New Models of the Cell Nucleus: Crowding, Entropic Forces, Phase Separation, and Fractals
- 1st Edition, Volume 307 - December 27, 2013
- Imprint: Academic Press
- Editors: Ronald Hancock, Kwang W. Jeon
- Language: English
- Hardback ISBN:9 7 8 - 0 - 1 2 - 8 0 0 0 4 6 - 5
- eBook ISBN:9 7 8 - 0 - 1 2 - 8 0 0 2 5 2 - 0
International Review of Cell and Molecular Biology presents current advances and comprehensive reviews in cell biology--both plant and animal. Articles address structure and… Read more
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Request a sales quoteInternational Review of Cell and Molecular Biology presents current advances and comprehensive reviews in cell biology--both plant and animal. Articles address structure and control of gene expression, nucleocytoplasmic interactions, control of cell development and differentiation, and cell transformation and growth. Impact factor for 2012: 4.973.
Ideas from the fields of biophysics, physical chemistry, of polymer and colloid, and soft matter science have helped clarify the structure and functions of the cell nucleus. The development of powerful methods for modeling conformations and interactions of macromolecules has also contributed. The book aims to encourage cell and molecular biologists to become more familiar with and understand these new concepts and methods, and the crucial contributions they are making to our perception of the nucleus.
- This is the first volume to present a comprehensive review of New Models of the Cell Nucleus
Cell biologists, molecular biologists, developmental biologists, physiologists (organ level), biomedical scientists, biochemists studying cell-cell interactions, cell variation and evolution
Contributors
Preface
Chapter One. The Nuclear Physique
Abstract
1 Introduction: A Brief History of Biophysics
2 The Biophysical Nucleus
Acknowledgments
References
Chapter Two. The Crowded Nucleus
Abstract
1 Introduction
2 Macromolecular Crowding in the Nucleus
3 Entropic (Depletion) Forces in the Nucleus
4 Compartmentalization in the Nucleus
5 Phase Separation in the Nucleus
6 Concluding Remarks
References
Further-Reading
Chapter Three. Crowding in Polymer–Nanoparticle Mixtures
Abstract
1 Introduction
2 Models of Macromolecules: Polymers and Nanoparticles
3 Theoretical and Computational Methods
4 Response of Polymer Conformations to Nanoparticle Crowding
5 Concluding Remarks
Acknowledgments
References
Chapter Four. Crowding-Induced Formation and Structural Alteration of Nuclear Compartments: Insights from Computer Simulations
Abstract
1 Introduction
2 Structural Properties of Nuclear Compartments
3 Crowded Nature of Cell Nucleus
4 Structural Alterations of Chromosome Subcompartments by Macromolecular Crowding
5 Formation and Maintenance of NBs Influenced by Macromolecular Crowding
6 Concluding Remarks
Acknowledgments
References
Chapter Five. Phase Separation as a Possible Means of Nuclear Compartmentalization
Abstract
1 Introduction
2 Macromolecule Solution Chemistry
3 Aqueous Phase Separation
4 Nuclear Compartments as Crowded and Dynamic Structures
5 Potential Functional Significance of Phase Separation for Nuclear Compartmentalization
6 Experimental Model Systems for Crowded, Phase-Separated Microcompartments
7 Looking Forward
Acknowledgment
References
Chapter Six. Formation of Multiprotein Assemblies in the Nucleus: The Spindle Assembly Checkpoint
Abstract
1 Introduction
2 SAC Signaling
3 Disorder-to-Order Transitions
4 Macromolecular Crowding of Nuclear Proteins
5 Cooperative Interactions of Nuclear Multiprotein Complexes
6 Concluding Remarks
References
Chapter Seven. Characteristic Behavior of Crowding Macromolecules Confined in Cell-Sized Droplets
Abstract
1 Introduction
2 Confinement of Long DNA Molecules in Droplets
3 Cross-Talk of DNA with Other Semiflexible Polymers
4 Gene Expression in Cell-Sized Droplets
5 From Cell-Sized Droplet in Oil Phase to Liposome in Aqueous Phase
6 Concluding Remarks
References
Chapter Eight. Noncanonical Structures and Their Thermodynamics of DNA and RNA Under Molecular Crowding: Beyond the Watson–Crick Double Helix
