Encyclopedia of Cell Biology

Encyclopedia of Cell Biology

1st Edition - August 7, 2015
This is the Latest Edition
  • Editors-in-Chief: Ralph Bradshaw, Philip Stahl
  • Hardcover ISBN: 9780123944474
  • eBook ISBN: 9780123947963

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Description

The Encyclopedia of Cell Biology, Four Volume Set offers a broad overview of cell biology, offering reputable, foundational content for researchers and students across the biological and medical sciences. This important work includes 285 articles from domain experts covering every aspect of cell biology, with fully annotated figures, abundant illustrations, videos, and references for further reading. Each entry is built with a layered approach to the content, providing basic information for those new to the area and more detailed material for the more experienced researcher. With authored contributions by experts in the field, the Encyclopedia of Cell Biology provides a fully cross-referenced, one-stop resource for students, researchers, and teaching faculty across the biological and medical sciences.

Key Features

  • Fully annotated color images and videos for full comprehension of concepts, with layered content for readers from different levels of experience
  • Includes information on cytokinesis, cell biology, cell mechanics, cytoskeleton dynamics, stem cells, prokaryotic cell biology, RNA biology, aging, cell growth, cell Injury, and more
  • In-depth linking to Academic Press/Elsevier content and additional links to outside websites and resources for further reading
  • A one-stop resource for students, researchers, and teaching faculty across the biological and medical sciences

Readership

Undergraduate and graduate students, researchers, scientists, and teaching faculty across the biological and medical sciences.

Table of Contents

  • Dedication

    Editors-in-Chief

    Volume Editors

    Section Editors

    Preface

    References

    Cell Biology: An Overview

    Imaging and Organelle Organization

    Signaling

    Concluding Remarks

    References

    Permission Acknowledgments

    Molecular Cell Biology

    Molecular Cell Biology: An Overview

    Basic Molecular Components and Technology

    Nucleic Acid Synthesis/Breakdown

    Protein Synthesis and Degradation

    Molecular Principles, Components, Technology, and Concepts

    Basic Principles

    MOLECULAR PRINCIPLES, COMPONENTS, TECHNOLOGY, AND CONCEPTS: BASIC PRINCIPLES | Chemical and Physical Principles

    Abstract

    Introduction

    The Laws of Thermodynamics and Living Cells

    Gibbs Free Energy Always Decreases for a Spontaneous Process at Constant Temperature and Pressure

    Gibbs Free Energy Changes are Additive

    Coupling of ATP Hydrolysis to Drive Thermodynamically Unfavorable Reactions

    Reaction Rate and Rate Constant

    Reaction Rate-Limiting Step

    Rate Constant and Activation Energy

    Enzyme Kinetics

    Allosteric Enzymes

    Concerted and Sequential Models

    Water as Life’s Aether

    Acid–Base Reactions Play a Central Role in Most Biochemical Processes

    Noncovalent Interactions Play Key Roles in Mediating Functions of Biomacromolecules

    Effect of Molecular Crowding in Living Cells

    Concluding Remarks

    References

    MOLECULAR PRINCIPLES, COMPONENTS, TECHNOLOGY, AND CONCEPTS: BASIC PRINCIPLES | Biocatalysis

    Abstract

    Introduction

    Enzymes

    Ribozymes

    See also

    References

    Relevant Websites

    Nucleic Acids

    MOLECULAR PRINCIPLES, COMPONENTS, TECHNOLOGY, AND CONCEPTS: NUCLEIC ACIDS | DNA, RNA Chemical Properties (Including Sequencing and Next-Generation Sequencing)

    Abstract

    Glossary

    Introduction

    Physical Structure of Nucleic Acid

    Chemical Modification of Nucleic Acids

    DNA Modification by Radiation

    DNA Mapping

    Nucleic Acid Sequencing

    Sanger DNA Sequencing

    NGS

    Library Preparation

    Sequencing through DNA Synthesis

    Data Analysis

    Future Directions

    See also

    References

    Further Reading

    MOLECULAR PRINCIPLES, COMPONENTS, TECHNOLOGY, AND CONCEPTS: NUCLEIC ACIDS | The Chemical Synthesis of DNA and RNA Oligonucleotides for Drug Development and Synthetic Biology Applications

    Abstract

    Introduction

    The Chemical Synthesis of Oligodeoxyribonucleotides

    The Chemical Synthesis of Oligoribonucleotides via the Phosphoramidite Approach

    DNA and RNA Microarrays

    Concluding Remarks

    See also

    References

    Proteins

    MOLECULAR PRINCIPLES, COMPONENTS, TECHNOLOGY, AND CONCEPTS: PROTEINS | Expression Systems

    Abstract

    Glossary

    Overview of Expression Systems

    Bacterial Expression Systems

    Yeast Expression Systems

    Cell-Free Expression Systems

    Insect Expression Systems

    Mammalian Expression Systems

    Summary/Conclusion

    See also

    References

    Further Reading

    MOLECULAR PRINCIPLES, COMPONENTS, TECHNOLOGY, AND CONCEPTS: PROTEINS | Isolation/Purification of Proteins

    Abstract

    Glossary

    Introduction

    The Protein Source

    Assays

    Considerations

    Initial Steps

    Chromatography

    Migration in an Electric Field

    Protein Crystallization

    Evaluating Purity

    A Final Word

    See also

    References

    Further Reading

    MOLECULAR PRINCIPLES, COMPONENTS, TECHNOLOGY, AND CONCEPTS: PROTEINS | Protein Sequence Determination: Methodology and Evolutionary Implications

    Abstract

    Sequencing Proteins by Chemical Techniques

    Other Sequencing Methodology

    Sequence Comparisons

    Concluding Remarks

    See also

    References

    MOLECULAR PRINCIPLES, COMPONENTS, TECHNOLOGY, AND CONCEPTS: PROTEINS | Posttranslational Modifications: Key Players in Health and Disease

    Abstract

    Introduction

    Proteolytic PTM of Proteins

    Phosphorylation

    Glycosylation (N- and O-linked)

    N-Acetylation

    Amidation

    Methylation

    Lipid Modification (Lipidation)

    Oxidative Stress-Related PTMs

    Hydroxylation

    Carbonylation

    Nitrosylation

    Ubiquitin and Targeted Protein Degradation

    γ-Carboxylation

    Conclusions: Many More PTMs Exist, and There Is Cross Talk between Them

    See also

    References

    Relevant Websites

    MOLECULAR PRINCIPLES, COMPONENTS, TECHNOLOGY, AND CONCEPTS: PROTEINS | Protein Domains: Structure, Function, and Methods

    Abstract

    Introduction

    Protein Structure: Motifs, Folds, and Domains

    Protein Domain Functions

    Identifying and Classifying Protein Domains

    Domains in Evolution: Modularity and Combinatorial Protein Structure

    Conclusions

    See also

    References

    MOLECULAR PRINCIPLES, COMPONENTS, TECHNOLOGY, AND CONCEPTS: PROTEINS | NMR in Structural and Cell Biology

    Abstract

    Introduction

    Brief Historical Perspective of NMR and Solution Structure Determination of Macromolecules

    Fundamentals of NMR Structure Determination

    Place of NMR Spectroscopy in Structural and Cell Biology

    Experimental and Computational Considerations

    Structural Proteomics of the Bacterial Phosphotransferase System

    Exploring Sparsely Populated States of Proteins and Their Complexes

    Acknowledgments

    See also

    References

    MOLECULAR PRINCIPLES, COMPONENTS, TECHNOLOGY, AND CONCEPTS | Proteins: Folding, Misfolding, Disordered Proteins, and Related Diseases

    Abstract

    Glossary

    Folding

    Misfolding

    Disordered Proteins

    Related Diseases

    See also

    References

    MOLECULAR PRINCIPLES, COMPONENTS, TECHNOLOGY, AND CONCEPTS: PROTEINS | Diseases of Protein Folding: Huntington’s Disease and Amyotrophic Lateral Sclerosis

    Abstract

    Introduction

    Genetic Basis of HD and ALS

    Effects of Protein Products on Protein Homeostasis

    Clearance Pathways of Aggregates – Cellular UPS

    Clearance Pathways of Aggregates – Autophagy Pathway

    Cellular Transfer of Aggregates on Toxic Fragments

    Cell Specificity and Susceptibility

    Symptoms and Treatments of the Disease

    Potential Treatments and Therapies

    See also

    References

    Further Reading

    MOLECULAR PRINCIPLES, COMPONENTS, TECHNOLOGY, AND CONCEPTS: PROTEINS | Site-Directed Mutagenesis

    Abstract

    Background

    Methods

    Applications

    Summary

    See also

    References

    MOLECULAR PRINCIPLES, COMPONENTS, TECHNOLOGY, AND CONCEPTS: PROTEINS | Chemical Biology

    Abstract

    Glossary

    Introduction

    Imaging

    Metabolic Labeling

    Affinity Labeling

    Activity-Based Probes

    Bioorthogonal Labeling

    Chemical Biology and Drug Development

    See also

    References

    Further Reading

    MOLECULAR PRINCIPLES, COMPONENTS, TECHNOLOGY, AND CONCEPTS: PROTEINS | Drug Design

    Abstract

    Glossary

    Introduction

    History of Drug Development

    Evolution of Drug Design

    Structural Biology and Drug Development

    HTS

    Virtual Screening

    Drug Design and Biologics

    Antibody–Drug Conjugates

    See also

    References

    Further Reading

    Relevant Website

    MOLECULAR PRINCIPLES, COMPONENTS, TECHNOLOGY, AND CONCEPTS: PROTEINS | Antibodies and Improved Engineered Formats (as Reagents)

    Abstract

    Introduction

    Antibodies for In Vitro Diagnosis, in Soluble (RIA), Surface-Bound (ELISA), Cell-Bound (Fluorescence-Activated Cell Sorting (FACS)), Tissue-Bound (IHC) and Modern E-Device Formats

    Antibodies for In Vivo Applications: Immunotherapy with Humanization and Deimmunisation

    Design of ‘Antibody Fragments’ for Unique Clinical Applications In Vivo

    Pharmacokinetics of Intact Antibodies versus Fragments

    Engineering Multiple Specificity in Antibody Fragments

    Antibody Libraries: Construction, Display, and Selection

    Production, Stability, and Expression Levels

    High-Value Clinical Applications

    Angiogenesis and Vascular Blockade/Transport

    Image-Guided Surgery: From Radioactive Image-Guided Surgery (RIGS) to Fluorescence Image-Guided Surgery (FIGS)

    Conclusion

    See also

    References

    Relevant Websites

    Lipids

    MOLECULAR PRINCIPLES, COMPONENTS, TECHNOLOGY, AND CONCEPTS: LIPIDS | Lipidomics

    Abstract

    Introduction

    Why Lipidomics?

    Description of How the Components of the Lipidome Are Usually Analyzed

    Lipidomics Databases and Other Online Tools

    Examples of Findings Using Lipidomics Approaches

    Summary

    See also

    References

    Relevant Websites

    MOLECULAR PRINCIPLES, COMPONENTS, TECHNOLOGY, AND CONCEPTS: LIPIDS | Synthesis and Structure of Glycerolipids

    Abstract

    Glossary

    Introduction

    Synthesis of Phosphatidic Acid

    Synthesis of Phospholipids in Bacteria

    Synthesis of Phospholipids in Eukaryotes

    Roles of Phospholipids in Cell Function

    See also

    References

    Further Reading

    MOLECULAR PRINCIPLES, COMPONENTS, TECHNOLOGY, AND CONCEPTS: LIPIDS | Cholesterol and Other Steroids

    Abstract

    Introduction

    Structure

    Cholesteryl Esters

    Cholesterol in Cell Membranes

    Cholesterol Biosynthesis

    Regulation of Cholesterol Biosynthesis

    Cellular Cholesterol Homeostasis

    Cholesterol in Brain

    Cholesterol in Diseases

    Steroids

    See also

    References

    MOLECULAR PRINCIPLES, COMPONENTS, TECHNOLOGY, AND CONCEPTS: LIPIDS | Glycolipids

    Abstract

    Introduction

    Definition of ‘Glycolipid’ and Subcategories of Glycolipids

    Glycosphingolipids – The Power of Combinatorial Biochemistry

    Analysis of Glycolipids by ‘Omic’ Technologies

    Perspective on the Future of Glycolipid Research

    See also

    References

    Relevant Websites

    MOLECULAR PRINCIPLES, COMPONENTS, TECHNOLOGY, AND CONCEPTS: LIPIDS | Lipid Signaling

    Abstract

    Glossary

    Introduction

    Lipid Classification and Nomenclature

    The Primary Mammalian Signaling Lipids

    Signaling Lipids are Spatially Restricted and Scarce

    The Complexity of Lipid Signaling

    Physiologic Roles of Signaling Lipids

    Signaling Lipids and Disease

    Recent Advances in Signaling Lipid Technologies

    See also

    References

    Further Reading

    Membranes

    MOLECULAR PRINCIPLES, COMPONENTS, TECHNOLOGY, AND CONCEPTS: MEMBRANES | Composition, Physical Properties, and Curvature

    Abstract

    Origins

    General Traits of Biological Membranes

    Membrane Electrostatics

    Lipid Packing

    Membrane Subdomains

    Mechanisms that Modifies the Bulk Lipid Composition of Organelles

    Membrane Curvature

    Conclusions

    See also

    References

    Relevant Website

    MOLECULAR PRINCIPLES, COMPONENTS, TECHNOLOGY, AND CONCEPTS: MEMBRANES | Lipid Rafts/Membrane Rafts

    Abstract

    Introduction

    The Physical States of Lipids in Lipid Bilayers

    Formulation of the Lipid Raft Hypothesis

    What Hold Rafts Together?

    The Basis of Membrane Protein Interaction with Rafts

    Lipid Domain Size

    Detecting Rafts in Model Membranes

    Detecting Rafts in Natural Membranes: Giant Plasma Membrane Vesicles

    Using Detergents to Detect Rafts in Cells: Rationale and Limitations

    Detecting Rafts in Cells: Microscopy and Spectroscopy

    Detecting Rafts in Cells Using Sterol Modification

    Biological Functions of Raft Domains in Cells

    Acknowledgment

    See also

    References

    MOLECULAR PRINCIPLES, COMPONENTS, TECHNOLOGY, AND CONCEPTS: MEMBRANES | Membrane Potential: Concepts

    Abstract

    Introduction

    Determinants of the Membrane Potential

    Measuring Membrane Potential and Relative Membrane Permeability

    Conclusion

    Acknowledgments

    References

    Relevant Websites

    MOLECULAR PRINCIPLES, COMPONENTS, TECHNOLOGY, AND CONCEPTS: MEMBRANES | The Outer Mitochondrial Membrane, a Smooth ‘Coat’ with Many Holes and Many Roles: Preparation, Protein Components, Interactions with Other Membranes, Involvement in Health, Disease, and as a Drug Target

    Abstract

    Introduction

    Separation and Isolation of the Four Mitochondrial Compartments

    Results: Protein/Enzyme Assignments of the Four Mitochondrial Compartments with an Emphasis on the Outer Mitochondrial Membrane

    ‘Moonlighting’ Roles of the Mitochondrial Outer Membrane with Its Intracellular Neighbors

    Involvement of the Outer Mitochondrial Membrane in Major Diseases and Potential Drug Target

    Concluding Remarks

    Acknowledgments

    See also

    References

    MOLECULAR PRINCIPLES, COMPONENTS, TECHNOLOGY, AND CONCEPTS: MEMBRANES | Neuronal Action Potentials and Ion Channel Allostery

