Principles of Developmental Genetics - Edition 2 - Edited by Sally A. Moody Elsevier Inspection Copies

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Principles of Developmental Genetics,

Edition 2

Edited by Sally A. Moody

Publication Date: 05 Sep 2014

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Providing expert coverage of all major events in early embryogenesis and the organogenesis of specific systems, and supplemented with representative clinical syndromes, Principles of Developmental Genetics, Second Edition discusses the processes of normal development in embryonic and prenatal animals, including humans. The new edition of this classic work supports clinical researchers developing future therapies with its all-new coverage of systems biology, stem cell biology, new technologies, and clinical disorders. A crystal-clear layout, exceptional full-color design, and bulleted summaries of major takeaways and clinical pathways assist comprehension and readability of the highly complex content.

Key Features

All-new coverage of systems biology and stem cell biology in context of evolving technologies places the work squarely on the modern sciences
Chapters are complemented with a bulleted summary for easy digestion of the major points, with a clinical summary for therapeutic application
Clinical highlights provides a bridge between basic developmental biology and clinical sciences in embryonic and prenatal syndromes

About the author

Edited by Sally A. Moody, George Washington University, Washington, DC, USA

Table of Contents

Preface
Section I. Emerging Technologies and Systems Biology
- Chapter 1. Generating Diversity and Specificity through Developmental Cell Signaling
  - Summary
  - 1.1. Introduction
  - 1.2. Identification of Signaling Pathway Components
  - 1.3. Functional Diversification of Related Signaling Proteins
  - 1.4. Roles of Cytoplasmic Extensions in Cell Signaling
  - 1.5. Formation and Interpretation of Signaling Gradients
  - 1.6. Transcriptional Regulation by Developmental Cell Signaling Pathways
  - 1.7. Transcription-Independent Responses to Cell Signaling
  - 1.8. Roles of Computational Biology in Developmental Cell Signaling Studies
  - 1.9. Closing Remarks
  - 1.10. Clinical Relevance: Developmental Cell Signaling and Human Disease
- Chapter 2. Applications of Deep Sequencing to Developmental Systems
  - Summary
  - 2.1. Introduction
  - 2.2. Using RNA-seq to Map and Quantify Transcripts
  - 2.3. Chromatin Immunoprecipitation for Identifying Protein-DNA Interactions
  - 2.4. DNAse I Hypersensitive Site Mapping to Identify Cis-Regulatory Regions
  - 2.5. Interactions at a Distance
  - 2.6. Prospects
  - 2.7. Clinical Relevance
- Chapter 3. Using Mutagenesis in Mice for Developmental Gene Discovery
  - Summary
  - 3.1. Use of ENU as a Mutagen
  - 3.2. ENU-Induced Mutations in Mice
  - 3.3. ENU-Induced Mutations Affecting Development
  - 3.4. Identification of Modifier loci
  - 3.5. Clinical Relevance
- Chapter 4. Chemical Approaches to Controlling Cell Fate
  - Summary
  - 4.1. Introduction
  - 4.2. Chemical Approaches to Controlling Cell Fate
  - 4.3. Clinical Relevance
- Chapter 5. BMP Signaling and Stem Cell Self-Renewal in the Drosophila Ovary
  - Summary
  - 5.1. Introduction
  - 5.2. The Drosophila Ovary
  - 5.3. The BMP Signaling Pathway
  - 5.4. Regulation of BMP Signaling by Extrinsic Factors
  - 5.5. Regulation of BMP Signaling by Intrinsic Factors
  - 5.6. Additional Regulators
  - 5.7. Selected Topics
  - 5.8. BMP Signaling and Stem Cell Homeostasis in Vertebrates
  - 5.9. Conclusions
  - 5.10. Clinical Relevance
- Chapter 6. Genomic Analyses of Neural Stem Cells
  - Summary
