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.

Table of Contents

• Dedication
• Editors-in-Chief
• Volume Editors
• Section Editors
• Preface
• Cell Biology: An Overview
• Permission Acknowledgments
• Volume 1: Molecular Cell Biology
• Molecular Cell Biology: An Overview
• MOLECULAR PRINCIPLES, COMPONENTS, TECHNOLOGY, AND CONCEPTS
• BASIC PRINCIPLES
• Chemical and Physical Principles
• Biocatalysis
• NUCLEIC ACIDS
• DNA, RNA Chemical Properties (Including Sequencing and Next-Generation Sequencing)
• The Chemical Synthesis of DNA and RNA Oligonucleotides for Drug Development and Synthetic Biology Applications
• PROTEINS
• Expression Systems
• Isolation/Purification of Proteins
• Protein Sequence Determination: Methodology and Evolutionary Implications
• Posttranslational Modifications: Key Players in Health and Disease
• Protein Domains: Structure, Function, and Methods
• NMR in Structural and Cell Biology
• Proteins: Folding, Misfolding, Disordered Proteins, and Related Diseases
• Diseases of Protein Folding: Huntington’s Disease and Amyotrophic Lateral Sclerosis
• Site-Directed Mutagenesis
• Chemical Biology
• Drug Design
• Antibodies and Improved Engineered Formats (as Reagents)
• LIPIDS
• Lipidomics
• Synthesis and Structure of Glycerolipids
• Cholesterol and Other Steroids
• Glycolipids
• Lipid Signaling
• MEMBRANES
• Composition, Physical Properties, and Curvature
• Lipid Rafts/Membrane Rafts
• Membrane Potential: Concepts
• 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
• Neuronal Action Potentials and Ion Channel Allostery
• Cystic Fibrosis
• CARBOHYDRATES
• Glycogen and Starch
• Proteoglycans
• Hyaluronan
• METABOLISM
• Metabolic Regulation
• A Structure Perspective on Organelle Bioenergetics
• NUCLEIC ACID SYNTHESIS/BREAKDOWN
• RNA SYNTHESIS/FUNCTION
• Transfer RNA
• Messenger RNA (mRNA): The Link between DNA and Protein
• The Interplay between Eukaryotic mRNA Degradation and Translation
• miRNAs/Small Noncoding RNAs
• Small RNAs/Cancer
• Riboswitches and Ribozymes
• Ribosomal RNAs and Protein Synthesis
• Comparison of Bacterial and Eukaryotic Replisome Components
• DNA SYNTHESIS/REPAIR
• Telomeres and Telomerase
• Telomere Biology
• Eukaryotic Nucleotide Excision Repair
• The Base Excision Repair Pathway
• Nonhomologous DNA End Joining
• DNA Repair by Homologous Recombination
• TRANSCRIPTION
• Prokaryotic Transcription
• Eukaryotic Transcriptional Regulation
• Distant Activation of Transcription by Enhancers
• The Spliceosome and Pre-mRNA Splicing
• Pre-mRNA Splicing: Function and Dysfunction
• NUCLEIC ACID TECHNOLOGY
• Transgenesis and Gene Replacement
• Viral Nucleic Acids
• PROTEIN SYNTHESIS/DEGRADATION
• TRANSLATION
• Components, Initiation, Elongation, Termination, and Regulation
• Biogenesis of Secretory Proteins
• The Protein Biosynthetic Machinery of Mitochondria
• Regulated Proteolysis of Signaling Molecules: The Proprotein Convertases
• PROTEIN DEGRADATION – GENERAL
• Mass Spectrometry-based Methodologies for Studying Proteolytic Networks and the Degradome
• PROTEIN DEGRADATION – INTRACELLULAR
• Ubiquitin, Ubiquitin-Like Proteins, and Proteasome-Mediated Degradation
• Endoplasmic Reticulum-Associated Degradation and Protein Quality Control
• Role of Lysosomes in Intracellular Degradation
• PROTEIN DEGRADATION – PROTEASE CLASSES
• Matrix Metalloproteinases
• ADAMTS Proteases: Mediators of Physiological and Pathogenic Extracellular Proteolysis
• ADAMs Regulate Cell–Cell Interactions by Controlling the Function of the EGF-Receptor, TNFα and Notch
