Encyclopedia of Cell Biology
1st Edition
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Description
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.
Key Features
- Fully annotated color images and videos for full comprehension of concepts, with layered content for readers from different levels of experience
- Includes information on cytokinesis, cell biology, cell mechanics, cytoskeleton dynamics, stem cells, prokaryotic cell biology, RNA biology, aging, cell growth, cell Injury, and more
- In-depth linking to Academic Press/Elsevier content and additional links to outside websites and resources for further reading
- A one-stop resource for students, researchers, and teaching faculty across the biological and medical sciences
Readership
Undergraduate and graduate students, researchers, scientists, and teaching faculty across the biological and medical sciences.
Table of Contents
Dedication
Editors-in-Chief
Volume Editors
Section Editors
Preface
References
Cell Biology: An Overview
Imaging and Organelle Organization
Signaling
Concluding Remarks
References
Permission Acknowledgments
Molecular Cell Biology
Molecular Cell Biology: An Overview
Basic Molecular Components and Technology
Nucleic Acid Synthesis/Breakdown
Protein Synthesis and Degradation
Molecular Principles, Components, Technology, and Concepts
Basic Principles
MOLECULAR PRINCIPLES, COMPONENTS, TECHNOLOGY, AND CONCEPTS: BASIC PRINCIPLES | Chemical and Physical Principles
Abstract
Introduction
The Laws of Thermodynamics and Living Cells
Gibbs Free Energy Always Decreases for a Spontaneous Process at Constant Temperature and Pressure
Gibbs Free Energy Changes are Additive
Coupling of ATP Hydrolysis to Drive Thermodynamically Unfavorable Reactions
Reaction Rate and Rate Constant
Reaction Rate-Limiting Step
Rate Constant and Activation Energy
Enzyme Kinetics
Allosteric Enzymes
Concerted and Sequential Models
Water as Life’s Aether
Acid–Base Reactions Play a Central Role in Most Biochemical Processes
Noncovalent Interactions Play Key Roles in Mediating Functions of Biomacromolecules
Effect of Molecular Crowding in Living Cells
Concluding Remarks
References
MOLECULAR PRINCIPLES, COMPONENTS, TECHNOLOGY, AND CONCEPTS: BASIC PRINCIPLES | Biocatalysis
Abstract
Introduction
Enzymes
Ribozymes
See also
References
Relevant Websites
Nucleic Acids
MOLECULAR PRINCIPLES, COMPONENTS, TECHNOLOGY, AND CONCEPTS: NUCLEIC ACIDS | DNA, RNA Chemical Properties (Including Sequencing and Next-Generation Sequencing)
Abstract
Glossary
Introduction
Physical Structure of Nucleic Acid
Chemical Modification of Nucleic Acids
DNA Modification by Radiation
DNA Mapping
Nucleic Acid Sequencing
Sanger DNA Sequencing
NGS
Library Preparation
Sequencing through DNA Synthesis
Data Analysis
Future Directions
See also
References
Further Reading
MOLECULAR PRINCIPLES, COMPONENTS, TECHNOLOGY, AND CONCEPTS: NUCLEIC ACIDS | The Chemical Synthesis of DNA and RNA Oligonucleotides for Drug Development and Synthetic Biology Applications
Abstract
Introduction
The Chemical Synthesis of Oligodeoxyribonucleotides
The Chemical Synthesis of Oligoribonucleotides via the Phosphoramidite Approach
DNA and RNA Microarrays
Concluding Remarks
See also
References
Proteins
MOLECULAR PRINCIPLES, COMPONENTS, TECHNOLOGY, AND CONCEPTS: PROTEINS | Expression Systems
Abstract
Glossary
Overview of Expression Systems
Bacterial Expression Systems
Yeast Expression Systems
Cell-Free Expression Systems
Insect Expression Systems
Mammalian Expression Systems
Summary/Conclusion
See also
References
Further Reading
MOLECULAR PRINCIPLES, COMPONENTS, TECHNOLOGY, AND CONCEPTS: PROTEINS | Isolation/Purification of Proteins
Abstract
Glossary
Introduction
The Protein Source
Assays
Considerations
Initial Steps
Chromatography
Migration in an Electric Field
Protein Crystallization
Evaluating Purity
A Final Word
See also
References
Further Reading
MOLECULAR PRINCIPLES, COMPONENTS, TECHNOLOGY, AND CONCEPTS: PROTEINS | Protein Sequence Determination: Methodology and Evolutionary Implications
Abstract
Sequencing Proteins by Chemical Techniques
Other Sequencing Methodology
Sequence Comparisons
Concluding Remarks
See also
References
MOLECULAR PRINCIPLES, COMPONENTS, TECHNOLOGY, AND CONCEPTS: PROTEINS | Posttranslational Modifications: Key Players in Health and Disease
Abstract
Introduction
Proteolytic PTM of Proteins
Phosphorylation
Glycosylation (N- and O-linked)
N-Acetylation
Amidation
Methylation
Lipid Modification (Lipidation)
Oxidative Stress-Related PTMs
Hydroxylation
Carbonylation
Nitrosylation
Ubiquitin and Targeted Protein Degradation
γ-Carboxylation
Conclusions: Many More PTMs Exist, and There Is Cross Talk between Them
See also
References
Relevant Websites
MOLECULAR PRINCIPLES, COMPONENTS, TECHNOLOGY, AND CONCEPTS: PROTEINS | Protein Domains: Structure, Function, and Methods
Abstract
Introduction
Protein Structure: Motifs, Folds, and Domains
Protein Domain Functions
Identifying and Classifying Protein Domains
Domains in Evolution: Modularity and Combinatorial Protein Structure
Conclusions
See also
References
MOLECULAR PRINCIPLES, COMPONENTS, TECHNOLOGY, AND CONCEPTS: PROTEINS | NMR in Structural and Cell Biology
Abstract
Introduction
Brief Historical Perspective of NMR and Solution Structure Determination of Macromolecules
Fundamentals of NMR Structure Determination
Place of NMR Spectroscopy in Structural and Cell Biology
Experimental and Computational Considerations
Structural Proteomics of the Bacterial Phosphotransferase System
Exploring Sparsely Populated States of Proteins and Their Complexes
Acknowledgments
See also
References
MOLECULAR PRINCIPLES, COMPONENTS, TECHNOLOGY, AND CONCEPTS | Proteins: Folding, Misfolding, Disordered Proteins, and Related Diseases
Abstract
Glossary
Folding
Misfolding
Disordered Proteins
Related Diseases
See also
References
MOLECULAR PRINCIPLES, COMPONENTS, TECHNOLOGY, AND CONCEPTS: PROTEINS | Diseases of Protein Folding: Huntington’s Disease and Amyotrophic Lateral Sclerosis
Abstract
Introduction
Genetic Basis of HD and ALS
Effects of Protein Products on Protein Homeostasis
Clearance Pathways of Aggregates – Cellular UPS
Clearance Pathways of Aggregates – Autophagy Pathway
Cellular Transfer of Aggregates on Toxic Fragments
Cell Specificity and Susceptibility
Symptoms and Treatments of the Disease
Potential Treatments and Therapies
See also
References
Further Reading
MOLECULAR PRINCIPLES, COMPONENTS, TECHNOLOGY, AND CONCEPTS: PROTEINS | Site-Directed Mutagenesis
Abstract
Background
Methods
Applications
Summary
See also
References
MOLECULAR PRINCIPLES, COMPONENTS, TECHNOLOGY, AND CONCEPTS: PROTEINS | Chemical Biology
Abstract
Glossary
Introduction
Imaging
Metabolic Labeling
Affinity Labeling
Activity-Based Probes
Bioorthogonal Labeling
Chemical Biology and Drug Development
See also
References
Further Reading
MOLECULAR PRINCIPLES, COMPONENTS, TECHNOLOGY, AND CONCEPTS: PROTEINS | Drug Design
Abstract
Glossary
Introduction
History of Drug Development
Evolution of Drug Design
Structural Biology and Drug Development
HTS
Virtual Screening
Drug Design and Biologics
Antibody–Drug Conjugates
See also
References
Further Reading
Relevant Website
MOLECULAR PRINCIPLES, COMPONENTS, TECHNOLOGY, AND CONCEPTS: PROTEINS | Antibodies and Improved Engineered Formats (as Reagents)
Abstract
Introduction
Antibodies for In Vitro Diagnosis, in Soluble (RIA), Surface-Bound (ELISA), Cell-Bound (Fluorescence-Activated Cell Sorting (FACS)), Tissue-Bound (IHC) and Modern E-Device Formats
Antibodies for In Vivo Applications: Immunotherapy with Humanization and Deimmunisation
Design of ‘Antibody Fragments’ for Unique Clinical Applications In Vivo
Pharmacokinetics of Intact Antibodies versus Fragments
Engineering Multiple Specificity in Antibody Fragments
Antibody Libraries: Construction, Display, and Selection
Production, Stability, and Expression Levels
High-Value Clinical Applications
Angiogenesis and Vascular Blockade/Transport
Image-Guided Surgery: From Radioactive Image-Guided Surgery (RIGS) to Fluorescence Image-Guided Surgery (FIGS)
Conclusion
See also
References
Relevant Websites
Lipids
MOLECULAR PRINCIPLES, COMPONENTS, TECHNOLOGY, AND CONCEPTS: LIPIDS | Lipidomics
Abstract
Introduction
Why Lipidomics?
Description of How the Components of the Lipidome Are Usually Analyzed
Lipidomics Databases and Other Online Tools
Examples of Findings Using Lipidomics Approaches
Summary
See also
References
Relevant Websites
MOLECULAR PRINCIPLES, COMPONENTS, TECHNOLOGY, AND CONCEPTS: LIPIDS | Synthesis and Structure of Glycerolipids
Abstract
Glossary
Introduction
Synthesis of Phosphatidic Acid
Synthesis of Phospholipids in Bacteria
Synthesis of Phospholipids in Eukaryotes
Roles of Phospholipids in Cell Function
See also
References
Further Reading
MOLECULAR PRINCIPLES, COMPONENTS, TECHNOLOGY, AND CONCEPTS: LIPIDS | Cholesterol and Other Steroids
Abstract
Introduction
Structure
Cholesteryl Esters
Cholesterol in Cell Membranes
Cholesterol Biosynthesis
Regulation of Cholesterol Biosynthesis
Cellular Cholesterol Homeostasis
Cholesterol in Brain
Cholesterol in Diseases
Steroids
See also
References
MOLECULAR PRINCIPLES, COMPONENTS, TECHNOLOGY, AND CONCEPTS: LIPIDS | Glycolipids
Abstract
Introduction
Definition of ‘Glycolipid’ and Subcategories of Glycolipids
Glycosphingolipids – The Power of Combinatorial Biochemistry
Analysis of Glycolipids by ‘Omic’ Technologies
Perspective on the Future of Glycolipid Research
See also
References
Relevant Websites
MOLECULAR PRINCIPLES, COMPONENTS, TECHNOLOGY, AND CONCEPTS: LIPIDS | Lipid Signaling
Abstract
Glossary
Introduction
Lipid Classification and Nomenclature
The Primary Mammalian Signaling Lipids
Signaling Lipids are Spatially Restricted and Scarce
The Complexity of Lipid Signaling
Physiologic Roles of Signaling Lipids
Signaling Lipids and Disease
Recent Advances in Signaling Lipid Technologies
See also
References
Further Reading
Membranes
MOLECULAR PRINCIPLES, COMPONENTS, TECHNOLOGY, AND CONCEPTS: MEMBRANES | Composition, Physical Properties, and Curvature
Abstract
Origins
General Traits of Biological Membranes
Membrane Electrostatics
Lipid Packing
Membrane Subdomains
Mechanisms that Modifies the Bulk Lipid Composition of Organelles
Membrane Curvature
Conclusions
See also
References
Relevant Website
MOLECULAR PRINCIPLES, COMPONENTS, TECHNOLOGY, AND CONCEPTS: MEMBRANES | Lipid Rafts/Membrane Rafts
Abstract
Introduction
The Physical States of Lipids in Lipid Bilayers
Formulation of the Lipid Raft Hypothesis
What Hold Rafts Together?
The Basis of Membrane Protein Interaction with Rafts
Lipid Domain Size
Detecting Rafts in Model Membranes
Detecting Rafts in Natural Membranes: Giant Plasma Membrane Vesicles
Using Detergents to Detect Rafts in Cells: Rationale and Limitations
Detecting Rafts in Cells: Microscopy and Spectroscopy
Detecting Rafts in Cells Using Sterol Modification
Biological Functions of Raft Domains in Cells
Acknowledgment
See also
References
MOLECULAR PRINCIPLES, COMPONENTS, TECHNOLOGY, AND CONCEPTS: MEMBRANES | Membrane Potential: Concepts
Abstract
Introduction
Determinants of the Membrane Potential
Measuring Membrane Potential and Relative Membrane Permeability
Conclusion
Acknowledgments
References
Relevant Websites
MOLECULAR PRINCIPLES, COMPONENTS, TECHNOLOGY, AND CONCEPTS: MEMBRANES | The Outer Mitochondrial Membrane, a Smooth ‘Coat’ with Many Holes and Many Roles: Preparation, Protein Components, Interactions with Other Membranes, Involvement in Health, Disease, and as a Drug Target
Abstract
Introduction
Separation and Isolation of the Four Mitochondrial Compartments
Results: Protein/Enzyme Assignments of the Four Mitochondrial Compartments with an Emphasis on the Outer Mitochondrial Membrane
‘Moonlighting’ Roles of the Mitochondrial Outer Membrane with Its Intracellular Neighbors
Involvement of the Outer Mitochondrial Membrane in Major Diseases and Potential Drug Target
Concluding Remarks
Acknowledgments
See also
References
MOLECULAR PRINCIPLES, COMPONENTS, TECHNOLOGY, AND CONCEPTS: MEMBRANES | Neuronal Action Potentials and Ion Channel Allostery
Abstract
Glossary
Introduction
Electrical Properties of Neurons
Anatomy of a Neuron and Flow of Information
Action Potentials
Action Potential Propagation
Action Potential Invasion of the Nerve Terminal
Fate of Neurotransmitter in the Synaptic Cleft
Postsynaptic Receptors/Ligand-Gated Ion Channels
Allosteric Effectors
See also
References
MOLECULAR PRINCIPLES, COMPONENTS, TECHNOLOGY, AND CONCEPTS: MEMBRANES | Cystic Fibrosis
Abstract
Glossary
Introduction
Key Highlights
Protein
Genetics
See also
References
Further Reading
Carbohydrates
MOLECULAR PRINCIPLES, COMPONENTS, TECHNOLOGY, AND CONCEPTS: CARBOHYDRATES | Glycogen and Starch
Abstract
Introduction
Structures of Glycogen and Starch
Glycogen Metabolism
Starch Metabolism
Genetic Modification of Starch and Glycogen Metabolism
References
MOLECULAR PRINCIPLES, COMPONENTS, TECHNOLOGY, AND CONCEPTS: CARBOHYDRATES | Proteoglycans
Abstract
Introduction
Structure and Synthesis of Proteoglycans
Cellular Functions of Proteoglycans in Health and Disease
References
Further Reading
MOLECULAR PRINCIPLES, COMPONENTS, TECHNOLOGY, AND CONCEPTS: CARBOHYDRATES | Hyaluronan
Abstract
Primary Sources
Introduction
Structure and Cellular Metabolism
Conclusions
References
Relevant Websites
Metabolism
MOLECULAR PRINCIPLES, COMPONENTS, TECHNOLOGY, AND CONCEPTS: METABOLISM | Metabolic Regulation
Abstract
Glossary
Introduction
Mechanisms for Regulation of Key Enzymes
Substrates (Fuel) Availability
Allosteric Modulation
Covalent Modification (or Posttranslational Modification)
Inhibitory Protein (Regulatory Protein) Interaction
Transcriptional and Degradational Control
Metabolism in the Fed State
Metabolism in the Fasted (Starvation) State
Dedication
See also
References
Further Reading
MOLECULAR PRINCIPLES, COMPONENTS, TECHNOLOGY, AND CONCEPTS: METABOLISM | A Structure Perspective on Organelle Bioenergetics
Abstract
Glossary
Energetics of Membrane-Based Adenosine Triphosphate Synthesis
Atomic Structures of Membrane Protein Complexes Responsible for Energization, That Is, Generation of the Δμ˜H+, of Mitochondria and Chloroplasts
Primary Charge Separation and Formation of a Membrane Potential; Photosynthetic Reaction Centers
Acknowledgments
See also
References
Further Reading
Nucleic Acid Synthesis/Breakdown
RNA Synthesis/Function
NUCLEIC ACID SYNTHESIS/BREAKDOWN: RNA SYNTHESIS/FUNCTION | Transfer RNA
Abstract
Glossary
Basis of Transfer RNA
Aminoacyl-tRNA Synthetases
tRNA in Translation
Surprising Number of Roles of tRNAs beyond Translation
tRNA-Like Molecules
tRNA and Human Diseases
Concluding Remarks
Acknowledgments
References
Relevant Websites
NUCLEIC ACID SYNTHESIS/BREAKDOWN: RNA SYNTHESIS/FUNCTION | Messenger RNA (mRNA): The Link between DNA and Protein
Abstract
Glossary
Messenger RNA (mRNA)
Prokaryotic mRNA Structure
Eukaryotic mRNA
See also
References
Further Reading
NUCLEIC ACID SYNTHESIS/BREAKDOWN: RNA SYNTHESIS/FUNCTION | The Interplay between Eukaryotic mRNA Degradation and Translation
Abstract
Overview of Eukaryotic mRNA turnover
mRNA Degradation is Intimately Linked to Translation
The Ying-Yang of Translational Initiation and Transcript Stability
Translation Elongation and mRNA Turnover
Translation Termination and mRNA Stability
Where Does Eukaryotic mRNA Degradation Occur Within the Cell?
