Coordinated regulation of gene expression by E ... - Jacobs University

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APPENDIX I gene blattner ratio p-value Function A/B ybiM b0806 0.3863 0.0240 conserved hypothetical protein ybjI b0844 1.9181 0.0193 conserved protein with a phophatase-like domain ycaM b0899 0.3822 0.0104 YcaM APC amino acid transporter ycaO b0905 0.5753 0.0151 conserved hypothetical protein ycbJ b0919 0.5051 0.0363 conserved hypothetical protein ycbX b0947 2.2239 0.0044 putative Fe-S protein yccK b0969 0.5751 0.0496 putative sulfite reductase (EC 1.8.-.-) yccS b0960 0.5639 0.0338 hypothetical protein yccV b0966 0.5070 0.0014 hemimethylated DNA-binding protein yceP b1060 2.4225 0.0246 conserved hypothetical protein ycfD b1128 0.5605 0.0362 putative enzyme ycgK b1178 1.8393 0.0309 hypothetical protein ycgV b1202 0.3754 0.0210 putative adhesion and penetration protein ychE b1242 0.6093 0.0360 putative membrane protein yciB b1254 0.5700 0.0437 hypothetical protein yciC b1255 0.6624 0.0484 hypothetical protein yciS b1279 0.6175 0.0026 conserved hypothetical protein ydbK b1378 0.6806 0.0083 putative pyruvate synthase ydcF b1414 0.2689 0.0238 conserved hypothetical protein ydcP b1435 0.2487 0.0276 putative collagenase ydgK b1626 0.4982 0.0446 putative oxidoreductase ydhF b1647 2.1014 0.0131 putative oxidoreductase, NAD(P)-linked ydiA b1703 0.4022 0.0020 conserved protein ydiH b1685 0.0411 0.0002 hypothetical protein ydiI b1686 0.6335 0.0373 conserved hypothetical protein ydiO b1695 0.4899 0.0220 putative acyl-CoA dehydrogenase ydiU b1706 0.7123 0.0018 conserved protein ydiY b1722 0.2336 0.0097 conserved hypothetical protein yeaC b1777 0.2907 0.0234 conserved hypothetical protein yeaD b1780 0.8053 0.0485 conserved hypothetical protein yeaK b1787 0.4458 0.0020 conserved hypothetical protein yeaL b1789 0.4155 0.0189 hypothetical protein yeaT b1799 3.0720 0.0141 putative transcriptional regulator LYSR-type yebE b1846 0.6028 0.0479 conserved hypothetical protein yebR b1832 3.1582 0.0092 conserved hypothetical protein yebU b1835 0.5220 0.0183 hypothetical protein yecN b1869 0.3001 0.0013 putative membrane protein yecP b1871 0.4509 0.0069 putative enzyme yedE b1929 0.5180 0.0037 putative transport system permease protein yedF b1930 0.6433 0.0118 conserved hypothetical protein; might bind RNA yedL b1932 0.7679 0.0407 putative acyl-CoA N-acyltransferase yeeZ b2016 0.7112 0.0403 putative enzyme of sugar metabolism yehU b2126 1.3634 0.0204 putative 2-component sensor protein yeiC b2166 0.5199 0.0069 putative kinase yeiH b2158 0.5810 0.0329 putative membrane protein yeiN b2165 0.6223 0.0224 conserved protein yeiP b2171 0.4453 0.0110 putative elongation factor yeiQ b2172 1.6577 0.0089 putative oxidoreductase yejE b2179 1.2788 0.0062 YejA/YejB/YejE/YejF ABC transporter yejM b2188 0.6919 0.0221 putative sulfatase yfbV b2295 0.1983 0.0066 conserved hypothetical protein yfcE b2300 0.5028 0.0272 putative metallo-dependent phosphatase yfeC b2398 3.6524 0.0085 hypothetical protein yfeD b2399 4.6195 0.0073 hypothetical protein yfeU b2428 2.5545 0.0178 putative regulator yfeZ b2433 0.8288 0.0423 putative membrane protein 87
