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Systems Biology Of Clostridium [Hardback]

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Edited by (Univ Of Ulm, Germany)
  • Formāts: Hardback, 292 pages
  • Izdošanas datums: 07-Jul-2014
  • Izdevniecība: Imperial College Press
  • ISBN-10: 1783264403
  • ISBN-13: 9781783264407
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Systems Biology Of ClostridiumPalielināt
  • Formāts: Hardback, 292 pages
  • Izdošanas datums: 07-Jul-2014
  • Izdevniecība: Imperial College Press
  • ISBN-10: 1783264403
  • ISBN-13: 9781783264407
Citas grāmatas par šo tēmu:
Permanent link: https://www.kriso.lv/db/9781783264407.html
Keywords:
Systems Biology of Clostridium provides a comprehensive overview of system biology approaches in clostridia, especially Clostridium acetobutylicum. Systems biology is a rapidly evolving scientific discipline that allows us to understand and predict the metabolism and its changes within the bacterium as a whole.Clostridia represent one of the largest bacterial genera. This group contains organisms with metabolic properties that hold enormous potential for biotechnological processes. A model organism is Clostridium acetobutylicum that has been, and is still used in large-scale industrial production of the solvents acetone and butanol. Systems biology offers a new way to elucidate and understand the complex regulatory network controlling the different metabolic pathways and their interactions. All aspects from the development of appropriate experimental tools to mathematical modeling are covered, including a fascinating historical account on acetone-butanol fermentation in World War II.Written by world-class experts in their fields, Systems Biology of Clostridium is an essential source of reference for all biologists, biochemists, chemists, and chemical engineers working on biotechnological fermentations or industrial applications, as well as biofuels.
Preface ix
Chapter 1 Metabolic and Regulatory Networks in Clostridium acetobutylicum
1(20)
1.1 Introduction
2(2)
1.2 Roadmap to modeling
4(9)
1.3 Regulators of solventogenesis and sporulation in C. acetobutylicum
13(8)
Supplementary material
19(1)
References
20(1)
Chapter 2 Clostridial Gene Tools
21(35)
2.1 Introduction
21(1)
2.2 Clostridial gene transfer
22(2)
2.3 Clostridial vector systems
24(3)
2.4 Tools for forward genetics studies
27(8)
2.4.1 Conjugative transposons
28(3)
2.4.2 Non-conjugative transposons
31(4)
2.5 Recombination-based tools for reverse genetic studies
35(5)
2.5.1 Mutants in pathogenic Clostridia
37(1)
2.5.2 Solventogenic Clostridia
38(1)
2.5.3 Negative selection markers
39(1)
2.6 Reverse genetic tools based on recombination-independent methods
40(3)
2.6.1 Group II introns
40(1)
2.6.2 Targetron-mediated inactivation of clostridial genes
41(1)
2.6.3 Positive selection of gene inactivation
42(1)
2.7 The ClosTron: a universal gene knock-out system for Clostridia
43(8)
2.7.1 ClosTron development
43(1)
2.7.2 The prototype ClosTron system
44(3)
2.7.3 ClosTron procedure refinements
47(4)
2.8 Conclusions
51(5)
Acknowledgement
52(1)
References
52(4)
Chapter 3 Supporting Systems Biology of Clostridium acetobutylicum by Proteome Analysis
56(29)
3.1 Introduction
57(3)
3.2 Stress proteomes of C. acetobutylicum
60(3)
3.3 Sample preparation and proteome reference maps of C. acetobutylicum
63(5)
3.4 Effects of the metabolic shift on the proteome of C. acetobutylicum
68(7)
3.5 Proteome data and transcriptome data, a comparison
75(6)
3.6 Conclusions and outlook
81(4)
Acknowledgement
83(1)
References
83(2)
Chapter 4 Comparative Genomic Analysis of the General Stress Response in Clostridium Acetobutylicum ATCC 824 and Clostridium Beijerinckii NCIMB 8052
85(18)
4.1 Introduction
85(2)
4.2 Class I heat shock proteins
87(6)
4.3 Class II heat shock proteins
93(1)
