Systems Biology E-Book

• Herausgeber: Wiley-VCH
• Kategorie: Wissenschaft und neue Technologien
• Serie: Current Topics from the Encyclopedia of Molecular Cell Biology and Molecular Medicine
• Sprache: Englisch

Seitenzahl: 1577

Veröffentlichungsjahr: 2012

Beschreibung

Systems biology is a relatively new biological study field that focuses on the systematic study of complex interactions in biological systems, thus using a new perspective (integration instead of reduction) to study them. Particularly from year 2000 onwards, the term is used widely in the biosciences, and in a variety of contexts. Systems biology is the study of the interconnected aspect of molecular, cellular, tissue, whole animal and ecological processes, and comprises mathematical and mechanistic studies of dynamical, mesoscopic, open, spatiotemporally defined, nonlinear, complex systems that are far from thermodynamic equilibrium.

Leseprobe

Table of Contents

Related Titles

Title Page

Copyright

Preface and Commentary

List of Contributors

Part I: Biological Basis of Systems Biology

1 Systems Biology

1 Introduction

2 What Is Systems Understanding?

3 Why Are Biological Systems Different?

4 Systems Biology Modeling

5 Future Prospects of Systems Biology

References

2 Developmental Cell Biology

1 Historical Perspective

2 Cell Activities Underlying Development

3 Cell Differentiation

4 The Cell Cycle and Development

5 Organogenesis

6 Stem Cells

7 Chimeras

8 microRNAs (miRNAs)

9 In vitro Fertilization

References

3 Principles and Applications of Embryogenomics

1 Introduction

2 Approaches

3 Model Organisms for Embryogenomics

4 Conclusions

References

4 Interactome

1 Introduction

2 Experimental Techniques for Detecting Protein Interactions

3 Computational Prediction of Protein Interactions

4 Exploring the Topology of the Interactome

5 Comparing Protein–Protein Interaction Networks

6 Databases of Protein and Domain Interactions

7 Applications

8 Looking Ahead: Towards the Dynamic Interactome

Acknowledgments

References

5 Protein Abundance Variation

1 Introduction

2 Biochemical Aspects Affecting Protein Abundance in Prokaryotes

3 Extracellular Causes Influencing Protein Abundance in Prokaryotes

4 Biochemical Aspects Affecting Protein Abundance in Eukaryotes

5 Other Factors Influencing Protein Abundance in Eukaryotes

6 Techniques Used to Measure Protein Abundance

7 Concluding Remarks and Outlook

Acknowledgments

References

Part II: Systems Biology of Evolution

6 Genetic Variation and Molecular Darwinism

1 Introduction

2 Principles of Molecular Evolution

3 Genetic Variation in Bacteria

4 Local Changes in the DNA Sequences

5 Intragenomic DNA Rearrangements

6 DNA Acquisition

7 The Three Natural Strategies Generating Genetic Variations Contribute Differently to the Evolutionary Process

8 Evolution Genes and Their Own Second-Order Selection

9 Arguments for a General Relevance of the Theory of Molecular Evolution for All Living Organisms

10 Systemic Aspects of Biological and Terrestrial Evolution

11 Conceptual Aspects of the Theory of Molecular Evolution

References

7 Systematics and Evolution

1 The Beginning of Molecular Systematics

2 The Molecular Assumption

3 DNA Hybridization

4 Mitochondrial DNA

5 DNA Sequences

6 Repeated (Retro)Transposons

7 “Evo-Devo”

8 Positional Information and Shape

9 “Mutation”