    Abstract

    Glossary

    Introduction

    Electrical Properties of Neurons

    Anatomy of a Neuron and Flow of Information

    Action Potentials

    Action Potential Propagation

    Action Potential Invasion of the Nerve Terminal

    Fate of Neurotransmitter in the Synaptic Cleft

    Postsynaptic Receptors/Ligand-Gated Ion Channels

    Allosteric Effectors

    See also

    References

    MOLECULAR PRINCIPLES, COMPONENTS, TECHNOLOGY, AND CONCEPTS: MEMBRANES | Cystic Fibrosis

    Abstract

    Glossary

    Introduction

    Key Highlights

    Protein

    Genetics

    See also

    References

    Further Reading

    Carbohydrates

    MOLECULAR PRINCIPLES, COMPONENTS, TECHNOLOGY, AND CONCEPTS: CARBOHYDRATES | Glycogen and Starch

    Abstract

    Introduction

    Structures of Glycogen and Starch

    Glycogen Metabolism

    Starch Metabolism

    Genetic Modification of Starch and Glycogen Metabolism

    References

    MOLECULAR PRINCIPLES, COMPONENTS, TECHNOLOGY, AND CONCEPTS: CARBOHYDRATES | Proteoglycans

    Abstract

    Introduction

    Structure and Synthesis of Proteoglycans

    Cellular Functions of Proteoglycans in Health and Disease

    References

    Further Reading

    MOLECULAR PRINCIPLES, COMPONENTS, TECHNOLOGY, AND CONCEPTS: CARBOHYDRATES | Hyaluronan

    Abstract

    Primary Sources

    Introduction

    Structure and Cellular Metabolism

    Conclusions

    References

    Relevant Websites

    Metabolism

    MOLECULAR PRINCIPLES, COMPONENTS, TECHNOLOGY, AND CONCEPTS: METABOLISM | Metabolic Regulation

    Abstract

    Glossary

    Introduction

    Mechanisms for Regulation of Key Enzymes

    Substrates (Fuel) Availability

    Allosteric Modulation

    Covalent Modification (or Posttranslational Modification)

    Inhibitory Protein (Regulatory Protein) Interaction

    Transcriptional and Degradational Control

    Metabolism in the Fed State

    Metabolism in the Fasted (Starvation) State

    Dedication

    See also

    References

    Further Reading

    MOLECULAR PRINCIPLES, COMPONENTS, TECHNOLOGY, AND CONCEPTS: METABOLISM | A Structure Perspective on Organelle Bioenergetics

    Abstract

    Glossary

    Energetics of Membrane-Based Adenosine Triphosphate Synthesis

    Atomic Structures of Membrane Protein Complexes Responsible for Energization, That Is, Generation of the Δμ˜H+, of Mitochondria and Chloroplasts

    Primary Charge Separation and Formation of a Membrane Potential; Photosynthetic Reaction Centers

    Acknowledgments

    See also

    References

    Further Reading

    Nucleic Acid Synthesis/Breakdown

    RNA Synthesis/Function

    NUCLEIC ACID SYNTHESIS/BREAKDOWN: RNA SYNTHESIS/FUNCTION | Transfer RNA

    Abstract

    Glossary

    Basis of Transfer RNA

    Aminoacyl-tRNA Synthetases

    tRNA in Translation

    Surprising Number of Roles of tRNAs beyond Translation

    tRNA-Like Molecules

    tRNA and Human Diseases

    Concluding Remarks

    Acknowledgments

    References

    Relevant Websites

    NUCLEIC ACID SYNTHESIS/BREAKDOWN: RNA SYNTHESIS/FUNCTION | Messenger RNA (mRNA): The Link between DNA and Protein

    Abstract

    Glossary

    Messenger RNA (mRNA)

    Prokaryotic mRNA Structure

    Eukaryotic mRNA

    See also

    References

    Further Reading

    NUCLEIC ACID SYNTHESIS/BREAKDOWN: RNA SYNTHESIS/FUNCTION | The Interplay between Eukaryotic mRNA Degradation and Translation

    Abstract

    Overview of Eukaryotic mRNA turnover

    mRNA Degradation is Intimately Linked to Translation

    The Ying-Yang of Translational Initiation and Transcript Stability

    Translation Elongation and mRNA Turnover

    Translation Termination and mRNA Stability

    Where Does Eukaryotic mRNA Degradation Occur Within the Cell?

    The mRNA Cycle Hypothesis – From Polysome to p-Bodies (and Perhaps Back)

    Parting on Polysomes

    What Does It All Mean?

    Perspectives

    References

    NUCLEIC ACID SYNTHESIS/BREAKDOWN: RNA SYNTHESIS/FUNCTION | miRNAs/Small Noncoding RNAs

    Abstract

    Glossary

    Introduction

    Biogenesis of miRNAs in Animals

    miRNAs in Plants

    Mutations in the miRNA and the Pathway Genes Cause Human Diseases

    Nomenclature of miRNA

    See also

    References

    Further Reading

    Relevant Website

    NUCLEIC ACID SYNTHESIS/BREAKDOWN: RNA SYNTHESIS/FUNCTION | Small RNAs/Cancer

    Abstract

    Glossary

    Introduction to Noncoding RNAs

    Introduction to miRNAs: Discovery, Biogenesis, and Nomenclature

    miRNAs and Cancer

    IsomiRs

    Other Forms of Noncoding RNAs and their Relevance to Cancer

    Summary

    See also

    References

    Relevant Websites

    NUCLEIC ACID SYNTHESIS/BREAKDOWN: RNA SYNTHESIS/FUNCTION | Riboswitches and Ribozymes

    Abstract

    Glossary

    Evolutionary Importance of RNA

    Catalytic RNAs: Ribozymes

    In Vitro Selection of Aptamers and Ribozymes

    From Aptamers to Riboswitches

    Control of Gene Expression by Riboswitches

    Ribozymes are Ubiquitous in Nature

    Ribozymes in the Replication of Viroids and Virusoids

    Ribozymes as Mobile Genetic Elements

    The Ribosome as a Ribozyme and Riboswitch

    The glmS Ribozyme–Riboswitch

    Ribozymes and Riboswitches as Cell Biological Tools

    Acknowledgment

    See also

    References

    NUCLEIC ACID SYNTHESIS/BREAKDOWN: RNA SYNTHESIS/FUNCTION | Ribosomal RNAs and Protein Synthesis

    Abstract

    Glossary

    Introduction

    Overview of Protein Synthesis

    Functional Role of 16S and 23S rRNAs During Initiation

    Functional Role of 16S and 23S RNAs During the Elongation Cycle

    Functional Role of 16S and 23S RNAs During Termination

    Functional Role of 16S and 23S RNAs During Recycling

    Functional Role of 5S rRNA

    Acknowledgments

    See also

    References

    NUCLEIC ACID SYNTHESIS/BREAKDOWN: RNA SYNTHESIS/FUNCTION | Comparison of Bacterial and Eukaryotic Replisome Components

    Abstract

    Glossary

    Introduction

    Bacterial Replicative DNA Polymerases Are Distinct from Those of Eukaryotes

    Sliding Clamps Are Conserved in All Cell Types

    The Clamp Loader Was Also Present in LUCA

    Bacterial and Eukaryotic Replicative Helicases

    Primases Are Very Different in Bacteria Compared to Eukaryotes

    Single-Strand DNA-Binding Protein

    Comparison of Bacterial and Eukaryotic Replisomes

    What Is Needed for the Future?

    Acknowledgment

    See also

    References

    DNA Synthesis/Repair

    NUCLEIC ACID SYNTHESIS/BREAKDOWN: DNA SYNTHESIS/REPAIR | Telomeres and Telomerase

    Abstract

    Glossary

    Telomeres

    The End-Replication Problem

    Telomeric DNA

    Telomeric Proteins

    Telomeric Repeat-Containing RNA

    Telomerase

    Telomerase Reverse Transcriptase

    Telomerase RNA

    Syndromes of Short Telomeres

    Alternative Lengthening of Telomeres

    See also

    References

    Further Reading

    NUCLEIC ACID SYNTHESIS/BREAKDOWN: DNA SYNTHESIS/REPAIR | Telomere Biology

    Abstract

    Glossary

    Introduction

    Telomere Structure and Proteins

    Telomere Replication and Length Maintenance

    Telomere Physiology

    See also

    References

    NUCLEIC ACID SYNTHESIS/BREAKDOWN: DNA SYNTHESIS/REPAIR | Eukaryotic Nucleotide Excision Repair

    Abstract

    Glossary

    Perspective

    Damage Recognition

    Damage Verification

    Assembly of the Incision Complex

    Excision, Repair Synthesis, and Ligation

    Human Diseases

    Acknowledgments

    See also

    References

    Relevant Website

    NUCLEIC ACID SYNTHESIS/BREAKDOWN: DNA SYNTHESIS/REPAIR | The Base Excision Repair Pathway

    Abstract

    Glossary

    Maintenance of Genome Stability and the Role of Base Excision Repair

    Basic Overview of the BER Pathway

    DNA Base Damage Recognition and Removal by DNA Glycosylases

    Abasic Site Incision and Processing of DNA Strand Break Ends

    Insertion of the Correct Undamaged Nucleotide

    DNA Nick Ligation

    The Long-Patch BER Pathway

    The Importance of Key BER Proteins is Highlighted by Knockout Mouse Models

    Regulation of BER Protein Levels

    Conclusions

    See also

    References

    Further Reading

    NUCLEIC ACID SYNTHESIS/BREAKDOWN: DNA SYNTHESIS/REPAIR | Nonhomologous DNA End Joining

    Abstract

    Introduction

    Mechanism of NHEJ

    A-NHEJ

    Choice of DSB Repair Pathway

    NHEJ and Disease

    NHEJ and Inhibitors

    Acknowledgments

    See also

    References

    NUCLEIC ACID SYNTHESIS/BREAKDOWN: DNA SYNTHESIS/REPAIR | DNA Repair by Homologous Recombination

    Abstract

    Glossary

    Introduction

    The Core Mechanism of Homologous Recombination

    Recombination and Double-Strand Break Repair

    Recombination and DNA Replication

    Recombination and Interstrand Cross-Link Repair

    Pathway Regulation and Crossover Control

    HR and Human Disease

    Conclusions

    Acknowledgments

    See also

    References

    Further Reading

    Transcription

    NUCLEIC ACID SYNTHESIS/BREAKDOWN: TRANSCRIPTION | Prokaryotic Transcription

    Abstract

    Glossary

    Introduction

    Core RNA Polymerase

    Bacterial RNA Polymerase Holoenzyme

    The Process of Transcription in Bacteria

    Mechanisms that Regulate Bacterial Transcription

    Transcription and Regulation in Archaea

    Summary

    Acknowledgments

    References

    Further Reading

    NUCLEIC ACID SYNTHESIS/BREAKDOWN: TRANSCRIPTION | Eukaryotic Transcriptional Regulation

    Abstract

    Introduction

    RNA Polymerases I, II, and III

    Promoters and Transcription Factors

    Transcription Initiation and Elongation

    Experimental Approaches

    See also

    References

    NUCLEIC ACID SYNTHESIS/BREAKDOWN: TRANSCRIPTION | Distant Activation of Transcription by Enhancers

    Abstract

    Glossary

    Introduction

    Bacterial Enhancer Action

    Enhancer Action in Eukaryotes

    Conclusions

    Acknowledgment

    See also

    References

    Relevant Websites

    NUCLEIC ACID SYNTHESIS/BREAKDOWN: TRANSCRIPTION | The Spliceosome and Pre-mRNA Splicing

    Abstract

    Glossary

    Introduction

    The Chemistry of Splicing and the Architecture of the Intron

    The Spliceosome is Composed of snRNAs and Proteins

    Spliceosomes are Assembled from snRNPs on Introns

    The Active Site of the Spliceosome

    DExD/H Box Proteins are Essential Cofactors of the Spliceosome

    Alternative Splicing Creates Multiple Products from a Single Gene

    Splicing is Coupled to Other Cellular Processes

    Defects in Splicing Cause Disease

    Conclusion

    See also

    References

    Further Reading

    NUCLEIC ACID SYNTHESIS/BREAKDOWN: TRANSCRIPTION | Pre-mRNA Splicing: Function and Dysfunction

    Abstract

    Introduction

    Splicing

    Alternative Splicing

    Diseases of the Spliceosome: Dysfunction Sheds Light on Function

    Summary

    Acknowledgments

    See also

    References

    Nucleic Acid Technology

    NUCLEIC ACID SYNTHESIS/BREAKDOWN: NUCLEIC ACID TECHNOLOGY | Transgenesis and Gene Replacement

    Abstract

    Introduction

    Transgenesis

    Temporal Regulation of Transgenes

    Loss of Function

    Gene Trap

    Homologous Recombination

    Precision Genome Editing

    Conclusion

    References

    NUCLEIC ACID SYNTHESIS/BREAKDOWN: NUCLEIC ACID TECHNOLOGY | Viral Nucleic Acids

    Abstract

    Glossary

    Introduction

    Group I: dsDNA Viruses

    Group II: ssDNA Viruses

    Group III: dsRNA Viruses

    Group IV: (+) Strand RNA Viruses

    Group V: (–) Strand RNA Viruses

    Group VI: (+) Strand RNA Viruses with DNA Intermediates

    Group VII: dsDNA Viruses with RNA Intermediates

    Gene Expression Strategies of RNA Viruses

    Concluding Remarks

    Note on Sources

    See also

    References

    Relevant Website

    Protein Synthesis/Degradation

    Translation

    PROTEIN SYNTHESIS/DEGRADATION: TRANSLATION | Components, Initiation, Elongation, Termination, and Regulation

    Abstract

    Glossary

    Components of Protein Synthesis

    Eukaryotic Translation Factors

    The Elongation Cycle

    Termination of Translation and Ribosome Recycling

    Molecular Mimicry

    Mistakes in Translation

    See also

    References

    PROTEIN SYNTHESIS/DEGRADATION: TRANSLATION | Biogenesis of Secretory Proteins

    Abstract

    Glossary

    Nascent Polypeptides Are Specifically Recognized and Delivered to the ER Membrane in a Co- or Posttranslational Manner

    Conducting Channels Made of Integrated Membrane Proteins Translocate Nascent Polypeptides across the ER Membrane

    The Nascent Polypeptides Form Their Native Structures in the ER Lumen with the Help of Multiple Factors

    A Comprehensive Quality Control System in the ER Lumen Ensures that Only Correctly Folded/Assembled Proteins Are Transported with the Misfolded/Misassembled Ones to be Degraded

    The Malfunctioning of Protein Folding in ER Are Known to Cause Folding Diseases

    See also

    References

    PROTEIN SYNTHESIS/DEGRADATION: TRANSLATION | The Protein Biosynthetic Machinery of Mitochondria

    Abstract

    General Background

    Information Content of Mitochondrial DNA

    Components of the Translational System

    Mechanism of Mitochondrial Protein Biosynthesis

    Future Directions

    See also

    References

    Further Reading

    PROTEIN SYNTHESIS/DEGRADATION: TRANSLATION | Regulated Proteolysis of Signaling Molecules: The Proprotein Convertases

    Abstract

    Glossary

    Introduction to Regulated Proteolysis

    The Proprotein Convertases

    Furin (PCSK3)

    Prohormone Convertase 1/3 (PCSK1)

    Prohormone Convertase 2 (PCSK2)

    Proprotein Convertase 4 (PCSK4)

    Paired Basic Amino Acid Cleaving Enzyme 4 (PACE4; PCSK6)

    Proprotein Convertase 5/6 (PCSK5)

    Proprotein Convertase 7 (PCSK7)

    Summary and Conclusions

    See also

    References

    Protein Degradation – General

    PROTEIN SYNTHESIS/DEGRADATION: PROTEIN DEGRADATION – GENERAL | Mass Spectrometry-based Methodologies for Studying Proteolytic Networks and the Degradome

    Abstract

    Glossary

    Introduction

    Degradomics

    Validation of Degradomic Data

    Conclusions

    See also

    References

    Relevant Website

    Protein Degradation – Intracellular

    PROTEIN SYNTHESIS/DEGRADATION: PROTEIN DEGRADATION – INTRACELLULAR | Ubiquitin, Ubiquitin-Like Proteins, and Proteasome-Mediated Degradation

    Abstract

    General Background

    Ubiquitin and Ubiquitin-like Proteins

    The 26S Proteasome

    The UPS as Drug Target

    Conclusion

    See also

    References

    Further Reading

    PROTEIN SYNTHESIS/DEGRADATION: PROTEIN DEGRADATION – INTRACELLULAR | Endoplasmic Reticulum-Associated Degradation and Protein Quality Control

