Muutke küpsiste eelistusi

Models of Cellular Regulation [Pehme köide]

(Director, Mathematical Biosciences Institute, The Ohio State University), (Visiting Associate Professor, The Ohio State University)
  • Formaat: Paperback / softback, 194 pages, kõrgus x laius x paksus: 245x173x12 mm, kaal: 366 g, 91 line drawings and halftones, 8 colour images
  • Sari: Oxford Graduate Texts
  • Ilmumisaeg: 13-Sep-2012
  • Kirjastus: Oxford University Press
  • ISBN-10: 0199657505
  • ISBN-13: 9780199657506
Teised raamatud teemal:
Models of Cellular RegulationSuurem pilt
  • Formaat: Paperback / softback, 194 pages, kõrgus x laius x paksus: 245x173x12 mm, kaal: 366 g, 91 line drawings and halftones, 8 colour images
  • Sari: Oxford Graduate Texts
  • Ilmumisaeg: 13-Sep-2012
  • Kirjastus: Oxford University Press
  • ISBN-10: 0199657505
  • ISBN-13: 9780199657506
Teised raamatud teemal:
Püsilink: https://www.kriso.ee/db/9780199657506.html
Märksõnad:
The human genome of three billion letters has been sequenced. So have the genomes of thousands of other organisms. With unprecedented resolution, modern technologies are allowing us to peek into the world of genes, biomolecules, and cells - and flooding us with data of immense complexity that we are just barely beginning to understand. A huge gap separates our knowledge of the components of a cell and what is known from our observations of its physiology. The authors have written this graduate textbook to explore what has been done to close this gap of understanding between the realms of molecules and biological processes. They have gathered together illustrative mechanisms and models of gene regulatory networks, DNA replication, the cell cycle, cell death, differentiation, cell senescence, and the abnormal state of cancer cells. The mechanisms are biomolecular in detail, and the models are mathematical in nature. The interdisciplinary presentation will be of interest to both biologists and mathematicians, and every discipline in between.
1 General introduction
1(5)
1.1 Goals
1(1)
1.2 Intracellular processes, cell states and cell fate: overview of the chapters
2(1)
1.3 On mathematical modelling of biological phenomena
3(2)
1.4 A brief note on the organization and use of the book
5(1)
References
5(1)
2 From molecules to a living cell
6(12)
2.1 Cell compartments and organelles
6(3)
2.2 The molecular machinery of gene expression
9(3)
2.3 Molecular pathways and networks
12(3)
2.4 The omics revolution
15(1)
References & further readings
16(2)
3 Mathematical and computational modelling tools
18(26)
3.1 Chemical kinetics
18(4)
3.2 Ordinary differential equations (ODEs)
22(3)
3.2.1 Theorems on uniqueness of solutions
22(1)
3.2.2 Vector fields, phase space, and trajectories
23(1)
3.2.3 Stability of steady states
24(1)
3.3 Phase portraits on the plane
25(2)
3.4 Bifurcations
27(2)
3.5 Bistability and hysteresis
29(1)
3.6 Hopf bifurcation
30(2)
3.7 Singular perturbations
32(1)
3.8 Partial differential equations (PDEs)
33(3)
3.8.1 Reaction-diffusion equations
33(1)
3.8.2 Cauchy problem
34(1)
3.8.3 Dirichlet, Neumann and third-boundary-value problems
35(1)
3.9 Well posed and ill posed problems
36(1)
3.10 Conservation laws
37(3)
3.10.1 Conservation of mass equation
37(1)
3.10.2 Method of characteristics
38(2)
3.11 Stochastic simulations
40(1)
3.12 Computer software platforms for cell modelling
41(1)
References
42(1)
Exercises
42(2)
4 Gene-regulatory networks: from DNA to metabolites and back
44(21)
4.1 Genome structure of Escherichia coli
44(1)
4.2 The Trp operon
45(2)
4.3 A model of the Trp operon