10 Toward a Theory of Evolutionary Change

11 Molecules and Systematics: Looking Toward the Future

References

8 Evolution of the Protein Repertoire

1 The First Proteins

2 Organization of the Modern Protein Repertoire

3 Protein Sequence and Its Evolution

4 Protein Structure and Its Evolution

5 Protein Function and Its Evolution

6 Protein Evolution in Human Hands

7 Lessons from the Evolution of the Protein Repertoire

References

Part III: Modeling of Biological Systems

9 Chaos in Biochemistry and Physiology

1 Introduction

2 Systems Biology and the Complex Systems Approach: Chaos in Context

3 Reconstructing the Underlying Dynamics of Complex Systems

4 Chaos, Randomness, and (Colored) Noise

5 Nonlinear Time Series Analysis: Conceptual Theoretical and Analytic Tools for Chaos Detection and Characterization

6 Periodic and Non-Periodic Dynamics

7 Biochemical and Physiological Chaos

8 Chaos in Dynamics of Heart and Brain?

9 Concluding Remarks: The Status and a Prospective for Chaos

10 Acknowledgments

References

10 Computational Biology

1 Introduction

2 Sequencing Genomes

3 Molecular Sequence Analysis

4 Molecular Structure Prediction

5 Analysis of Molecular Interactions

6 Molecular Networks

7 Analysis of Expression Data

8 Protein Function Prediction

9 Computational Biology of Diseases

10 Perspectives

Acknowledgments

Note on the Second Edition on This Chapter

References

11 Dynamics of Biomolecular Networks

1 Introduction

2 Boolean Dynamics Models

3 Continuous Dynamics Models

References

12 AR E-Cell

1 Introduction

2 Biological Modeling and Simulation Tools

3 The E-Cell System

4 Practical Applications

5 Concluding Remarks

References

13 Fractals in Biology and Medicine

1 Introduction

2 The Irruption of Fractal Geometry in Biology and Medicine

3 Fractal Criteria

4 Fractalomics

5 Concluding Remarks

Acknowledgments

References

14 Models of Cell Migration

1 Overview

2 Phenomenology and Mechanisms of Cell Motility

3 Mechanics of Migration

4 Chemotaxis

5 Multi-Photon Imaging of Lymphocyte Migration

6 Mathematical Models of Cell Migration

7 Mathematical Models of Tissue Organization

8 Conclusions

References

15 Protein Modeling

1 Introduction

2 Structure Prediction Methods

3 Structure-Based Modeling

4 Simulations of Protein Dynamics

5 Example Applications

6 Perspectives

Acknowledgments

References

16 System Models for Inference on Mechanisms of Neuronal Dynamics

1 General System Theory and Systems Biology

2 A General Form for System Models

3 System Models for Inferring Functional Integration and Effective Connectivity from Neuroimaging Data

4 Regression-Based Models of Effective Connectivity

5 Vector Autoregressive Models and Granger Causality

6 The Importance of Biophysical Forward Models

7 Dynamic Causal Modeling (DCM) for fMRI

8 Bayesian Model Selection (BMS)

9 Nonlinear, Two-State and Stochastic DCMs for fMRI

10 DCM for Electrophysiological Data

11 Future Applications and Challenges for Inferring Effective Connectivity from Neuroimaging and Electrophysiological Data