Abstract
1 Introduction
2 Thermodynamic Studies on Nucleic Acids
3 Molecular Crowding Effects on the Canonical Structures of Nucleic Acids
4 Molecular Crowding Effects on Noncanonical Structures of Nucleic Acids
5 Molecular Crowding Effects on Functional RNAs
6 Molecular Crowding Effects Under Extreme Environments
7 Molecular Crowding Effects on Transcription and Translation
8 Perspectives
Acknowledgments
References
Chapter Nine. Computational Models of Large-Scale Genome Architecture
Abstract
1 Introduction
2 Direct Models of Genome Architecture
3 Inverse Models of Genome Architecture
4 Concluding Remarks
Acknowledgments
References
Chapter Ten. How Chromatin Looping and Nuclear Envelope Attachment Affect Genome Organization in Eukaryotic Cell Nuclei
Abstract
1 Introduction
2 The Model
3 Results
4 Perspectives
Acknowledgments
References
Chapter Eleven. Crowding, Diffusion, and Biochemical Reactions
Abstract
1 Introduction
2 Diffusion and Random Walks
3 Quantifying Diffusion in Living Cells
4 Diffusion as a Driving Force for Biochemical Reactions
5 Concluding Remarks
References
Chapter Twelve. Importance of Crowding in Signaling, Genetic, and Metabolic Networks
Abstract
1 Introduction
2 Diffusion of Transcription Factors Can Increase Noise in Gene Expression
3 Diffusion Between Compartments Can Reduce Protein Concentration Fluctuations
4 Crowding Can Enhance Information Transmission by Removing Correlations
5 Crowding Can Promote Membrane Rebinding, Which Can Enhance Downstream Signal Propagation
6 Crowding Can Qualitatively Change the Response of Biochemical Networks
7 Diffusion Can Affect Metabolic Flux
8 How to Model Biochemical Networks in the Presence of Crowding
9 Effect of Crowding: Diffusion or Entropy?
10 Perspectives
Acknowledgments
References
Further Reading
Chapter Thirteen. Relevance and Limitations of Crowding, Fractal, and Polymer Models to Describe Nuclear Architecture
Abstract
1 Introduction
2 First Glance at Methods to Investigate Nuclear Organization
3 Molecular Crowding
4 Fractal Models
5 Polymer Models for Chromosomes
6 Evaluating Chromosome Structural Properties with Combined Techniques
7 Uniformity of Chromatin Mechanical Parameters
8 Concluding Remarks
Acknowledgments
References
Index
- Edition: 1
- Volume: 307
- Published: December 27, 2013
- No. of pages (Hardback): 512
- Imprint: Academic Press
- Language: English
- Hardback ISBN: 9780128000465
- eBook ISBN: 9780128002520
RH
Ronald Hancock
Ronald Hancock obtained a PhD in Microbiology at Cambridge, UK and was a postdoc at Harvard Medical School. He worked at the Swiss Cancer Institute and is now a professor in the Department of Molecular Biology and the Cancer Research Centre of Laval University in Québec, Canada.
His research focuses on the structure of the cell nucleus and chromosomes, and he also teaches and collaborates on studies of DNA repair with scientists in the Biosystems Group of the Silesian University, Gliwice, Poland. He is Editor of two volumes on "The Nucleus" in the series "Methods in Molecular Biology" (Springer) and of a Chapter entitled "The crowded environment of the genome" in the book "Genome organization and function in the cell nucleus" (Wiley). He represents Canada on the International Committee of the International (William Bernhard) Workshop on the Cell Nucleus.
Affiliations and expertise
Laval University Cancer Research Centre, Québec, CanadaKJ
Kwang W. Jeon
Kwang Jeon received his Ph.D. in cell physiology at King’s College, University of London, UK, in 1964 and taught at SUNY Buffalo and University of Tennessee. His research was concerned with the biogenesis and function of cell components in two major areas: Integration of intracellular symbionts into host cells leading to the acquisition of new cell components and cell variation; Membrane-protein recycling during endo- and exocytosis.
Affiliations and expertise
University of Tennessee, Knoxville, TN, USARead New Models of the Cell Nucleus: Crowding, Entropic Forces, Phase Separation, and Fractals on ScienceDirect