    Abstract

    Glossary

    Introduction

    The Manufacturing of a Secretory Protein

    Unforgivable Errors: The ERADication of an Unfolded Protein

    Acknowledgments

    See also

    References

    PROTEIN SYNTHESIS/DEGRADATION: PROTEIN DEGRADATION – INTRACELLULAR | Role of Lysosomes in Intracellular Degradation

    Abstract

    Glossary

    Introduction

    Lysosomal Proteins

    Cathepsins

    Lipases

    Glycosidases

    Pathways to the Lysosome

    See also

    References

    Protein Degradation – Protease Classes

    PROTEIN SYNTHESIS/DEGRADATION: PROTEIN DEGRADATION – PROTEASE CLASSES | Matrix Metalloproteinases

    Abstract

    Glossary

    Structure

    Substrate Profiles: Biological and Biomedical Implications

    Cellular Regulation of MMPs

    MMPs as Therapeutic Targets and Anti-Targets: The Use of Synthetic Inhibitors

    Imaging of MMPs

    MMP Activity in Drug Delivery Mechanisms

    Future Directions

    See also

    References

    Relevant Websites

    PROTEIN SYNTHESIS/DEGRADATION: PROTEIN DEGRADATION – PROTEASE CLASSES | ADAMTS Proteases: Mediators of Physiological and Pathogenic Extracellular Proteolysis

    Abstract

    Glossary

    Introduction, Defining Characteristics and Phylogeny of A Disintegrin-Like and Metalloprotease Domain with Thrombospondin Type 1 Motif Proteinases

    Domain Organization and 3-Dimensional Structure

    Biosynthesis and Regulation

    Mechanistic Basis of Genetic and Acquired Disorders Involving ADAMTS Proteases

    Functions in Mammalian Development Gleaned from Mouse Mutants

    See also

    References

    Further Reading

    PROTEIN SYNTHESIS/DEGRADATION: PROTEIN DEGRADATION – PROTEASE CLASSES | ADAMs Regulate Cell–Cell Interactions by Controlling the Function of the EGF-Receptor, TNFα and Notch

    Abstract

    Glossary

    Introduction

    ADAM17, the TNFα Convertase

    ADAM17 is Crucial for EGFR Signaling

    ADAM17-Dependent EGFR Activation Protects the Skin and Intestinal Barrier

    ADAM17/TNFα and ADAM17/EGFR Signaling are Controlled by Upstream Regulators Called iRhoms

    ADAM10, A Crucial Regulator of Notch Signaling

    Other Substrates of ADAM10 and ADAM17

    Summary

    See also

    References

    PROTEIN SYNTHESIS/DEGRADATION: PROTEIN DEGRADATION – PROTEASE CLASSES | Extracellular: Plasma Membrane Proteases – Serine Proteases

    Abstract

    Introduction

    Membrane-Anchored Serine Proteases

    The GPI-Anchored Serine Proteases

    The Type I Transmembrane Serine Proteases

    The Type II Transmembrane Serine Proteases

    Conclusion

    See also

    References

    PROTEIN SYNTHESIS/DEGRADATION: PROTEIN DEGRADATION – PROTEASE CLASSES | Aspartic Proteases of Alzheimer’s Disease: β- and γ-Secretases

    Abstract

    Glossary

    Amyloid and Alzheimer’s Disease

    β-Secretase

    γ-Secretase

    See also

    References

    Further Reading

    PROTEIN SYNTHESIS/DEGRADATION: PROTEIN DEGRADATION – PROTEASE CLASSES | The Calpain Proteolytic System

    Abstract

    Introduction

    Structure of Conventional Calpains

    Classification of Calpains

    Regulation and Activation of Calpains

    Calpains in Apoptosis

    Physiological Functions of Calpains and the Role of Dysregulation in Human Disease

    Conclusion

    See also

    References

    PROTEIN SYNTHESIS/DEGRADATION: PROTEIN DEGRADATION – PROTEASE CLASSES | Cathepsin E: An Aspartic Protease with Diverse Functions and Biomedical Implications

    Abstract

    Aspartic Peptidases

    Cathepsin E

    Conclusion Remarks

    Acknowledgments

    See also

    References

    Relevant Website

    PROTEIN SYNTHESIS/DEGRADATION: PROTEIN DEGRADATION – PROTEASE CLASSES | Metalloproteases Meprin α and Meprin β in Health and Disease

    Abstract

    Introduction

    Structural Features of Meprin α and Meprin β

    Inhibition of Meprin Metalloproteases

    Cleavage Specificity and Identification of Substrates by Proteomics

    Physiologic and Pathologic Role of Meprin α and Meprin β

    Conclusion

    See also

    References

    PROTEIN SYNTHESIS/DEGRADATION: PROTEIN DEGRADATION – PROTEASE CLASSES | Kallikrein

    Abstract

    Glossary

    Introduction

    Plasma KLK

    Tissue KLK

    Kinins

    Kallikrein-Related Peptidases

    KLK–Cell Interactions

    KLK and Cancer

    See also

    References

    Further Reading

    PROTEIN SYNTHESIS/DEGRADATION: PROTEIN DEGRADATION – PROTEASE CLASSES | Naturally-Occurring Polypeptide Inhibitors: Cystatins/Stefins, Inhibitors of Apoptosis (IAPs), Serpins, and Tissue Inhibitors of Metalloproteinases (TIMPs)

    Abstract

    Glossary

    General Introduction

    Cystatins/Stefins

    Inhibitors of Apoptosis

    Serpins

    Tissue Inhibitors of Metalloproteinases

    See also

    References

    Relevant Website

    Proteolytic Pathways

    PROTEIN SYNTHESIS/DEGRADATION: PROTEOLYTIC PATHWAYS | Overview of Blood Coagulation and the Pathophysiology of Blood Coagulation Disorders

    Abstract

    Overview of Blood Coagulation

    Primary Hemostasis

    Secondary Hemostasis

    Regulation of Blood Coagulation

    Coagulation Disorders Overview

    Conclusions

    See also

    References

    PROTEIN SYNTHESIS/DEGRADATION: PROTEOLYTIC PATHWAYS | Molecular Mechanisms Underlying the Actions of the Complement System

    Abstract

    The Complement System

    Classical Pathway

    Lectin Pathway

    The Alternative Pathway

    Regulation of Complement Activation by Proteases and Binding Factors

    See also

    References

    Relevant Websites

    PROTEIN SYNTHESIS/DEGRADATION: PROTEOLYTIC PATHWAYS | Digestive Proteases: Roles in the Human Alimentary Tract

    Abstract

    Glossary

    Introduction

    Role of the Oral Cavity in Proteolysis

    Role of the Stomach in Proteolysis

    Role of the Small Intestine in Proteolysis

    Role of the Large Intestine in Proteolysis

    Summary

    References

    Relevant Websites

    Protein Degradation – Pathological Aspects

    PROTEIN SYNTHESIS/DEGRADATION: PROTEIN DEGRADATION – PATHOLOGICAL ASPECTS | Inhibitors of HIV Protease

    Abstract

    Glossary

    Introduction

    Structure and Enzymatic Mechanism of HIV Protease

    Inhibitors of Retroviral Proteases

    First generation of HIV-1 PR Inhibitors Approved as AIDS Drugs

    Emergence of Resistance to Clinical Inhibitors of HIV-1 PR

    Roads Not Taken – Inhibitors of HIV-1 PR That Did Not Become Drugs

    Where Will the HIV-1 PR Inhibitors Be in the Future?

    See also

    References

    Relavant Website

    PROTEIN SYNTHESIS/DEGRADATION: PROTEIN DEGRADATION – PATHOLOGICAL ASPECTS | Blood Pressure, Proteases and Inhibitors

    Abstract

    Glossary

    Introduction

    Proteolytic Regulation of Blood Pressure

    The Natriuretic Peptide Family and Their Proteases (Corin, Furin, and NEP)

    The Endothelin Peptide Family and Their Proteases

    Summary

    References

    Further Reading

    PROTEIN SYNTHESIS/DEGRADATION: PROTEIN DEGRADATION – PATHOLOGICAL ASPECTS | Cancer – Proteases in the Progression and Metastasis

    Abstract

    Introduction

    Aspartic Proteases

    Cysteine Proteases

    Metalloproteases

    Serine Proteases

    Threonine Proteases

    Concluding Remarks

    See also

    References

    Further Reading

    PROTEIN SYNTHESIS/DEGRADATION: PROTEIN DEGRADATION – PATHOLOGICAL ASPECTS | Lysosomal Diseases

    Abstract

    Introduction

    Lysosomal Diseases

    Nomenclature

    Other Lysosomal Diseases

    Related Conditions Affecting Organelle Biogenesis

    Functional Complementation of Lysosomal Diseases

    Treatment of Lysosomal Diseases

    Therapeutic Stratagems for Lysosomal Diseases with Neurological Manifestations

    Advances in the Field

    Pathogenesis and Physiological Understanding

    Conclusion

    Acknowledgments

    References

    PROTEIN SYNTHESIS/DEGRADATION: PROTEIN DEGRADATION – PATHOLOGICAL ASPECTS | Alpha-1-Antitrypsin Deficiency: A Misfolded Secretory Glycoprotein Damages the Liver by Proteotoxicity and Its Reduced Secretion Predisposes to Emphysematous Lung Disease Because of Protease-Inhibitor Imbalance

    Abstract

    Glossary

    Introduction

    Physiology and Function of AT

    Mechanism of Deficiency in the Classical form of ATD

    Cellular Mechanisms of Liver Disease

    Cellular Mechanisms of Lung Disease

    Cellular Responses to Misfolding of Mutant ATZ

    Therapies for ATD Liver Disease

    Therapies for ATD Lung Disease

    See also

    References

    Organizational Cell Biology

    Organizational Cell Biology: An Overview

    Imaging the Cell

    Organelles

    Interorganellar Communication

    Cytoskeleton and Motors

    Intracellular Infectiology

    Reference

    Imaging the Cell

    Electron Microscopy

    IMAGING THE CELL: ELECTRON MICROSCOPY | Single-Particle CryoEM of Macromolecular Complexes

    Abstract

    Introduction

    CryoEM Sample Consideration

    Frozen, Hydrated Specimen Preparation

    CryoEM Image Acquisition

    CryoEM Image Processing

    Resolution of CryoEM Density Maps

    CryoEM Model Building and Model Validation

    High-Resolution CryoEM Structures

    Identifying Different Populations Within a Heterogeneous Sample

    Delineating the Conformational Changes of a Molecular Machine

    Conclusion

    Acknowledgments

    See also

    References

    Relevant Website

    IMAGING THE CELL: ELECTRON MICROSCOPY | Scanning Electron Microscopy in Cell Biology

    Abstract

    Introduction

    Scanning Electron Microscopy ‘Versus’ Transmission Electron Microscopy

    Construction of the SEM

    Scanning the Specimen

    Beam – Specimen Interactions

    Image Formation

    A Brief History of SEM

    Specimen Preparation for SEM

    Critical Point Drying

    Sputter Coating

    Labeling for SEM

    Cryoscanning EM

    Environmental SEM

    Serial Block Face Imaging

    Merging SEM and TEM

    Freeze Etching

    SEM and the Nuclear Envelope

    SEM in Cell Biology

    See also

    References

    Further Reading

    IMAGING THE CELL: ELECTRON MICROSCOPY | Electron Tomography

    Abstract

    Glossary

    Introduction

    Specimen Preparation Methods

    Methods of Cryo-ET

    Techniques to Combine with Cryo-ET

    Examples

    Future Outlook

    Supplementary Video

    See also

    References

    Further Reading

    IMAGING THE CELL: ELECTRON MICROSCOPY | Immunoelectron Microscopy: High-Resolution Immunocytochemistry

    Abstract

    Glossary

    Introduction

    Sample Preparation Strategies

    Immunolabeling Strategies

    CLEM

    Immunogold Label Quantification and Labeling Specificity

    Conclusions

    See also

    References

    Further Reading

    IMAGING THE IMAGING THE CELL: ELECTRON MICROSCOPY | Imaging Cellular Architecture with 3D SEM

    Abstract

    Introduction

    Sample Preparation for 3D SEM

    Orientation and Location of Region of Interest

    3D SEM Techniques

    Data Handling and Segmentation

    New Methods and Future Developments

    Acknowledgments

    See also

    References

    Light Microscopy

    IMAGING THE CELL: LIGHT MICROSCOPY | Genetically Encoded Fluorescent Probes and Live Cell Imaging

    Abstract

    Introduction – Fluorescent Proteins

    Fluorescent Proteins as Probes for Function

    Imaging Cells in Whole Organisms

    Breaking the Diffraction Barrier

    Technical Considerations for Live Imaging

    Looking Forward

    See also

    References

    IMAGING THE CELL: LIGHT MICROSCOPY | Total Internal Reflection Fluorescence Microscopy

    Abstract

    Introduction

    Theoretical Basis

    Applications and Combinations in Cell Biology

    Optical Configurations and Setup

    Additional Features

    TIRF versus Other Optical Sectioning Microscopies

    See also

    References

    IMAGING THE CELL: LIGHT MICROSCOPY | Super Resolution Fluorescence Localization Microscopy

    Abstract

    Glossary

    Introduction

    Concept

    Experimental Methods

    Data Analysis

    Discussion

    Acknowledgments

    See also

    References

    IMAGING THE CELL: LIGHT MICROSCOPY | Super-Resolution Light Microscopy: Stimulated Emission Depletion and Ground-State Depletion

    Abstract

    Introduction

    STED and GSD for Super-Resolution: Principle and Technology

    Biological Applications of STED and GSDIM

    Conclusion

    Acknowledgment

    See also

    References

    Relevant Websites

    IMAGING THE CELL: LIGHT MICROSCOPY | Structured Illumination Microscopy

    Abstract

    Introduction

    Principles of SIM

    Microscope Hardware, Software, and Data Acquisition

    Imaging Artifacts: Causes and Manifestations

    Applications

    Recent Developments

    References

    Relevant Website

    IMAGING THE CELL: LIGHT MICROSCOPY | Fluorescence Correlation Spectroscopy: A Tool for Measuring Dynamic and Equilibrium Properties of Molecules in Cells

    Abstract

    Glossary

    Introduction

    Basic Concepts and Theory

    Experimental Considerations

    Measurement of Molecular Association and Aggregation

    Summary

    Appendix

    Acknowledgments

    See also

    References

    IMAGING THE CELL: LIGHT MICROSCOPY | Fluorescence Lifetime Imaging – Applications and Instrumental Principles

    Abstract

    Glossary

    Fluorescence

    FLIM Applications in Life Sciences

    Clinical FLIM Applications

    Technical Aspects of FLIM

    Latest Developments

    See also

    References

    IMAGING THE CELL: LIGHT MICROSCOPY | High-Speed Localization Microscopy and Single-Particle Tracking

    Abstract

    Introduction

    The Localization Concept

    Experimental Requirements

    High-Speed LM

    SPT

    Future Trends/Avenues

    Conclusion

    See also

    References

    IMAGING THE CELL: LIGHT MICROSCOPY | Intravital Microscopy in Mammalian Organisms: From Tissue Physiology to Cell Biology

    Abstract

    Brief Historical Background on Intravital Microscopy

    Imaging Techniques Used to Perform IVM

    Current Applications of IVM

    Concluding Remarks

    Acknowledgments

    References

    IMAGING THE CELL: LIGHT MICROSCOPY | Optogenetics

    Abstract

    Glossary

    Light As a Tool in Biology

    Optogenetics – Manipulating Molecules, Cells, and Organisms with Light

    Light-Sensitive Proteins to Control Cellular Excitability

    Optochemical Approaches to Control Specific Receptors and Ion Channels

    Summary – From Molecules to Systems

    Acknowledgments

    See also

    References

    Further Reading

    Organelles

    Structure and Function

    ORGANELLES: STRUCTURE AND FUNCTION | The Endoplasmic Reticulum

    Abstract

    Introduction

    Origin and Function of the ER

    Morphology of the ER

    Membrane Contact Sites of the ER with Other Organelles

    Translocation and Membrane Embedding of ER Client Proteins

    Posttranslational Modifications of ER Client Proteins

    Protein Folding in the ER

    Export from and Retrieval to the ER

    ER Homeostasis

    Perspectives

    Acknowledgments

    See also

    References

    Further Reading

    ORGANELLES: STRUCTURE AND FUNCTION | Intermediate Compartment: A Sorting Station between the Endoplasmic Reticulum and the Golgi Apparatus