References

17 Systems Biology of the Liver

1 Background

2 Liver Physiology, Biochemistry, and Disease

3 Modeling of Genetic and Metabolic Phenomena in the Liver

4 Modeling Liver Physiology

5 A Composite Systems Biology Model to Predict Glucose Homeostasis

6 Conclusions and Future Developments

References

Part IV: Systems Biology in Medicine and Disease

18 Inferring Networks for Diseases

1 Common Diseases Are Complex

2 Network-Based Analysis: A Brief Summary

3 Networks in Diseases

4 Disease-Scale Network-Based Analyses of a Model Disease: Seasonal Allergic Rhinitis

5 Graph Theoretical Tools for Network-Based Analysis

6 An Example of a Combinatorial, Network-Based Study to Identify a Disease Module in SAR

7 Problems in Applying Network-Based Analyses to Clinical Research

8 Future Perspectives

9 Conclusions

References

19 Personalized Medicine (Predictive and Preventive)

1 Some History and Some Fundamentals

2 Where Are We Today?

3 Summing Up

4 Examples of Recent Advances in Personalized Medicine Based on Pharmacogenomic Findings

5 Analysis of Variability in Drug Response: Sources, Surprises, and Solutions

6 How Variance Aggregates in a Multicomponent System

7 Some Provisos

8 An Overview

References

Part V: Systems Biology of Organisms

20 Microbiomes

1 Introduction

2 History of Microbial Diversity Studies

3 Microbiomes

4 Single-Cell Genomics

5 Sequence Technologies and Tools

6 Future Perspectives

Acknowledgments

References

21 AR Synthetic Biology

1 Introduction

2 DNA Assembly and Modification

3 Modular Parts and Circuits

4 Spatial Regulation

5 The Synthetic Cell

6 Societal Challenges Posed by Synthetic Biology

7 Concluding Remarks

Acknowledgments

References

22 Plant Systems Biology

1 Introduction

2 Network Analysis

3 Plant Systems Biology

4 Concluding Remarks

References

Index

Related Titles

Meyers, R. A. (ed.)

Encyclopedia of Molecular Cell Biology and Molecular Medicine

Online version: www.meyers-emcbmm.com

Klipp, E., Liebermeister, W.,

Wierling, C., Kowald, A., Lehrach, H., Herwig, R.

Systems Biology

A Textbook

ISBN: 978-3-527-31874-2

Fu, P., Panke, S. (eds.)

Systems Biology and Synthetic Biology

ISBN: 978-0-471-76778-7

Dehmer, M., Emmert-Streib, F. (eds.)

Analysis of Complex Networks

From Biology to Linguistics

ISBN: 978-3-527-32345-6

Junker, B. H., Schreiber, F.

Analysis of Biological Networks

ISBN: 978-0-470-04144-4

Mandoiu, I., Zelikovsky, A.

Bioinformatics Algorithms

Techniques and Applications

ISBN: 978-0-470-09773-1

The Editor

The Editor

Dr. Robert A. Meyers

Editor in Chief

RAMTECH Limited

122, Escalle Lane

Larkspur, CA 94939

USA

Cover

Network-based analysis of DNA microarray data, with kind permission by Mikael Benson (for more information see Chapter 18, Figure 5).

Limit of Liability/Disclaimer of Warranty: While the publisher and author have used their best efforts in preparing this book, they make no representations or warranties with respect to the accuracy or completeness of the contents of this book and specifically disclaim any implied warranties of merchantability or fitness for a particular purpose. No warranty can be created or extended by sales representatives or written sales materials. The Advice and strategies contained herein may not be suitable for your situation. You should consult with a professional where appropriate. Neither the publisher nor authors shall be liable for any loss of profit or any other commercial damages, including but not limited to special, incidental, consequential, or other damages.

Library of Congress Card No.: applied for

British Library Cataloguing-in-Publication Data

A catalogue record for this book is available from the British Library.

Bibliographic information published by the Deutsche Nationalbibliothek

The Deutsche Nationalbibliothek lists this publication in the Deutsche Nationalbibliografie; detailed bibliographic data are available on the Internet at <http://dnb.d-nb.de>.

© 2012 Wiley-VCH Verlag & Co. KGaA, Boschstr. 12, 69469 Weinheim, Germany

Wiley-Blackwell is an imprint of John Wiley & Sons, formed by the merger of Wiley's global Scientific, Technical, and Medical business with Blackwell Publishing.

All rights reserved (including those of translation into other languages). No part of this book may be reproduced in any form — by photoprinting, microfilm, or any other means — nor transmitted or translated into a machine language without written permission from the publishers. Registered names, trademarks, etc. used in this book, even when not specifically marked as such, are not to be considered unprotected by law.