The mRNA Cycle Hypothesis – From Polysome to p-Bodies (and Perhaps Back)
Parting on Polysomes
What Does It All Mean?
Perspectives
References
NUCLEIC ACID SYNTHESIS/BREAKDOWN: RNA SYNTHESIS/FUNCTION | miRNAs/Small Noncoding RNAs
Abstract
Glossary
Introduction
Biogenesis of miRNAs in Animals
miRNAs in Plants
Mutations in the miRNA and the Pathway Genes Cause Human Diseases
Nomenclature of miRNA
See also
References
Further Reading
Relevant Website
NUCLEIC ACID SYNTHESIS/BREAKDOWN: RNA SYNTHESIS/FUNCTION | Small RNAs/Cancer
Abstract
Glossary
Introduction to Noncoding RNAs
Introduction to miRNAs: Discovery, Biogenesis, and Nomenclature
miRNAs and Cancer
IsomiRs
Other Forms of Noncoding RNAs and their Relevance to Cancer
Summary
See also
References
Relevant Websites
NUCLEIC ACID SYNTHESIS/BREAKDOWN: RNA SYNTHESIS/FUNCTION | Riboswitches and Ribozymes
Abstract
Glossary
Evolutionary Importance of RNA
Catalytic RNAs: Ribozymes
In Vitro Selection of Aptamers and Ribozymes
From Aptamers to Riboswitches
Control of Gene Expression by Riboswitches
Ribozymes are Ubiquitous in Nature
Ribozymes in the Replication of Viroids and Virusoids
Ribozymes as Mobile Genetic Elements
The Ribosome as a Ribozyme and Riboswitch
The glmS Ribozyme–Riboswitch
Ribozymes and Riboswitches as Cell Biological Tools
Acknowledgment
See also
References
NUCLEIC ACID SYNTHESIS/BREAKDOWN: RNA SYNTHESIS/FUNCTION | Ribosomal RNAs and Protein Synthesis
Abstract
Glossary
Introduction
Overview of Protein Synthesis
Functional Role of 16S and 23S rRNAs During Initiation
Functional Role of 16S and 23S RNAs During the Elongation Cycle
Functional Role of 16S and 23S RNAs During Termination
Functional Role of 16S and 23S RNAs During Recycling
Functional Role of 5S rRNA
Acknowledgments
See also
References
NUCLEIC ACID SYNTHESIS/BREAKDOWN: RNA SYNTHESIS/FUNCTION | Comparison of Bacterial and Eukaryotic Replisome Components
Abstract
Glossary
Introduction
Bacterial Replicative DNA Polymerases Are Distinct from Those of Eukaryotes
Sliding Clamps Are Conserved in All Cell Types
The Clamp Loader Was Also Present in LUCA
Bacterial and Eukaryotic Replicative Helicases
Primases Are Very Different in Bacteria Compared to Eukaryotes
Single-Strand DNA-Binding Protein
Comparison of Bacterial and Eukaryotic Replisomes
What Is Needed for the Future?
Acknowledgment
See also
References
DNA Synthesis/Repair
NUCLEIC ACID SYNTHESIS/BREAKDOWN: DNA SYNTHESIS/REPAIR | Telomeres and Telomerase
Abstract
Glossary
Telomeres
The End-Replication Problem
Telomeric DNA
Telomeric Proteins
Telomeric Repeat-Containing RNA
Telomerase
Telomerase Reverse Transcriptase
Telomerase RNA
Syndromes of Short Telomeres
Alternative Lengthening of Telomeres
See also
References
Further Reading
NUCLEIC ACID SYNTHESIS/BREAKDOWN: DNA SYNTHESIS/REPAIR | Telomere Biology
Abstract
Glossary
Introduction
Telomere Structure and Proteins
Telomere Replication and Length Maintenance
Telomere Physiology
See also
References
NUCLEIC ACID SYNTHESIS/BREAKDOWN: DNA SYNTHESIS/REPAIR | Eukaryotic Nucleotide Excision Repair
Abstract
Glossary
Perspective
Damage Recognition
Damage Verification
Assembly of the Incision Complex
Excision, Repair Synthesis, and Ligation
Human Diseases
Acknowledgments
See also
References
Relevant Website
NUCLEIC ACID SYNTHESIS/BREAKDOWN: DNA SYNTHESIS/REPAIR | The Base Excision Repair Pathway
Abstract
Glossary
Maintenance of Genome Stability and the Role of Base Excision Repair
Basic Overview of the BER Pathway
DNA Base Damage Recognition and Removal by DNA Glycosylases
Abasic Site Incision and Processing of DNA Strand Break Ends
Insertion of the Correct Undamaged Nucleotide
DNA Nick Ligation
The Long-Patch BER Pathway
The Importance of Key BER Proteins is Highlighted by Knockout Mouse Models
Regulation of BER Protein Levels
Conclusions
See also
References
Further Reading
NUCLEIC ACID SYNTHESIS/BREAKDOWN: DNA SYNTHESIS/REPAIR | Nonhomologous DNA End Joining
Abstract
Introduction
Mechanism of NHEJ
A-NHEJ
Choice of DSB Repair Pathway
NHEJ and Disease
NHEJ and Inhibitors
Acknowledgments
See also
References
NUCLEIC ACID SYNTHESIS/BREAKDOWN: DNA SYNTHESIS/REPAIR | DNA Repair by Homologous Recombination
Abstract
Glossary
Introduction
The Core Mechanism of Homologous Recombination
Recombination and Double-Strand Break Repair
Recombination and DNA Replication
Recombination and Interstrand Cross-Link Repair
Pathway Regulation and Crossover Control
HR and Human Disease
Conclusions
Acknowledgments
See also
References
Further Reading
Transcription
NUCLEIC ACID SYNTHESIS/BREAKDOWN: TRANSCRIPTION | Prokaryotic Transcription
Abstract
Glossary
Introduction
Core RNA Polymerase
Bacterial RNA Polymerase Holoenzyme
The Process of Transcription in Bacteria
Mechanisms that Regulate Bacterial Transcription
Transcription and Regulation in Archaea
Summary
Acknowledgments
References
Further Reading
NUCLEIC ACID SYNTHESIS/BREAKDOWN: TRANSCRIPTION | Eukaryotic Transcriptional Regulation
Abstract
Introduction
RNA Polymerases I, II, and III
Promoters and Transcription Factors
Transcription Initiation and Elongation
Experimental Approaches
See also
References
NUCLEIC ACID SYNTHESIS/BREAKDOWN: TRANSCRIPTION | Distant Activation of Transcription by Enhancers
Abstract
Glossary
Introduction
Bacterial Enhancer Action
Enhancer Action in Eukaryotes
Conclusions
Acknowledgment
See also
References
Relevant Websites
NUCLEIC ACID SYNTHESIS/BREAKDOWN: TRANSCRIPTION | The Spliceosome and Pre-mRNA Splicing
Abstract
Glossary
Introduction
The Chemistry of Splicing and the Architecture of the Intron
The Spliceosome is Composed of snRNAs and Proteins
Spliceosomes are Assembled from snRNPs on Introns
The Active Site of the Spliceosome
DExD/H Box Proteins are Essential Cofactors of the Spliceosome
Alternative Splicing Creates Multiple Products from a Single Gene
Splicing is Coupled to Other Cellular Processes
Defects in Splicing Cause Disease
Conclusion
See also
References
Further Reading
NUCLEIC ACID SYNTHESIS/BREAKDOWN: TRANSCRIPTION | Pre-mRNA Splicing: Function and Dysfunction
Abstract
Introduction
Splicing
Alternative Splicing
Diseases of the Spliceosome: Dysfunction Sheds Light on Function
Summary
Acknowledgments
See also
References
Nucleic Acid Technology
NUCLEIC ACID SYNTHESIS/BREAKDOWN: NUCLEIC ACID TECHNOLOGY | Transgenesis and Gene Replacement
Abstract
Introduction
Transgenesis
Temporal Regulation of Transgenes
Loss of Function
Gene Trap
Homologous Recombination
Precision Genome Editing
Conclusion
References
NUCLEIC ACID SYNTHESIS/BREAKDOWN: NUCLEIC ACID TECHNOLOGY | Viral Nucleic Acids
Abstract
Glossary
Introduction
Group I: dsDNA Viruses
Group II: ssDNA Viruses
Group III: dsRNA Viruses
Group IV: (+) Strand RNA Viruses
Group V: (–) Strand RNA Viruses
Group VI: (+) Strand RNA Viruses with DNA Intermediates
Group VII: dsDNA Viruses with RNA Intermediates
Gene Expression Strategies of RNA Viruses
Concluding Remarks
Note on Sources
See also
References
Relevant Website
Protein Synthesis/Degradation
Translation
PROTEIN SYNTHESIS/DEGRADATION: TRANSLATION | Components, Initiation, Elongation, Termination, and Regulation
Abstract
Glossary
Components of Protein Synthesis
Eukaryotic Translation Factors
The Elongation Cycle
Termination of Translation and Ribosome Recycling
Molecular Mimicry
Mistakes in Translation
See also
References
PROTEIN SYNTHESIS/DEGRADATION: TRANSLATION | Biogenesis of Secretory Proteins
Abstract
Glossary
Nascent Polypeptides Are Specifically Recognized and Delivered to the ER Membrane in a Co- or Posttranslational Manner
Conducting Channels Made of Integrated Membrane Proteins Translocate Nascent Polypeptides across the ER Membrane
The Nascent Polypeptides Form Their Native Structures in the ER Lumen with the Help of Multiple Factors
A Comprehensive Quality Control System in the ER Lumen Ensures that Only Correctly Folded/Assembled Proteins Are Transported with the Misfolded/Misassembled Ones to be Degraded
The Malfunctioning of Protein Folding in ER Are Known to Cause Folding Diseases
See also
References
PROTEIN SYNTHESIS/DEGRADATION: TRANSLATION | The Protein Biosynthetic Machinery of Mitochondria
Abstract
General Background
Information Content of Mitochondrial DNA
Components of the Translational System
Mechanism of Mitochondrial Protein Biosynthesis
Future Directions
See also
References
Further Reading
PROTEIN SYNTHESIS/DEGRADATION: TRANSLATION | Regulated Proteolysis of Signaling Molecules: The Proprotein Convertases
Abstract
Glossary
Introduction to Regulated Proteolysis
The Proprotein Convertases
Furin (PCSK3)
Prohormone Convertase 1/3 (PCSK1)
Prohormone Convertase 2 (PCSK2)
Proprotein Convertase 4 (PCSK4)
Paired Basic Amino Acid Cleaving Enzyme 4 (PACE4; PCSK6)
Proprotein Convertase 5/6 (PCSK5)
Proprotein Convertase 7 (PCSK7)
Summary and Conclusions
See also
References
Protein Degradation – General
PROTEIN SYNTHESIS/DEGRADATION: PROTEIN DEGRADATION – GENERAL | Mass Spectrometry-based Methodologies for Studying Proteolytic Networks and the Degradome
Abstract
Glossary
Introduction
Degradomics
Validation of Degradomic Data
Conclusions
See also
References
Relevant Website
Protein Degradation – Intracellular
PROTEIN SYNTHESIS/DEGRADATION: PROTEIN DEGRADATION – INTRACELLULAR | Ubiquitin, Ubiquitin-Like Proteins, and Proteasome-Mediated Degradation
Abstract
General Background
Ubiquitin and Ubiquitin-like Proteins
The 26S Proteasome
The UPS as Drug Target
Conclusion
See also
References
Further Reading
PROTEIN SYNTHESIS/DEGRADATION: PROTEIN DEGRADATION – INTRACELLULAR | Endoplasmic Reticulum-Associated Degradation and Protein Quality Control
Abstract
Glossary
Introduction
The Manufacturing of a Secretory Protein
Unforgivable Errors: The ERADication of an Unfolded Protein
Acknowledgments
See also
References
PROTEIN SYNTHESIS/DEGRADATION: PROTEIN DEGRADATION – INTRACELLULAR | Role of Lysosomes in Intracellular Degradation
Abstract
Glossary
Introduction
Lysosomal Proteins
Cathepsins
Lipases
Glycosidases
Pathways to the Lysosome
See also
References
Protein Degradation – Protease Classes
PROTEIN SYNTHESIS/DEGRADATION: PROTEIN DEGRADATION – PROTEASE CLASSES | Matrix Metalloproteinases
Abstract
Glossary
Structure
Substrate Profiles: Biological and Biomedical Implications
Cellular Regulation of MMPs
MMPs as Therapeutic Targets and Anti-Targets: The Use of Synthetic Inhibitors
Imaging of MMPs
MMP Activity in Drug Delivery Mechanisms
Future Directions
See also
References
Relevant Websites
PROTEIN SYNTHESIS/DEGRADATION: PROTEIN DEGRADATION – PROTEASE CLASSES | ADAMTS Proteases: Mediators of Physiological and Pathogenic Extracellular Proteolysis
Abstract
Glossary
Introduction, Defining Characteristics and Phylogeny of A Disintegrin-Like and Metalloprotease Domain with Thrombospondin Type 1 Motif Proteinases
Domain Organization and 3-Dimensional Structure
Biosynthesis and Regulation
Mechanistic Basis of Genetic and Acquired Disorders Involving ADAMTS Proteases
Functions in Mammalian Development Gleaned from Mouse Mutants
See also
References
Further Reading
PROTEIN SYNTHESIS/DEGRADATION: PROTEIN DEGRADATION – PROTEASE CLASSES | ADAMs Regulate Cell–Cell Interactions by Controlling the Function of the EGF-Receptor, TNFα and Notch
Abstract
Glossary
Introduction
ADAM17, the TNFα Convertase
ADAM17 is Crucial for EGFR Signaling
ADAM17-Dependent EGFR Activation Protects the Skin and Intestinal Barrier
ADAM17/TNFα and ADAM17/EGFR Signaling are Controlled by Upstream Regulators Called iRhoms
ADAM10, A Crucial Regulator of Notch Signaling
Other Substrates of ADAM10 and ADAM17
Summary
See also
References
PROTEIN SYNTHESIS/DEGRADATION: PROTEIN DEGRADATION – PROTEASE CLASSES | Extracellular: Plasma Membrane Proteases – Serine Proteases
Abstract
Introduction
Membrane-Anchored Serine Proteases
The GPI-Anchored Serine Proteases
The Type I Transmembrane Serine Proteases
The Type II Transmembrane Serine Proteases
Conclusion
See also
References