    Abstract

    Glossary

    Introduction

    Historical Perspective

    Compositional Aspects

    Structure, Distribution, and Dynamics

    Different IC Models

    Functional Aspects

    Links to Disease

    See also

    References

    Further Reading

    ORGANELLES: STRUCTURE AND FUNCTION | Golgi and TGN

    Abstract

    The Golgi Apparatus – An Introduction

    The Structure of the Golgi Apparatus

    Transport through the Golgi

    Molecular Mechanism of Transport

    Glycosylation at the Golgi

    Regulation of the Golgi Apparatus Structure and Function

    Role of Golgi in Disease

    Evolution of the Golgi Apparatus

    Perspectives

    See also

    References

    ORGANELLES: STRUCTURE AND FUNCTION | Early Endosomal Compartments

    Abstract

    Endosomes

    Endosome Heterogeneity Reflects Functional Compartmentalization

    Epithelial Cells Have Spatially Separated, Connected Endosomal Circuits

    (Ultra)structure and Specialization

    Regulation of Endosome Traffic

    Early Endosome Maturation and Conversion to Late Endosomes

    Retrieval of Proteins from Endosomes to the Trans Golgi Network

    Recycling from Early Endosomes to the Plasma Membrane

    Conclusion and Perspectives

    See also

    References

    ORGANELLES: STRUCTURE AND FUNCTION | The Late Endosome

    Abstract

    Introduction

    The Early/Recycling Endosome Network

    Biogenesis of the Multivesicular Body

    The Late Endosome–Lysosome Network

    Endosomes in Plants and Fungi

    Lysosome Enzymes and Lysosomal Membrane Proteins

    Composition and Fate of Intralumenal Membranes

    Other Destinations: All Roads Do Not Lead to the Lysosomes

    The Late Endosome: A Signaling Platform

    See also

    References

    Further Reading

    ORGANELLES: STRUCTURE AND FUNCTION | Signaling from Endosomes

    Abstract

    Endocytosis

    Different Cell Types Employ Signaling Endosomes for Distinct Purposes

    Endocytic Routes Specify Signaling Outcome

    Endocytosis Regulates Signal Termination and Cellular Response to Ligand Gradient

    Endosomes – A World of Their Own

    Endocytosis Regulates Spatial Signaling and Signal Amplification

    Signaling Regulates Endocytosis

    Endocytosis and Implications in Cancer

    Conclusions and Future Perspectives

    See also

    References

    ORGANELLES: STRUCTURE AND FUNCTION | Conventional and Secretory Lysosomes

    Abstract

    Introduction

    Conventional Lysosomes

    Cell Type-Specific Secretory Lysosomes

    Biogenesis of Lysosomes and Secretory Lysosomes

    Exocytosis of Secretory Lysosomes

    Genetic Diseases Associate with Defects in Conventional or Secretory Lysosomes

    Conclusions

    See also

    References

    Further Reading

    ORGANELLES: STRUCTURE AND FUNCTION | Lysosome-Related Organelles

    Abstract

    Glossary

    Morphology, Composition, and Function of Lysosome-Related Organelles

    Biogenesis and Transport of LROs

    Genetic Diseases Associated with Defects in LRO Biogenesis and Transport

    Multi-Media Annexes

    See also

    References

    Relevant Websites

    ORGANELLES: STRUCTURE AND FUNCTION | At the Center of Autophagy: Autophagosomes

    Abstract

    Glossary

    Macroautophagy and Autophagosomes

    Acknowledgments

    See also

    References

    Further Reading

    ORGANELLES: STRUCTURE AND FUNCTION | Peroxisomes

    Abstract

    Introduction and Morphology

    Some Important, Specialized Physiological Functions of Peroxisomes

    Conserved Biochemical Pathways Present in Most Peroxisomes

    Other Peroxisome Functions

    Metabolic Cooperation and Interaction with Other Organelles

    Peroxisome Abundance, Adaptability, and Regulation

    Peroxisome Division, Transport, and Inheritance

    Peroxisome Biogenesis

    Remodeling, Random Turnover, and Selective Degradation

    Evolution

    Human Disease and Peroxisomes

    Conclusion

    See also

    References

    ORGANELLES: STRUCTURE AND FUNCTION | Lipid Droplets

    Abstract

    Glossary

    Basic Structure

    LD Proteins

    Adipocyte LDs

    LD Subpopulations

    Biogenesis of LDs

    Neutral Lipid Synthesis and Lipolysis

    Droplet Dynamics

    Lipid Droplets and Disease

    See also

    References

    Further Reading

    ORGANELLES: STRUCTURE AND FUNCTION | Mechanisms and Functions of Mitochondrial Dynamics

    Abstract

    Glossary

    Introduction

    Mitochondrial Fusion Machinery and Regulation

    Molecular Insights into Drp1 Actions During Mitochondrial Fission

    Physiologic Importance of Mitochondrial Dynamics

    Perspective

    Acknowledgments

    See also

    References

    ORGANELLES: STRUCTURE AND FUNCTION | Synaptosomes and Synaptic Vesicles

    Abstract

    Introduction

    Synaptosomes

    SVs

    See also

    References

    Further Reading

    Organelles: Structure and Function | Extracellular Vesicles

    Abstract

    Extracellular Vesicles

    The Physiological Role of EVs: From Waste Bin to Versatile Transporter of Biological Signals

    EVs in Cross-Kingdom Communication

    EV Biogenesis

    EVs in Disease

    Clinical Applications of EVs

    Concluding Remarks

    See also

    References

    Further Reading

    ORGANELLES: STRUCTURE AND FUNCTION | Nuclear Organization (Nuclear Structure and Dynamics)

    Abstract

    Introduction

    Nuclear Structure and Function

    Conclusion

    See also

    References

    ORGANELLES: STRUCTURE AND FUNCTION | Nuclear Pores

    Abstract

    Structure of the Nuclear Pore Complex

    Nucleoporins (Nups)

    Dynamic Behavior of Nuceloporin

    Nucleocytoplasmic Transport

    Nucleoporin and Diesease

    See also

    References

    ORGANELLES: STRUCTURE AND FUNCTION | Plastids: The Anabolic Factories of Plant Cells

    Abstract

    Introduction

    Plastids of the Viridiplantae

    References

    Further Reading

    Interorganellar Communication

    Interplay and Processes

    INTERORGANELLAR COMMUNICATION: INTERPLAY AND PROCESSES | ER–Golgi Transport

    Abstract

    The COPII Coat

    Cargo Capture during Vesicle Formation

    Regulation of COPII Biogenesis: The GTPase Cycle

    Cellular Regulation of COPII Vesicle Biogenesis

    Regulation of Vesicle Size

    Vesicle Tethering

    Vesicle Fusion

    Conclusions

    See also

    References

    INTERORGANELLAR COMMUNICATION: INTERPLAY AND PROCESSES | N-Linked Glycans (N-Glycans)

    Abstract

    Glossary

    Introduction

    Initiation of an N-Glycan on Dolichol-Phosphate

    Maturation of the Dol-P-P-Oligosaccharide

    En-Bloc Transfer of an N-Glycan to Protein

    Processing and Folding of Glycoproteins in the ER

    Unique Modification of Lysosomal Hydrolases

    Maturation of N-Glycans During Transit Through Golgi Compartments

    Functions of N-Glycans

    Summary

    See also

    References

    Further Reading

    INTERORGANELLAR COMMUNICATION: INTERPLAY AND PROCESSES | Extracellular O-Glycans

    Abstract

    Glossary

    Introduction

    Mucin-Type O-Glycans/O-GalNAc Glycans

    O-Mannose Glycans

    O-Fuc Glycans

    O-Glc Glycans

    O-GlcNAc Glycans

    O-Gal Glycans

    Proteoglycans/O-Xyl Glycans

    Conclusions

    See also

    References

    Further Reading

    INTERORGANELLAR COMMUNICATION: INTERPLAY AND PROCESSES | Intra-Golgi Transport

    Abstract

    Glossary

    Introduction

    Conclusions/perspectives

    Acknowledgment

    See also

    References

    INTERORGANELLAR COMMUNICATION: INTERPLAY AND PROCESSES | Post-Golgi Transport – Cargo, Carriers, and Pathways

    Abstract

    Introduction

    Overview of Pathways

    Cargo Sorting and Packaging at the TGN

    Concluding Remarks

    Acknowledgments

    See also

    References

    INTERORGANELLAR COMMUNICATION: INTERPLAY AND PROCESSES | Regulation of the Secretory Pathway

    Abstract

    Constitutive and Regulated Secretion

    The Regulation of Constitutive Secretion

    Extent of the Regulation Network of the Secretory Pathway

    Traffic Regulation in Response to Environmental Signals and Demands

    Signaling Pathways that Support Homeostasis and Coordination of the Secretory Apparatus with Other Cellular Modules

    The Conceptual Framework

    Summary and Conclusions

    See also

    References

    INTERORGANELLAR COMMUNICATION: INTERPLAY AND PROCESSES | Regulated versus Constitutive Secretion – A Major Form of Intercellular Communication

    Abstract

    Glossary

    Summary

    Overview

    How Do We Know about Regulated versus Constitutive Secretion?

    Tour of Regulated Secretion

    The Steps of Regulated Exocytosis

    Constitutive Secretion

    Conclusion

    See also

    References

    Relevant Websites

    INTERORGANELLAR COMMUNICATION: INTERPLAY AND PROCESSES | Clathrin and Clathrin-Dependent Endocytosis

    Abstract

    Introduction

    Biochemistry of Clathrin

    Cellular Function and Regulation of Clathrin

    Conclusions

    See also

    References

    Further Reading

    INTERORGANELLAR COMMUNICATION: INTERPLAY AND PROCESSES | Clathrin Independent Endocytosis

    Abstract

    Introduction

    Macropinocytosis

    Caveolae

    Clathrin- and Caveolin-Independent Micropinocytic Pathways

    Conclusions and Perspectives

    Acknowledgments

    See also

    References

    Further Reading

    INTERORGANELLAR COMMUNICATION: INTERPLAY AND PROCESSES | Rabs of the Endosomal Recycling Pathway

    Abstract

    Overview

    Rab4 and the ‘Short-Loop’ Recycling Pathway

    Rab11 and the Endosomal Recycling Compartment

    Other Rabs of the Endosomal Recycling Pathway

    Intracellular Pathogens Subvert the Function of Rab GTPases

    Summary

    Acknowledgments

    See also

    References

    INTERORGANELLAR COMMUNICATION: INTERPLAY AND PROCESSES | Endosome to Lysosome Transport

    Abstract

    Introduction

    Endocytic Vesicles and Early Endosomes

    Biogenesis of MVBs and Cargo Sorting

    Late Endosomes

    Role of pH and Ion Concentrations in Endosomal Maturation

    Perinuclear Clustering of LE and Fusion Events

    Role of Rab Proteins

    Role of Cytoskeletal Elements and of Molecular Motors

    Conclusions and Perspectives

    See also

    References

    Further Reading

    INTERORGANELLAR COMMUNICATION: INTERPLAY AND PROCESSES | Endocytosis of Cargo Proteins: LDL

    Abstract

    Glossary

    Introduction

    Low Density Lipoprotein Biosynthesis

    The LDL Receptor

    Cargo-Selective Clathrin Adaptors for the LDL Receptor

    Endosomal Dynamics

    Dynamic Modulation of LDL Receptor Surface Levels

    Concluding Remarks

    Acknowledgment

    References

    Relevant Websites

    INTERORGANELLAR COMMUNICATION: INTERPLAY AND PROCESSES | Retrograde Transport

    Abstract

    Introduction

    Different Retrograde Pathways

    Biophysical Mechanisms for Retrograde Trafficking

    Biomedical Applications of Retrograde Trafficking

    See also

    References

    INTERORGANELLAR COMMUNICATION: INTERPLAY AND PROCESSES | Rabs and Other G Proteins

    Abstract

    Introduction

    Rab Family of G Proteins and Membrane Trafficking

    Biosynthesis and Membrane Targeting of Rab Proteins

    Structure and GTPase cycle of Rab Proteins

    Effectors and Functions of Rab Proteins

    Other G Proteins

    Acknowledgement

    See also

    References

    Further Reading

    Components

    INTERORGANELLAR COMMUNICATION: COMPONENTS | Adaptor Proteins: Inter-Organelle Traffic Controllers

    Abstract

    Adaptor Proteins

    Heterotetrameric Adaptor Complexes

    GGAs

    The Epsin and Eps15 Families

    AP180 and Clathrin Assembly Lymphoid Myeloid Leukemia

    PTB Domain Containing Family (DAB, ARH, and Numb)

    Arrestin Family

    The Adaptor Protein Network

    See also

    References

    INTERORGANELLAR COMMUNICATION: COMPONENTS | SNAREs: Membrane Fusion and Beyond

    Abstract

    Introduction: A Brief Historical Perspective on Soluble N-Ethylmaleimide-Sensitive Factor Attachment Protein Receptors (SNAREs)

    SNAREs: Membrane Fusion Nanomachines

    The Regulators of the SNARE Nanomachine

    SNAREs: More than Fusogenic Proteins? The Case of the Longin v-SNAREs Sec22b and TI-VAMP/VAMP7

    Conclusion

    See also

    References

    Further Reading

    INTERORGANELLAR COMMUNICATION: COMPONENTS | ESCRTing around the Cell

    Abstract

    History

    ESCRT Machinery

    Models of ESCRT Function

    ESCRTs in the Endolysosomal System

    ESCRTs in Virus Budding

    ESCRTs in Cytokinesis

    ESCRTs in Extracellular Vesicle Biogenesis

    Non-Endosomal Roles for the ESCRT Machinery

    Summary and Perspectives

    See also

    References

    INTERORGANELLAR COMMUNICATION: COMPONENTS | The Retromer Complex

    Abstract

    Introduction

    A Brief History of Retromer

    The Assembly and Structure of Retromer

    How Membrane Tubules are Stabilized

    Recruitment of Retromer

    Recognition of Cargo

    Accessory Proteins that Modulate Retromer Function

    The Physiological Processes That Depend on Retromer

    Retromer and Disease

    Acknowledgments

    See also

    References

    INTERORGANELLAR COMMUNICATION: COMPONENTS | Vesicle Tethers

    Abstract

    Glossary

    Introduction

    Interactions with Small GTPases and SNARE Proteins

    Coiled-Coil Tethers

    Multisubunit Tethering Complexes

    Conclusions

    See also

    References

    Further Reading

    INTERORGANELLAR COMMUNICATION: COMPONENTS | BAR Domains and BAR Domain Superfamily Proteins

    Abstract

    Introduction

    See also

    References

    Interplay and Processes

    INTERORGANELLAR COMMUNICATION: INTERPLAY AND PROCESSES | Role of Phosphoinositides in Membrane Traffic

    Abstract

    Glossary

    Phosphoinositides at the Membrane–Cytosol Interface

    Organelle Compartments the Spatial Restriction of Phosphoinositide Species and Organelle Identity

    Phosphoinositides in Plasma Membrane Trafficking

    Phosphoinositides in the Endosomal Compartment – Early Endosomes, Recycling Endosomes, and Late Endosomes

    Phosphoinositides in Golgi Trafficking

    Retrograde Trafficking from Endosomes to Golgi

    Phosphoinositides in the Regulation of Autophagy

    Concluding Remarks

    See also

    References

    INTERORGANELLAR COMMUNICATION: INTERPLAY AND PROCESSES | Unconventional Protein Secretion: Fibroblast Growth Factor 2 and Interleukin-1β as Examples

    Abstract

    Mechanisms of Eukaryotic Protein Secretion

    Hallmarks of FGF2 Membrane Translocation during Unconventional Secretion

    The Molecular Mechanism of FGF2 Membrane Translocation and Its Path of Discovery

    PI(4,5)P2-Induced FGF2 Oligomerization and Membrane Pore Formation: A Transient Intermediate in FGF2 Membrane Translocation

    Understanding the Regulation of IL-1β Processing

    IL-1β Secretion and Cell Death

    Mechanisms of IL-1β Release

    Unconventional Secretion – What Is It Good for?