Print ISBN: 978-3-527-32607-5

Preface and Commentary

Our project is based on the recognition that a true and complete understanding of biology and indeed, human disease must go beyond genomics. Genes and their transcripts and translation products are of course crucial, but in fact these molecules never act alone; they rather operate in tremendously complex and noisy networks. Consider it is now estimated that the human genome encodes about 20 000 to 32 000 distinct proteins, while the expression and alternative splicing of mRNAs indicates that humans may be able to produce 106 different proteins. Hence the need for the emerging discipline of Systems Biology. Thus, Systems Biology is a recently established field in life sciences that aims at promoting a global, top-down, mathematical, systems understanding of living matter through the integration of various scientific domains.

Our compendium is written for university undergraduates, graduate students, faculty and investigators at research institutes and is a team effort which began with overall guidance from our Board, which includes 11 Nobel Prize winners. Each article and author selection was then validated by several reviewers from major university research centers and each manuscript was then reviewed by peers from other universities. There is a glossary of terms with definitions provided at the beginning of each article for students and the articles average close to 30 print pages – which provides significantly more depth for advanced researchers than other systems biology reviews.

Our treatment consists of 22 articles or chapters, and begins with an overview of Systems Biology which the reader, at any level, can use as a roadmap to the content of our book. Then, the detailed articles are organized into five sections, the first of which is: the Biological Basis of Systems Biology (the chapters range from developmental biology to the Interactome and protein abundance variation); the section on Systems Biology of Evolution includes a chapter by Nobel Laureate and Board Member, Werner Arber; the Modeling of Biological Systems section includes chapters ranging from computer simulation methodology of specific systems such as the brain and cell migration as well as protein modeling. Considering that there are now about 21 000 distinct proteins encoded directly by the human genome while the expression and alternative splicing of mRNAs indicates that humans may be able to produce 106 different proteins, and we can only surmise the function of nearly half of these proteins – a systems approach is clearly needed. This section then includes top down mathematical modeling methods involving chaos, fractals, dynamics of biomolecular networks and informatics; the Systems Biology in Medicine and Disease section includes chapters on inferring networks for disease (termed the diseasome) and culminates in a chapter on systems aspects in personalized medicine for prediction and prevention. Our concluding section is Systems Biology of Organisms which includes plant systems biology as well as two chapters from scientists at the J. Craig Venter Institute, one on microbiomes which encompasses metagenomics as well as the human gut microbiome which has recently been discovered to contribute to viral infection cycles, and the other on synthetic biology which describes methods and the recent creation of a synthetic cell.

Our team hopes that you, the reader, will benefit from our hard work – finding the content useful in your research and education. We wish to thank our Managing Editor, Sarah Mellor as well as our Executive Editor, Gregor Cicchetti for both their advice and hard work in the course of this project.

Larkspur, California, March 2012

Robert A. Meyers

RAMTECH Limited

List of Contributors

Mario Albrecht

Max Planck Institute for Informatics

Department of Computational Biology and Applied Algorithmics

Campus E1 4

66123 Saarbrücken

Germany

Mikkel A. Algire

J. Craig Venter Institute

Synthetic Biology

9704 Medical Center Drive

Rockville, MD 20850

USA

Miguel Antonio Aon

Johns Hopkins University

Department of Medicine

720 Rutland Avenue

Baltimore, MD 21205

USA

Werner Arber

University of Basel

Department of Microbiology

Biozentrum

Klingelbergstrasse 70

4056 Basel

Switzerland

Mikael Benson

University of Linköping

The Center for Individualized Medicine

Linköping

58185

Sweden

Tilo Beyer

Institute for Molecular and Clinical Immunology

Otto-von-Guericke University

Leipziger Str. 44

39120 Magdeburg

Germany

Robert R. Bies

Indiana University School of Medicine

Department of Clinical Pharmacology

Department of Medicine

1001 W. 10th Street

W.D. Myers Bldg W7125

Indianapolis, IN 46202

USA

Melanie Boerries

Freiburg Institute for Advanced Studies – LifeNet

School of Life Sciences

Albertstraße 19

79104 Freiburg

Germany

Ian David Lockhart Bogle

University College London

CoMPLEX – Centre for Mathematics

and Physics in the Life Sciences and Experimental Biology

Gower Street

London WC1E 6BT

UK

Hauke Busch

Freiburg Institute for Advanced Studies – LifeNet

School of Life Sciences

Albertstraße 19

79104 Freiburg

Germany

Dong-Yeon Cho

National Institute of Health (NIH)