PROTEIN SYNTHESIS/DEGRADATION: PROTEIN DEGRADATION – PROTEASE CLASSES | Aspartic Proteases of Alzheimer’s Disease: β- and γ-Secretases
Abstract
Glossary
Amyloid and Alzheimer’s Disease
β-Secretase
γ-Secretase
See also
References
Further Reading
PROTEIN SYNTHESIS/DEGRADATION: PROTEIN DEGRADATION – PROTEASE CLASSES | The Calpain Proteolytic System
Abstract
Introduction
Structure of Conventional Calpains
Classification of Calpains
Regulation and Activation of Calpains
Calpains in Apoptosis
Physiological Functions of Calpains and the Role of Dysregulation in Human Disease
Conclusion
See also
References
PROTEIN SYNTHESIS/DEGRADATION: PROTEIN DEGRADATION – PROTEASE CLASSES | Cathepsin E: An Aspartic Protease with Diverse Functions and Biomedical Implications
Abstract
Aspartic Peptidases
Cathepsin E
Conclusion Remarks
Acknowledgments
See also
References
Relevant Website
PROTEIN SYNTHESIS/DEGRADATION: PROTEIN DEGRADATION – PROTEASE CLASSES | Metalloproteases Meprin α and Meprin β in Health and Disease
Abstract
Introduction
Structural Features of Meprin α and Meprin β
Inhibition of Meprin Metalloproteases
Cleavage Specificity and Identification of Substrates by Proteomics
Physiologic and Pathologic Role of Meprin α and Meprin β
Conclusion
See also
References
PROTEIN SYNTHESIS/DEGRADATION: PROTEIN DEGRADATION – PROTEASE CLASSES | Kallikrein
Abstract
Glossary
Introduction
Plasma KLK
Tissue KLK
Kinins
Kallikrein-Related Peptidases
KLK–Cell Interactions
KLK and Cancer
See also
References
Further Reading
PROTEIN SYNTHESIS/DEGRADATION: PROTEIN DEGRADATION – PROTEASE CLASSES | Naturally-Occurring Polypeptide Inhibitors: Cystatins/Stefins, Inhibitors of Apoptosis (IAPs), Serpins, and Tissue Inhibitors of Metalloproteinases (TIMPs)
Abstract
Glossary
General Introduction
Cystatins/Stefins
Inhibitors of Apoptosis
Serpins
Tissue Inhibitors of Metalloproteinases
See also
References
Relevant Website
Proteolytic Pathways
PROTEIN SYNTHESIS/DEGRADATION: PROTEOLYTIC PATHWAYS | Overview of Blood Coagulation and the Pathophysiology of Blood Coagulation Disorders
Abstract
Overview of Blood Coagulation
Primary Hemostasis
Secondary Hemostasis
Regulation of Blood Coagulation
Coagulation Disorders Overview
Conclusions
See also
References
PROTEIN SYNTHESIS/DEGRADATION: PROTEOLYTIC PATHWAYS | Molecular Mechanisms Underlying the Actions of the Complement System
Abstract
The Complement System
Classical Pathway
Lectin Pathway
The Alternative Pathway
Regulation of Complement Activation by Proteases and Binding Factors
See also
References
Relevant Websites
PROTEIN SYNTHESIS/DEGRADATION: PROTEOLYTIC PATHWAYS | Digestive Proteases: Roles in the Human Alimentary Tract
Abstract
Glossary
Introduction
Role of the Oral Cavity in Proteolysis
Role of the Stomach in Proteolysis
Role of the Small Intestine in Proteolysis
Role of the Large Intestine in Proteolysis
Summary
References
Relevant Websites
Protein Degradation – Pathological Aspects
PROTEIN SYNTHESIS/DEGRADATION: PROTEIN DEGRADATION – PATHOLOGICAL ASPECTS | Inhibitors of HIV Protease
Abstract
Glossary
Introduction
Structure and Enzymatic Mechanism of HIV Protease
Inhibitors of Retroviral Proteases
First generation of HIV-1 PR Inhibitors Approved as AIDS Drugs
Emergence of Resistance to Clinical Inhibitors of HIV-1 PR
Roads Not Taken – Inhibitors of HIV-1 PR That Did Not Become Drugs
Where Will the HIV-1 PR Inhibitors Be in the Future?
See also
References
Relavant Website
PROTEIN SYNTHESIS/DEGRADATION: PROTEIN DEGRADATION – PATHOLOGICAL ASPECTS | Blood Pressure, Proteases and Inhibitors
Abstract
Glossary
Introduction
Proteolytic Regulation of Blood Pressure
The Natriuretic Peptide Family and Their Proteases (Corin, Furin, and NEP)
The Endothelin Peptide Family and Their Proteases
Summary
References
Further Reading
PROTEIN SYNTHESIS/DEGRADATION: PROTEIN DEGRADATION – PATHOLOGICAL ASPECTS | Cancer – Proteases in the Progression and Metastasis
Abstract
Introduction
Aspartic Proteases
Cysteine Proteases
Metalloproteases
Serine Proteases
Threonine Proteases
Concluding Remarks
See also
References
Further Reading
PROTEIN SYNTHESIS/DEGRADATION: PROTEIN DEGRADATION – PATHOLOGICAL ASPECTS | Lysosomal Diseases
Abstract
Introduction
Lysosomal Diseases
Nomenclature
Other Lysosomal Diseases
Related Conditions Affecting Organelle Biogenesis
Functional Complementation of Lysosomal Diseases
Treatment of Lysosomal Diseases
Therapeutic Stratagems for Lysosomal Diseases with Neurological Manifestations
Advances in the Field
Pathogenesis and Physiological Understanding
Conclusion
Acknowledgments
References
PROTEIN SYNTHESIS/DEGRADATION: PROTEIN DEGRADATION – PATHOLOGICAL ASPECTS | Alpha-1-Antitrypsin Deficiency: A Misfolded Secretory Glycoprotein Damages the Liver by Proteotoxicity and Its Reduced Secretion Predisposes to Emphysematous Lung Disease Because of Protease-Inhibitor Imbalance
Abstract
Glossary
Introduction
Physiology and Function of AT
Mechanism of Deficiency in the Classical form of ATD
Cellular Mechanisms of Liver Disease
Cellular Mechanisms of Lung Disease
Cellular Responses to Misfolding of Mutant ATZ
Therapies for ATD Liver Disease
Therapies for ATD Lung Disease
See also
References
Organizational Cell Biology
Organizational Cell Biology: An Overview
Imaging the Cell
Organelles
Interorganellar Communication
Cytoskeleton and Motors
Intracellular Infectiology
Reference
Imaging the Cell
Electron Microscopy
IMAGING THE CELL: ELECTRON MICROSCOPY | Single-Particle CryoEM of Macromolecular Complexes
Abstract
Introduction
CryoEM Sample Consideration
Frozen, Hydrated Specimen Preparation
CryoEM Image Acquisition
CryoEM Image Processing
Resolution of CryoEM Density Maps
CryoEM Model Building and Model Validation
High-Resolution CryoEM Structures
Identifying Different Populations Within a Heterogeneous Sample
Delineating the Conformational Changes of a Molecular Machine
Conclusion
Acknowledgments
See also
References
Relevant Website
IMAGING THE CELL: ELECTRON MICROSCOPY | Scanning Electron Microscopy in Cell Biology
Abstract
Introduction
Scanning Electron Microscopy ‘Versus’ Transmission Electron Microscopy
Construction of the SEM
Scanning the Specimen
Beam – Specimen Interactions
Image Formation
A Brief History of SEM
Specimen Preparation for SEM
Critical Point Drying
Sputter Coating
Labeling for SEM
Cryoscanning EM
Environmental SEM
Serial Block Face Imaging
Merging SEM and TEM
Freeze Etching
SEM and the Nuclear Envelope
SEM in Cell Biology
See also
References
Further Reading
IMAGING THE CELL: ELECTRON MICROSCOPY | Electron Tomography
Abstract
Glossary
Introduction
Specimen Preparation Methods
Methods of Cryo-ET
Techniques to Combine with Cryo-ET
Examples
Future Outlook
Supplementary Video
See also
References
Further Reading
IMAGING THE CELL: ELECTRON MICROSCOPY | Immunoelectron Microscopy: High-Resolution Immunocytochemistry
Abstract
Glossary
Introduction
Sample Preparation Strategies
Immunolabeling Strategies
CLEM
Immunogold Label Quantification and Labeling Specificity
Conclusions
See also
References
Further Reading
IMAGING THE IMAGING THE CELL: ELECTRON MICROSCOPY | Imaging Cellular Architecture with 3D SEM
Abstract
Introduction
Sample Preparation for 3D SEM
Orientation and Location of Region of Interest
3D SEM Techniques
Data Handling and Segmentation
New Methods and Future Developments
Acknowledgments
See also
References
Light Microscopy
IMAGING THE CELL: LIGHT MICROSCOPY | Genetically Encoded Fluorescent Probes and Live Cell Imaging
Abstract
Introduction – Fluorescent Proteins
Fluorescent Proteins as Probes for Function
Imaging Cells in Whole Organisms
Breaking the Diffraction Barrier
Technical Considerations for Live Imaging
Looking Forward
See also
References
IMAGING THE CELL: LIGHT MICROSCOPY | Total Internal Reflection Fluorescence Microscopy
Abstract
Introduction
Theoretical Basis
Applications and Combinations in Cell Biology
Optical Configurations and Setup
Additional Features
TIRF versus Other Optical Sectioning Microscopies
See also
References
IMAGING THE CELL: LIGHT MICROSCOPY | Super Resolution Fluorescence Localization Microscopy
Abstract
Glossary
Introduction
Concept
Experimental Methods
Data Analysis
Discussion
Acknowledgments
See also
References
IMAGING THE CELL: LIGHT MICROSCOPY | Super-Resolution Light Microscopy: Stimulated Emission Depletion and Ground-State Depletion
Abstract
Introduction
STED and GSD for Super-Resolution: Principle and Technology
Biological Applications of STED and GSDIM
Conclusion
Acknowledgment
See also
References
Relevant Websites
IMAGING THE CELL: LIGHT MICROSCOPY | Structured Illumination Microscopy
Abstract
Introduction
Principles of SIM
Microscope Hardware, Software, and Data Acquisition
Imaging Artifacts: Causes and Manifestations
Applications
Recent Developments
References
Relevant Website
IMAGING THE CELL: LIGHT MICROSCOPY | Fluorescence Correlation Spectroscopy: A Tool for Measuring Dynamic and Equilibrium Properties of Molecules in Cells
Abstract
Glossary
Introduction
Basic Concepts and Theory
Experimental Considerations
Measurement of Molecular Association and Aggregation
Summary
Appendix
Acknowledgments
See also
References
IMAGING THE CELL: LIGHT MICROSCOPY | Fluorescence Lifetime Imaging – Applications and Instrumental Principles
Abstract
Glossary
Fluorescence
FLIM Applications in Life Sciences
Clinical FLIM Applications
Technical Aspects of FLIM
Latest Developments
See also
References
IMAGING THE CELL: LIGHT MICROSCOPY | High-Speed Localization Microscopy and Single-Particle Tracking
Abstract
Introduction
The Localization Concept
Experimental Requirements
High-Speed LM
SPT
Future Trends/Avenues
Conclusion
See also
References
IMAGING THE CELL: LIGHT MICROSCOPY | Intravital Microscopy in Mammalian Organisms: From Tissue Physiology to Cell Biology
Abstract
Brief Historical Background on Intravital Microscopy
Imaging Techniques Used to Perform IVM
Current Applications of IVM
Concluding Remarks
Acknowledgments
References
IMAGING THE CELL: LIGHT MICROSCOPY | Optogenetics
Abstract
Glossary
Light As a Tool in Biology
Optogenetics – Manipulating Molecules, Cells, and Organisms with Light
Light-Sensitive Proteins to Control Cellular Excitability
Optochemical Approaches to Control Specific Receptors and Ion Channels
Summary – From Molecules to Systems
Acknowledgments
See also
References
Further Reading
Organelles
Structure and Function
ORGANELLES: STRUCTURE AND FUNCTION | The Endoplasmic Reticulum
Abstract
Introduction
Origin and Function of the ER
Morphology of the ER
Membrane Contact Sites of the ER with Other Organelles
Translocation and Membrane Embedding of ER Client Proteins
Posttranslational Modifications of ER Client Proteins
Protein Folding in the ER
Export from and Retrieval to the ER
ER Homeostasis
Perspectives
Acknowledgments
See also
References
Further Reading
ORGANELLES: STRUCTURE AND FUNCTION | Intermediate Compartment: A Sorting Station between the Endoplasmic Reticulum and the Golgi Apparatus
Abstract
Glossary
Introduction
Historical Perspective
Compositional Aspects
Structure, Distribution, and Dynamics
Different IC Models
Functional Aspects
Links to Disease
See also
References
Further Reading
ORGANELLES: STRUCTURE AND FUNCTION | Golgi and TGN
Abstract
The Golgi Apparatus – An Introduction
The Structure of the Golgi Apparatus
Transport through the Golgi
Molecular Mechanism of Transport
Glycosylation at the Golgi
Regulation of the Golgi Apparatus Structure and Function
Role of Golgi in Disease
Evolution of the Golgi Apparatus
Perspectives
See also
References
ORGANELLES: STRUCTURE AND FUNCTION | Early Endosomal Compartments
Abstract
Endosomes
Endosome Heterogeneity Reflects Functional Compartmentalization
Epithelial Cells Have Spatially Separated, Connected Endosomal Circuits
(Ultra)structure and Specialization
Regulation of Endosome Traffic
Early Endosome Maturation and Conversion to Late Endosomes
Retrieval of Proteins from Endosomes to the Trans Golgi Network
Recycling from Early Endosomes to the Plasma Membrane