APPENDIX I gene blattner ratio p-value Function A/B yfgD b2495 1.3436 0.0280 putative oxidoreductase yfhQ b2532 0.7396 0.0351 putative ATP synthase beta subunit yfiD b2579 2.1520 0.0130 stress-induced alternate pyruvate formate-lyase subunit yfiF b2581 0.7263 0.0437 hypothetical protein yfjD b4461 0.6709 0.0382 putative membrane protein, hemolysin-like yfjF b2618 0.8164 0.0194 conserved hypothetical protein yfjK b2627 1.8469 0.0067 hypothetical protein yfjW b2642 2.9798 0.0025 hypothetical protein ygaH b2683 2.3469 0.0029 putative transport protein ygaW b2670 0.2097 0.0395 putative membrane protein ygbT b2755 1.5803 0.0209 conserved hypothetical protein ygcE b2776 0.6769 0.0395 putative kinase ygcO b2767 2.1793 0.0250 putative ferredoxin ygeY b2872 0.3333 0.0367 putative deacetylase yggE b2922 0.7072 0.0229 putative actin-like protein yghU b2989 0.6145 0.0305 glutathione transferase-like protein possibly involved in glutathionylspermidine metabolism ygiR b3015 0.1712 0.0020 conserved protein yhaI b3104 1.8901 0.0167 putative cytochrome yhbG b3201 0.7306 0.0489 YhbG/YhbN ABC transporter yhbW b3160 2.5842 0.0205 putative enzyme yhcE b3217 1.8476 0.0321 hypothetical protein yhcH b3221 1.4134 0.0166 conserved hypothetical protein; gene is in sialic acid catabolic operon yhdE b3248 1.4099 0.0332 conserved hypothetical protein yhdN b3293 0.3490 0.0092 conserved hypothetical protein yhfG b3362 2.0525 0.0319 conserved hypothetical protein yhfT b3377 0.5275 0.0096 putative transport protein yhfX b3381 0.8420 0.0430 conserved protein yhjK b3529 0.8141 0.0360 conserved protein yhjR b3535 3.3058 0.0027 hypothetical protein yhjV b3539 0.4101 0.0312 YhjV STP transporter yiaJ b3574 0.4842 0.0009 YiaJ transcriptional repressor yibG b3596 0.9825 0.0318 conserved hypothetical protein yibI b3598 1.7891 0.0258 hypothetical protein yidI b3677 3.0250 0.0389 hypothetical protein yidZ b3711 0.5369 0.0092 putative transcriptional regulator LysR-type yifE b3764 1.9633 0.0245 hypothetical protein yifK b3795 2.3518 0.0138 YifK APC transporter yjcG b4067 0.7076 0.0091 YjcG SSS transporter yjcZ b4110 1.5987 0.0010 hypothetical protein yjdF b4121 1.6223 0.0050 putative membrane protein yjeI b4144 1.6231 0.0306 conserved protein yjeO b4158 0.7234 0.0164 conserved hypothetical protein yjgM b4256 1.3106 0.0028 putative acyltransferase yjhB b4279 0.2981 0.0096 YjhB MFS transporter yjhC b4280 0.3673 0.0052 KpLE2 phage-like element; putative NAD(P)-binding dehydrogenase yjhP b4306 0.6759 0.0413 putative methyltransferase yjhT b4310 0.4662 0.0446 putative enzyme contains galactose oxidase-like domain yjiA b4352 1.7339 0.0199 P-loop guanosine triphosphatase yjiG b4329 0.5318 0.0394 putative membrane protein yjiT b4342 10.7703 0.0111 conserved protein yjiX b4353 1.7994 0.0423 hypothetical protein yjiY b4354 15.2032 0.0105 putative carbon starvation protein yjjI b4380 1.3283 0.0003 conserved hypothetical protein yjjK b4391 0.6653 0.0186 YjjK yjjM b4357 2.3936 0.0179 hypothetical protein 88
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Coordinated regulation of gene expr
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Parts of this work has been publish
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ABSTRACT promoter region determines
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ACKNOWLEDGEMENTS first impression o
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TABLE OF CONTENTS 2.2.5 Preparation
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LIST OF TABLES List of tables Table
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LIST OF FIGURES List of Figures Fig
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ABBREVIATIONS Abbreviations ∆61
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ABBREVIATIONS TBE Tris TS tyrT35U t