  - 6.1. Introduction
  - 6.2. The Importance of Global Analysis and Caveats when Comparing Cell Samples
  - 6.3. The Use of a Reference Standard
  - 6.4. Epigenetic Modulation
  - 6.5. MicroRNA
  - 6.6. Mitochondrial Sequencing
  - 6.7. Transcriptome Mapping
  - 6.8. Data Mining: Chromosome Mapping, Pathway Analysis, Data Representation
  - 6.9. General Observations about the Properties of Neural Stem Cells
  - 6.10. Species Differences
  - 6.11. Lack of a “Stemness” Phenotype
  - 6.12. Allelic Variability
  - 6.13. Age Dependent Changes in NSCs
  - 6.14. Cancer Stem Cells
  - 6.15. Conclusions
  - 6.16. Clinical Relevance
- Chapter 7. Genomic and Evolutionary Insights into Chordate Origins
  - Summary
  - 7.1. Introduction
  - 7.2. Hox Gene Cluster Organization and Expression in Deuterostomes: Anterior-Posterior Axis Development
  - 7.3. Pharyngeal Gills and Gill Bar Development
  - 7.4. The Post-Anal Tail and the Endostyle of Hemichordates: Gene Expression Studies
  - 7.5. The Central Nervous System and the Dorsal-Ventral Inversion Hypothesis
  - 7.6. Evidence for the Hemichordate Stomochord Homology to Chordate Notochord
  - 7.7. The Evolution of Placodes and the Neural Crest in Chordates
  - 7.8. Stem Cells and Regeneration in Hemichordates
  - 7.9. Summary and Conclusions
  - 7.10. Clinical Relevance
Section II. Early Embryology and Morphogenesis
- Chapter 8. Signaling Cascades, Gradients, and Gene Networks in Dorsal/Ventral Patterning
  - Summary
  - 8.1. Introduction
  - 8.2. AP and DV Polarity is Specified in the Developing Ovariole
  - 8.3. From the Oocyte to the Fertilized Egg: Formation of the DL Nuclear Concentration Gradient
  - 8.4. Dpp/Sog Activity Gradients are Responsible for Further Patterning of the DV Axis
  - 8.5. The DV Regulatory Network
  - 8.6. Comparison of DV Patterning in Drosophila and Vertebrates
  - 8.7. Clinical Relevance
- Chapter 9. Building Dimorphic Forms: The Intersection of Sex Determination and Embryonic Patterning
  - Summary
  - 9.1. Introduction
  - 9.2. Sex determination in Drosophila melanogaster
  - 9.3. Sex Determination in Mammals
  - 9.4. Dimorphism in the Fly Olfactory System
  - 9.5. Integration of Sex Determination and Embryonic Pattern Formation
  - 9.6. Clinical implications of Sexual Determination and Dimorphism
  - 9.7. Conclusions
  - 9.8. Clinical Relevance
- Chapter 10. Formation of the Anterior-Posterior Axis in Mammals
  - Summary
  - 10.1. Introduction
  - 10.2. Discovery and Importance of the AVE
  - 10.3. The DVE is a Heterogeneous and Dynamic Cell Population, which forms after the Proximo-Distal Regionalization of the VE
  - 10.4. Mechanisms of DVE Cell Movement
  - 10.5. Evolutionary Perspective
  - 10.6. Conclusions
  - 10.7. Clinical Relevance
- Chapter 11. Early Development of Epidermis and Neural Tissue
  - Summary
  - 11.1. Introduction
  - 11.2. Specification of Ectoderm and Mesendoderm by Mutually Antagonistic Factors
  - 11.3. Specification of Epidermis and Neural Tissue
  - 11.4. Ectodermal Cell Type Specification and Cell Polarity
  - 11.5. Clinical Relevance
- Chapter 12. Taking the Middle Road: Vertebrate Mesoderm Formation and the Blastula-Gastrula Transition
  - Summary
  - 12.1. The Discovery of Mesoderm and Germ Layers
  - 12.2. Germ Layer Phylogeny
  - 12.3. Mesoderm’s Fossil Record
  - 12.4. Embryonic Organizers and Induction
  - 12.5. Cell Lineage Tracing
  - 12.6. The Blastula-Gastrula Transition in Vertebrates
  - 12.7. The Cryptic Homology of Vertebrate Fate Maps
  - 12.8. Exceptions to Presumed Cell Lineage Restrictions
  - 12.9. Beyond the Blastula-Gastrula Transition: Caudal Mesoderm and the Left-Right Axis