Conclusion and Perspectives
See also
References
ORGANELLES: STRUCTURE AND FUNCTION | The Late Endosome
Abstract
Introduction
The Early/Recycling Endosome Network
Biogenesis of the Multivesicular Body
The Late Endosome–Lysosome Network
Endosomes in Plants and Fungi
Lysosome Enzymes and Lysosomal Membrane Proteins
Composition and Fate of Intralumenal Membranes
Other Destinations: All Roads Do Not Lead to the Lysosomes
The Late Endosome: A Signaling Platform
See also
References
Further Reading
ORGANELLES: STRUCTURE AND FUNCTION | Signaling from Endosomes
Abstract
Endocytosis
Different Cell Types Employ Signaling Endosomes for Distinct Purposes
Endocytic Routes Specify Signaling Outcome
Endocytosis Regulates Signal Termination and Cellular Response to Ligand Gradient
Endosomes – A World of Their Own
Endocytosis Regulates Spatial Signaling and Signal Amplification
Signaling Regulates Endocytosis
Endocytosis and Implications in Cancer
Conclusions and Future Perspectives
See also
References
ORGANELLES: STRUCTURE AND FUNCTION | Conventional and Secretory Lysosomes
Abstract
Introduction
Conventional Lysosomes
Cell Type-Specific Secretory Lysosomes
Biogenesis of Lysosomes and Secretory Lysosomes
Exocytosis of Secretory Lysosomes
Genetic Diseases Associate with Defects in Conventional or Secretory Lysosomes
Conclusions
See also
References
Further Reading
ORGANELLES: STRUCTURE AND FUNCTION | Lysosome-Related Organelles
Abstract
Glossary
Morphology, Composition, and Function of Lysosome-Related Organelles
Biogenesis and Transport of LROs
Genetic Diseases Associated with Defects in LRO Biogenesis and Transport
Multi-Media Annexes
See also
References
Relevant Websites
ORGANELLES: STRUCTURE AND FUNCTION | At the Center of Autophagy: Autophagosomes
Abstract
Glossary
Macroautophagy and Autophagosomes
Acknowledgments
See also
References
Further Reading
ORGANELLES: STRUCTURE AND FUNCTION | Peroxisomes
Abstract
Introduction and Morphology
Some Important, Specialized Physiological Functions of Peroxisomes
Conserved Biochemical Pathways Present in Most Peroxisomes
Other Peroxisome Functions
Metabolic Cooperation and Interaction with Other Organelles
Peroxisome Abundance, Adaptability, and Regulation
Peroxisome Division, Transport, and Inheritance
Peroxisome Biogenesis
Remodeling, Random Turnover, and Selective Degradation
Evolution
Human Disease and Peroxisomes
Conclusion
See also
References
ORGANELLES: STRUCTURE AND FUNCTION | Lipid Droplets
Abstract
Glossary
Basic Structure
LD Proteins
Adipocyte LDs
LD Subpopulations
Biogenesis of LDs
Neutral Lipid Synthesis and Lipolysis
Droplet Dynamics
Lipid Droplets and Disease
See also
References
Further Reading
ORGANELLES: STRUCTURE AND FUNCTION | Mechanisms and Functions of Mitochondrial Dynamics
Abstract
Glossary
Introduction
Mitochondrial Fusion Machinery and Regulation
Molecular Insights into Drp1 Actions During Mitochondrial Fission
Physiologic Importance of Mitochondrial Dynamics
Perspective
Acknowledgments
See also
References
ORGANELLES: STRUCTURE AND FUNCTION | Synaptosomes and Synaptic Vesicles
Abstract
Introduction
Synaptosomes
SVs
See also
References
Further Reading
Organelles: Structure and Function | Extracellular Vesicles
Abstract
Extracellular Vesicles
The Physiological Role of EVs: From Waste Bin to Versatile Transporter of Biological Signals
EVs in Cross-Kingdom Communication
EV Biogenesis
EVs in Disease
Clinical Applications of EVs
Concluding Remarks
See also
References
Further Reading
ORGANELLES: STRUCTURE AND FUNCTION | Nuclear Organization (Nuclear Structure and Dynamics)
Abstract
Introduction
Nuclear Structure and Function
Conclusion
See also
References
ORGANELLES: STRUCTURE AND FUNCTION | Nuclear Pores
Abstract
Structure of the Nuclear Pore Complex
Nucleoporins (Nups)
Dynamic Behavior of Nuceloporin
Nucleocytoplasmic Transport
Nucleoporin and Diesease
See also
References
ORGANELLES: STRUCTURE AND FUNCTION | Plastids: The Anabolic Factories of Plant Cells
Abstract
Introduction
Plastids of the Viridiplantae
References
Further Reading
Interorganellar Communication
Interplay and Processes
INTERORGANELLAR COMMUNICATION: INTERPLAY AND PROCESSES | ER–Golgi Transport
Abstract
The COPII Coat
Cargo Capture during Vesicle Formation
Regulation of COPII Biogenesis: The GTPase Cycle
Cellular Regulation of COPII Vesicle Biogenesis
Regulation of Vesicle Size
Vesicle Tethering
Vesicle Fusion
Conclusions
See also
References
INTERORGANELLAR COMMUNICATION: INTERPLAY AND PROCESSES | N-Linked Glycans (N-Glycans)
Abstract
Glossary
Introduction
Initiation of an N-Glycan on Dolichol-Phosphate
Maturation of the Dol-P-P-Oligosaccharide
En-Bloc Transfer of an N-Glycan to Protein
Processing and Folding of Glycoproteins in the ER
Unique Modification of Lysosomal Hydrolases
Maturation of N-Glycans During Transit Through Golgi Compartments
Functions of N-Glycans
Summary
See also
References
Further Reading
INTERORGANELLAR COMMUNICATION: INTERPLAY AND PROCESSES | Extracellular O-Glycans
Abstract
Glossary
Introduction
Mucin-Type O-Glycans/O-GalNAc Glycans
O-Mannose Glycans
O-Fuc Glycans
O-Glc Glycans
O-GlcNAc Glycans
O-Gal Glycans
Proteoglycans/O-Xyl Glycans
Conclusions
See also
References
Further Reading
INTERORGANELLAR COMMUNICATION: INTERPLAY AND PROCESSES | Intra-Golgi Transport
Abstract
Glossary
Introduction
Conclusions/perspectives
Acknowledgment
See also
References
INTERORGANELLAR COMMUNICATION: INTERPLAY AND PROCESSES | Post-Golgi Transport – Cargo, Carriers, and Pathways
Abstract
Introduction
Overview of Pathways
Cargo Sorting and Packaging at the TGN
Concluding Remarks
Acknowledgments
See also
References
INTERORGANELLAR COMMUNICATION: INTERPLAY AND PROCESSES | Regulation of the Secretory Pathway
Abstract
Constitutive and Regulated Secretion
The Regulation of Constitutive Secretion
Extent of the Regulation Network of the Secretory Pathway
Traffic Regulation in Response to Environmental Signals and Demands
Signaling Pathways that Support Homeostasis and Coordination of the Secretory Apparatus with Other Cellular Modules
The Conceptual Framework
Summary and Conclusions
See also
References
INTERORGANELLAR COMMUNICATION: INTERPLAY AND PROCESSES | Regulated versus Constitutive Secretion – A Major Form of Intercellular Communication
Abstract
Glossary
Summary
Overview
How Do We Know about Regulated versus Constitutive Secretion?
Tour of Regulated Secretion
The Steps of Regulated Exocytosis
Constitutive Secretion
Conclusion
See also
References
Relevant Websites
INTERORGANELLAR COMMUNICATION: INTERPLAY AND PROCESSES | Clathrin and Clathrin-Dependent Endocytosis
Abstract
Introduction
Biochemistry of Clathrin
Cellular Function and Regulation of Clathrin
Conclusions
See also
References
Further Reading
INTERORGANELLAR COMMUNICATION: INTERPLAY AND PROCESSES | Clathrin Independent Endocytosis
Abstract
Introduction
Macropinocytosis
Caveolae
Clathrin- and Caveolin-Independent Micropinocytic Pathways
Conclusions and Perspectives
Acknowledgments
See also
References
Further Reading
INTERORGANELLAR COMMUNICATION: INTERPLAY AND PROCESSES | Rabs of the Endosomal Recycling Pathway
Abstract
Overview
Rab4 and the ‘Short-Loop’ Recycling Pathway
Rab11 and the Endosomal Recycling Compartment
Other Rabs of the Endosomal Recycling Pathway
Intracellular Pathogens Subvert the Function of Rab GTPases
Summary
Acknowledgments
See also
References
INTERORGANELLAR COMMUNICATION: INTERPLAY AND PROCESSES | Endosome to Lysosome Transport
Abstract
Introduction
Endocytic Vesicles and Early Endosomes
Biogenesis of MVBs and Cargo Sorting
Late Endosomes
Role of pH and Ion Concentrations in Endosomal Maturation
Perinuclear Clustering of LE and Fusion Events
Role of Rab Proteins
Role of Cytoskeletal Elements and of Molecular Motors
Conclusions and Perspectives
See also
References
Further Reading
INTERORGANELLAR COMMUNICATION: INTERPLAY AND PROCESSES | Endocytosis of Cargo Proteins: LDL
Abstract
Glossary
Introduction
Low Density Lipoprotein Biosynthesis
The LDL Receptor
Cargo-Selective Clathrin Adaptors for the LDL Receptor
Endosomal Dynamics
Dynamic Modulation of LDL Receptor Surface Levels
Concluding Remarks
Acknowledgment
References
Relevant Websites
INTERORGANELLAR COMMUNICATION: INTERPLAY AND PROCESSES | Retrograde Transport
Abstract
Introduction
Different Retrograde Pathways
Biophysical Mechanisms for Retrograde Trafficking
Biomedical Applications of Retrograde Trafficking
See also
References
INTERORGANELLAR COMMUNICATION: INTERPLAY AND PROCESSES | Rabs and Other G Proteins
Abstract
Introduction
Rab Family of G Proteins and Membrane Trafficking
Biosynthesis and Membrane Targeting of Rab Proteins
Structure and GTPase cycle of Rab Proteins
Effectors and Functions of Rab Proteins
Other G Proteins
Acknowledgement
See also
References
Further Reading
Components
INTERORGANELLAR COMMUNICATION: COMPONENTS | Adaptor Proteins: Inter-Organelle Traffic Controllers
Abstract
Adaptor Proteins
Heterotetrameric Adaptor Complexes
GGAs
The Epsin and Eps15 Families
AP180 and Clathrin Assembly Lymphoid Myeloid Leukemia
PTB Domain Containing Family (DAB, ARH, and Numb)
Arrestin Family
The Adaptor Protein Network
See also
References
INTERORGANELLAR COMMUNICATION: COMPONENTS | SNAREs: Membrane Fusion and Beyond
Abstract
Introduction: A Brief Historical Perspective on Soluble N-Ethylmaleimide-Sensitive Factor Attachment Protein Receptors (SNAREs)
SNAREs: Membrane Fusion Nanomachines
The Regulators of the SNARE Nanomachine
SNAREs: More than Fusogenic Proteins? The Case of the Longin v-SNAREs Sec22b and TI-VAMP/VAMP7
Conclusion
See also
References
Further Reading
INTERORGANELLAR COMMUNICATION: COMPONENTS | ESCRTing around the Cell
Abstract
History
ESCRT Machinery
Models of ESCRT Function
ESCRTs in the Endolysosomal System
ESCRTs in Virus Budding
ESCRTs in Cytokinesis
ESCRTs in Extracellular Vesicle Biogenesis
Non-Endosomal Roles for the ESCRT Machinery
Summary and Perspectives
See also
References
INTERORGANELLAR COMMUNICATION: COMPONENTS | The Retromer Complex
Abstract
Introduction
A Brief History of Retromer
The Assembly and Structure of Retromer
How Membrane Tubules are Stabilized
Recruitment of Retromer
Recognition of Cargo
Accessory Proteins that Modulate Retromer Function
The Physiological Processes That Depend on Retromer
Retromer and Disease
Acknowledgments
See also
References
INTERORGANELLAR COMMUNICATION: COMPONENTS | Vesicle Tethers
Abstract
Glossary
Introduction
Interactions with Small GTPases and SNARE Proteins
Coiled-Coil Tethers
Multisubunit Tethering Complexes
Conclusions
See also
References
Further Reading
INTERORGANELLAR COMMUNICATION: COMPONENTS | BAR Domains and BAR Domain Superfamily Proteins
Abstract
Introduction
See also
References
Interplay and Processes
INTERORGANELLAR COMMUNICATION: INTERPLAY AND PROCESSES | Role of Phosphoinositides in Membrane Traffic
Abstract
Glossary
Phosphoinositides at the Membrane–Cytosol Interface
Organelle Compartments the Spatial Restriction of Phosphoinositide Species and Organelle Identity
Phosphoinositides in Plasma Membrane Trafficking
Phosphoinositides in the Endosomal Compartment – Early Endosomes, Recycling Endosomes, and Late Endosomes
Phosphoinositides in Golgi Trafficking
Retrograde Trafficking from Endosomes to Golgi
Phosphoinositides in the Regulation of Autophagy
Concluding Remarks
See also
References
INTERORGANELLAR COMMUNICATION: INTERPLAY AND PROCESSES | Unconventional Protein Secretion: Fibroblast Growth Factor 2 and Interleukin-1β as Examples
Abstract
Mechanisms of Eukaryotic Protein Secretion
Hallmarks of FGF2 Membrane Translocation during Unconventional Secretion
The Molecular Mechanism of FGF2 Membrane Translocation and Its Path of Discovery
PI(4,5)P2-Induced FGF2 Oligomerization and Membrane Pore Formation: A Transient Intermediate in FGF2 Membrane Translocation
Understanding the Regulation of IL-1β Processing
IL-1β Secretion and Cell Death
Mechanisms of IL-1β Release
Unconventional Secretion – What Is It Good for?