    Future Perspectives

    Acknowledgments

    See also

    References

    INTERORGANELLAR COMMUNICATION: INTERPLAY AND PROCESSES | Endoplasmic Reticulum Stress in Disease

    Abstract

    Glossary

    Introduction

    The Role of the UPR in Human Health and Disease

    Conclusions

    Acknowledgments

    See also

    References

    Further Reading

    Cytoskeleton and Motors

    Cytoskeletal Components

    CYTOSKELETON AND MOTORS: CYTOSKELETAL COMPONENTS | Microtubules and Microtubule-Associated Proteins (MAPs)

    Abstract

    Glossary

    Microtubule Structure

    Microtubule Dynamics

    Cellular Functions of Microtubules

    MAPs

    Regulation of Microtubule Structure and Mechanics by MAPs

    Regulation of Microtubule Dynamics by MAPs

    Arrangement of Microtubules into Higher-Order Structures by MAPs

    Microtubules in Human Disease

    See also

    References

    Relevant Websites

    CYTOSKELETON AND MOTORS: CYTOSKELETAL COMPONENTS | Actin Assembly Dynamics and Its Regulation in Motile and Morphogenetic Processes

    Abstract

    Glossary

    Introduction

    Actin: Structural and Mechanical Properties

    Actin Self-Assembly: Nucleation-Growth, Thermodynamics, Polarity, ATP Hydrolysis

    Regulation of Actin Assembly by Associated Proteins

    Site-directed Branching of Actin Filaments by WASP Protein Family and Arp2/3 Complex

    Integrated Protein Modules in Reconstituted Actin-Based Motility

    Actin Regulators in Adhesion Structures

    Actin-Based Molecular Motors: The Family of Myosins

    Actin in the Nucleus? Potential Role of Actin in the Regulation of Gene Expression

    Bacterial Actin Ancestors

    See also

    References

    Further Reading

    CYTOSKELETON AND MOTORS: CYTOSKELETAL COMPONENTS | Intermediate Filaments

    Abstract

    Glossary

    The Intermediate Filament Protein Family is Subdivided into Six Types with Cell Type-Specific Expression Patterns

    Intermediate Filament Proteins Are Reliable Markers of Cellular Differentiation

    Intermediate Filaments Share a Common Secondary Structure

    Intermediate Filaments Can Be Assigned to Three Different Assembly Groups

    Intermediate Filament Networks Have Distinct Properties That Render Them Different from the Other Cytoskeletal Systems

    Cytoplasmic Intermediate Filament Network Organization Is Determined by Interaction with Major Cellular Components through Associated Proteins

    Lamin Intermediate Filaments Contribute to Nuclear Structure and Function

    Intermediate Filament Proteins Are Posttranslationally Modified

    Intermediate Filaments Serve Many Functions

    Cytoplasmic Intermediate Filament Dysfunctions Cause Tissue-Specific Diseases

    Lamin Intermediate Filament Mutations Cause Complex Syndromes

    Highly Diverse Intermediate Filament Proteins Occur Throughout the Animal Kingdom

    See also

    References

    Further Reading

    CYTOSKELETON AND MOTORS: CYTOSKELETAL COMPONENTS | Septins: Cytoskeletal Filaments with Structural and Regulatory Functions

    Abstract

    Septin Structure, Assembly, and Dynamics

    Septins and the Membrane Skeleton

    Septins and the Actin Cytoskeleton

    Septins and the Microtubule Cytoskeleton

    Conclusions

    See also

    References

    Further Reading

    CYTOSKELETON AND MOTORS: CYTOSKELETAL COMPONENTS | Bacterial and Archaeal Cytoskeletons

    Abstract

    Introduction

    Cytokinesis

    DNA Segregation

    Cell Shape Determination

    Organization of Intracellular Membrane Compartments

    Conclusion

    See also

    References

    Further Reading

    CYTOSKELETON AND MOTORS: CYTOSKELETAL COMPONENTS | Myosins

    Abstract

    Glossary

    Introduction

    Myosin Structure and Organization

    Mechanochemical ATPase Cycle

    Pathophysiology

    Class-1 Myosins

    Class-2 Myosins

    Class-3 and -9 Myosins

    Class-5 Myosins

    Class-6 Myosins

    Class-7, -10, and -15 Myosins

    Class-8 and 11 Myosins

    Class-14 Myosins and -21 Myosins

    Class-16 and -18 Myosins

    Class-19 Myosins

    Summary and Perspectives

    Acknowledgment

    See also

    References

    Further Reading

    CYTOSKELETON AND MOTORS: CYTOSKELETAL COMPONENTS | Kinesin Superfamily Proteins (KIFs) as a Fundamental Component of Life: Intracellular Transport and Beyond

    Abstract

    Glossary

    Introduction

    Molecular Phylogeny and Nomenclature of Kinesins

    Motor–Cargo Relationship and Pathophysiological Relevance

    Regulation and Synergy of Kinesins

    Concluding Remarks

    See also

    References

    Further Reading

    CYTOSKELETON AND MOTORS: CYTOSKELETAL COMPONENTS | Dyneins

    Abstract

    Glossary

    Introduction

    Architecture of Dyneins

    Dynein Motility

    Regulation of Dynein Motility

    Functions of Cytoplasmic Dynein In Vivo

    Axonemal Dyneins: Overall Arrangement and Structure

    Function of Axonemal Dynein HCs in Cilia

    Regulatory Components

    Axonemal Dynein-Related Ciliopathies

    See also

    References

    Further Reading

    Complex Cytoskeletal Structures

    CYTOSKELETON AND MOTORS: COMPLEX CYTOSKELETAL STRUCTURES | The Mitotic Spindle

    Abstract

    Architecture and Dynamics of the Mitotic Spindle

    Different Paths of Spindle Assembly

    The Role of Motors and MAPs in Mitotic Spindle Assembly

    Mitotic Spindle Properties

    Mitotic Spindle Function

    Spindle Disassembly and Cytokinesis

    See also

    References

    Relevant Websites

    CYTOSKELETON AND MOTORS: COMPLEX CYTOSKELETAL STRUCTURES | Centrioles and the Centrosome

    Abstract

    Glossary

    Introduction

    Structure of the Centrosome

    Centriole Duplication

    Functions of the Centrosome

    The Centrosome in Development

    Centrosome in Disease

    Summary

    References

    CYTOSKELETON AND MOTORS: COMPLEX CYTOSKELETAL STRUCTURES | Cilia and Flagella

    Abstract

    Glossary

    Introduction

    Structure of Cilia and Flagella

    Ciliogenesis

    Signaling Pathways Coordinated by Cilia

    Diseases Caused by Defects in Cilia

    See also

    References

    Further Reading

    CYTOSKELETON AND MOTORS: COMPLEX CYTOSKELETAL STRUCTURES | Skeletal Muscle

    Abstract

    Sarcomeres Are the Basic Unit of Contraction

    Sarcomere Contraction Is Driven by Sliding of Myosin and Actin Filaments

    Calcium Release from the SR Activates Contraction

    Muscle Disorders Associated with Skeletal Muscle

    See also

    References

    Further Reading

    CYTOSKELETON AND MOTORS: COMPLEX CYTOSKELETAL STRUCTURES | Filopodia and Lamellipodia

    Abstract

    Glossary

    Introduction

    General Principles of Actin Polymerization-Driven Protrusion

    Filopodia

    Lamellipodia

    See also

    References

    CYTOSKELETON AND MOTORS: COMPLEX CYTOSKELETAL STRUCTURES | The Extracellular Matrix

    Abstract

    Extracellular Matrix

    Basement Membranes

    Laminins

    Collagen IV

    Nidogens

    Heparan Sulfate Proteoglycans

    Other ECM Proteins Associated with Basement Membranes

    Fibronectin

    Connective Tissue/Interstitium

    Fibrillar Collagens

    FACIT Collagens and SLRPs

    Elastic Fibers

    Matricellular Proteins

    Conclusions

    See also

    References

    Relevant Websites

    CYTOSKELETON AND MOTORS: COMPLEX CYTOSKELETAL STRUCTURES | Cell–Cell Adhesion and the Cytoskeleton

    Abstract

    Introduction

    Cell–Cell Adhesion and the Actin Cytoskeleton

    Cell–Cell Adhesion and the Intermediate Filament Cytoskeleton

    Cell–Cell Adhesion and MTs

    Concluding Comments

    See also

    References

    CYTOSKELETON AND MOTORS: COMPLEX CYTOSKELETAL STRUCTURES | Cell Adhesion to the Extracellular Matrix

    Abstract

    Glossary

    The Extracellular Matrix (ECM)

    Diversity of ECM Adhesions

    The Integrin Adhesome

    Geometric and Mechanical Sensory (Mechanosensing) Functions of ECM Adhesions

    The Cross-Talk between the Cell and the ECM

    Acknowledgments

    See also

    References

    Relevant Websites

    CYTOSKELETON AND MOTORS: COMPLEX CYTOSKELETAL STRUCTURES | Cell Migration

    Abstract

    Introduction

    Alone or in the Company of Others: Modes of Eukaryotic Cell Migration

    Building a Migrating Cell

    Migration in Development and Homeostasis

    Migration in Pathology

    Harnessing Cell Migration in Therapy

    Conclusions

    Acknowledgments

    See also

    References

    CYTOSKELETON AND MOTORS: COMPLEX CYTOSKELETAL STRUCTURES | Rho GTPases

    Abstract

    General Features

    Regulation of the GTP-Binding/GTP-Hydrolytic Cycles of Rho GTPases

    Rho GTPases and Their Roles in Regulating the Actin Cytoskeleton

    Other Targets and Multiple Roles in Biology

    Rho GTPases in Oncogenic Transformation

    Rho GTPases in Mammalian Tumors

    Rho GTPases and Cancer Cell Metabolism

    Rho GTPases and Cancer Cell Microvesicles

    Concluding Remarks

    Key Points

    See also

    References

    CYTOSKELETON AND MOTORS: COMPLEX CYTOSKELETAL STRUCTURES | Cell Polarity

    Abstract

    Glossary

    Basic Principles of Cell Polarity and Common Mechanisms of Control

    Epithelial Cells

    Apical–Basal Polarity of Epithelial Cells

    Planar Cell Polarity

    Relationship between Cell Polarity and Spindle Orientation Control

    Loss of Cell Polarity and Disease

    Conclusions

    See also

    References

    Further Reading

    Intracellular Infectiology

    Cell Processes

    INTRACELLULAR INFECTIOLOGY: CELL PROCESSES | Phagocytosis

    Abstract

    Glossary

    Introduction

    Phagocytic Receptors

    Signaling to Actin Polymerization

    Other Receptors and Signaling Pathways to Actin Polymerization

    Membrane Remodeling and Focal Exocytosis

    Linking Actin the Polymerization/Depolymerization Cycle with Vesicular Trafficking

    Maturation of Phagosomes into Phagolysosomes

    Conclusion

    See also

    References

    INTRACELLULAR INFECTIOLOGY: CELL PROCESSES | Macropinocytosis

    Abstract

    Introduction

    Functions of Macropinocytosis

    Solute Flow During Pinocytosis

    Mechanisms of Macropinosome Formation

    The Organization of Cytoplasm for Macropinosome Formation

    Experimental Diagnosis

    Dysregulation

    Therapeutics

    See also

    References

    INTRACELLULAR INFECTIOLOGY: CELL PROCESSES | Microbicidal Mechanisms

    Abstract

    Glossary

    Phagocytes and Phagocytosis

    Phagocytic Killing

    Autophagy and Xenophagy

    Cell Death Mechanisms and Host Defense

    Pathogen Subversion of Host Defense

    Summary

    See also

    References

    Further Reading

    INTRACELLULAR INFECTIOLOGY: CELL PROCESSES | Bacterial Subversion of Phagocytic Killing

    Abstract

    Introduction

    Interference of Uptake by Bacterial Pathogens

    The Replication Vacuole 1: Manipulation of the Endocytic Pathway to Support Bacterial Replication

    The Replication Vacuole 2: Manipulation of the Secretory Pathway to Support Bacterial Replication

    The Replication Vacuole 3: Multi-Organelle Interactions

    Breaking Free to Avoid Host Cell Killing

    Bypass and Exploitation of Host Autophagic Clearing of Microorganisms

    Bacterial Embrace of Autophagy

    Perspective

    See also

    References

    INTRACELLULAR INFECTIOLOGY: CELL PROCESSES | Cellular Invasion by Bacterial Pathogens

    Abstract

    Introduction

    Entry Mechanisms

    Intracellular Lifestyle and Manipulation of Host Intracellular Trafficking

    Cellular Responses to Bacterial Invasion

    Concluding Remarks

    See also

    References

    Infectious Agents

    INTRACELLULAR INFECTIOLOGY: INFECTIOUS AGENTS | Bacterial Protein Toxins as Tools in Cell Biology and Physiology

    Abstract

    Introduction

    Final Considerations

    See also

    References

    INTRACELLULAR INFECTIOLOGY: INFECTIOUS AGENTS | The Gut Microbiome

    Abstract

    The Gut Microbiome

    Microbiome Research Methodology (Approaches and Tools)

    Constituents of the Microbiome

    The Roles of the Microbiome

    Changes in the Gut Microbiome Throughout Life

    Factors Influencing the Microbiome

    The Microbiome and Disease

    Future Microbiome Research

    See also

    References

    INTRACELLULAR INFECTIOLOGY: INFECTIOUS AGENTS | Cell Biology of Virus Infection

    Abstract

    The Virus Particle

    Transmission

    Introduction to the Replication Cycle

    Virus Entry

    Replication and Synthesis of Viral mRNAs

    Virus Assembly and Release

    See also

    References

    Relevant Websites

    INTRACELLULAR INFECTIOLOGY: INFECTIOUS AGENTS | Virus Factories and Mini-Organelles Generated for Virus Replication

    Abstract

    Introduction

    RNA Viruses

    DNA Viruses

    See also

    References

    INTRACELLULAR INFECTIOLOGY: INFECTIOUS AGENTS | HIV – The Cell Biology of Virus Infection and Replication

    Abstract

    Glossary

    Introduction

    The HIV Replication Cycle

    Virus Assembly

    Virus Transmission

    Virus Entry

    Cell Killing

    Host Defences against HIV

    Drugs Interfering with HIV Replication

    Conclusion

    Acknowledgments

    See also

    References

    Further Reading

    INTRACELLULAR INFECTIOLOGY: INFECTIOUS AGENTS | Prions

    Abstract

    Introduction

    History of the Prion Discovery

    Prion Diseases

    The Prion Protein

    Conversion and Replication

    Transmission

    Strains

    Neurotoxicity

    Conclusion

    See also

    References

    Cell Processes

    INTRACELLULAR INFECTIOLOGY: CELL PROCESSES | Cellular Responses to Infections in Caenorhabditis elegans

    Abstract

    Caenorhabditis elegans as a Model System to Study Responses to Pathogens

    Overview of C. elegans Pathogens

    Pathogen Recognition by C. elegans

    Immune Effectors

    Immune Signaling Pathways

    Conclusions and Perspectives

    See also

    References

    Functional Cell Biology

    Functional Cell Biology: An Overview

    Introduction

    Cell Signaling and Intercellular Communication

    Cell Growth

    Functional Cell Biology of Immunity

    Stem Cell Biology

    References

    Cell Communication

    Growth Factor Mediated Cell Signaling

    CELL COMMUNICATION: GROWTH FACTOR MEDIATED CELL SIGNALING | Receptor Tyrosine Kinases and Their Ligands

    Abstract

    Glossary

    Introduction

    Families of RTKs and Their Ligands

    RTKs Undergo Ligand-Induced Dimerization

    Dimerization Activates the Kinase Activity of RTKs

    Signaling Downstream of RTKs

    RTK Coreceptors

    Feedback and Amplification of RTK Signaling

    Internalization of RTKs

    Structural and Functional Properties of RTK Families

    RTKs in Disease

    See also

    References

    CELL COMMUNICATION: GROWTH FACTOR MEDIATED CELL SIGNALING | Cytokine Receptors and Their Ligands