National Center of Biotechnology Information

NLM, 8600 Rockville Pike

Bethesda, MD 20894

USA

Valentina Corradi

Department of Biological Sciences and Institute for Biocomplexity and Informatics

2500 University Dr. NW

Calgary, AB T21N4

Canada

Sonia Cortassa

Johns Hopkins University

Department of Medicine

720 Rutland Avenue

Baltimore, MD 21205

USA

Emanuele Cozzo

University of Zaragoza

Institute for Biocomputation and Physics of Complex Systems (BIFI)

50018 Zaragoza

Spain

Pawan K. Dhar

Symbiosis International University

School of Biomedical Sciences

Pune 411 042

India

Francisco S. Domingues

Max Planck Institute for Informatics

Department of Computational Biology and Applied Algorithmics

Campus E1 4

66123 Saarbrücken

Germany

Frank John Dye

Western Connecticut State University

Biological and Environmental Sciences

181 White Street

Danbury, CT 06810

USA

Roland Eils

German Cancer Research Institute

Im Neuenheimer Feld 280

69120 Heidelberg

Germany

Alisdair R. Fernie

Max Planck Institut für Molekulare Pflanzenphysiologie

Am Mühlenberg 1

14476 Potsdam-Golm

Germany

Antony Finkelstein

University College London

CoMPLEX – Centre for Mathematics and Physics in the Life Sciences and Experimental Biology

Gower Street

London WC1E 6BT

UK

Karl J. Friston

University College London

Wellcome Trust Centre for Neuroimaging

Institute of Neurology

12 Queen Square

London WC1N 3BG

UK

Michele S. Garfinkel

J. Craig Venter Institute

Synthetic Biology

9704 Medical Center Drive

Rockville, MD 20850

USA

Aaron David Goldman

Princeton University

Department of Ecology and Evolutionary Biology

106A Guyot Hall

Princeton, NJ 08542

USA

and

NASA Astrobiology Institute

Center for Ribosomal Origins and Evolution at Georgia Institute of Technology

NASA Postdoctoral Program

225 North Ave. NW

Atlanta, GA 30332

USA

Greco Hernández

National Institute for Cancer

Division of Basic Research

Av. San Fernando No. 22, Col.

Sección XVI, Tlalpan

C. P. 14080 Mexico City

Mexico

and

McGill University

Department of Biology and Developmental Biology Research Initiative, Bellini Life Sciences

3649, Sir-William-Osler Street

Montréal, H3A 1B1

Canada

Jeremy A. Horst

University of California San Francisco School of Pediatric Dentistry

Department of Orofacial Sciences

707 Parnassus Ave

San Francisco, CA 94143

USA

and

University of Washington

Department of Microbiology

960 Republican Street

Seattle, WA 98109

USA

Ling-Hong Hung

University of Washington

Department of Microbiology

960 Republican Street

Seattle, WA 98109

USA

Rajiv Jalan

University College London

CoMPLEX – Centre for Mathematics and Physics in the Life Sciences and Experimental Biology

Gower Street

London WC1E 6BT

UK

Konstantinos Krampis

J. Craig Venter Institute

9704 Medical Center Drive

Rockville, MD 20850

USA

Michael A. Langston

University of Tennessee

Department of Electrical Engineering

and Computer Science

203 Claxton Complex

1122 Volunteer Boulevard

Knoxville, TN 37996-3450

USA

Thomas Lengauer

Max Planck Institute for Informatics

Department of Computational Biology and Applied Algorithmics

Campus E1 4

66123 Saarbrücken

Germany

David Lloyd

Cardiff University

Microbiology (BIOSI 1)