Future Perspectives
Acknowledgments
See also
References
INTERORGANELLAR COMMUNICATION: INTERPLAY AND PROCESSES | Endoplasmic Reticulum Stress in Disease
Abstract
Glossary
Introduction
The Role of the UPR in Human Health and Disease
Conclusions
Acknowledgments
See also
References
Further Reading
Cytoskeleton and Motors
Cytoskeletal Components
CYTOSKELETON AND MOTORS: CYTOSKELETAL COMPONENTS | Microtubules and Microtubule-Associated Proteins (MAPs)
Abstract
Glossary
Microtubule Structure
Microtubule Dynamics
Cellular Functions of Microtubules
MAPs
Regulation of Microtubule Structure and Mechanics by MAPs
Regulation of Microtubule Dynamics by MAPs
Arrangement of Microtubules into Higher-Order Structures by MAPs
Microtubules in Human Disease
See also
References
Relevant Websites
CYTOSKELETON AND MOTORS: CYTOSKELETAL COMPONENTS | Actin Assembly Dynamics and Its Regulation in Motile and Morphogenetic Processes
Abstract
Glossary
Introduction
Actin: Structural and Mechanical Properties
Actin Self-Assembly: Nucleation-Growth, Thermodynamics, Polarity, ATP Hydrolysis
Regulation of Actin Assembly by Associated Proteins
Site-directed Branching of Actin Filaments by WASP Protein Family and Arp2/3 Complex
Integrated Protein Modules in Reconstituted Actin-Based Motility
Actin Regulators in Adhesion Structures
Actin-Based Molecular Motors: The Family of Myosins
Actin in the Nucleus? Potential Role of Actin in the Regulation of Gene Expression
Bacterial Actin Ancestors
See also
References
Further Reading
CYTOSKELETON AND MOTORS: CYTOSKELETAL COMPONENTS | Intermediate Filaments
Abstract
Glossary
The Intermediate Filament Protein Family is Subdivided into Six Types with Cell Type-Specific Expression Patterns
Intermediate Filament Proteins Are Reliable Markers of Cellular Differentiation
Intermediate Filaments Share a Common Secondary Structure
Intermediate Filaments Can Be Assigned to Three Different Assembly Groups
Intermediate Filament Networks Have Distinct Properties That Render Them Different from the Other Cytoskeletal Systems
Cytoplasmic Intermediate Filament Network Organization Is Determined by Interaction with Major Cellular Components through Associated Proteins
Lamin Intermediate Filaments Contribute to Nuclear Structure and Function
Intermediate Filament Proteins Are Posttranslationally Modified
Intermediate Filaments Serve Many Functions
Cytoplasmic Intermediate Filament Dysfunctions Cause Tissue-Specific Diseases
Lamin Intermediate Filament Mutations Cause Complex Syndromes
Highly Diverse Intermediate Filament Proteins Occur Throughout the Animal Kingdom
See also
References
Further Reading
CYTOSKELETON AND MOTORS: CYTOSKELETAL COMPONENTS | Septins: Cytoskeletal Filaments with Structural and Regulatory Functions
Abstract
Septin Structure, Assembly, and Dynamics
Septins and the Membrane Skeleton
Septins and the Actin Cytoskeleton
Septins and the Microtubule Cytoskeleton
Conclusions
See also
References
Further Reading
CYTOSKELETON AND MOTORS: CYTOSKELETAL COMPONENTS | Bacterial and Archaeal Cytoskeletons
Abstract
Introduction
Cytokinesis
DNA Segregation
Cell Shape Determination
Organization of Intracellular Membrane Compartments
Conclusion
See also
References
Further Reading
CYTOSKELETON AND MOTORS: CYTOSKELETAL COMPONENTS | Myosins
Abstract
Glossary
Introduction
Myosin Structure and Organization
Mechanochemical ATPase Cycle
Pathophysiology
Class-1 Myosins
Class-2 Myosins
Class-3 and -9 Myosins
Class-5 Myosins
Class-6 Myosins
Class-7, -10, and -15 Myosins
Class-8 and 11 Myosins
Class-14 Myosins and -21 Myosins
Class-16 and -18 Myosins
Class-19 Myosins
Summary and Perspectives
Acknowledgment
See also
References
Further Reading
CYTOSKELETON AND MOTORS: CYTOSKELETAL COMPONENTS | Kinesin Superfamily Proteins (KIFs) as a Fundamental Component of Life: Intracellular Transport and Beyond
Abstract
Glossary
Introduction
Molecular Phylogeny and Nomenclature of Kinesins
Motor–Cargo Relationship and Pathophysiological Relevance
Regulation and Synergy of Kinesins
Concluding Remarks
See also
References
Further Reading
CYTOSKELETON AND MOTORS: CYTOSKELETAL COMPONENTS | Dyneins
Abstract
Glossary
Introduction
Architecture of Dyneins
Dynein Motility
Regulation of Dynein Motility
Functions of Cytoplasmic Dynein In Vivo
Axonemal Dyneins: Overall Arrangement and Structure
Function of Axonemal Dynein HCs in Cilia
Regulatory Components
Axonemal Dynein-Related Ciliopathies
See also
References
Further Reading
Complex Cytoskeletal Structures
CYTOSKELETON AND MOTORS: COMPLEX CYTOSKELETAL STRUCTURES | The Mitotic Spindle
Abstract
Architecture and Dynamics of the Mitotic Spindle
Different Paths of Spindle Assembly
The Role of Motors and MAPs in Mitotic Spindle Assembly
Mitotic Spindle Properties
Mitotic Spindle Function
Spindle Disassembly and Cytokinesis
See also
References
Relevant Websites
CYTOSKELETON AND MOTORS: COMPLEX CYTOSKELETAL STRUCTURES | Centrioles and the Centrosome
Abstract
Glossary
Introduction
Structure of the Centrosome
Centriole Duplication
Functions of the Centrosome
The Centrosome in Development
Centrosome in Disease
Summary
References
CYTOSKELETON AND MOTORS: COMPLEX CYTOSKELETAL STRUCTURES | Cilia and Flagella
Abstract
Glossary
Introduction
Structure of Cilia and Flagella
Ciliogenesis
Signaling Pathways Coordinated by Cilia
Diseases Caused by Defects in Cilia
See also
References
Further Reading
CYTOSKELETON AND MOTORS: COMPLEX CYTOSKELETAL STRUCTURES | Skeletal Muscle
Abstract
Sarcomeres Are the Basic Unit of Contraction
Sarcomere Contraction Is Driven by Sliding of Myosin and Actin Filaments
Calcium Release from the SR Activates Contraction
Muscle Disorders Associated with Skeletal Muscle
See also
References
Further Reading
CYTOSKELETON AND MOTORS: COMPLEX CYTOSKELETAL STRUCTURES | Filopodia and Lamellipodia
Abstract
Glossary
Introduction
General Principles of Actin Polymerization-Driven Protrusion
Filopodia
Lamellipodia
See also
References
CYTOSKELETON AND MOTORS: COMPLEX CYTOSKELETAL STRUCTURES | The Extracellular Matrix
Abstract
Extracellular Matrix
Basement Membranes
Laminins
Collagen IV
Nidogens
Heparan Sulfate Proteoglycans
Other ECM Proteins Associated with Basement Membranes
Fibronectin
Connective Tissue/Interstitium
Fibrillar Collagens
FACIT Collagens and SLRPs
Elastic Fibers
Matricellular Proteins
Conclusions
See also
References
Relevant Websites
CYTOSKELETON AND MOTORS: COMPLEX CYTOSKELETAL STRUCTURES | Cell–Cell Adhesion and the Cytoskeleton
Abstract
Introduction
Cell–Cell Adhesion and the Actin Cytoskeleton
Cell–Cell Adhesion and the Intermediate Filament Cytoskeleton
Cell–Cell Adhesion and MTs
Concluding Comments
See also
References
CYTOSKELETON AND MOTORS: COMPLEX CYTOSKELETAL STRUCTURES | Cell Adhesion to the Extracellular Matrix
Abstract
Glossary
The Extracellular Matrix (ECM)
Diversity of ECM Adhesions
The Integrin Adhesome
Geometric and Mechanical Sensory (Mechanosensing) Functions of ECM Adhesions
The Cross-Talk between the Cell and the ECM
Acknowledgments
See also
References
Relevant Websites
CYTOSKELETON AND MOTORS: COMPLEX CYTOSKELETAL STRUCTURES | Cell Migration
Abstract
Introduction
Alone or in the Company of Others: Modes of Eukaryotic Cell Migration
Building a Migrating Cell
Migration in Development and Homeostasis
Migration in Pathology
Harnessing Cell Migration in Therapy
Conclusions
Acknowledgments
See also
References
CYTOSKELETON AND MOTORS: COMPLEX CYTOSKELETAL STRUCTURES | Rho GTPases
Abstract
General Features
Regulation of the GTP-Binding/GTP-Hydrolytic Cycles of Rho GTPases
Rho GTPases and Their Roles in Regulating the Actin Cytoskeleton
Other Targets and Multiple Roles in Biology
Rho GTPases in Oncogenic Transformation
Rho GTPases in Mammalian Tumors
Rho GTPases and Cancer Cell Metabolism
Rho GTPases and Cancer Cell Microvesicles
Concluding Remarks
Key Points
See also
References
CYTOSKELETON AND MOTORS: COMPLEX CYTOSKELETAL STRUCTURES | Cell Polarity
Abstract
Glossary
Basic Principles of Cell Polarity and Common Mechanisms of Control
Epithelial Cells
Apical–Basal Polarity of Epithelial Cells
Planar Cell Polarity
Relationship between Cell Polarity and Spindle Orientation Control
Loss of Cell Polarity and Disease
Conclusions
See also
References
Further Reading
Intracellular Infectiology
Cell Processes
INTRACELLULAR INFECTIOLOGY: CELL PROCESSES | Phagocytosis
Abstract
Glossary
Introduction
Phagocytic Receptors
Signaling to Actin Polymerization
Other Receptors and Signaling Pathways to Actin Polymerization
Membrane Remodeling and Focal Exocytosis
Linking Actin the Polymerization/Depolymerization Cycle with Vesicular Trafficking
Maturation of Phagosomes into Phagolysosomes
Conclusion
See also
References
INTRACELLULAR INFECTIOLOGY: CELL PROCESSES | Macropinocytosis
Abstract
Introduction
Functions of Macropinocytosis
Solute Flow During Pinocytosis
Mechanisms of Macropinosome Formation
The Organization of Cytoplasm for Macropinosome Formation
Experimental Diagnosis
Dysregulation
Therapeutics
See also
References
INTRACELLULAR INFECTIOLOGY: CELL PROCESSES | Microbicidal Mechanisms
Abstract
Glossary
Phagocytes and Phagocytosis
Phagocytic Killing
Autophagy and Xenophagy
Cell Death Mechanisms and Host Defense
Pathogen Subversion of Host Defense
Summary
See also
References
Further Reading
INTRACELLULAR INFECTIOLOGY: CELL PROCESSES | Bacterial Subversion of Phagocytic Killing
Abstract
Introduction
Interference of Uptake by Bacterial Pathogens
The Replication Vacuole 1: Manipulation of the Endocytic Pathway to Support Bacterial Replication
The Replication Vacuole 2: Manipulation of the Secretory Pathway to Support Bacterial Replication
The Replication Vacuole 3: Multi-Organelle Interactions
Breaking Free to Avoid Host Cell Killing
Bypass and Exploitation of Host Autophagic Clearing of Microorganisms
Bacterial Embrace of Autophagy
Perspective
See also
References
INTRACELLULAR INFECTIOLOGY: CELL PROCESSES | Cellular Invasion by Bacterial Pathogens
Abstract
Introduction
Entry Mechanisms
Intracellular Lifestyle and Manipulation of Host Intracellular Trafficking
Cellular Responses to Bacterial Invasion
Concluding Remarks
See also
References
Infectious Agents
INTRACELLULAR INFECTIOLOGY: INFECTIOUS AGENTS | Bacterial Protein Toxins as Tools in Cell Biology and Physiology
Abstract
Introduction
Final Considerations
See also
References
INTRACELLULAR INFECTIOLOGY: INFECTIOUS AGENTS | The Gut Microbiome
Abstract
The Gut Microbiome
Microbiome Research Methodology (Approaches and Tools)
Constituents of the Microbiome
The Roles of the Microbiome
Changes in the Gut Microbiome Throughout Life
Factors Influencing the Microbiome
The Microbiome and Disease
Future Microbiome Research
See also
References
INTRACELLULAR INFECTIOLOGY: INFECTIOUS AGENTS | Cell Biology of Virus Infection
Abstract
The Virus Particle
Transmission
Introduction to the Replication Cycle
Virus Entry
Replication and Synthesis of Viral mRNAs
Virus Assembly and Release
See also
References
Relevant Websites
INTRACELLULAR INFECTIOLOGY: INFECTIOUS AGENTS | Virus Factories and Mini-Organelles Generated for Virus Replication
Abstract
Introduction
RNA Viruses
DNA Viruses
See also
References
INTRACELLULAR INFECTIOLOGY: INFECTIOUS AGENTS | HIV – The Cell Biology of Virus Infection and Replication
Abstract
Glossary
Introduction
The HIV Replication Cycle
Virus Assembly
Virus Transmission
Virus Entry
Cell Killing
Host Defences against HIV
Drugs Interfering with HIV Replication
Conclusion
Acknowledgments
See also
References
Further Reading
INTRACELLULAR INFECTIOLOGY: INFECTIOUS AGENTS | Prions
Abstract
Introduction
History of the Prion Discovery
Prion Diseases
The Prion Protein
Conversion and Replication
Transmission
Strains
Neurotoxicity
Conclusion
See also
References
Cell Processes
INTRACELLULAR INFECTIOLOGY: CELL PROCESSES | Cellular Responses to Infections in Caenorhabditis elegans
Abstract
Caenorhabditis elegans as a Model System to Study Responses to Pathogens
Overview of C. elegans Pathogens
Pathogen Recognition by C. elegans
Immune Effectors
Immune Signaling Pathways
Conclusions and Perspectives
See also
References
Functional Cell Biology
Functional Cell Biology: An Overview
Introduction
Cell Signaling and Intercellular Communication
Cell Growth
Functional Cell Biology of Immunity
Stem Cell Biology
References
Cell Communication
Growth Factor Mediated Cell Signaling
CELL COMMUNICATION: GROWTH FACTOR MEDIATED CELL SIGNALING | Receptor Tyrosine Kinases and Their Ligands
Abstract
Glossary
Introduction
Families of RTKs and Their Ligands
RTKs Undergo Ligand-Induced Dimerization
Dimerization Activates the Kinase Activity of RTKs
Signaling Downstream of RTKs
RTK Coreceptors
Feedback and Amplification of RTK Signaling
Internalization of RTKs
Structural and Functional Properties of RTK Families
RTKs in Disease
See also
References