• Extracellular: Plasma Membrane Proteases – Serine Proteases
• Aspartic Proteases of Alzheimer’s Disease: β- and γ-Secretases
• The Calpain Proteolytic System
• Cathepsin E: An Aspartic Protease with Diverse Functions and Biomedical Implications
• Metalloproteases Meprin α and Meprin β in Health and Disease
• Kallikrein
• Naturally-Occurring Polypeptide Inhibitors: Cystatins/Stefins, Inhibitors of Apoptosis (IAPs), Serpins, and Tissue Inhibitors of Metalloproteinases (TIMPs)
• PROTEOLYTIC PATHWAYS
• Overview of Blood Coagulation and the Pathophysiology of Blood Coagulation Disorders
• Molecular Mechanisms Underlying the Actions of the Complement System
• Digestive Proteases: Roles in the Human Alimentary Tract
• PROTEIN DEGRADATION – PATHOLOGICAL ASPECTS
• Inhibitors of HIV Protease
• Blood Pressure, Proteases and Inhibitors
• Cancer – Proteases in the Progression and Metastasis
• Lysosomal Diseases
• 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
• Volume 2: Organizational Cell Biology
• Organizational Cell Biology: An Overview
• IMAGING THE CELL
• ELECTRON MICROSCOPY
• Single-Particle CryoEM of Macromolecular Complexes
• Scanning Electron Microscopy in Cell Biology
• Electron Tomography
• Immunoelectron Microscopy: High-Resolution Immunocytochemistry
• Imaging Cellular Architecture with 3D SEM
• LIGHT MICROSCOPY
• Genetically Encoded Fluorescent Probes and Live Cell Imaging
• Total Internal Reflection Fluorescence Microscopy
• Super Resolution Fluorescence Localization Microscopy
• Super-Resolution Light Microscopy: Stimulated Emission Depletion and Ground-State Depletion
• Structured Illumination Microscopy
• Fluorescence Correlation Spectroscopy: A Tool for Measuring Dynamic and Equilibrium Properties of Molecules in Cells
• Fluorescence Lifetime Imaging – Applications and Instrumental Principles
• High-Speed Localization Microscopy and Single-Particle Tracking
• Intravital Microscopy in Mammalian Organisms: From Tissue Physiology to Cell Biology
• Optogenetics
• ORGANELLES
• STRUCTURE AND FUNCTION
• The Endoplasmic Reticulum
• Intermediate Compartment: A Sorting Station between the Endoplasmic Reticulum and the Golgi Apparatus
• Golgi and TGN
• Early Endosomal Compartments
• The Late Endosome
• Signaling from Endosomes
• Conventional and Secretory Lysosomes
• Lysosome-Related Organelles
• At the Center of Autophagy: Autophagosomes
• Peroxisomes
• Lipid Droplets
• Mechanisms and Functions of Mitochondrial Dynamics
• Synaptosomes and Synaptic Vesicles
• Extracellular Vesicles
• Nuclear Organization (Nuclear Structure and Dynamics)
• Nuclear Pores
• Plastids: The Anabolic Factories of Plant Cells
• INTERORGANELLAR COMMUNICATION
• INTERPLAY AND PROCESSES
• ER–Golgi Transport
• N-Linked Glycans (N-Glycans)
• Extracellular O-Glycans
• Intra-Golgi Transport
• Post-Golgi Transport – Cargo, Carriers, and Pathways
• Regulation of the Secretory Pathway
• Regulated versus Constitutive Secretion – A Major Form of Intercellular Communication
• Clathrin and Clathrin-Dependent Endocytosis
• Clathrin Independent Endocytosis
• Rabs of the Endosomal Recycling Pathway
• Endosome to Lysosome Transport
• Endocytosis of Cargo Proteins: LDL
• Retrograde Transport
• Rabs and Other G Proteins
• COMPONENTS
• Adaptor Proteins: Inter-Organelle Traffic Controllers
• SNAREs: Membrane Fusion and Beyond
• ESCRTing around the Cell
• The Retromer Complex
• Vesicle Tethers
• BAR Domains and BAR Domain Superfamily Proteins
• INTERPLAY AND PROCESSES
• Role of Phosphoinositides in Membrane Traffic