    Abstract

    Glossary

    Introduction

    hGHR and Related Receptors

    Beta Common Receptors

    Gamma Common Receptors

    Shared Glycoprotein 130 Receptors

    IL-1 Receptors

    IL-10/IL-22 Receptors

    IL-17 Receptors

    IFN Receptors

    Intracellular Signaling Complexes

    Concluding Remarks

    Acknowledgments

    See also

    References

    Further Reading

    CELL COMMUNICATION: GROWTH FACTOR MEDIATED CELL SIGNALING | TGF-β Superfamily Signaling

    Abstract

    Introduction

    Function of TGF-β Superfamily Signaling

    TGF-β Superfamily Ligands

    TGF-β Receptors

    Pathway Modulation

    TGF-β Superfamily Signaling and Disease

    Acknowledgments

    See also

    References

    Relevant Websites

    CELL COMMUNICATION: GROWTH FACTOR-MEDIATED CELL SIGNALING | G Protein-Coupled Receptors

    Abstract

    G Protein-Coupled Receptors

    Growth Factor Receptors and GPCRs

    NGF Induces Neurite Outgrowth through G Protein

    Conclusion

    Acknowledgment

    See also

    References

    Further Reading

    CELL COMMUNICATION: GROWTH FACTOR MEDIATED CELL SIGNALING | Guanylyl Cyclase Receptors

    Abstract

    Introduction

    Soluble GCs

    pGCs

    PDE

    Conclusion

    See also

    References

    CELL COMMUNICATION: GROWTH FACTOR MEDIATED CELL SIGNALING | Tumor Necrosis Factor Receptors: A Brief Digestion

    Abstract

    Introduction

    Classification of TNFRSF

    Structural Basis of Ligand–Receptor Interaction

    Signal Transduction through TNFR Activation

    The Double-Edged Sword in Cancer: Signaling through TNFR1/2 as an Example

    Clinical Targeting of TNFSF and TNFRSF Members: Focusing on Cancer Immunotherapy

    Concluding Remarks

    See also

    References

    CELL COMMUNICATION: GROWTH FACTOR MEDIATED CELL SIGNALING | Signaling and Function of Death Receptors of the Tumor Necrosis Factor Receptor Superfamily

    Abstract

    Glossary

    Introduction to Cell Death

    DR Signaling Activates Multiple Signal Pathways

    Function and Signaling Pathway of Each DR

    Summary

    See also

    References

    Further Reading

    CELL COMMUNICATION: GROWTH FACTOR MEDIATED CELL SIGNALING | Hedgehog Signaling in Development and Disease

    Abstract

    Introduction

    The Basic Mechanisms of HH Signaling

    Newer Aspects of HH Signal Transduction

    HH Signaling in Human Disease

    See also

    References

    CELL COMMUNICATION: GROWTH FACTOR MEDIATED CELL SIGNALING | The Wnt/β-Catenin Pathway

    Abstract

    Introduction

    Wnt Proteins

    Wnt Protein Biogenesis

    Wnt Receptors: Frizzled and LRP5/6

    Wnt Antagonists

    Wnt Agonists

    The ‘Wnt-Off’ State: Keeping β-Catenin Levels Low

    The ‘Wnt-On’ State: Raising β-Catenin Levels High

    β-Catenin Stabilization

    Wnt Signaling in the Nucleus

    Conclusions

    Acknowledgments

    References

    Relevant Website

    CELL COMMUNICATION: GROWTH FACTOR MEDIATED CELL SIGNALING | The Hippo Pathway

    Abstract

    Introduction

    The Hippo Pathway in D. melanogaster

    Upstream Regulators of Hippo Signaling in D. melanogaster

    The Hippo Pathway in Mammals

    Upstream Regulators of Hippo Signaling in Mammals

    Regulation of Organ Size, Stem Cell Self-Renewal, and Tissue Regeneration

    Hippo Pathway Deregulation in Cancer

    Conclusions

    See also

    References

    Further Reading

    CELL COMMUNICATION: GROWTH FACTOR MEDIATED CELL SIGNALING | The Notch Pathway

    Abstract

    The Notch Signaling Pathway

    Developmental Biology

    Pathology

    Summary

    See also

    References

    Intracellular Pathways

    CELL COMMUNICATION: INTRACELLULAR PATHWAYS | SH3 and SH2: Prototypic Domains to Mediate Regulatory Mechanisms in the Cell

    Abstract

    Glossary

    The Domain Perspective of Protein Architecture and Function

    A Brief History of the Discovery of SH Domains

    SH3

    SH2

    Specificity and Promiscuity

    Function

    SH Domains and Diseases

    Conclusions

    See also

    References

    Further Reading

    Relevant Website

    CELL COMMUNICATION: INTRACELLULAR PATHWAYS | The MAPK Signaling Cascades

    Abstract

    Glossary

    General Overview

    Components of MAPK Cascades

    Regulation of the MAPK Cascades

    MAPK Signaling in Diseases

    See also

    References

    CELL COMMUNICATION: INTRACELLULAR PATHWAYS | The PI3K/Akt/mTOR Pathway

    Abstract

    Brief History

    PI3K

    Akt

    mTOR

    Regulation of the PI3K/Akt/mTOR Pathway

    PI3K/Akt/mTOR Signaling in Human Disorders

    Highlights

    See also

    References

    CELL COMMUNICATION: INTRACELLULAR PATHWAYS | The JAK–STAT–SOCS Signaling Cascade

    Abstract

    Introduction

    The JAK Family

    STAT Proteins

    The SOCS

    JAK–STAT–SOCS and Human Disease

    Concluding Remarks

    Acknowledgments

    See also

    References

    Further Reading

    CELL COMMUNICATION: INTRACELLULAR PATHWAYS | The PLC Pathway

    Abstract

    Families of Phosphoinoside-Specific Phospholipase C Enzymes

    See also

    References

    CELL COMMUNICATION: INTRACELLULAR PATHWAYS | Calcium and Calmodulin Signaling

    Abstract

    Glossary

    The EF-Hand Calcium-Binding Principle

    CaM

    Regulation of Ca2+ by Proteins that Mediate Its Membrane Transport

    CaM Targets

    The Dark Side of Ca2+ Signaling: Ca2+-Related Pathologies

    See also

    References

    Further Reading

    Cellular Machineries

    CELL COMMUNICATION: CELLULAR MACHINERIES | Macromolecular Communication between Nucleus and Cytoplasm

    Abstract

    Glossary

    Introduction

    History – Overview

    Transport Signals and the Importin β Superfamily: A Code

    Directionality of Translocation by Importin β Superfamily Members

    mRNA Export

    Nucleoporins

    Regulation of Transport

    Shuttling

    Related Issues/Unanticipated Roles of the Nucleus

    Evolutionary Considerations

    Concluding Remarks

    Acknowledgments

    See also

    References

    CELL COMMUNICATION: CELLULAR MACHINERIES | The Molecular Architecture of Cell–Cell Adhesions

    Abstract

    Cell–Cell Adhesion: The Essence of Multicellularity

    Structural and Functional Diversity of Cell–Cell Junctions

    The Cadherin Family and Diversity of AJs

    The Molecular Basis for Cadherin–Cadherin Binding

    The Cytoplasmic Plaque

    Dynamic Connections between Cadherin and the Actin Cytoskeleton

    Regulatory Elements of the Cadherin Adhesome

    Dynamics of Actin at AJs

    Cadherin and Embryonic Development

    AJs in Disease

    Concluding Comments

    Acknowledgments

    See also

    References

    CELL COMMUNICATION: CELLULAR MACHINERIES | Extracellular Regulation of Cell-to-Matrix Adhesion

    Abstract

    Introduction

    Early Studies of Cell Adhesion

    Specific versus Generic Attractive and Repulsive Interactions

    Stiffness, Spacing, and Curvature

    How Extracellular Signals Alter Adhesion to Matrix

    Cell Adhesions and Matrix Molecules in Connective Tissue Function

    Role of Cell–Matrix Adhesions in Pathological Processes: Fibrosis

    Role of Cell–Matrix Adhesions in Pathological Processes: Platelets and Thrombosis

    Conclusion

    See also

    References

    Relevant Websites

    Cellular Outcomes

    CELL COMMUNICATION: CELLULAR OUTCOMES | Regulation of Cell Polarity

    Abstract

    Introduction

    A Modular Signaling System

    Principles of Collective Polarization

    Feedback Control of Core Amplification

    System Architecture

    Outlook

    See also

    References

    CELL COMMUNICATION: CELLULAR OUTCOMES | Regulation of Cell Migration

    Abstract

    Signals to Migrate

    Cytoskeletal Changes Underlying Migration

    Cell Migration Is Regulated Through Interactions with the Environment

    See also

    References

    Prototypic Integrative Processes

    CELL COMMUNICATION: PROTOTYPIC INTEGRATIVE PROCESSES | Wound Healing: An Orchestrated Process of Cell Cycle, Adhesion, and Signaling

    Abstract

    Glossary

    Molecular and Cellular Biology of Normal Wound Healing and Scar Formation

    Wound Healing versus Regeneration

    Impaired Wound Healing and Clinical Problems

    Parallels between Wound Healing and Cancer

    See also

    References

    Relevant Websites

    CELL COMMUNICATION: PROTOTYPIC INTEGRATIVE PROCESSES | Cancer Cell Invasion through Tissue Barriers

    Abstract

    Introduction

    EMT

    Invadopodia

    Modes of Cell Migration

    Anoikis

    Microtentacles

    Conclusion

    See also

    References

    CELL COMMUNICATION: PROTOTYPIC INTEGRATIVE PROCESSES | Neuronal Transport and Spatial Signaling Mechanisms in Neural Repair

    Abstract

    Glossary

    Introduction

    Constituents for Intracellular Communication and Trafficking in Neurons

    Neural Repair Mechanisms

    Perspectives

    Acknowledgments

    See also

    References

    Further Reading

    Cell Division/Death

    Regulation of Cell Growth

    CELL DIVISION/DEATH: REGULATION OF CELL GROWTH | mTORC1: Upstream and Downstream

    Abstract

    Introduction

    mTORC1 and mTORC2

    Downstream of mTORC1

    Upstream of mTORC1

    Concluding Remarks

    Acknowledgment

    See also

    References

    CELL DIVISION/DEATH: REGULATION OF CELL GROWTH | The Nucleolus

    Abstract

    Nucleolar Architecture

    Nucleoli and Ribosome Subunit Biogenesis

    Ribosomal DNA

    rRNA Transcription

    Regulation of rDNA Expression

    Interchange of Nucleoli with Other Nuclear Bodies

    The Dynamic Nucleolus

    Nucleoli and Viruses

    Proteomic Studies on Nucleolar Architecture, Function, and Dynamics

    Conclusion

    Methods

    Acknowledgments

    See also

    References

    Further Reading

    CELL DIVISION/DEATH: REGULATION OF CELL GROWTH | Ribosomes and Stress – Linked from Birth to Death

    Abstract

    Glossary

    Introduction

    Ribosome Birth in the Nucleolus

    The Busy Life of the Ribosome

    The End of the Line – Ribosome Degradation

    Conclusion

    See also

    References

    Further Reading

    CELL DIVISION/DEATH: REGULATION OF CELL GROWTH | Extra-Ribosome Functions of Ribosomal Proteins

    Abstract

    Introduction to Basic Ribosome Structure and Function

    Ribosome Biogenesis Is Intrinsically Connected to Cancerous Growth

    Ribosomopathies Are Associated with Increased Cancer Risk

    Non-ribosomal Functions of RPs Independent of the MDM2-p53 Pathway

    Ribosomal Protein-MDM2-p53 Pathway

    The RP-MDM2-p53 Pathway as a Putative Target in Cancer Therapy

    Conclusions

    See also

    References

    CELL DIVISION/DEATH: REGULATION OF CELL GROWTH | Ribosomal RNA Processing

    Abstract

    Introduction

    Ribosomal RNA Processing in Yeast

    rRNA Processing in Other Eukaryotes

    rRNA Processing in Prokaryotes

    5S rRNA Processing

    Human Diseases Caused by rRNA Processing Defects

    Perspectives

    Conclusions

    Acknowledgments

    See also

    References

    CELL DIVISION/DEATH: REGULATION OF CELL GROWTH | Eukaryotic Ribosome Assembly and Export

    Abstract

    Introduction

    Ribosomal Pre-rRNA Processing

    Trans-Acting Factors Involved in Ribosome Assembly

    Nuclear Export of Pre-Ribosomal Particles

    Cytoplasmic Events in Ribosome Biogenesis

    Concluding Remarks

    Acknowledgments

    See also

    References

    Further Reading

    CELL DIVISION/DEATH: REGULATION OF CELL GROWTH | Internal Ribosome Entry Site-Mediated Translation

    Abstract

    Glossary

    Introduction: The Canonical Cap-Dependent Mechanism of Translation Initiation in Eukaryotes

    Internal Ribosome Entry Site-Mediated Translation Initiation

    Conclusion and Perspective

    See also

    References

    Further Reading

    CELL DIVISION/DEATH: REGULATION OF CELL GROWTH | Targeted mRNA Degradation

    Abstract

    Introduction

    mRNA Surveillance Mechanisms

    Substrate Choice

    Substrate Recognition

    Substrate Fate

    Targeted mRNA Degradation in Gene Regulation

    mRNA Degradation Control by Short RNAs

    Targeted mRNA Degradation by RBPs

    Combined Action of Short RNAs and RBPs

    See also

    References

    Apoptosis

    CELL DIVISION/DEATH: APOPTOSIS | Apoptosis

    Abstract

    Apoptosis, Death as Part of Life

    Of Life and Apoptosis: The Anti-Apoptotic versus Pro-Apoptotic Machinery

    Acknowledgment

    See also

    References

    Relevant Website

    CELL DIVISION/DEATH: APOPTOSIS | Anoikis

    Abstract

    Introduction

    Why Leave?

    The Challenges of Being a Tumor Cell in its Primary Microenvironment

    ROS and Anoikis – A Double-edged Sword?

    What Otto Warburg Said, How It Was Misinterpreted, and the Idea of Metabolic Coupling in Tumors

    Summary

    See also

    References

    CELL DIVISION/DEATH: APOPTOSIS | Mitochondria in Cell Death Regulation

    Abstract

    Glossary

    Introduction

    Mitochondrial Control of Regulated Cell Death

    Mitochondrial Membrane Permeabilization

    Concluding Remarks

    See also

    References

    CELL DIVISION/DEATH: APOPTOSIS | Tumor Necrosis Factor Signaling Pathways

    Abstract

    Glossary

    Introduction

    The TNF and TNFR Superfamilies

    Structural Features of TNF, TNFR1, and TNFR2

    TNF-Induced TNFR Signaling

    TNFR-Induced NF-κB Activation

    TNFR-Induced Cell Death

    Regulation of TNF Signaling by Ubiquitin Ligases and Deubiquitinases

    TNF-Induced Activation of MAPK Pathways

    Physiologic Functions of TNF and Disease Relevance

    TNF Inhibitors

    Impact of TNF Blockade in Inflammatory Diseases

    See also

    References

    Further Reading

    CELL DIVISION/DEATH: APOPTOSIS | Caspases

    Abstract

    Introduction

    Structure, Classification, and Non-Apoptotic Biological Roles

    Activation Mechanisms

    Substrate Specificity and Targets

    Caspase Activation and Function in Cell Death and Inflammation

    New Modes of Caspase-Regulated Cell Death

    Acknowledgments

    See also

    References

    Relevant Websites

    CELL DIVISION/DEATH: APOPTOSIS | Efferocytosis in the Tumor Microenvironment

    Abstract

    Glossary

    Introduction

    A Historical Overview of Efferocytosis

    Efferocytosis Is an Established Process That Is Rapidly Deployed in the Breast

    Efferocytosis in the Tumor Microenvironment

    Efferocytosis and Postpartum Breast Cancer

    Conclusion and Future Directions

    References

    Further Reading

    CELL DIVISION/DEATH: APOPTOSIS | The Bcl-2 Family Proteins: Insights into Their Mechanism of Action and Therapeutic Potential

    Abstract

    Apoptosis and the Bcl-2 Family: A Historical Perspective

    How Do Bcl-2 Family Proteins Regulate MOMP?