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INTRODUCTION Salmonella: “In more
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INTRODUCTION Figure 1: Schematic il
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INTRODUCTION UP element -35 -10 Spa
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INTRODUCTION can also influence elo
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INTRODUCTION have more base-pairs t
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INTRODUCTION Figure 6: Graphical re
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INTRODUCTION shown that H-NS reache
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INTRODUCTION formed as a repercussi
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MATERIALS AND METHODS 2 Materials a
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MATERIALS AND METHODS NaCl 10 gm YT
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MATERIALS AND METHODS LZ41 3 pyrF28
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MATERIALS AND METHODS 2.2 Methods 2
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MATERIALS AND METHODS given using a
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MATERIALS AND METHODS phenol: chlor
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MATERIALS AND METHODS Filtered (by
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MATERIALS AND METHODS free water (A
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RESULTS 3 Results Growth phase-depe
Page 53 and 54: RESULTS Neither the fis nor the hns
Page 55 and 56: RESULTS these identified genes (by
Page 57 and 58: RESULTS furthermore the colour of t
Page 59 and 60: RESULTS During the entire growth cy
Page 61 and 62: RESULTS transcripts of a growth pha
Page 63 and 64: RESULTS phosphorylation, are associ
Page 65 and 66: RESULTS Table 4: RT-PCR analysis of
Page 67 and 68: RESULTS Figure 16: Schematic repres
Page 69 and 70: RESULTS parC) which allows the supe
Page 71 and 72: RESULTS Figure 19: In vitro transcr
Page 73 and 74: RESULTS contrast the tyrTD promoter
Page 75 and 76: DISCUSSION 4 Discussion The idea of
Page 77 and 78: DISCUSSION In a study by Balke & Gr
Page 79 and 80: DISCUSSION cells maintain viability
Page 81 and 82: DISCUSSION writhe in the UAS by FIS
Page 83 and 84: DISCUSSION 4.3.2 Mechanism of trans
Page 85 and 86: CONCLUSION 5 Conclusion Regulation
Page 87 and 88: REFERENCES Bordes, P., Conter, A.,
Page 89 and 90: REFERENCES Gruber, T.M., and Gross,
Page 91 and 92: REFERENCES molecular basis for sele
Page 93 and 94: REFERENCES Pan, C.Q., Finkel, S.E.,
Page 95 and 96: REFERENCES Schroder, O., and Wagner
Page 97 and 98: REFERENCES Willenbrock, H., and Uss
Page 99 and 100: APPENDIX I gene blattner ratio p-va
Page 103: APPENDIX I gene blattner ratio p-va
Page 127 and 128: APPENDIX I Supplementary table - VI
Page 129 and 130: APPENDIX I fabB b2323 0.6336 0.0043
Page 131 and 132: APPENDIX I ibpA b3687 2.4960 0.0181
Page 133 and 134: APPENDIX I pepP b2908 1.2182 0.0368
Page 135 and 136: APPENDIX I speG b1584 0.4151 0.0001
Page 137 and 138: APPENDIX I ycjX b1321 4.0841 0.0141
Page 139 and 140: APPENDIX I yhfY b3382 1.4063 0.0453
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APPENDIX I gene blattner ratio p-va
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APPENDIX I gene blattner ratio A/B
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Statement of sources Declaration I
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