Models of cellular regulation / Baltazar D. Aguda, Avner Friedman.

Format:

Book

Author/Creator:

Aguda, B. (Baltazar)

Contributor:

Friedman, Avner.

Series:

Oxford graduate texts.

Oxford graduate texts

Language:

English

Subjects (All):

Cellular control mechanisms.

Physical Description:

1 online resource (199 p.)

Place of Publication:

Oxford ; New York : Oxford University Press, 2008.

Language Note:

English

Summary:

This text illustrates the mechanisms and models linking the realms of molecular interactions and biological processes or functions. It addresses the need of mathematical modelers to learn how to formulate models of cellular processes.

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)

3.2.1 Theorems on uniqueness of solutions3.2.2 Vector fields, phase space, and trajectories; 3.2.3 Stability of steady states; 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); 3.8.1 Reaction-diffusion equations; 3.8.2 Cauchy problem; 3.8.3 Dirichlet, Neumann and third-boundary-value problems; 3.9 Well posed and ill posed problems; 3.10 Conservation laws; 3.10.1 Conservation of mass equation; 3.10.2 Method of characteristics; 3.11 Stochastic simulations

3.12 Computer software platforms for cell modellingReferences; 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. coli5.2 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; 5.4.1 DnaA protein synthesis; 5.4.2 DnaA binding to boxes and initiation of replication; 5.4.3 Changing numbers of oriCs and dnaA boxes during chromosome replication; 5.4.4 Death and birth of oriCs; 5.4.5 Inactivation of dnaA-ATP; 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 cycle6.2 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; 7.3.1 The G1-S regulatory network; 7.3.2 A switching module; 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

Notes:

Description based upon print version of record.

Includes bibliographical references and index.

Description based on print version record.

Description based on publisher supplied metadata and other sources.

ISBN:

0-19-965750-5

1-281-85241-4

9786611852412

0-19-154723-9

OCLC:

301989864