CELL COMMUNICATION: GROWTH FACTOR MEDIATED CELL SIGNALING | Cytokine Receptors and Their Ligands
Abstract
Glossary
Introduction
hGHR and Related Receptors
Beta Common Receptors
Gamma Common Receptors
Shared Glycoprotein 130 Receptors
IL-1 Receptors
IL-10/IL-22 Receptors
IL-17 Receptors
IFN Receptors
Intracellular Signaling Complexes
Concluding Remarks
Acknowledgments
See also
References
Further Reading
CELL COMMUNICATION: GROWTH FACTOR MEDIATED CELL SIGNALING | TGF-β Superfamily Signaling
Abstract
Introduction
Function of TGF-β Superfamily Signaling
TGF-β Superfamily Ligands
TGF-β Receptors
Pathway Modulation
TGF-β Superfamily Signaling and Disease
Acknowledgments
See also
References
Relevant Websites
CELL COMMUNICATION: GROWTH FACTOR-MEDIATED CELL SIGNALING | G Protein-Coupled Receptors
Abstract
G Protein-Coupled Receptors
Growth Factor Receptors and GPCRs
NGF Induces Neurite Outgrowth through G Protein
Conclusion
Acknowledgment
See also
References
Further Reading
CELL COMMUNICATION: GROWTH FACTOR MEDIATED CELL SIGNALING | Guanylyl Cyclase Receptors
Abstract
Introduction
Soluble GCs
pGCs
PDE
Conclusion
See also
References
CELL COMMUNICATION: GROWTH FACTOR MEDIATED CELL SIGNALING | Tumor Necrosis Factor Receptors: A Brief Digestion
Abstract
Introduction
Classification of TNFRSF
Structural Basis of Ligand–Receptor Interaction
Signal Transduction through TNFR Activation
The Double-Edged Sword in Cancer: Signaling through TNFR1/2 as an Example
Clinical Targeting of TNFSF and TNFRSF Members: Focusing on Cancer Immunotherapy
Concluding Remarks
See also
References
CELL COMMUNICATION: GROWTH FACTOR MEDIATED CELL SIGNALING | Signaling and Function of Death Receptors of the Tumor Necrosis Factor Receptor Superfamily
Abstract
Glossary
Introduction to Cell Death
DR Signaling Activates Multiple Signal Pathways
Function and Signaling Pathway of Each DR
Summary
See also
References
Further Reading
CELL COMMUNICATION: GROWTH FACTOR MEDIATED CELL SIGNALING | Hedgehog Signaling in Development and Disease
Abstract
Introduction
The Basic Mechanisms of HH Signaling
Newer Aspects of HH Signal Transduction
HH Signaling in Human Disease
See also
References
CELL COMMUNICATION: GROWTH FACTOR MEDIATED CELL SIGNALING | The Wnt/β-Catenin Pathway
Abstract
Introduction
Wnt Proteins
Wnt Protein Biogenesis
Wnt Receptors: Frizzled and LRP5/6
Wnt Antagonists
Wnt Agonists
The ‘Wnt-Off’ State: Keeping β-Catenin Levels Low
The ‘Wnt-On’ State: Raising β-Catenin Levels High
β-Catenin Stabilization
Wnt Signaling in the Nucleus
Conclusions
Acknowledgments
References
Relevant Website
CELL COMMUNICATION: GROWTH FACTOR MEDIATED CELL SIGNALING | The Hippo Pathway
Abstract
Introduction
The Hippo Pathway in D. melanogaster
Upstream Regulators of Hippo Signaling in D. melanogaster
The Hippo Pathway in Mammals
Upstream Regulators of Hippo Signaling in Mammals
Regulation of Organ Size, Stem Cell Self-Renewal, and Tissue Regeneration
Hippo Pathway Deregulation in Cancer
Conclusions
See also
References
Further Reading
CELL COMMUNICATION: GROWTH FACTOR MEDIATED CELL SIGNALING | The Notch Pathway
Abstract
The Notch Signaling Pathway
Developmental Biology
Pathology
Summary
See also
References
Intracellular Pathways
CELL COMMUNICATION: INTRACELLULAR PATHWAYS | SH3 and SH2: Prototypic Domains to Mediate Regulatory Mechanisms in the Cell
Abstract
Glossary
The Domain Perspective of Protein Architecture and Function
A Brief History of the Discovery of SH Domains
SH3
SH2
Specificity and Promiscuity
Function
SH Domains and Diseases
Conclusions
See also
References
Further Reading
Relevant Website
CELL COMMUNICATION: INTRACELLULAR PATHWAYS | The MAPK Signaling Cascades
Abstract
Glossary
General Overview
Components of MAPK Cascades
Regulation of the MAPK Cascades
MAPK Signaling in Diseases
See also
References
CELL COMMUNICATION: INTRACELLULAR PATHWAYS | The PI3K/Akt/mTOR Pathway
Abstract
Brief History
PI3K
Akt
mTOR
Regulation of the PI3K/Akt/mTOR Pathway
PI3K/Akt/mTOR Signaling in Human Disorders
Highlights
See also
References
CELL COMMUNICATION: INTRACELLULAR PATHWAYS | The JAK–STAT–SOCS Signaling Cascade
Abstract
Introduction
The JAK Family
STAT Proteins
The SOCS
JAK–STAT–SOCS and Human Disease
Concluding Remarks
Acknowledgments
See also
References
Further Reading
CELL COMMUNICATION: INTRACELLULAR PATHWAYS | The PLC Pathway
Abstract
Families of Phosphoinoside-Specific Phospholipase C Enzymes
See also
References
CELL COMMUNICATION: INTRACELLULAR PATHWAYS | Calcium and Calmodulin Signaling
Abstract
Glossary
The EF-Hand Calcium-Binding Principle
CaM
Regulation of Ca2+ by Proteins that Mediate Its Membrane Transport
CaM Targets
The Dark Side of Ca2+ Signaling: Ca2+-Related Pathologies
See also
References
Further Reading
Cellular Machineries
CELL COMMUNICATION: CELLULAR MACHINERIES | Macromolecular Communication between Nucleus and Cytoplasm
Abstract
Glossary
Introduction
History – Overview
Transport Signals and the Importin β Superfamily: A Code
Directionality of Translocation by Importin β Superfamily Members
mRNA Export
Nucleoporins
Regulation of Transport
Shuttling
Related Issues/Unanticipated Roles of the Nucleus
Evolutionary Considerations
Concluding Remarks
Acknowledgments
See also
References
CELL COMMUNICATION: CELLULAR MACHINERIES | The Molecular Architecture of Cell–Cell Adhesions
Abstract
Cell–Cell Adhesion: The Essence of Multicellularity
Structural and Functional Diversity of Cell–Cell Junctions
The Cadherin Family and Diversity of AJs
The Molecular Basis for Cadherin–Cadherin Binding
The Cytoplasmic Plaque
Dynamic Connections between Cadherin and the Actin Cytoskeleton
Regulatory Elements of the Cadherin Adhesome
Dynamics of Actin at AJs
Cadherin and Embryonic Development
AJs in Disease
Concluding Comments
Acknowledgments
See also
References
CELL COMMUNICATION: CELLULAR MACHINERIES | Extracellular Regulation of Cell-to-Matrix Adhesion
Abstract
Introduction
Early Studies of Cell Adhesion
Specific versus Generic Attractive and Repulsive Interactions
Stiffness, Spacing, and Curvature
How Extracellular Signals Alter Adhesion to Matrix
Cell Adhesions and Matrix Molecules in Connective Tissue Function
Role of Cell–Matrix Adhesions in Pathological Processes: Fibrosis
Role of Cell–Matrix Adhesions in Pathological Processes: Platelets and Thrombosis
Conclusion
See also
References
Relevant Websites
Cellular Outcomes
CELL COMMUNICATION: CELLULAR OUTCOMES | Regulation of Cell Polarity
Abstract
Introduction
A Modular Signaling System
Principles of Collective Polarization
Feedback Control of Core Amplification
System Architecture
Outlook
See also
References
CELL COMMUNICATION: CELLULAR OUTCOMES | Regulation of Cell Migration
Abstract
Signals to Migrate
Cytoskeletal Changes Underlying Migration
Cell Migration Is Regulated Through Interactions with the Environment
See also
References
Prototypic Integrative Processes
CELL COMMUNICATION: PROTOTYPIC INTEGRATIVE PROCESSES | Wound Healing: An Orchestrated Process of Cell Cycle, Adhesion, and Signaling
Abstract
Glossary
Molecular and Cellular Biology of Normal Wound Healing and Scar Formation
Wound Healing versus Regeneration
Impaired Wound Healing and Clinical Problems
Parallels between Wound Healing and Cancer
See also
References
Relevant Websites
CELL COMMUNICATION: PROTOTYPIC INTEGRATIVE PROCESSES | Cancer Cell Invasion through Tissue Barriers
Abstract
Introduction
EMT
Invadopodia
Modes of Cell Migration
Anoikis
Microtentacles
Conclusion
See also
References
CELL COMMUNICATION: PROTOTYPIC INTEGRATIVE PROCESSES | Neuronal Transport and Spatial Signaling Mechanisms in Neural Repair
Abstract
Glossary
Introduction
Constituents for Intracellular Communication and Trafficking in Neurons
Neural Repair Mechanisms
Perspectives
Acknowledgments
See also
References
Further Reading
Cell Division/Death
Regulation of Cell Growth
CELL DIVISION/DEATH: REGULATION OF CELL GROWTH | mTORC1: Upstream and Downstream
Abstract
Introduction
mTORC1 and mTORC2
Downstream of mTORC1
Upstream of mTORC1
Concluding Remarks
Acknowledgment
See also
References
CELL DIVISION/DEATH: REGULATION OF CELL GROWTH | The Nucleolus
Abstract
Nucleolar Architecture
Nucleoli and Ribosome Subunit Biogenesis
Ribosomal DNA
rRNA Transcription
Regulation of rDNA Expression
Interchange of Nucleoli with Other Nuclear Bodies
The Dynamic Nucleolus
Nucleoli and Viruses
Proteomic Studies on Nucleolar Architecture, Function, and Dynamics
Conclusion
Methods
Acknowledgments
See also
References
Further Reading
CELL DIVISION/DEATH: REGULATION OF CELL GROWTH | Ribosomes and Stress – Linked from Birth to Death
Abstract
Glossary
Introduction
Ribosome Birth in the Nucleolus
The Busy Life of the Ribosome
The End of the Line – Ribosome Degradation
Conclusion
See also
References
Further Reading
CELL DIVISION/DEATH: REGULATION OF CELL GROWTH | Extra-Ribosome Functions of Ribosomal Proteins
Abstract
Introduction to Basic Ribosome Structure and Function
Ribosome Biogenesis Is Intrinsically Connected to Cancerous Growth
Ribosomopathies Are Associated with Increased Cancer Risk
Non-ribosomal Functions of RPs Independent of the MDM2-p53 Pathway
Ribosomal Protein-MDM2-p53 Pathway
The RP-MDM2-p53 Pathway as a Putative Target in Cancer Therapy
Conclusions
See also
References
CELL DIVISION/DEATH: REGULATION OF CELL GROWTH | Ribosomal RNA Processing
Abstract
Introduction
Ribosomal RNA Processing in Yeast
rRNA Processing in Other Eukaryotes
rRNA Processing in Prokaryotes
5S rRNA Processing
Human Diseases Caused by rRNA Processing Defects
Perspectives
Conclusions
Acknowledgments
See also
References
CELL DIVISION/DEATH: REGULATION OF CELL GROWTH | Eukaryotic Ribosome Assembly and Export
Abstract
Introduction
Ribosomal Pre-rRNA Processing
Trans-Acting Factors Involved in Ribosome Assembly
Nuclear Export of Pre-Ribosomal Particles
Cytoplasmic Events in Ribosome Biogenesis
Concluding Remarks
Acknowledgments
See also
References
Further Reading
CELL DIVISION/DEATH: REGULATION OF CELL GROWTH | Internal Ribosome Entry Site-Mediated Translation
Abstract
Glossary
Introduction: The Canonical Cap-Dependent Mechanism of Translation Initiation in Eukaryotes
Internal Ribosome Entry Site-Mediated Translation Initiation
Conclusion and Perspective
See also
References
Further Reading
CELL DIVISION/DEATH: REGULATION OF CELL GROWTH | Targeted mRNA Degradation
Abstract
Introduction
mRNA Surveillance Mechanisms
Substrate Choice
Substrate Recognition
Substrate Fate
Targeted mRNA Degradation in Gene Regulation
mRNA Degradation Control by Short RNAs
Targeted mRNA Degradation by RBPs
Combined Action of Short RNAs and RBPs
See also
References
Apoptosis
CELL DIVISION/DEATH: APOPTOSIS | Apoptosis
Abstract
Apoptosis, Death as Part of Life
Of Life and Apoptosis: The Anti-Apoptotic versus Pro-Apoptotic Machinery
Acknowledgment
See also
References
Relevant Website
CELL DIVISION/DEATH: APOPTOSIS | Anoikis
Abstract
Introduction
Why Leave?
The Challenges of Being a Tumor Cell in its Primary Microenvironment
ROS and Anoikis – A Double-edged Sword?
What Otto Warburg Said, How It Was Misinterpreted, and the Idea of Metabolic Coupling in Tumors
Summary
See also
References
CELL DIVISION/DEATH: APOPTOSIS | Mitochondria in Cell Death Regulation
Abstract
Glossary
Introduction
Mitochondrial Control of Regulated Cell Death
Mitochondrial Membrane Permeabilization
Concluding Remarks
See also
References
CELL DIVISION/DEATH: APOPTOSIS | Tumor Necrosis Factor Signaling Pathways
Abstract
Glossary
Introduction
The TNF and TNFR Superfamilies
Structural Features of TNF, TNFR1, and TNFR2
TNF-Induced TNFR Signaling
TNFR-Induced NF-κB Activation
TNFR-Induced Cell Death
Regulation of TNF Signaling by Ubiquitin Ligases and Deubiquitinases
TNF-Induced Activation of MAPK Pathways
Physiologic Functions of TNF and Disease Relevance
TNF Inhibitors
Impact of TNF Blockade in Inflammatory Diseases
See also
References
Further Reading
CELL DIVISION/DEATH: APOPTOSIS | Caspases
Abstract
Introduction
Structure, Classification, and Non-Apoptotic Biological Roles
Activation Mechanisms
Substrate Specificity and Targets
Caspase Activation and Function in Cell Death and Inflammation
New Modes of Caspase-Regulated Cell Death
Acknowledgments
See also
References
Relevant Websites
CELL DIVISION/DEATH: APOPTOSIS | Efferocytosis in the Tumor Microenvironment
Abstract
Glossary
Introduction
A Historical Overview of Efferocytosis
Efferocytosis Is an Established Process That Is Rapidly Deployed in the Breast
Efferocytosis in the Tumor Microenvironment
Efferocytosis and Postpartum Breast Cancer
Conclusion and Future Directions
References
Further Reading
CELL DIVISION/DEATH: APOPTOSIS | The Bcl-2 Family Proteins: Insights into Their Mechanism of Action and Therapeutic Potential
Abstract
Apoptosis and the Bcl-2 Family: A Historical Perspective
How Do Bcl-2 Family Proteins Regulate MOMP?