4.4 Class III heat shock proteins
94(2)
4.5 Class IV--VI heat shock proteins
96(2)
4.6 Heat shock proteins (HSPs) and solvent tolerance
98(1)
4.7 Conclusions
99(4)
Acknowledgement
100(1)
References
100(3)
Chapter 5 Mathematical Modeling of the pH-Induced Metabolic Shift in Clostridium Acetobutylicum
103(28)
5.1 Industrial application of C. acetobutylicum
103(2)
5.2 AB fermentation in C. acetobuylicum
105(3)
5.3 Modeling the pH-dependent metabolic switch
108(18)
5.3.1 The AB fermentation in a continuously fed well-stirred isothermal tank reactor
109(2)
5.3.2 pH-induced changes of transcriptome and proteome
111(7)
5.3.3 The impact of the pH value on biochemical reactions
118(4)
5.3.4 Dynamic modeling of the pH-dependent metabolic shift
122(4)
5.4 Conclusions and outlook
126(5)
Acknowledgement
128(1)
References
129(2)
Chapter 6 Mathematical Models for Clostridia: From Cultivation Description to Systems Biology
131(42)
6.1 Introduction
131(5)
6.2 Models for the ABE fermentation process with Clostridia
136(24)
6.2.1 History
136(1)
6.2.2 The ABE fermentation with C. acetobutylicum in batch processes
137(18)
6.2.3 The ABE fermentation with C. acetobutylicum in continuous processes
155(5)
6.3 Models for processes with Clostridia beyond the ABE fermentation
160(7)
6.3.1 Growth models for C. perfringens
161(3)
6.3.2 Fermentative biohydrogen production by Clostridia
164(3)
6.4 Outlook
167(6)
Nomenclature
169(1)
References
170(3)
Chapter 7 Modelling agr-Dependent Quorum Sensing in Gram-Positive Bacteria
173(20)
7.1 Quorum sensing: gene regulation in response to cell population density
174(1)
7.2 agr-type quorum sensing systems
175(3)
7.3 Mathematical models of quorum sensing
178(3)
7.4 Model formulation
181(5)
7.5 Numerical solutions
186(4)
7.6 The relevance of modelling the agr operon to clostridial systems biology
190(3)
Acknowledgement
191(1)
References
191(2)
Chapter 8 Comparative Genomic Analysis of the Central Metabolism of the Solventogenic Species Clostridium Acetobutylicum ATCC 824 and Clostridium Beijerinckii NCIMB 8052
193(27)
8.1 Introduction
194(1)
8.2 General genome features
195(5)
8.3 The central catabolic pathways
200(16)
8.3.1 Glucose uptake
201(5)
8.3.2 Glycolysis
206(2)
8.3.3 Gluconeogenesis
208(1)
8.3.4 Pyruvate conversion
209(1)
8.3.5 Acetyl-CoA conversion
210(2)
8.3.6 Energy generation and disposal of reducing equivalents
212(4)
8.4 Conclusion
216(4)
Acknowledgement
217(1)
References
217(3)
Chapter 9 The Strategic Importance of Butanol for Japan During WWII: A Case Study of the Butanol Fermentation Process in Taiwan and Japan
220(53)
9.1 Introduction
220(3)
9.2 Historical events that led to the establishment and development of the ABE fermentation process in Japan prior to WWII
223(1)
9.3 The key role played by Japanese air power
224(2)
9.4 The importance of high-octane aviation fuel
226(4)
9.5 Japan's vulnerability with respect to oil and aviation fuel
230(1)
9.6 The establishment of the Japanese ABE fermentation industry
231(3)
9.7 Japan's acquisition of US aviation fuel technology
234(6)
9.8 Developments leading to use of biobutanol for iso-octane production
240(2)
9.9 Reasons for the establishment of a major butanol fermentation industry in Taiwan
242(2)
9.10 The main butanol plant at Kagi in Taiwan
244(5)
9.11 Japan's fuel situation at the outbreak of WWII
249(3)
9.12 The development of a sugar-based butanol fermentation process
252(3)
9.13 The role of the Japanese Navy fuel depots in butanol and iso-octane production
255(4)
9.14 The USAAF bombing campaign in Taiwan, 1944--1945
259(2)
9.15 The impact on Japan's fuel supplies
261(3)
9.16 Post-war developments in Taiwan leading to the re-establishment of the butanol fermentation process
264(4)
9.17 The post-war butanol fermentation process in Japan and China
268(5)
Acknowledgement
270(1)
References
270(3)
Index 273