Cardiff

Wales CF10 3AT

UK

Gabriele Angelo Losa

Institute of Scientific Interdisciplinary Studies

v.F. Rusca 1

6600 Locarno

Switzerland

Ramana Madupu

J. Craig Venter Institute

9704 Medical Center Drive

Rockville, MD 20850

USA

Michael Meyer-Hermann

Helmholtz Centre for Infection Research

Department of Systems Immunology

Inhoffenstr. 7

38124 Braunschweig

Germany

and

Bio Center for Life Science

University of Technology Braunschweig

Spielmannstr. 7

38106 Braunschweig

Germany

Jason Miller

J. Craig Venter Institute

9704 Medical Center Drive

Rockville, MD 20850

USA

Michael G. Montague

J. Craig Venter Institute

Synthetic Biology

9704 Medical Center Drive

Rockville, MD 20850

USA

Yamir Moreno

University of Zaragoza

Institute for Biocomputation and Physics of Complex Systems (BIFI)

50018 Zaragoza

Spain

and

University of Zaragoza

Department of Theoretical Physics

Faculty of Sciences

50009 Zaragoza

Spain

Yoichi Nakayama

Keio University

Institute for Advanced Biosciences

Tsuruoka

Yamagata 997-0035

Japan

Karen E. Nelson

J. Craig Venter Institute

9704 Medical Center Drive

Rockville, MD 20850

USA

Sonia Osorio

Max Planck Institut für Molekulare Pflanzenphysiologie

Am Mühlenberg 1

14476 Potsdam-Golm

Germany

Teresa M. Przytycka

National Institute of Health (NIH)

National Center of Biotechnology Information

NLM, 8600 Rockville Pike

Bethesda, MD 20894

USA

Yu-Hui Rogers

J. Craig Venter Institute

9704 Medical Center Drive

Rockville, MD 20850

USA

Doug Rusch

Center for Genomics and Bioinformatics at Indiana University

Bloomington

Jordan Hall A302D 1001 E. 3rd Street

Bloomington, IN 47405-3700

USA

Ram Samudrala

University of Washington

Department of Microbiology

960 Republican Street

Seattle, WA 98109

USA

Joaquín Sanz

University of Zaragoza

Institute for Biocomputation and Physics of Complex Systems (BIFI)

50018 Zaragoza

Spain

Jeffrey H. Schwartz

University of Pittsburgh

Departments of Anthropology and History and Philosophy of Science

3302 Posvar Hall

University of Pittsburgh

Pittsburgh, PA 15260

USA

Robert Seymour

University College London

CoMPLEX – Centre for Mathematics and Physics in the Life Sciences and Experimental Biology

Gower Street

London WC1E 6BT

UK

Elizabeth Shephard

University College London

CoMPLEX – Centre for Mathematics and Physics in the Life Sciences and Experimental Biology

Gower Street

London WC1E 6BT

UK

Klaas E. Stephan

University of Zurich

Laboratory for Social and Neural Systems Research

Department of Economics

Bluemlisalpstr. 10

8006 Zurich

Switzerland

and

University College London

Wellcome Trust Centre for Neuroimaging

Institute of Neurology

12 Queen Square

London WC1N 3BG

UK

Thomas Sumner

University College London

CoMPLEX – Centre for Mathematics and Physics in the Life Sciences and Experimental Biology

Gower Street

London WC1E 6BT

UK

Kouichi Takahashi

Keio University

Institute for Advanced Biosciences

Tsuruoka

Yamagata 997-0035

Japan

Gritta Tettweiler

McGill University

Department of Biology and Developmental Biology Research Initiative, Bellini Life Sciences

3649, Sir-William-Osler Street

Montréal, H3A 1B1

Canada

D. Peter Tieleman

Department of Biological Sciences

and Institute for Biocomplexity and Informatics

2500 University Dr. NW

Calgary, AB T21N4

Canada

Masaru Tomita

Keio University

Institute for Advanced Biosciences

Tsuruoka

Yamagata 997-0035

Japan

John Urquhart

AARDEX Group, S.A.