Physiology and Regulation of Bcl-2 Family Members
Bcl-2 Proteins at the Endoplasmic Reticulum
Bcl-2 Family Proteins and Cancer
Summary
See also
References
Further Reading
CELL DIVISION/DEATH: APOPTOSIS | Inhibitor of Apoptosis Proteins, the Sentinels of Cell Death and Signaling
Abstract
Glossary
Structural Organization of IAPs
IAP Protein Characteristics and Function
Targeting IAP Proteins
Concluding Remarks
See also
References
CELL DIVISION/DEATH: APOPTOSIS | Mitotic Catastrophe
Abstract
Introduction
Mitotic Catastrophe
Inducing Mitotic Catastrophe
Mechanisms of Mitotic Catastrophe
Concluding Remarks
Acknowledgment
References
CELL DIVISION/DEATH: APOPTOSIS | Autophagy
Abstract
Autophagic Pathways
Autophagy Step-by-Step
The Autophagic Cargo and Purpose of Its Degradation
Pathophysiology of Autophagy
Concluding Remarks
See also
References
Cell Cycle
CELL DIVISION/DEATH: CELL CYCLE | Interplay between Oncogenes and Tumor Suppressor Genes in Human Disease
Abstract
Glossary
Introduction: Scope and Intent of Article
Oncogenes and Tumor Suppressor Genes and Human Cancer
Interplay between Oncogenes and Tumor Suppressor Genes in Human Cancer
Role of Oncogenes and Tumor Suppressor Genes in Human Developmental Diseases
See also
References
Relevant Websites
CELL DIVISION/DEATH: CELL CYCLE | Cyclins and Cyclin-Dependent Kinases
Abstract
Introduction
The Discovery of Regulators of the Cell Cycle
The Cyclins
The Cyclin-Dependent Kinases
Functions of Cyclin-CDK in the Cell Cycle and Quiescence
CKIs: CDK Inhibitors
Cyclins, CDKs, and CKIs in Cancer
Beyond the Cell Cycle: Other Functions of Cyclins and CDKs
See also
References
CELL DIVISION/DEATH: CELL CYCLE | The Restriction Point
Abstract
Glossary
The Restriction Point
The Role of RB and p53 in Establishing the Restriction Point
Conclusions
See also
References
CELL DIVISION/DEATH: CELL CYCLE | CDK Inhibitors in Normal and Malignant Cells
Abstract
Cyclins, CDKs, and Cell Cycle Progression
The INK4 Family
The CIP/KIP Family
Prognostic Significance of CDK Inhibitor Deregulation in Human Cancers
CDK Inhibitors as Predictors of Drug Response
Concluding Remarks
See also
References
CELL DIVISION/DEATH: CELL CYCLE | The INK4a/ARF Locus
Abstract
Introduction
Control and Significance of G1–S Phase Progression in Mammals
p16INK4a and RB1-Mediated Senescence
INK4a/ARF – a Dual Coding Locus in Mammals
INK4a/ARF – One Locus, Two Important Tumor Suppressors
ARF, a Multi-Faceted Tumor Suppressor
Regulation and Loss of INK4a/ARF in Cancer
INK4a/ARF in Aging
Unique Roles of ARF in Development
Conclusions
See also
References
Relevant Websites
CELL DIVISION/DEATH: CELL CYCLE | S Phase
Abstract
Introduction
S Phase Activation
DNA Replication
DNA Damage Response
Conclusions
See also
References
CELL DIVISION/DEATH: CELL CYCLE | Traveling through Mitosis with the Chromosomal Passenger Complex
Abstract
Introduction
Identification of the Core CPC Members
Putting the CPC Together
CPC during the Approach to Mitosis
CPC in Mitosis
The Spindle Assembly Checkpoint
Spindle Assembly Checkpoint and Inter-Kinetochore Tension
CPC and Error Correction
The Two-Histone Model of CPC Localization to Centromeres
Modified View of CPC Targeting
CPC during Anaphase, Telophase, and Cytokinesis
Conclusion
See also
References
CELL DIVISION/DEATH: CELL CYCLE | Mitosis in Animal Cells
Abstract
Introduction
Stages of Mitosis
Mitosis As an Anticancer Drug Target
Conclusion
Acknowledgments
See also
References
Relevant Website
CELL DIVISION/DEATH: CELL CYCLE | Regulating Cytokinesis
Abstract
Positioning the Site of Cell Division
Formation of the Cleavage Furrow
Formation of the Midbody
Abscission
Temporal Regulation of Cytokinesis
The Abscission Checkpoint Protects against the Deleterious Effects of Chromatin Bridges
Conclusions and Future Perspectives
Acknowledgments
See also
References
CELL DIVISION/DEATH: CELL CYCLE | Regulation of the p53 Pathway
Abstract
Introduction
Control of p53 through the Ubiquitin-Proteasome Pathway
E3 Ligases in the p53 Pathway
The p53–Mdm2–HAUSP Connection
DUBs in the p53 Pathway
Transactivation of p53 through Posttranslational Modifications
Involvement of p53 in Metabolism
Conclusions
See also
References
CELL DIVISION/DEATH: CELL CYCLE | Cellular Senescence
Abstract
Introduction
What Defines Cellular Senescence?
Molecular Signaling Pathways
Epigenetic Control of Senescence
Secreted Factors
Senescence in Aging
Senescence in Cancer
Senescence and Tissue Repair
Senescence in Development
Conclusion
See also
References
Cellular Immunology
Overview
CELLULAR IMMUNOLOGY: OVERVIEW | Introduction to Functional Cell Biology of Immunity
Abstract
Glossary
Introduction
Elements of Innate and Adaptive Immunity
Barriers and Tissue Cells
Chemical Defenses
Sensing Mechanisms
Phagocytes and Their Receptors
Innate Lymphoid Cells
Lymphocytes
Immunological Synapses
Lymphoid Tissues
Evolution
Perspective
See also
References
Transcriptional Basis of B and T Cell Lineages and Memory Cells
CELLULAR IMMUNOLOGY: TRANSCRIPTIONAL BASIS OF B AND T CELL LINEAGES AND MEMORY CELLS | The T-Cell Receptor Signalosome
Abstract
Introduction
The TCR and Its Ligands: Structural and Functional Topology
The Signaling Code Used by the TCR Signalosome to Convert Extracellular Signals into Biological Responses
Biochemical Modules and Assembly of the TCR Signalosome
Conclusions
See also
References
Further Reading
CELLULAR IMMUNOLOGY: TRANSCRIPTIONAL BASIS OF B AND T CELL LINEAGES AND MEMORY CELLS | T Follicular Helper Cells
Abstract
Introduction
T Follicular Helper Cell Differentiation
Acknowledgments
See also
References
CELLULAR IMMUNOLOGY: TRANSCRIPTIONAL BASIS OF B AND T CELL LINEAGES AND MEMORY CELLS | V(D)J Recombination: Orchestrating Diversity without Damage
Abstract
Introduction
Developmental and Epigenetic Regulation of V(D)J Recombination
Molecular Mechanisms of RAG-Mediated V(D)J Recombination
V(D)J Recombination and Malignancies of the Immune System
Acknowledgments
References
Further Reading
CELLULAR IMMUNOLOGY: TRANSCRIPTIONAL BASIS OF B AND T CELL LINEAGES AND MEMORY CELLS | T Cell Memory to Viral Infections
Abstract
Background
Memory Formation
Phenotypes of Memory T Cells
Tissue-Resident Memory
Different Phenotypes Characterize Different Viral Infections
Immune Exhaustion
Memory Inflation
Atypical Memory
Impact on Vaccine Design
Conclusions and Future Directions
See also
References
Further Reading
CELLULAR IMMUNOLOGY: TRANSCRIPTIONAL BASIS OF B AND T CELL LINEAGES AND MEMORY CELLS | Nuclear Factor of Activated T Cells and Tolerance
Abstract
Introduction
NFAT Domain Structure
Regulation of NFAT Activation
NFAT-Regulated Transcription
Functions of NFAT in T cells
NFAT and T Cell Tolerance
Conclusions
See also
References
Further Reading
CELLULAR IMMUNOLOGY: TRANSCRIPTIONAL BASIS OF B AND T CELL LINEAGES AND MEMORY CELLS | NF-kappaB and the Immune System
Abstract
Glossary
Introduction
NF-κB in Normal Immune Cell Function and Development
Role of NF-κB in Innate Immunity
Misregulation of NF-κB in Human Immune Diseases
Human Immune Cell Viruses Use NF-κB for Replication and Pathogenesis
Targeting NF-κB for Therapy in Immune Diseases
See also
References
Further Reading
Cell–Cell Interactions and the Immune System
CELLULAR IMMUNOLOGY: CELL–CELL INTERACTIONS AND THE IMMUNE SYSTEM | Functional Specialization of Dendritic Cell Subsets
Abstract
Discovery of Dendritic Cells
Antigen Processing and Presentation
DC Development and DC Characterization
Functional Specialization in Antigen Presentation of Mouse DC Subpopulations
Functional Specialization in Antigen Presentation of Human DC Subpopulations
Conclusions
Acknowledgments
See also
References
CELLULAR IMMUNOLOGY: CELL–CELL INTERACTIONS AND THE IMMUNE SYSTEM | CD28 Costimulation and Regulatory T Cells
Abstract
Introduction
How Is the Self-Tolerance Established?
The Biology of the CD28/CTLA-4 Pathway
CTLA-4 – A Key Negative Regulator of T cell Activation
How Does CTLA-4 Function?
Manipulation of CD28/CTLA-4 Pathway: Antagonist, Agonists, and Superagonists
Conclusions
See also
References
CELLULAR IMMUNOLOGY: CELL–CELL INTERACTIONS AND THE IMMUNE SYSTEM | Roles of Stromal Cells in the Immune System
Abstract
Introduction to Stromal Cells
Stromal Cell Regulation of Lymphoid Tissue Structure and Function
Stromal Cell Regulation of Immune Responses in Peripheral Tissues
See also
References
CELLULAR IMMUNOLOGY: CELL–CELL INTERACTIONS AND THE IMMUNE SYSTEM | CXCL12/SDF-1 and Hematopoiesis
Abstract
Introduction
Role of CXCL12 in Homing to BM
Role of CXCL12 in HSC and HPC Maintenance within BM Niches
CXCL12 in HSC and HPC Mobilization
Role of CXCL12 in Maintenance of Neutrophils in BM
Role of CXCL12 in Maintenance of the B cell Lineage in BM
The Role of CXCL12 in Balancing Granulopoiesis and Lymphopoiesis during Inflammation
Conclusion
References
CELLULAR IMMUNOLOGY: CELL–CELL INTERACTIONS AND THE IMMUNE SYSTEM | Lymphocyte–Endothelial Interactions
Abstract
Glossary
Introduction
The Endothelium as a Barrier for the Vascular and Lymphatic Systems
Contexts for Lymphocyte–Endothelial Interactions
Mechanisms for T Lymphocyte Adhesion to and Diapedesis across Endothelia
Information Exchange at the T Lymphocyte–Endothelial Interface
Summary
Supplementary Material
Acknowledgment
See also
References
CELLULAR IMMUNOLOGY: CELL–CELL INTERACTIONS AND THE IMMUNE SYSTEM | T Cell Receptor Triggering
Abstract
Introduction
Time of Interaction and Recruitment of Modulators
Exclusion of Negative Regulators
Changes in Conformation and Accessibility of Intracellular Domains
TCRs as Mechanoreceptors
Clustering
Quantity and Valency of Cognate pMHC Ligands
Conclusions
See also
References
CELLULAR IMMUNOLOGY: CELL–CELL INTERACTIONS AND THE IMMUNE SYSTEM | Single Molecule Methods to Measure Receptor–Ligand Interaction in Immunological Synapses
Abstract
Introduction
Mechanical Assays to Measure 2D-kinetics
Imaging TCR–pMHC Interactions In Situ
Pulling Forces Enhance Discriminative Power of Peptide Recognition
Conclusion and Outlook
Acknowledgments
See also
References
CELLULAR IMMUNOLOGY: CELL–CELL INTERACTIONS AND THE IMMUNE SYSTEM | Single-Cell Interrogation of the Immune System Using Microtools
Abstract
Single-Cell Secretion
Cell Migration
Cell–Cell Communication
Other Applications
Acknowledgments
References
CELLULAR IMMUNOLOGY: CELL–CELL INTERACTIONS AND THE IMMUNE SYSTEM | Cellular Structures Controlling T Cell Signaling in Time and Space
Abstract
Introduction
Studying the Organization of T Cell Signaling
Signaling Organization and the Structures Driving It
Signaling Organization Varies with T Cell Activation Conditions
The Function of Signaling Organization
See also
References
Further Reading
Innate Immunity
CELLULAR IMMUNOLOGY: INNATE IMMUNITY | Function of Epithelial Barriers
Abstract
Glossary
Introduction
Structure of the Epithelial Layer
Epithelial Cell Types
Defense
Loss of Barrier Function in Disease
Perspective
See also
References
CELLULAR IMMUNOLOGY: INNATE IMMUNITY | Phagocytic Synapses
Abstract
Glossary
Introduction
Dectin-1 Activation by β-Glucans
FcγR Activation by Immunoglobulin G (IgG)
The Phagocytic Synapse Model
Regulation of the Phagocytic Synapse by CD47
Summary
See also
References
CELLULAR IMMUNOLOGY: INNATE IMMUNITY | The Phagocyte NADPH Oxidase: Structure and Assembly of the Key Multicomponent Enzyme of Innate Immunity
Abstract
The Phagocyte Oxidative Burst
The Phagocyte NADPH Oxidase NOX2
Conclusion
Acknowledgments
See also
References
CELLULAR IMMUNOLOGY: INNATE IMMUNITY | Cytoplasmic Sensing in Innate Immunity
Abstract
Introduction
Classes, Structure, and Activation of Innate Sensors
Role of Intracellular Organelles and Spatial Relocation
Combinatorial Sensing and PRR Crosstalk
Multiscale Regulation of Cytosolic Sensing Pathways
Acknowledgments
See also
References
CELLULAR IMMUNOLOGY: INNATE IMMUNITY | Scavenger Receptors
Abstract
Introduction
Evolutionary Origins of SRs and Functions in Host Physiology
SRs in Innate Immunity
SRs as Causes and Therapeutic Targets in Disease
See also
References
Relevant Website
CELLULAR IMMUNOLOGY: INNATE IMMUNITY | Dendritic Cells
Abstract
Discovery of Dendritic Cells
DC Development and Homeostasis
Features Enable DCs as the Orchestrator of Immunity
DCs in Clinical Immunology
See also
References
CELLULAR IMMUNOLOGY: INNATE IMMUNITY | Neutrophil Biology
Abstract
Introduction
Neutrophil Development
Neutrophil Migration into Sites of Inflammation
Neutrophil Defense Mechanisms
Neutrophil Subsets
Genetic Defects That Affect Neutrophil Numbers and/or Function
Neutrophils in Systemic Autoimmune Diseases
Conclusion
See also
References
CELLULAR IMMUNOLOGY: INNATE IMMUNITY | Specialized Subsets of Tissue-Resident Macrophages in Secondary Lymphoid Organs
Abstract
Macrophage Subsets in the Spleen
LN Macrophages
Conclusions
See also
References
CELLULAR IMMUNOLOGY: INNATE IMMUNITY | CD4 T Cell Memory and Role of TNF Receptor Family
Abstract
Overview
CD4 T Cell Responses
Members of the TNFRSF and CD4 T Cells
Concluding Remarks
See also
References
Stem Cell Biology
Structure and Function
STEM CELL BIOLOGY: STRUCTURE AND FUNCTION | Stem Cells and Aging
Abstract
Introduction
Determinants of Stem Cell Aging
Aging in Adult Stem Cells
Concluding Remarks
Acknowledgments
See also
References
STEM CELL BIOLOGY: STRUCTURE AND FUNCTION | Epigenetic Regulation of Stem Cells
Abstract
Introduction: Regulation of Gene Expression in Stem Cells
Effectors and Mechanisms of Epigenetic Regulation of Gene Expression in ESCs
Epigenetic Signatures and Control of Nuclear Architecture in ESCs
Epigenetic Control of Quiescence/Stemness and Lineage Determination in Adult
See also
References
Relevant Website
STEM CELL BIOLOGY: STRUCTURE AND FUNCTION | The Adult Stem Cell Niche: Multiple Cellular Players in Tissue Homeostasis and Regeneration
Abstract
The Skin Hair Follicle
Skeletal Muscle
The Adult Central Nervous System Stem Cell Niche
The Heart-Evidence for a Cardiac Stem Cell Niche?