• Unconventional Protein Secretion: Fibroblast Growth Factor 2 and Interleukin-1β as Examples
• Endoplasmic Reticulum Stress in Disease
• CYTOSKELETON AND MOTORS
• CYTOSKELETAL COMPONENTS
• Microtubules and Microtubule-Associated Proteins (MAPs)
• Actin Assembly Dynamics and Its Regulation in Motile and Morphogenetic Processes
• Intermediate Filaments
• Septins: Cytoskeletal Filaments with Structural and Regulatory Functions
• Bacterial and Archaeal Cytoskeletons
• Myosins
• Kinesin Superfamily Proteins (KIFs) as a Fundamental Component of Life: Intracellular Transport and Beyond
• Dyneins
• COMPLEX CYTOSKELETAL STRUCTURES
• The Mitotic Spindle
• Centrioles and the Centrosome
• Cilia and Flagella
• Skeletal Muscle
• Filopodia and Lamellipodia
• The Extracellular Matrix
• Cell–Cell Adhesion and the Cytoskeleton
• Cell Adhesion to the Extracellular Matrix
• Cell Migration
• Rho GTPases
• Cell Polarity
• INTRACELLULAR INFECTIOLOGY
• CELL PROCESSES
• Phagocytosis
• Macropinocytosis
• Microbicidal Mechanisms
• Bacterial Subversion of Phagocytic Killing
• Cellular Invasion by Bacterial Pathogens
• INFECTIOUS AGENTS
• Bacterial Protein Toxins as Tools in Cell Biology and Physiology
• The Gut Microbiome
• Cell Biology of Virus Infection
• Virus Factories and Mini-Organelles Generated for Virus Replication
• HIV – The Cell Biology of Virus Infection and Replication
• Prions
• CELL PROCESSES
• Cellular Responses to Infections in Caenorhabditis elegans
• Volume 3: Functional Cell Biology
• Functional Cell Biology: An Overview
• CELL COMMUNICATION
• GROWTH FACTOR MEDIATED CELL SIGNALING
• Receptor Tyrosine Kinases and Their Ligands
• Cytokine Receptors and Their Ligands
• TGF-β Superfamily Signaling
• G Protein-Coupled Receptors
• Guanylyl Cyclase Receptors
• Tumor Necrosis Factor Receptors: A Brief Digestion
• Signaling and Function of Death Receptors of the Tumor Necrosis Factor Receptor Superfamily
• Hedgehog Signaling in Development and Disease
• The Wnt/β-Catenin Pathway
• The Hippo Pathway
• The Notch Pathway
• INTRACELLULAR PATHWAYS
• SH3 and SH2: Prototypic Domains to Mediate Regulatory Mechanisms in the Cell
• The MAPK Signaling Cascades
• The PI3K/Akt/mTOR Pathway
• The JAK–STAT–SOCS Signaling Cascade
• The PLC Pathway
• Calcium and Calmodulin Signaling
• CELLULAR MACHINERIES
• Macromolecular Communication between Nucleus and Cytoplasm
• The Molecular Architecture of Cell–Cell Adhesions
• Extracellular Regulation of Cell-to-Matrix Adhesion
• CELLULAR OUTCOMES
• Regulation of Cell Polarity
• Regulation of Cell Migration
• PROTOTYPIC INTEGRATIVE PROCESSES
• Wound Healing: An Orchestrated Process of Cell Cycle, Adhesion, and Signaling
• Cancer Cell Invasion through Tissue Barriers
• Neuronal Transport and Spatial Signaling Mechanisms in Neural Repair
• CELL DIVISION/DEATH
• REGULATION OF CELL GROWTH
• mTORC1: Upstream and Downstream
• The Nucleolus
• Ribosomes and Stress – Linked from Birth to Death
• Extra-Ribosome Functions of Ribosomal Proteins
• Ribosomal RNA Processing
• Eukaryotic Ribosome Assembly and Export
• Internal Ribosome Entry Site-Mediated Translation
• Targeted mRNA Degradation
• APOPTOSIS
• Apoptosis
• Anoikis
• Mitochondria in Cell Death Regulation
• Tumor Necrosis Factor Signaling Pathways
• Caspases
• Efferocytosis in the Tumor Microenvironment
• The Bcl-2 Family Proteins: Insights into Their Mechanism of Action and Therapeutic Potential
• Inhibitor of Apoptosis Proteins, the Sentinels of Cell Death and Signaling
• Mitotic Catastrophe
• Autophagy
• CELL CYCLE
• Interplay between Oncogenes and Tumor Suppressor Genes in Human Disease
