Transactions on Computational Systems Biology IX (Lecture Notes in Computer Science, 5121)

✍ Scribed by Corrado Priami (editor)

• Publisher: Springer
• Year: 2008
• Tongue: English
• Leaves: 160
• Category: Library

✦ Synopsis

The LNCS journal Transactions on Computational Systems Biology is devoted to inter- and multidisciplinary research in the fields of computer science and life sciences and supports a paradigmatic shift in the techniques from computer and information science to cope with the new challenges arising from the systems oriented point of view of biological phenomena. This issue contains four highly detailed papers. The first paper focuses on quantitative aspects of the bgl operon for E.coli. The second contribution deals with ecosystem transitions affecting phenotype expressions and selection mechanisms. The third paper presents the Stochastic Calculus of Looping Sequences (SCLS) suitable for the description of microbiological systems, such as cellular pathways, and their evolution. The final contribution describes the use of biological transactions to make atomic sequences of interactions in the BlenX language.

✦ Table of Contents

Title Page
Preface
Organization
Table of Contents
A Quantitative $bgl$ Operon Model for $E. coli$ Requires BglF Conformational Change for Sugar Transport
Introduction
Computational Model Derivation of $bgl$ Transcription
Model Approximations
Model Equations
Computational Details
Results and Discussion
Steady State Levels with and without Inducer
Induction of the $bgl$ Operon
The Dynamics of Induction When Inducer Is Present in Limiting Amounts
Inducer Concentration vs. Induction Intensity
Sensitivity of the Model to the Kinetic RNA-Binding Parameters Kter1 and Kter2
The Failure of BglF to Change Its Conformation While Transporting the Sugar Results in Loss of Induction
Mutations in $bglG$ and $bglF$ Make the Expression of bgl Operon Constitutive
Predictions Made by the Model
Conclusions
References
Punctuated Equilibrium in Statistical Models of Generalized Coevolutionary Resilience: How Sudden Ecosystem Transitions Can Entrain Both Phenotype Expression and Darwinian Selection
Introduction
Ecosystems as Information Sources
Coarse-Graining a Simple Model
Ecosystems and Information
Cognition as an Information Source
Immune Cognition
Tumor Control
A Cognitive Paradigm for Gene Expression
Darwinian Genetic Inheritance as an Information Source
Interacting Information Sources: Punctuated Crosstalk
Dynamic Manifolds
Directed Homotopy
Red Queen Coevolution
The Basic Idea
Recursive Interaction
Extending the Model
Second Order Theory: Farming a Coevolutionary System
Generalized Stochastic Resonance: Many Baldwin Effects
Discussion and Conclusions
Mathematical Appendix
The Shannon-McMillan Theorem
The Rate Distortion Theorem
Morse Theory
The Mean Field Model
References
Stochastic Calculus of Looping Sequences for the Modelling and Simulation of Cellular Pathways
Introduction
Summary
The Calculus of Looping Sequences
Modelling Guidelines
The Stochastic Calculus of Looping Sequences
Modelling the Lactose Operon
Stochastic CLS Model
Simulation Results
Modelling Quorum Sensing
Stochastic CLS Model
Experimental Results
Conclusions
Related Work
References
The BlenX Language with Biological Transactions
Introduction
Related Works
TheBlenX Language
The Syntax
The Operational Semantics
The Stochastic Algorithm
Example: Three-Reactant One-Product Reaction
TheBlenX Language with Biological Transactions
Biological Transactions
General Ideas
Syntax
Semantics
Rates
Observation
Example: System with a Three-Reactant One-Product Reaction (Continued)
Some Definitions
Properties
Examples
Multiple-Reactant Multiple-Product Reactions
Phosphorylation of p53 at Serine 15 by Two Enzymes
The Citric Acid Cycle
Discussion and Conclusion
References
Author Index