Overall Conclusions and Future Directions
Acknowledgments
See also
References
STEM CELL BIOLOGY: STRUCTURE AND FUNCTION | Cancer Stem Cells
Abstract
Definitions and History
Tumor Heterogeneity
Terminology
Modes of Identification
Regulation of Cancer Stemness
Plasticity
Markers for the Identification of Cancer Stem Cells in Major Malignancies
Clinical Significance of Cancer Stem Cells
Conclusions
See also
References
STEM CELL BIOLOGY: STRUCTURE AND FUNCTION | Metabolic and Energetic Regulation of Stem Cells
Abstract
Hypoxia-Inducible Factor 1α and Glycolysis in Stem Cells
Fatty Acid Metabolism and Mitochondrial Function
Nutrient-Sensing Pathways
Redox Homeostasis
Other Stem Cell Niches
Conclusions
See also
References
STEM CELL BIOLOGY: STRUCTURE AND FUNCTION | Pluripotent Cells: New Tools for Disease Research and Therapies
Abstract
Glossary
Naturally Occurring Pluripotent Cells
Engineered Pluripotent Cells
New Tools to Provide Mechanistic Insights on Determining Cell Fates and Disease States
New Tools for Cell-Based Regenerative Therapy
Clinical Trials and Contributions to Future Cell-Based Regenerative Therapy
See also
References
Further Reading
Systems Cell Biology
Systems Cell Biology: An Overview
Dynamic Integration
Vertical Integration
Horizontal Integration
References
Relevant Websites
Dynamic Integration
Dynamics
DYNAMIC INTEGRATION: DYNAMICS | Dynamics of Gradient Sensing and Chemotaxis
Abstract
Introduction
Strategies for Chemotaxis
Adaptation in Chemotactic Systems
Signal Amplification and Sensitivity
Conclusions
See also
References
Further Reading
DYNAMIC INTEGRATION: DYNAMICS | Modeling Actin Dynamics
Abstract
Introduction
Conceptual Models of Mechano-Chemical Control of Cell Motility and Shape
Detailed Biochemical Modeling
Conclusion
Acknowledgments
See also
References
Relevant Websites
DYNAMIC INTEGRATION: DYNAMICS | Metabolism
Abstract
Introduction
Metabolism
Fundamentals
Enzyme Response
Pathway Responses
Control Coefficients
Connectivity Theorems
Metabolic Motifs
Conclusion
Acknowledgments
See also
References
Further Reading
DYNAMIC INTEGRATION: DYNAMICS | Dynamics of Microtubule Self-Assembly
Abstract
Glossary
Cellular Functions of Microtubules
Microtubule Structure
Microtubule Self-Assembly Dynamics
Theoretical Framework for Microtubule Self-Assembly
Microtubule-Targeting Agents Attenuate Microtubule Dynamics
See also
References
Further Reading
DYNAMIC INTEGRATION: DYNAMICS | Dynamics of Protein Kinase Cascades
Abstract
Glossary
Introduction
Signal Amplification and Decision Making
Cellular Decisions Encoded in the Dynamics of Signaling
Robustness of Signaling Pathways
See also
References
Further Reading
DYNAMIC INTEGRATION: DYNAMICS | Cdc42 and the Mechanisms of Yeast Cell Polarization – A Paradigm for Mesoscale Systems Biology
Abstract
Introduction
Cue-Dependent Cell Polarization
Breaking Symmetry
Inhibitory Interactions and Reinforcements in Polarity Regulation
See also
References
DYNAMIC INTEGRATION: DYNAMICS | Theory of Cargo and Membrane Trafficking
Abstract
Introduction
Theory of the Endosomal Network
Regulation of the Microscopic Processes
Relation to Kinetics of Total Cargo Pool
Implications for Cargo Sorting
Conclusion
See also
References
Further Reading
DYNAMIC INTEGRATION: DYNAMICS | Transcription Factor Networks
Abstract
Introduction
Local Properties of GRNs
Motifs
Global Properties of GRNs
Conclusions
See also
References
Further Reading
Vertical Integration
Modeling
VERTICAL INTEGRATION: MODELING | Vertical Integration
Abstract
Introduction
The Multiple Time and Spatial Scales Associated with Cellular Biology
Approaches for Linking Scales in Multiscale Models: ‘Top-Down’, ‘Bottom-Up,’ and ‘Middle-Out’
Mathematical and Computational Representations of the Components of a Multiscale Model
Assembling Multiscale Modeling
Software for Multiscale Modeling
Applications of Multiscale Modeling and Two Case Studies
Challenges Associated with Multiscale Modeling
Summary
Conclusions
See also
References
Further Reading
VERTICAL INTEGRATION: MODELING | Computational Approaches for Multiscale Modeling
Abstract
Glossary
Introduction
Multiscale Modeling
Discussion
Acknowledgments
See also
References
Further Reading
Relevant Website
VERTICAL INTEGRATION: MODELING | Cardiac Modeling
Abstract
State-of-the-Art in Cardiac Cell Modeling
Human Models of Cardiac Cell Electrophysiology
Modeling Variability in Cardiac Cell Electrophysiology
Whole Organ Cardiac Modeling
Conclusions and Outlook
References
Relevant Website
Applications
VERTICAL INTEGRATION: APPLICATIONS | Mathematical Approaches to Studying Inflammation
Abstract
Introduction
A Simple Mathematical Model Capturing the Resolution of Inflammation
Current Mathematical and Computational Models of Inflammation
Early Events, Leukocyte Responses to Bacteria
Inflammatory Cytokines, TNF-Therapy
Tissue Damage and Wound Healing
Inflammation and Progression to the Immune Response
Conclusions and Future Challenges
See also
References
VERTICAL INTEGRATION: APPLICATIONS | Angiogenesis
Abstract
Glossary
Vascular Evolution
Developmental Vasculogenesis
Capillary Structure
Primary Factors Controlling Angiogenesis
Hypoxic Induction of Angiogenesis
Sprouting Angiogenesis
Intussusceptive Angiogenesis
Arterial and Venous Vessels
Summary
References
VERTICAL INTEGRATION: APPLICATIONS | A Review on Various Mathematical Modeling Approaches for Wound Healing
Abstract
Wound Healing and the Need for Modeling
Evaluation of Several Mathematical Approaches
Conclusions
See also
References
VERTICAL INTEGRATION: APPLICATIONS | Multiscale Analysis of Morphogenesis
Abstract
Introduction
Vertical Integration
Analyzing Cell Behavior
Mathematical Models for Studying Collective Cell Behavior
Examples of Vertical Integration Studies
Conclusion
Acknowledgments
References
Further Reading
VERTICAL INTEGRATION: APPLICATIONS | Neurogenesis in the Adult Brain
Abstract
Introduction
Historical Perspective
Identity of Adult NSCs
Cell Proliferation in the SVZ
Neuronal Migration in the RMS
Neuronal Differentiation in the Olfactory Bulb
Potential Functions of Adult Neurogenesis
Potential Applications
Conclusion
References
Further Reading
Horizontal Integration
Networks
HORIZONTAL INTEGRATION: NETWORKS | Understanding of ‘Networks’ In Vitro and/or In Vivo
Introduction
Networks in Cancer
Concluding Remarks
See also
References
Relevant Website
Omics
HORIZONTAL INTEGRATION: OMICS | Connecting Evolutionary Genomics to Cell Biology
Abstract
Genomics for Old and New Questions
Case Studies: New Genes for Old and New Functions
Gene Traffic
Gene Regulatory Networks
Cell Division
Protein Traffic
Perspectives
Acknowledgments
References
HORIZONTAL INTEGRATION: OMICS | Transcriptomics
Abstract
Glossary
Introduction
Evolution of High-Throughput Transcriptomic Technologies
Exploring the Interactive Transcriptome
New Technologies for mRNA Transcriptomics
Integrating Transcriptomics with Other Omics
Conclusion
See also
References
HORIZONTAL INTEGRATION: OMICS | The Advent of Mass Spectrometry-Based Proteomics in Systems Biology Research
Abstract
Systems Biology and Proteomics
Liquid Chromatography-Coupled Tandem Mass Spectrometry
Systems Biology Application for High-Throughput Proteomics
Outlook
Acknowledgments
See also
References
HORIZONTAL INTEGRATION: OMICS | Phosphoproteomics: Approaches, Developments, and Challenges
Abstract
Introduction to Posttranslational Modifications
Protein Phosphorylation
Phosphopeptide Enrichment
Large-Scale Phosphoproteomics Strategies
Phosphopeptide Fragmentation
Quantitative Phosphoproteomics
PTM Cross Talk and PTM Coding
Challenges in Phosphoproteomics
Conclusions
See also
References
HORIZONTAL INTEGRATION: OMICS | Interactomes – Scaffolds of Cellular Systems
Abstract
Introduction
Methods to Map Interactomes
Applications of Interactome Maps
Perspectives
See also
References
HORIZONTAL INTEGRATION: OMICS | Metabolomics in Cell Biology
Abstract
Introduction
Conducting a Successful Metabolomics Study
See also
References
Analyses and Tools
HORIZONTAL INTEGRATION: ANALYSES AND TOOLS | Network Modeling of Heterogeneous Datasets
Abstract
Introduction
Overview
Network Algorithms
See also
References
HORIZONTAL INTEGRATION: ANALYSES AND TOOLS | Stochastic Analysis of Nongenetic Cell-to-Cell Heterogeneity
Abstract
Glossary
Introduction
Cell Signaling
Variability in Gene Expression
Single-Cell Analysis
Modeling and Analysis of Stochastic Data
Connecting Heterogeneity at Multiple Levels
Conclusion
See also
References
HORIZONTAL INTEGRATION: ANALYSES AND TOOLS | Systematic Methods to Interrogate Genetic Perturbations and Map Phosphorylation-Dependent Signaling
Abstract
Acknowledgments
See also
References
HORIZONTAL INTEGRATION: ANALYSES AND TOOLS | High-Content Screening in Cell Biology
Abstract
Glossary
Introduction
History
Experimental Setup
High-Content or Low-Content?
Conclusion
See also
References
Further Reading
HORIZONTAL INTEGRATION: ANALYSES AND TOOLS | Integrative Systems Biology
Abstract
Introduction
Challenges
Solutions
Conclusions
See also
References
Relevant Websites
Disease
HORIZONTAL INTEGRATION: DISEASE | Computational and Systems Cancer Biology
Abstract
Integrative and Systems Biology Methodologies
Assembly and Analysis of Cancer Regulatory Models
Interactome Reverse Engineering
Interrogating Pathways and Networks
Recent Trends and Future Perspective
See also
References
Relevant Website
HORIZONTAL INTEGRATION: DISEASE | Drug Targeting
Abstract
Drug Targeting – An Introduction
A Historical Perspective
From Molecules to Systems
Network Medicine
New Methods for Drug Targeting
See also
References
Authors
Index
Details
- No. of pages:
- 3008
- Language:
- English
- Copyright:
- © Academic Press 2016
- Published:
- 2nd September 2015
- Imprint:
- Academic Press
- Hardcover ISBN:
- 9780123944474
- eBook ISBN:
- 9780123947963
About the Editors in Chief
Ralph Bradshaw
Ralph A. Bradshaw is Professor Emeritus in the Department of Physiology and biophysics at the University of California, Irvine. Prior to that he was on the faculty of the Department of Biological Chemistry, Washington University School of Medicine in St. Louis, MO and was Professor and Chair of the Department of Biological Chemistry at the University of California, Irvine. From 2006 to 2015, he was a member of the Mass Spectrometry Facility and Professor of Pharmaceutical Chemistry at the University of California, San Francisco. He holds degrees from Colby College and Duke University and was a post-doctoral fellow at Indiana University and the University of Washington. He has served as president for FASEB, was the founding president of the Protein Society and was the treasurer of the American Society for Biochemistry and Molecular Biology. His research has focused on protein chemistry and proteomics, with emphasis on the structure and function of growth factors and their receptors, particularly nerve growth factor and fibroblast growth factor, and the involvement of receptor tyrosine kinases in cell signalling. He has also studied in the role of proteolytic processing and N-terminal modification in protein stability and turnover.
Affiliations and Expertise
Department of Chemistry and Pharmaceutical Chemistry; and Mass Spectrometry Facility, University of California, San Francisco, Department of Physiology and Biophysics, College of Medicine, University of California, Irvine, Irvine, CA
Philip Stahl
Philip D. Stahl is Mallinckrodt Jr. Professor Emeritus at Washington University School of Medicine in St. Louis, MO. He was educated at West Virginia University with post-doctoral work at Vanderbilt University. He served as Head of the Department of Cell Biology and Physiology and Director of the Division of Biology and Biomedical Sciences at Washington University. He has been the recipient of many awards including a MERIT award from the NIH and the WICB Senior Recognition award given by the American Society for Cell Biology in recognition of his work supporting the advancement of women in science. Among StahlLab contributions are the discovery of the lysosomal enzyme clearance pathway now implemented in the treatment of lysosomal storage disease, discovery of the innate immune receptor, the mannose receptor, discovery of the exosome secretion pathway, and the role of Rab5 and Arf6 in endocytosis. Currently his research focuses on endocytosis, signal transduction, and exosome biogenesis and secretion.
Affiliations and Expertise
Washington University, St. Louis, MO, USA
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