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Models of cellular regulation / Baltazar D. Aguda, Avner Friedman. — Oxford : Oxford University Press, c2008. – (58.1574/A282) |
Contents
Contents
1 General introduction
1.1 Goals
1.2 Intracellular processes， cell states and cell fate: overview of the chapters
1.3 On mathematical modelling of biological phenomena
1.4 A brief note on the organization and use of the book
References
2 From molecules to a living cell
2.1 Cell compartments and organelles
2.2 The molecular machinery of gene expression
2.3 Molecular pathways and networks
2.4 The omics revolution
References & further readings
3 Mathematical and computational modelling tools
3.1 Chemical kinetics
3.2 Ordinary differential equations (ODEs)
3.3 Phase portraits on the plane
3.4 Bifurcations
3.5 Bistability and hysteresis
3.6 Hopf bifurcation
3.7 Singular perturbations
3.8 Partial differential equations (PDEs)
3.9 Well posed and ill posed problems
3.10 Conservation laws
3.11 Stochastic simulations
3.12 Computer software platforms for cell modelling
References
Exercises
4 Gene-regulatory networks: from DNA to metabolites and back
4.1 Genome structure of Escherichia coli
4.2 The Trp operon
4.3 A model of the Trp operon
4.4 Roles of the negative feedbacks in the Trp operon
4.5 The lac operon
4.6 Experimental evidence and modelling of bistable behavior of the lac operon
4.7 A reduced model derived from the detailed lac operon network
4.8 The challenge ahead: complexity of the global transcriptional network
References
Exercises
5 Control of DNA replication in a prokaryote
5.1 The cell cycle of E. coli
5.2 Overlapping cell cycles: coordinating growth and DNA replication
5.3 The oriC and the initiation of DNA replication
5.4 The initiation-titration-activation model of replication initiation
5.5 Model dynamics
5.6 Robustness of initiation control
References
Exercises
6 The eukaryotic cell-cycle engine
6.1 Physiology of the eukaryotic cell cycle
6.2 The biochemistry of the cell-cycle engine
6.3 Embryonic cell cycles
6.4 Control of MPF activity in embryonic cell cycles
6.5 Essential elements of the basic eukaryotic cell-cycle engine
6.6 Summary
References
Exercises
7 Cell-cycle control
7.1 Cell-cycle checkpoints
7.2 The restriction point
7.3 Modelling the restriction point
7.4 The G2 DNA damage checkpoint
7.5 The mitotic spindle checkpoint
References
Exercises
8 Cell death
8.1 Background on the biology of apoptosis
8.2 Intrinsic and extrinsic caspase pathways
8.3 A bistable model for caspase-3 activation
8.4 DISC formation and caspase-8 activation
8.5 Combined intrinsic and extrinsic apoptosis pathways
8.6 Summary and future modelling
References
Exercises
9 Cell differentiation
9.1 Cell differentiation in the hematopoietic system
9.2 Modelling the differentiation of Th lymphocytes
9.3 Cytokine memory in single cells
9.4 Population of differentiating Th lymphocytes
9.5 High-dimensional switches in cellular differentiation
9.6 Summary
References
Exercises
10 Cell aging and renewal
10.1 Cellular senescence and telomeres
10.2 Models of tissue aging and maintenance
10.3 Asymmetric stem-cell division
10.4 Maintaining the stem-cell reservoir
References
Exercises
11 Multiscale modelling of cancer
11.1 Attributes of cancer
11.2 A multiscale model of avascular tumor growth
11.3 A multiscale model of colorectal cancer
11.4 Continuum models of solid tumor growth
References
Exercises
Glossary
Index
