A computational study of bacterial gene regulation and adaptation ...

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BibliographyKalir, S., Mangan, S., and Alon, U. 2005. A coherent feed-forward loop with a SUM input functionprolongs flagella expression in Escherichia coli. Molecular Systems Biology 1: 2005 0006.Kalujnaia, S., Wilson, G.D., Feilen, A.L., and Cramb, G. 2009. Guanylin-like peptides, guanylatecyclase and osmoregulation in the European eel (Anguilla anguilla). General and ComparativeEndocrinology. 161: 103-114Kanehisa, M., Araki, M., Goto, S., Hattori, M., Hirakawa, M., Itoh, M., Katayama, T., Kawashima,S., Okuda, S., Tokimatsu, T., et al. 2008. KEGG for linking genomes to life and the environment.Nucleic Acids Research 36: D480-484.Kanehisa, M., Goto, S., Hattori, M., Aoki-Kinoshita, K.F., Itoh, M., Kawashima, S., Katayama,T.,Araki, M., and Hirakawa, M. 2006. From genomics to chemical genomics: new developments inKEGG. Nucleic Acids Research 34: D354-357.Kapanidis, A.N., Margeat, E., Laurence, T.A., Doose, S., Ho, S.O., Mukhopadhyay, J., Kortkhonjia,E., Mekler, V., Ebright, R.H., and Weiss, S. 2005. Retention of transcription initiation factorsigma70 in transcription elongation: single-molecule analysis. Molecular Cell 20: 347-356.Kaplan, S., Bren, A., Zaslaver, A., Dekel, E., and Alon, U. 2008. Diverse two-dimensional inputfunctions control bacterial sugar genes. Molecular Cell 29: 786-792.Kato, A., and Groisman, E.A. 2008. The PhoQ/PhoP regulatory network of Salmonella enterica.Advances in Experimental Medicine and Biology 631: 7-21.Kazmierczak, B.I., Lebron, M.B., and Murray. T.S. 2006. Analysis of FimX, a phosphodiesterasethat governs twitching motility in Pseudomonas aeruginosa. Molecular Microbiology 60: 1026-1043.Keseler, I.M., Bonavides-Martinez, C., Collado-Vides, J., Gama-Castro, S., Gunsalus, R.P., Johnson,D.A., Krummenacker, M., Nolan, L.M., Paley, S., Paulsen, I.T., et al. 2009. EcoCyc: a comprehensiveview of Escherichia coli biology. Nucleic Acids Research 37: D464-470.B15
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Statement of lengthThis thesis does
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molecules also bind to enzymes dire
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Table of ContentsTitlePagesIntroduc
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TitlePageFigure 4.5: Catalytic and
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IntroductionFunctional and comparat
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egulation owing to the large amount
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(A) Closed complex formationRNA pol
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Intuitively negative supercoiling,
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I.3. Transcription factors: domain
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I.4. Transcriptional regulatory net
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(Balazsi et al. 2005). Gene express
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metabolism / carbon nutrition with
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I.4.5. Signal sensing in transcript
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I.5. Non-transcriptional output: cy
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transcriptional initiation by c-di-
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phosphatase activity of the kinases
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I.7. ConclusionIn this chapter, we
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Chapter 1: Global regulators of bac
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Chapter 2: Transcriptional control
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Chapter 3: Transcriptional and post
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Chapter 4: Comparative genomics of
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Page 157 and 158: Discussion and conclusionsD2. Futur
Page 159 and 160: BibliographyAmikam, D., Steinberger
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Page 167 and 168: Bibliographysystem level analysis o
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Page 189 and 190: BibliographyYanofsky, C. 1981. Atte
Page 191 and 192: Appendix 1Appendix 1.1: Differences
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Page 195 and 196: Appendix 1Appendix 1.5: Gene expres
Page 197 and 198: Appendix 2Appendix 2.1: Differences
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Page 214 and 215: Reaction ID Regulatory metabolite I
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Appendix 4Motile organisms are rich
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Appendix 4We can expand the analysi
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Appendix 5Appendix 5.1A: PFAMs for
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Appendix 5Appendix 5.1C: PFAMs for
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Appendix 5Appendix 5.2B: Small-mole
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Appendix 5Appendix 5.3: Organisms s
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Appendix 5Appendix 5.5: Partner dom
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Appendix 5fraction of SDRRs would a
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Appendix 5Appendix 5.6C: Non-hybrid
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Appendix 5Appendix 5.8: List of org
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Appendix 6Appendix 6List of genomes
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Appendix 648. Mycobacterium tubercu
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Appendix 6144. Bacillus cereus ATCC
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Appendix 6240. Nitrobacter winograd
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Appendix 6336. Cytophaga hutchinson
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Appendix 6432. Acinetobacter bauman
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Appendix 6528. Enterobacter sakazak
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Appendix 6624. Polynucleobacter nec
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Appendix 7Appendix 7List of genomes
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Appendix 748. Bordetella parapertus
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Appendix 7144. Haemophilus somnus14
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Appendix 7240. Prochlorococcus mari
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Appendix 7336. Synechococcus sp. CC
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Downloaded from genome.cshlp.org on
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JOURNAL OF BACTERIOLOGY, June 2008,
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VOL. 190, 2008 P. MIRABILIS GENOME
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2 Nucleic Acids Research, 2008PCR a
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4 Nucleic Acids Research, 2008Table
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6 Nucleic Acids Research, 2008Table
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8 Nucleic Acids Research, 2008solve
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An Assessment of the Role of DNA Ad
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DAM and Transcriptionpotential of s
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