Encyclopedia of Cell Biology

The Encyclopedia of Cell Biology 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.

• 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

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

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