Ave de la Gare, 29

1950 Sion

Switzerland

and

University of California

San Francisco Medical Center

Department of Biomedical Engineering and Therapeutic Sciences

505 Parnassus Ave

San Francisco, CA 94122

USA

Vincent VanBuren

Texas A&M Health Science Center College of Medicine

Systems Biology and Translational Medicine

702 SW HK Dodgen Loop

Medical Research Building

Temple, TX 76504

USA

Sanjay Vashee

J. Craig Venter Institute

Synthetic Biology

9704 Medical Center Drive

Rockville, MD 20850

USA

Anne Warner

University College London

CoMPLEX – Centre for Mathematics

and Physics in the Life Sciences and Experimental Biology

Gower Street

London WC1E 6BT

UK

Alette M. Wessels

Indiana University School of Medicine

Department of Clinical Pharmacology

Department of Medicine

1001 W. 10th Street

W.D. Myers Bldg W7125

Indianapolis, IN 46202

USA

Marian R. Zlomislic

Department of Biological Sciences

and Institute for Biocomplexity and Informatics

2500 University Dr. NW

Calgary, AB T21N4

Canada

Part I

Biological Basis of Systems Biology

1

Systems Biology

Melanie Boerries1, Roland Eils2, and Hauke Busch1

1Freiburg Institute for Advanced Studies – LifeNet, School of Life Sciences, Albertstraße 19, 79104 Freiburg, Germany

2German Cancer Research Institute, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany

1 Introduction

2 What Is Systems Understanding?

3 Why Are Biological Systems Different?

3.1 Biological Complexity

3.2 Global Properties of Biological Systems

3.2.1 Robustness of Biological Systems

3.2.2 System Adaptation and Control

3.2.3 Modules and Protocols

4 Systems Biology Modeling

4.1 Network Biology

4.2 Dynamic Network Models

4.3 ReactionDiffusion Models

4.4 Holism versus Reductionism: The Global Dynamics of Networks

4.5 Modeling Resources and Standards

5 Future Prospects of Systems Biology

5.1 Synthetic Biology

5.2 Conclusions: Where Are We?

References

Keywords

Systems biology

A new field of biology that studies the functional structure and dynamics of intercellular and intracellular networks with the help signal- and systems-oriented methods.

Synthetic biology

Studies life as networks of biological objects such as DNA proteins RNA and metabolites.

Network biology

Studies the static organization of life as networks made up of biological entities such as DNA proteins RNA or metabolites.

System

A set of interacting parts functioning as a whole and distinguishable from its surroundings by identifiable boundaries.

Systems theory

This denotes the cross-disciplinary investigation of the abstract organization of systems irrespective of their substance type or spatiotemporal scale of existence. The goal is the study of emerging properties that arise from the interconnectedness of the individual parts making up the system.

Robustness

The robustness of biological systems denotes the maintenance of specific system functionalities in the presence of fluctuations or change in environmental parameters.

Control

Control is defined as the response action taken by a system to counteract parameter changes to maintain system functions at a certain predefined level.

Modularity

A design concept of complex systems to integrate simpler self-contained functional building-blocks into the framework of one larger system.

Model

The concept of representing causal relationships from real systems in the language of mathematics

Systems Biology is a new field of biology, which places the theoretical foundations of systems analysis of living matter into the context of modern high-throughput quantitative experimental data, mathematics, and in silico simulations. The aim is to analyze the organization and to gain engineering-control of metabolic and genetic pathways. The ultimate goal is to gain an “holistic” view of the complex workings of life. The need for a system level understanding of biology is reviewed in this chapter, and comments are provided on the current scientific progress in this field. The current and future directions of experimental design strategies and theoretical approaches are also highlighted.