 7 and 8:
Maren Depke Zusammenfassung der Dis
Page 9 and 10:
Maren Depke S U M M A R Y O F D I S
Page 11 and 12:
Maren Depke Summary of Dissertation
Page 13 and 14:
Maren Depke I N T R O D U C T I O N
Page 15 and 16:
Maren Depke Introduction Besides op
Page 17 and 18:
Maren Depke Introduction Extracellu
Page 19 and 20:
Maren Depke Introduction with heigh
Page 21 and 22:
Maren Depke Introduction 2005). SaP
Page 23 and 24:
Maren Depke Introduction contains a
Page 25 and 26:
Maren Depke Introduction via fibron
Page 27 and 28:
Maren Depke Introduction cathelicid
Page 29 and 30:
Maren Depke Introduction shock are
Page 31 and 32:
Maren Depke Introduction STUDIES OF
Page 33 and 34:
Maren Depke Introduction are effect
Page 35 and 36:
Maren Depke Introduction cell stimu
Page 37 and 38:
Maren Depke Introduction channel CF
Page 39 and 40:
Maren Depke M A T E R I A L A N D M
Page 41:
Maren Depke Material and Methods Li
Page 44 and 45:
Maren Depke Material and Methods Ki
Page 47 and 48:
Maren Depke Material and Methods GE
Page 49:
Maren Depke Material and Methods Ge
Page 52 and 53:
Maren Depke Material and Methods Ho
Page 54 and 55:
Maren Depke Material and Methods Ho
Page 56 and 57:
Maren Depke Material and Methods Pa
Page 58 and 59: Maren Depke Material and Methods Pa
Page 60 and 61: Maren Depke Material and Methods Pa
Page 63 and 64: corticosterone [pg/ml plasma] corti
Page 65 and 66: Maren Depke Results Liver Gene Expr
Page 67 and 68: lood glucose levels [nmol/l] resist
Page 69 and 70: LBP [ng/ml] CPR [ng/ml] Maren Depke
Page 71 and 72: Maren Depke Results Liver Gene Expr
Page 73 and 74: liver weight [g] Maren Depke Result
Page 75 and 76: infection rate cfu / 10 mg tissue c
Page 77 and 78: Maren Depke Results Kidney Gene Exp
Page 79 and 80: Table R.2.1: Genes displaying stati
Page 81 and 82: Maren Depke BR1 sign DsigB vs wt BR
Page 91 and 92: Maren Depke Results GENE EXPRESSION
Page 93 and 94: Maren Depke Results Gene Expression
Page 95 and 96: log2(ratio C57BL/6 / BALB/c) at IFN
Page 107: Maren Depke Results Gene Expression
Page 112 and 113: Maren Depke Results Host Cell Gene
Page 132 and 133: Maren Depke Results Pathogen Gene E
Page 138 and 139: S. aureus RN1HG sample conditions a
Page 148 and 149: mean normalized intensity mean norm
Page 158 and 159:
mean normalized intensity Maren Dep
Page 160 and 161:
Maren Depke Results Pathogen Gene E
Page 162 and 163:
mean normalized intensity mean norm
Page 164 and 165:
Page 166 and 167:
Page 168 and 169:
log 2 (ratio) log 2 (ratio) log 2 (
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
Page 175 and 176:
Page 177 and 178:
Page 179 and 180:
Page 181 and 182:
Page 183 and 184:
Page 185 and 186:
Page 187 and 188:
Page 189 and 190:
Page 191 and 192:
Page 193 and 194:
Page 195 and 196:
Page 197 and 198:
Page 199 and 200:
Page 201 and 202:
Page 203 and 204:
Page 205:
Page 208 and 209:
Maren Depke References Athanasopoul
Page 210 and 211:
Maren Depke References Byrne GI, Le
Page 212 and 213:
Maren Depke References Demling R. T
Page 214 and 215:
Maren Depke References Foss GS, Pry
Page 216 and 217:
Maren Depke References Hagopian K,
Page 218 and 219:
Maren Depke References Jin T, Bokar
Page 220 and 221:
Maren Depke References Kwan T, Liu
Page 222 and 223:
Maren Depke References Luster AD, U
Page 224 and 225:
Maren Depke References Namiki S, Na
Page 226 and 227:
Maren Depke References Puccetti P.
Page 228 and 229:
Maren Depke References Siewert E, B
Page 230 and 231:
Maren Depke References van den Akke
Page 232 and 233:
Maren Depke References Yang XL, Sch
Page 235:
Maren Depke A F F I D A V I T / E R
Page 238 and 239:
Maren Depke Acknowledgments Kidney
show all

genomewide characterization of host-pathogen interactions by ...

Create successful ePaper yourself

Delete template?

Save as template?