47(3)
4.4 Roles of the negative feedbacks in the Trp operon
50(2)
4.5 The lac operon
52(2)
4.6 Experimental evidence and modelling of bistable behavior of the lac operon
54(1)
4.7 A reduced model derived from the detailed lac operon network
55(6)
4.8 The challenge ahead: complexity of the global transcriptional network
61(1)
References
62(1)
Exercises
63(2)
5 Control of DNA replication in a prokaryote
65(14)
5.1 The cell cycle of E. coli
65(2)
5.2 Overlapping cell cycles: coordinating growth and DNA replication
67(1)
5.3 The oriC and the initiation of DNA replication
67(2)
5.4 The initiation-titration-activation model of replication initiation
69(5)
5.4.1 DnaA protein synthesis
70(1)
5.4.2 DnaA binding to boxes arid initiation of replication
71(2)
5.4.3 Changing numbers of oriCs and dnaA boxes during chromosome replication
73(1)
5.4.4 Death and birth of oriCs
74(1)
5.4.5 Inactivation of dnaA-ATP
74(1)
5.5 Model dynamics
74(1)
5.6 Robustness of initiation control
75(2)
References
77(1)
Exercises
78(1)
6 The eukaryotic cell-cycle engine
79(17)
6.1 Physiology of the eukaryotic cell cycle
79(1)
6.2 The biochemistry of the cell-cycle engine
80(2)
6.3 Embryonic cell cycles
82(3)
6.4 Control of MPF activity in embryonic cell cycles
85(2)
6.5 Essential elements of the basic eukaryotic cell-cycle engine
87(6)
6.6 Summary
93(2)
References
95(1)
Exercises
95(1)
7 Cell-cycle control
96(12)
7.1 Cell-cycle checkpoints
96(1)
7.2 The restriction point
97(1)
7.3 Modelling the restriction point
98(3)
7.3.1 The G1-S regulatory network
98(2)
7.3.2 A switching module
100(1)
7.4 The G2 DNA damage checkpoint
101(3)
7.5 The mitotic spindle checkpoint
104(2)
References
106(1)
Exercises
107(1)
8 Cell death
108(17)
8.1 Background on the biology of apoptosis
108(1)
8.2 Intrinsic and extrinsic caspase pathways
109(2)
8.3 A bistable model for caspase-3 activation
111(4)
8.4 DISC formation and caspase-8 activation
115(5)
8.5 Combined intrinsic and extrinsic apoptosis pathways
120(2)
8.6 Summary and future modelling
122(2)
References
124(1)
Exercises
124(1)
9 Cell differentiation
125(14)
9.1 Cell differentiation in the hematopoietic system
126(1)
9.2 Modelling the differentiation of Th lymphocytes
127(3)
9.3 Cytokine memory in single cells
130(1)
9.4 Population of differentiating Th lymphocytes
131(3)
9.4.1 Equation for population density φ
131(2)
9.4.2 Determining the population density φ
133(1)
9.5 High-dimensional switches in cellular differentiation
134(2)
9.6 Summary
136(1)
References
137(1)
Exercises
137(2)
10 Cell aging and renewal
139(16)
10.1 Cellular senescence and telomeres
139(1)
10.2 Models of tissue aging and maintenance
140(5)
10.2.1 The probabilistic model of Op den Buijs et al.
140(2)
10.2.2 A continuum model
142(3)
10.3 Asymmetric stem-cell division
145(3)
10.4 Maintaining the stem-cell reservoir
148(5)
10.4.1 The Roeder-Loeffler model
148(3)
10.4.2 A deterministic model
151(2)
References
153(1)
Exercises
153(2)
11 Multiscale modelling of cancer
155(21)
11.1 Attributes of cancer
155(1)
11.2 A multiscale model of avaseular tumor growth
156(4)
11.2.1 Cellular scale
157(1)
11.2.2 Extracellular scale
158(1)
11.2.3 Subcellular scale
159(1)
11.3 A multiscale model of colorectal cancer
160(7)
11.3.1 Gene level: a Boolean network
161(2)
11.3.2 Cell level: a discrete cell-cycle model
163(1)
11.3.3 Tissue level: colonies of cells and oxygen supply
164(3)
11.4 Continuum models of solid tumor growth
167(7)
11.4.1 Three types of cells
167(5)
11.4.2 One type of cells
172(2)
References
174(1)
Exercises
174(2)
Glossary 176(5)
Index 181