    Physiology and Regulation of Bcl-2 Family Members

    Bcl-2 Proteins at the Endoplasmic Reticulum

    Bcl-2 Family Proteins and Cancer

    Summary

    See also

    References

    Further Reading

    CELL DIVISION/DEATH: APOPTOSIS | Inhibitor of Apoptosis Proteins, the Sentinels of Cell Death and Signaling

    Abstract

    Glossary

    Structural Organization of IAPs

    IAP Protein Characteristics and Function

    Targeting IAP Proteins

    Concluding Remarks

    See also

    References

    CELL DIVISION/DEATH: APOPTOSIS | Mitotic Catastrophe

    Abstract

    Introduction

    Mitotic Catastrophe

    Inducing Mitotic Catastrophe

    Mechanisms of Mitotic Catastrophe

    Concluding Remarks

    Acknowledgment

    References

    CELL DIVISION/DEATH: APOPTOSIS | Autophagy

    Abstract

    Autophagic Pathways

    Autophagy Step-by-Step

    The Autophagic Cargo and Purpose of Its Degradation

    Pathophysiology of Autophagy

    Concluding Remarks

    See also

    References

    Cell Cycle

    CELL DIVISION/DEATH: CELL CYCLE | Interplay between Oncogenes and Tumor Suppressor Genes in Human Disease

    Abstract

    Glossary

    Introduction: Scope and Intent of Article

    Oncogenes and Tumor Suppressor Genes and Human Cancer

    Interplay between Oncogenes and Tumor Suppressor Genes in Human Cancer

    Role of Oncogenes and Tumor Suppressor Genes in Human Developmental Diseases

    See also

    References

    Relevant Websites

    CELL DIVISION/DEATH: CELL CYCLE | Cyclins and Cyclin-Dependent Kinases

    Abstract

    Introduction

    The Discovery of Regulators of the Cell Cycle

    The Cyclins

    The Cyclin-Dependent Kinases

    Functions of Cyclin-CDK in the Cell Cycle and Quiescence

    CKIs: CDK Inhibitors

    Cyclins, CDKs, and CKIs in Cancer

    Beyond the Cell Cycle: Other Functions of Cyclins and CDKs

    See also

    References

    CELL DIVISION/DEATH: CELL CYCLE | The Restriction Point

    Abstract

    Glossary

    The Restriction Point

    The Role of RB and p53 in Establishing the Restriction Point

    Conclusions

    See also

    References

    CELL DIVISION/DEATH: CELL CYCLE | CDK Inhibitors in Normal and Malignant Cells

    Abstract

    Cyclins, CDKs, and Cell Cycle Progression

    The INK4 Family

    The CIP/KIP Family

    Prognostic Significance of CDK Inhibitor Deregulation in Human Cancers

    CDK Inhibitors as Predictors of Drug Response

    Concluding Remarks

    See also

    References

    CELL DIVISION/DEATH: CELL CYCLE | The INK4a/ARF Locus

    Abstract

    Introduction

    Control and Significance of G1–S Phase Progression in Mammals

    p16INK4a and RB1-Mediated Senescence

    INK4a/ARF – a Dual Coding Locus in Mammals

    INK4a/ARF – One Locus, Two Important Tumor Suppressors

    ARF, a Multi-Faceted Tumor Suppressor

    Regulation and Loss of INK4a/ARF in Cancer

    INK4a/ARF in Aging

    Unique Roles of ARF in Development

    Conclusions

    See also

    References

    Relevant Websites

    CELL DIVISION/DEATH: CELL CYCLE | S Phase

    Abstract

    Introduction

    S Phase Activation

    DNA Replication

    DNA Damage Response

    Conclusions

    See also

    References

    CELL DIVISION/DEATH: CELL CYCLE | Traveling through Mitosis with the Chromosomal Passenger Complex

    Abstract

    Introduction

    Identification of the Core CPC Members

    Putting the CPC Together

    CPC during the Approach to Mitosis

    CPC in Mitosis

    The Spindle Assembly Checkpoint

    Spindle Assembly Checkpoint and Inter-Kinetochore Tension

    CPC and Error Correction

    The Two-Histone Model of CPC Localization to Centromeres

    Modified View of CPC Targeting

    CPC during Anaphase, Telophase, and Cytokinesis

    Conclusion

    See also

    References

    CELL DIVISION/DEATH: CELL CYCLE | Mitosis in Animal Cells

    Abstract

    Introduction

    Stages of Mitosis

    Mitosis As an Anticancer Drug Target

    Conclusion

    Acknowledgments

    See also

    References

    Relevant Website

    CELL DIVISION/DEATH: CELL CYCLE | Regulating Cytokinesis

    Abstract

    Positioning the Site of Cell Division

    Formation of the Cleavage Furrow

    Formation of the Midbody

    Abscission

    Temporal Regulation of Cytokinesis

    The Abscission Checkpoint Protects against the Deleterious Effects of Chromatin Bridges

    Conclusions and Future Perspectives

    Acknowledgments

    See also

    References

    CELL DIVISION/DEATH: CELL CYCLE | Regulation of the p53 Pathway

    Abstract

    Introduction

    Control of p53 through the Ubiquitin-Proteasome Pathway

    E3 Ligases in the p53 Pathway

    The p53–Mdm2–HAUSP Connection

    DUBs in the p53 Pathway

    Transactivation of p53 through Posttranslational Modifications

    Involvement of p53 in Metabolism

    Conclusions

    See also

    References

    CELL DIVISION/DEATH: CELL CYCLE | Cellular Senescence

    Abstract

    Introduction

    What Defines Cellular Senescence?

    Molecular Signaling Pathways

    Epigenetic Control of Senescence

    Secreted Factors

    Senescence in Aging

    Senescence in Cancer

    Senescence and Tissue Repair

    Senescence in Development

    Conclusion

    See also

    References

    Cellular Immunology

    Overview

    CELLULAR IMMUNOLOGY: OVERVIEW | Introduction to Functional Cell Biology of Immunity

    Abstract

    Glossary

    Introduction

    Elements of Innate and Adaptive Immunity

    Barriers and Tissue Cells

    Chemical Defenses

    Sensing Mechanisms

    Phagocytes and Their Receptors

    Innate Lymphoid Cells

    Lymphocytes

    Immunological Synapses

    Lymphoid Tissues

    Evolution

    Perspective

    See also

    References

    Transcriptional Basis of B and T Cell Lineages and Memory Cells

    CELLULAR IMMUNOLOGY: TRANSCRIPTIONAL BASIS OF B AND T CELL LINEAGES AND MEMORY CELLS | The T-Cell Receptor Signalosome

    Abstract

    Introduction

    The TCR and Its Ligands: Structural and Functional Topology

    The Signaling Code Used by the TCR Signalosome to Convert Extracellular Signals into Biological Responses

    Biochemical Modules and Assembly of the TCR Signalosome

    Conclusions

    See also

    References

    Further Reading

    CELLULAR IMMUNOLOGY: TRANSCRIPTIONAL BASIS OF B AND T CELL LINEAGES AND MEMORY CELLS | T Follicular Helper Cells

    Abstract

    Introduction

    T Follicular Helper Cell Differentiation

    Acknowledgments

    See also

    References

    CELLULAR IMMUNOLOGY: TRANSCRIPTIONAL BASIS OF B AND T CELL LINEAGES AND MEMORY CELLS | V(D)J Recombination: Orchestrating Diversity without Damage

    Abstract

    Introduction

    Developmental and Epigenetic Regulation of V(D)J Recombination

    Molecular Mechanisms of RAG-Mediated V(D)J Recombination

    V(D)J Recombination and Malignancies of the Immune System

    Acknowledgments

    References

    Further Reading

    CELLULAR IMMUNOLOGY: TRANSCRIPTIONAL BASIS OF B AND T CELL LINEAGES AND MEMORY CELLS | T Cell Memory to Viral Infections

    Abstract

    Background

    Memory Formation

    Phenotypes of Memory T Cells

    Tissue-Resident Memory

    Different Phenotypes Characterize Different Viral Infections

    Immune Exhaustion

    Memory Inflation

    Atypical Memory

    Impact on Vaccine Design

    Conclusions and Future Directions

    See also

    References

    Further Reading

    CELLULAR IMMUNOLOGY: TRANSCRIPTIONAL BASIS OF B AND T CELL LINEAGES AND MEMORY CELLS | Nuclear Factor of Activated T Cells and Tolerance

    Abstract

    Introduction

    NFAT Domain Structure

    Regulation of NFAT Activation

    NFAT-Regulated Transcription

    Functions of NFAT in T cells

    NFAT and T Cell Tolerance

    Conclusions

    See also

    References

    Further Reading

    CELLULAR IMMUNOLOGY: TRANSCRIPTIONAL BASIS OF B AND T CELL LINEAGES AND MEMORY CELLS | NF-kappaB and the Immune System

    Abstract

    Glossary

    Introduction

    NF-κB in Normal Immune Cell Function and Development

    Role of NF-κB in Innate Immunity

    Misregulation of NF-κB in Human Immune Diseases

    Human Immune Cell Viruses Use NF-κB for Replication and Pathogenesis

    Targeting NF-κB for Therapy in Immune Diseases

    See also

    References

    Further Reading

    Cell–Cell Interactions and the Immune System

    CELLULAR IMMUNOLOGY: CELL–CELL INTERACTIONS AND THE IMMUNE SYSTEM | Functional Specialization of Dendritic Cell Subsets

    Abstract

    Discovery of Dendritic Cells

    Antigen Processing and Presentation

    DC Development and DC Characterization

    Functional Specialization in Antigen Presentation of Mouse DC Subpopulations

    Functional Specialization in Antigen Presentation of Human DC Subpopulations

    Conclusions

    Acknowledgments

    See also

    References

    CELLULAR IMMUNOLOGY: CELL–CELL INTERACTIONS AND THE IMMUNE SYSTEM | CD28 Costimulation and Regulatory T Cells

    Abstract

    Introduction

    How Is the Self-Tolerance Established?

    The Biology of the CD28/CTLA-4 Pathway

    CTLA-4 – A Key Negative Regulator of T cell Activation

    How Does CTLA-4 Function?

    Manipulation of CD28/CTLA-4 Pathway: Antagonist, Agonists, and Superagonists

    Conclusions

    See also

    References

    CELLULAR IMMUNOLOGY: CELL–CELL INTERACTIONS AND THE IMMUNE SYSTEM | Roles of Stromal Cells in the Immune System

    Abstract

    Introduction to Stromal Cells

    Stromal Cell Regulation of Lymphoid Tissue Structure and Function

    Stromal Cell Regulation of Immune Responses in Peripheral Tissues

    See also

    References

    CELLULAR IMMUNOLOGY: CELL–CELL INTERACTIONS AND THE IMMUNE SYSTEM | CXCL12/SDF-1 and Hematopoiesis

    Abstract

    Introduction

    Role of CXCL12 in Homing to BM

    Role of CXCL12 in HSC and HPC Maintenance within BM Niches

    CXCL12 in HSC and HPC Mobilization

    Role of CXCL12 in Maintenance of Neutrophils in BM

    Role of CXCL12 in Maintenance of the B cell Lineage in BM

    The Role of CXCL12 in Balancing Granulopoiesis and Lymphopoiesis during Inflammation

    Conclusion

    References

    CELLULAR IMMUNOLOGY: CELL–CELL INTERACTIONS AND THE IMMUNE SYSTEM | Lymphocyte–Endothelial Interactions

    Abstract

    Glossary

    Introduction

    The Endothelium as a Barrier for the Vascular and Lymphatic Systems

    Contexts for Lymphocyte–Endothelial Interactions

    Mechanisms for T Lymphocyte Adhesion to and Diapedesis across Endothelia

    Information Exchange at the T Lymphocyte–Endothelial Interface

    Summary

    Supplementary Material

    Acknowledgment

    See also

    References

    CELLULAR IMMUNOLOGY: CELL–CELL INTERACTIONS AND THE IMMUNE SYSTEM | T Cell Receptor Triggering

    Abstract

    Introduction

    Time of Interaction and Recruitment of Modulators

    Exclusion of Negative Regulators

    Changes in Conformation and Accessibility of Intracellular Domains

    TCRs as Mechanoreceptors

    Clustering

    Quantity and Valency of Cognate pMHC Ligands

    Conclusions

    See also

    References

    CELLULAR IMMUNOLOGY: CELL–CELL INTERACTIONS AND THE IMMUNE SYSTEM | Single Molecule Methods to Measure Receptor–Ligand Interaction in Immunological Synapses

    Abstract

    Introduction

    Mechanical Assays to Measure 2D-kinetics

    Imaging TCR–pMHC Interactions In Situ

    Pulling Forces Enhance Discriminative Power of Peptide Recognition

    Conclusion and Outlook

    Acknowledgments

    See also

    References

    CELLULAR IMMUNOLOGY: CELL–CELL INTERACTIONS AND THE IMMUNE SYSTEM | Single-Cell Interrogation of the Immune System Using Microtools

    Abstract

    Single-Cell Secretion

    Cell Migration

    Cell–Cell Communication

    Other Applications

    Acknowledgments

    References

    CELLULAR IMMUNOLOGY: CELL–CELL INTERACTIONS AND THE IMMUNE SYSTEM | Cellular Structures Controlling T Cell Signaling in Time and Space

    Abstract

    Introduction

    Studying the Organization of T Cell Signaling

    Signaling Organization and the Structures Driving It

    Signaling Organization Varies with T Cell Activation Conditions

    The Function of Signaling Organization

    See also

    References

    Further Reading

    Innate Immunity

    CELLULAR IMMUNOLOGY: INNATE IMMUNITY | Function of Epithelial Barriers

    Abstract

    Glossary

    Introduction

    Structure of the Epithelial Layer

    Epithelial Cell Types

    Defense

    Loss of Barrier Function in Disease

    Perspective

    See also

    References

    CELLULAR IMMUNOLOGY: INNATE IMMUNITY | Phagocytic Synapses

    Abstract

    Glossary

    Introduction

    Dectin-1 Activation by β-Glucans

    FcγR Activation by Immunoglobulin G (IgG)

    The Phagocytic Synapse Model

    Regulation of the Phagocytic Synapse by CD47

    Summary

    See also

    References

    CELLULAR IMMUNOLOGY: INNATE IMMUNITY | The Phagocyte NADPH Oxidase: Structure and Assembly of the Key Multicomponent Enzyme of Innate Immunity

    Abstract

    The Phagocyte Oxidative Burst

    The Phagocyte NADPH Oxidase NOX2

    Conclusion

    Acknowledgments

    See also

    References

    CELLULAR IMMUNOLOGY: INNATE IMMUNITY | Cytoplasmic Sensing in Innate Immunity

    Abstract

    Introduction

    Classes, Structure, and Activation of Innate Sensors

    Role of Intracellular Organelles and Spatial Relocation

    Combinatorial Sensing and PRR Crosstalk

    Multiscale Regulation of Cytosolic Sensing Pathways

    Acknowledgments

    See also

    References

    CELLULAR IMMUNOLOGY: INNATE IMMUNITY | Scavenger Receptors

    Abstract

    Introduction

    Evolutionary Origins of SRs and Functions in Host Physiology

    SRs in Innate Immunity

    SRs as Causes and Therapeutic Targets in Disease

    See also

    References

    Relevant Website

    CELLULAR IMMUNOLOGY: INNATE IMMUNITY | Dendritic Cells

    Abstract

    Discovery of Dendritic Cells

    DC Development and Homeostasis

    Features Enable DCs as the Orchestrator of Immunity

    DCs in Clinical Immunology

    See also

    References

    CELLULAR IMMUNOLOGY: INNATE IMMUNITY | Neutrophil Biology

    Abstract

    Introduction

    Neutrophil Development

    Neutrophil Migration into Sites of Inflammation

    Neutrophil Defense Mechanisms

    Neutrophil Subsets

    Genetic Defects That Affect Neutrophil Numbers and/or Function

    Neutrophils in Systemic Autoimmune Diseases

    Conclusion

    See also

    References

    CELLULAR IMMUNOLOGY: INNATE IMMUNITY | Specialized Subsets of Tissue-Resident Macrophages in Secondary Lymphoid Organs

    Abstract

    Macrophage Subsets in the Spleen

    LN Macrophages

    Conclusions

    See also

    References

    CELLULAR IMMUNOLOGY: INNATE IMMUNITY | CD4 T Cell Memory and Role of TNF Receptor Family

    Abstract

    Overview

    CD4 T Cell Responses

    Members of the TNFRSF and CD4 T Cells

    Concluding Remarks

    See also

    References

    Stem Cell Biology

    Structure and Function

    STEM CELL BIOLOGY: STRUCTURE AND FUNCTION | Stem Cells and Aging

    Abstract

    Introduction

    Determinants of Stem Cell Aging

    Aging in Adult Stem Cells

    Concluding Remarks

    Acknowledgments

    See also

    References

    STEM CELL BIOLOGY: STRUCTURE AND FUNCTION | Epigenetic Regulation of Stem Cells

    Abstract

    Introduction: Regulation of Gene Expression in Stem Cells

    Effectors and Mechanisms of Epigenetic Regulation of Gene Expression in ESCs

    Epigenetic Signatures and Control of Nuclear Architecture in ESCs

    Epigenetic Control of Quiescence/Stemness and Lineage Determination in Adult

    See also

    References

    Relevant Website

    STEM CELL BIOLOGY: STRUCTURE AND FUNCTION | The Adult Stem Cell Niche: Multiple Cellular Players in Tissue Homeostasis and Regeneration

    Abstract

    The Skin Hair Follicle

    Skeletal Muscle

    The Adult Central Nervous System Stem Cell Niche

    The Heart-Evidence for a Cardiac Stem Cell Niche?