• Cyclins and Cyclin-Dependent Kinases
• The Restriction Point
• CDK Inhibitors in Normal and Malignant Cells
• The INK4a/ARF Locus
• S Phase
• Traveling through Mitosis with the Chromosomal Passenger Complex
• Mitosis in Animal Cells
• Regulating Cytokinesis
• Regulation of the p53 Pathway
• Cellular Senescence
• CELLULAR IMMUNOLOGY
• OVERVIEW
• Introduction to Functional Cell Biology of Immunity
• TRANSCRIPTIONAL BASIS OF B AND T CELL LINEAGES AND MEMORY CELLS
• The T-Cell Receptor Signalosome
• T Follicular Helper Cells
• V(D)J Recombination: Orchestrating Diversity without Damage
• T Cell Memory to Viral Infections
• Nuclear Factor of Activated T Cells and Tolerance
• NF-kappaB and the Immune System
• CELL–CELL INTERACTIONS AND THE IMMUNE SYSTEM
• Functional Specialization of Dendritic Cell Subsets
• CD28 Costimulation and Regulatory T Cells
• Roles of Stromal Cells in the Immune System
• CXCL12/SDF-1 and Hematopoiesis
• Lymphocyte–Endothelial Interactions
• T Cell Receptor Triggering
• Single Molecule Methods to Measure Receptor–Ligand Interaction in Immunological Synapses
• Single-Cell Interrogation of the Immune System Using Microtools
• Cellular Structures Controlling T Cell Signaling in Time and Space
• INNATE IMMUNITY
• Function of Epithelial Barriers
• Phagocytic Synapses
• The Phagocyte NADPH Oxidase: Structure and Assembly of the Key Multicomponent Enzyme of Innate Immunity
• Cytoplasmic Sensing in Innate Immunity
• Scavenger Receptors
• Dendritic Cells
• Neutrophil Biology
• Specialized Subsets of Tissue-Resident Macrophages in Secondary Lymphoid Organs
• CD4 T Cell Memory and Role of TNF Receptor Family
• STEM CELL BIOLOGY
• STRUCTURE AND FUNCTION
• Stem Cells and Aging
• Epigenetic Regulation of Stem Cells
• The Adult Stem Cell Niche: Multiple Cellular Players in Tissue Homeostasis and Regeneration
• Cancer Stem Cells
• Metabolic and Energetic Regulation of Stem Cells
• Pluripotent Cells: New Tools for Disease Research and Therapies
• Volume 4: Systems Cell Biology
• Systems Cell Biology: An Overview
• DYNAMIC INTEGRATION
• DYNAMICS
• Dynamics of Gradient Sensing and Chemotaxis
• Modeling Actin Dynamics
• Metabolism
• Dynamics of Microtubule Self-Assembly
• Dynamics of Protein Kinase Cascades
• Cdc42 and the Mechanisms of Yeast Cell Polarization – A Paradigm for Mesoscale Systems Biology
• Theory of Cargo and Membrane Trafficking
• Transcription Factor Networks
• VERTICAL INTEGRATION
• MODELING
• Vertical Integration
• Computational Approaches for Multiscale Modeling
• Cardiac Modeling
• APPLICATIONS
• Mathematical Approaches to Studying Inflammation
• Angiogenesis
• A Review on Various Mathematical Modeling Approaches for Wound Healing
• Multiscale Analysis of Morphogenesis
• Neurogenesis in the Adult Brain
• HORIZONTAL INTEGRATION
• NETWORKS
• Understanding of ‘Networks’ In Vitro and/or In Vivo
• OMICS
• Connecting Evolutionary Genomics to Cell Biology
• Transcriptomics
• The Advent of Mass Spectrometry-Based Proteomics in Systems Biology Research
• Phosphoproteomics: Approaches, Developments, and Challenges
• Interactomes – Scaffolds of Cellular Systems
• Metabolomics in Cell Biology
• ANALYSES AND TOOLS
• Network Modeling of Heterogeneous Datasets
• Stochastic Analysis of Nongenetic Cell-to-Cell Heterogeneity
• Systematic Methods to Interrogate Genetic Perturbations and Map Phosphorylation-Dependent Signaling
• High-Content Screening in Cell Biology
• Integrative Systems Biology
• DISEASE
• Computational and Systems Cancer Biology
• Drug Targeting