    Overall Conclusions and Future Directions

    Acknowledgments

    See also

    References

    STEM CELL BIOLOGY: STRUCTURE AND FUNCTION | Cancer Stem Cells

    Abstract

    Definitions and History

    Tumor Heterogeneity

    Terminology

    Modes of Identification

    Regulation of Cancer Stemness

    Plasticity

    Markers for the Identification of Cancer Stem Cells in Major Malignancies

    Clinical Significance of Cancer Stem Cells

    Conclusions

    See also

    References

    STEM CELL BIOLOGY: STRUCTURE AND FUNCTION | Metabolic and Energetic Regulation of Stem Cells

    Abstract

    Hypoxia-Inducible Factor 1α and Glycolysis in Stem Cells

    Fatty Acid Metabolism and Mitochondrial Function

    Nutrient-Sensing Pathways

    Redox Homeostasis

    Other Stem Cell Niches

    Conclusions

    See also

    References

    STEM CELL BIOLOGY: STRUCTURE AND FUNCTION | Pluripotent Cells: New Tools for Disease Research and Therapies

    Abstract

    Glossary

    Naturally Occurring Pluripotent Cells

    Engineered Pluripotent Cells

    New Tools to Provide Mechanistic Insights on Determining Cell Fates and Disease States

    New Tools for Cell-Based Regenerative Therapy

    Clinical Trials and Contributions to Future Cell-Based Regenerative Therapy

    See also

    References

    Further Reading

    Systems Cell Biology

    Systems Cell Biology: An Overview

    Dynamic Integration

    Vertical Integration

    Horizontal Integration

    References

    Relevant Websites

    Dynamic Integration

    Dynamics

    DYNAMIC INTEGRATION: DYNAMICS | Dynamics of Gradient Sensing and Chemotaxis

    Abstract

    Introduction

    Strategies for Chemotaxis

    Adaptation in Chemotactic Systems

    Signal Amplification and Sensitivity

    Conclusions

    See also

    References

    Further Reading

    DYNAMIC INTEGRATION: DYNAMICS | Modeling Actin Dynamics

    Abstract

    Introduction

    Conceptual Models of Mechano-Chemical Control of Cell Motility and Shape

    Detailed Biochemical Modeling

    Conclusion

    Acknowledgments

    See also

    References

    Relevant Websites

    DYNAMIC INTEGRATION: DYNAMICS | Metabolism

    Abstract

    Introduction

    Metabolism

    Fundamentals

    Enzyme Response

    Pathway Responses

    Control Coefficients

    Connectivity Theorems

    Metabolic Motifs

    Conclusion

    Acknowledgments

    See also

    References

    Further Reading

    DYNAMIC INTEGRATION: DYNAMICS | Dynamics of Microtubule Self-Assembly

    Abstract

    Glossary

    Cellular Functions of Microtubules

    Microtubule Structure

    Microtubule Self-Assembly Dynamics

    Theoretical Framework for Microtubule Self-Assembly

    Microtubule-Targeting Agents Attenuate Microtubule Dynamics

    See also

    References

    Further Reading

    DYNAMIC INTEGRATION: DYNAMICS | Dynamics of Protein Kinase Cascades

    Abstract

    Glossary

    Introduction

    Signal Amplification and Decision Making

    Cellular Decisions Encoded in the Dynamics of Signaling

    Robustness of Signaling Pathways

    See also

    References

    Further Reading

    DYNAMIC INTEGRATION: DYNAMICS | Cdc42 and the Mechanisms of Yeast Cell Polarization – A Paradigm for Mesoscale Systems Biology

    Abstract

    Introduction

    Cue-Dependent Cell Polarization

    Breaking Symmetry

    Inhibitory Interactions and Reinforcements in Polarity Regulation

    See also

    References

    DYNAMIC INTEGRATION: DYNAMICS | Theory of Cargo and Membrane Trafficking

    Abstract

    Introduction

    Theory of the Endosomal Network

    Regulation of the Microscopic Processes

    Relation to Kinetics of Total Cargo Pool

    Implications for Cargo Sorting

    Conclusion

    See also

    References

    Further Reading

    DYNAMIC INTEGRATION: DYNAMICS | Transcription Factor Networks

    Abstract

    Introduction

    Local Properties of GRNs

    Motifs

    Global Properties of GRNs

    Conclusions

    See also

    References

    Further Reading

    Vertical Integration

    Modeling

    VERTICAL INTEGRATION: MODELING | Vertical Integration

    Abstract

    Introduction

    The Multiple Time and Spatial Scales Associated with Cellular Biology

    Approaches for Linking Scales in Multiscale Models: ‘Top-Down’, ‘Bottom-Up,’ and ‘Middle-Out’

    Mathematical and Computational Representations of the Components of a Multiscale Model

    Assembling Multiscale Modeling

    Software for Multiscale Modeling

    Applications of Multiscale Modeling and Two Case Studies

    Challenges Associated with Multiscale Modeling

    Summary

    Conclusions

    See also

    References

    Further Reading

    VERTICAL INTEGRATION: MODELING | Computational Approaches for Multiscale Modeling

    Abstract

    Glossary

    Introduction

    Multiscale Modeling

    Discussion

    Acknowledgments

    See also

    References

    Further Reading

    Relevant Website

    VERTICAL INTEGRATION: MODELING | Cardiac Modeling

    Abstract

    State-of-the-Art in Cardiac Cell Modeling

    Human Models of Cardiac Cell Electrophysiology

    Modeling Variability in Cardiac Cell Electrophysiology

    Whole Organ Cardiac Modeling

    Conclusions and Outlook

    References

    Relevant Website

    Applications

    VERTICAL INTEGRATION: APPLICATIONS | Mathematical Approaches to Studying Inflammation

    Abstract

    Introduction

    A Simple Mathematical Model Capturing the Resolution of Inflammation

    Current Mathematical and Computational Models of Inflammation

    Early Events, Leukocyte Responses to Bacteria

    Inflammatory Cytokines, TNF-Therapy

    Tissue Damage and Wound Healing

    Inflammation and Progression to the Immune Response

    Conclusions and Future Challenges

    See also

    References

    VERTICAL INTEGRATION: APPLICATIONS | Angiogenesis

    Abstract

    Glossary

    Vascular Evolution

    Developmental Vasculogenesis

    Capillary Structure

    Primary Factors Controlling Angiogenesis

    Hypoxic Induction of Angiogenesis

    Sprouting Angiogenesis

    Intussusceptive Angiogenesis

    Arterial and Venous Vessels

    Summary

    References

    VERTICAL INTEGRATION: APPLICATIONS | A Review on Various Mathematical Modeling Approaches for Wound Healing

    Abstract

    Wound Healing and the Need for Modeling

    Evaluation of Several Mathematical Approaches

    Conclusions

    See also

    References

    VERTICAL INTEGRATION: APPLICATIONS | Multiscale Analysis of Morphogenesis

    Abstract

    Introduction

    Vertical Integration

    Analyzing Cell Behavior

    Mathematical Models for Studying Collective Cell Behavior

    Examples of Vertical Integration Studies

    Conclusion

    Acknowledgments

    References

    Further Reading

    VERTICAL INTEGRATION: APPLICATIONS | Neurogenesis in the Adult Brain

    Abstract

    Introduction

    Historical Perspective

    Identity of Adult NSCs

    Cell Proliferation in the SVZ

    Neuronal Migration in the RMS

    Neuronal Differentiation in the Olfactory Bulb

    Potential Functions of Adult Neurogenesis

    Potential Applications

    Conclusion

    References

    Further Reading

    Horizontal Integration

    Networks

    HORIZONTAL INTEGRATION: NETWORKS | Understanding of ‘Networks’ In Vitro and/or In Vivo

    Introduction

    Networks in Cancer

    Concluding Remarks

    See also

    References

    Relevant Website

    Omics

    HORIZONTAL INTEGRATION: OMICS | Connecting Evolutionary Genomics to Cell Biology

    Abstract

    Genomics for Old and New Questions

    Case Studies: New Genes for Old and New Functions

    Gene Traffic

    Gene Regulatory Networks

    Cell Division

    Protein Traffic

    Perspectives

    Acknowledgments

    References

    HORIZONTAL INTEGRATION: OMICS | Transcriptomics

    Abstract

    Glossary

    Introduction

    Evolution of High-Throughput Transcriptomic Technologies

    Exploring the Interactive Transcriptome

    New Technologies for mRNA Transcriptomics

    Integrating Transcriptomics with Other Omics

    Conclusion

    See also

    References

    HORIZONTAL INTEGRATION: OMICS | The Advent of Mass Spectrometry-Based Proteomics in Systems Biology Research

    Abstract

    Systems Biology and Proteomics

    Liquid Chromatography-Coupled Tandem Mass Spectrometry

    Systems Biology Application for High-Throughput Proteomics

    Outlook

    Acknowledgments

    See also

    References

    HORIZONTAL INTEGRATION: OMICS | Phosphoproteomics: Approaches, Developments, and Challenges

    Abstract

    Introduction to Posttranslational Modifications

    Protein Phosphorylation

    Phosphopeptide Enrichment

    Large-Scale Phosphoproteomics Strategies

    Phosphopeptide Fragmentation

    Quantitative Phosphoproteomics

    PTM Cross Talk and PTM Coding

    Challenges in Phosphoproteomics

    Conclusions

    See also

    References

    HORIZONTAL INTEGRATION: OMICS | Interactomes – Scaffolds of Cellular Systems

    Abstract

    Introduction

    Methods to Map Interactomes

    Applications of Interactome Maps

    Perspectives

    See also

    References

    HORIZONTAL INTEGRATION: OMICS | Metabolomics in Cell Biology

    Abstract

    Introduction

    Conducting a Successful Metabolomics Study

    See also

    References

    Analyses and Tools

    HORIZONTAL INTEGRATION: ANALYSES AND TOOLS | Network Modeling of Heterogeneous Datasets

    Abstract

    Introduction

    Overview

    Network Algorithms

    See also

    References

    HORIZONTAL INTEGRATION: ANALYSES AND TOOLS | Stochastic Analysis of Nongenetic Cell-to-Cell Heterogeneity

    Abstract

    Glossary

    Introduction

    Cell Signaling

    Variability in Gene Expression

    Single-Cell Analysis

    Modeling and Analysis of Stochastic Data

    Connecting Heterogeneity at Multiple Levels

    Conclusion

    See also

    References

    HORIZONTAL INTEGRATION: ANALYSES AND TOOLS | Systematic Methods to Interrogate Genetic Perturbations and Map Phosphorylation-Dependent Signaling

    Abstract

    Acknowledgments

    See also

    References

    HORIZONTAL INTEGRATION: ANALYSES AND TOOLS | High-Content Screening in Cell Biology

    Abstract

    Glossary

    Introduction

    History

    Experimental Setup

    High-Content or Low-Content?

    Conclusion

    See also

    References

    Further Reading

    HORIZONTAL INTEGRATION: ANALYSES AND TOOLS | Integrative Systems Biology

    Abstract

    Introduction

    Challenges

    Solutions

    Conclusions

    See also

    References

    Relevant Websites

    Disease

    HORIZONTAL INTEGRATION: DISEASE | Computational and Systems Cancer Biology

    Abstract

    Integrative and Systems Biology Methodologies

    Assembly and Analysis of Cancer Regulatory Models

    Interactome Reverse Engineering

    Interrogating Pathways and Networks

    Recent Trends and Future Perspective

    See also

    References

    Relevant Website

    HORIZONTAL INTEGRATION: DISEASE | Drug Targeting

    Abstract

    Drug Targeting – An Introduction

    A Historical Perspective

    From Molecules to Systems

    Network Medicine

    New Methods for Drug Targeting

    See also

    References

    Authors

    Index

Product details

  • No. of pages: 3008
  • Language: English
  • Copyright: © Academic Press 2015
  • Published: August 7, 2015
  • Imprint: Academic Press
  • Hardcover ISBN: 9780123944474
  • eBook ISBN: 9780123947963

About the Editors in Chief

Ralph Bradshaw

Ralph Bradshaw
Ralph A. Bradshaw is Professor Emeritus in the Department of Physiology and biophysics at the University of California, Irvine. Prior to that he was on the faculty of the Department of Biological Chemistry, Washington University School of Medicine in St. Louis, MO and was Professor and Chair of the Department of Biological Chemistry at the University of California, Irvine. From 2006 to 2015, he was a member of the Mass Spectrometry Facility and Professor of Pharmaceutical Chemistry at the University of California, San Francisco. He holds degrees from Colby College and Duke University and was a post-doctoral fellow at Indiana University and the University of Washington. He has served as president for FASEB, was the founding president of the Protein Society and was the treasurer of the American Society for Biochemistry and Molecular Biology. His research has focused on protein chemistry and proteomics, with emphasis on the structure and function of growth factors and their receptors, particularly nerve growth factor and fibroblast growth factor, and the involvement of receptor tyrosine kinases in cell signalling. He has also studied in the role of proteolytic processing and N-terminal modification in protein stability and turnover.

Affiliations and Expertise

Department of Chemistry and Pharmaceutical Chemistry; and Mass Spectrometry Facility, University of California, San Francisco, Department of Physiology and Biophysics, College of Medicine, University of California, Irvine, Irvine, CA

Philip Stahl

Philip Stahl
Philip D. Stahl is Mallinckrodt Jr. Professor Emeritus at Washington University School of Medicine in St. Louis, MO. He was educated at West Virginia University with post-doctoral work at Vanderbilt University. He served as Head of the Department of Cell Biology and Physiology and Director of the Division of Biology and Biomedical Sciences at Washington University. He has been the recipient of many awards including a MERIT award from the NIH and the WICB Senior Recognition award given by the American Society for Cell Biology in recognition of his work supporting the advancement of women in science. Among StahlLab contributions are the discovery of the lysosomal enzyme clearance pathway now implemented in the treatment of lysosomal storage disease, discovery of the innate immune receptor, the mannose receptor, discovery of the exosome secretion pathway, and the role of Rab5 and Arf6 in endocytosis. Currently his research focuses on endocytosis, signal transduction, and exosome biogenesis and secretion.

Affiliations and Expertise

Washington University, St. Louis, MO, USA