  - 12.10. Molecular-Genetic Dissection of Mesoderm Formation
  - 12.11. A Gene Regulatory Network View of Development
  - 12.12. GRNs of Vertebrate Mesoderm Formation
  - 12.13. Maternal Activation of Nodal Signaling: X. laevis and Zebrafish
  - 12.14. Zygotic Regulation of Nodal Signaling: Chick and Mouse
  - 12.15. Establishing T Expression
  - 12.16. Establishing Homogenous Cellular Fields
  - 12.17. The SMO Proximodistal Axis
  - 12.18. Separating Mesendoderm from Ectoderm
  - 12.19. Separating Mesoderm from Endoderm
  - 12.20. Early Zygotic Genes are Poised for Action
  - 12.21. The Phylotypic Egg Timer
  - 12.22. Mesoderm Specification Defects in Humans
  - 12.23. Human Gene Variants Associated with Mesoderm Specification Defects
  - 12.24. Implications of a Pan-N-M Caudal Axis
  - 12.25. Concluding Remarks
  - 12.26. Clinical Relevance
- Chapter 13. Vertebrate Endoderm Formation
  - Summary
  - 13.1. Introduction
  - 13.2. Overview of Endoderm Morphogenesis in Vertebrates
  - 13.3. Molecular Mechanisms of Endoderm Development
  - 13.4. Endoderm GRN Transcription Factors
  - 13.5. Modulation of the Endoderm GRN by other Signaling Pathways
  - 13.6. Human Endoderm Differentiation in Pluripotent Stem Cells
  - 13.5. Clinical Relevance
- Chapter 14. Epithelial Branching: Mechanisms of Patterning and Self-Organization
  - Summary
  - 14.1. Introduction: The Importance of Epithelial Branching to Organogenesis
  - 14.2. Types and Scales of Branching Morphogenesis
  - 14.3. The Role of Genetics in Studying Mechanisms of Branching Morphogenesis
  - 14.4. The Problems: What most Needs to be Explained
  - 14.5. Symmetry-Breaking: Why do Epithelia Branch Rather than Just Balloon?
  - 14.6. Tips and Stalks
  - 14.7. Patterning: How to make a Tree not a Tangle
  - 14.8. Imposing Subtlety: Making Organ-Specific Patterns
  - 14.9. Clinical Relevance
- Chapter 15. Lessons from the Zebrafish Lateral Line System
  - Summary
  - 15.1. Introduction
  - 15.2. Emergence of the PLL System
  - 15.3. Morphogenesis and Sequential Formation of Protoneuromasts in the PLLP
  - 15.4. Establishment of Polarized Wnt and FGF Signaling Systems in the PLLP
  - 15.5. Specification of a Central Hair Cell Progenitor by Lateral Inhibition Mediated by Notch Signaling
  - 15.6. The Hair Cell Progenitor Becomes a New Localized Source of FGF
  - 15.7. Notch Signaling – an Essential Node in the Self-Organization of the PLLP
  - 15.8. Periodic Formation of Protoneuromasts
  - 15.9. Termination of the PLLP System
  - 15.10. Polarized Migration of the PLLP Along a Path Defined by Chemokine Signals
  - 15.11. Regulation of Neuromast Spacing
  - 15.12. Conclusions
  - 15.13. Clinical Relevance
Section III. Organogenesis
- Chapter 16. Neural Cell Fate Determination
  - Summary
  - 16.1. Introduction
  - 16.2. Fundamentals of Neurogenesis
  - 16.3. The Generation of Specific Cell Types within the Vertebrate Nervous System: Spinal Cord Development
  - 16.4. Common Themes in CNS Development
  - 16.5. Postmitotic Refinement of Subtype Identity
  - 16.6. Applying Developmental Principles to Stem Cell Research: Directed Differentiation from Pluripotent Stem Cells
  - 16.7. Using Transcription Factor Codes to Directly Specify Cell Fate
  - 16.8. Modeling Human Neurological Disorders and Diseases
  - Clinical Relevance
- Chapter 17. Retinal Development
  - Vignette: Drosophila Genetics: What the Fly told the Vertebrate Eye
- Chapter 18. Neural Crest Determination and Migration
  - Summary
  - 18.1. Introduction
  - 18.2. Techniques to Identify Neural Crest Development
  - 18.3. Specification of Neural Crest Cells
  - 18.4. Neural Crest Cell Migration
  - 18.5. Human Pathologies
  - 18.6. Clinical Relevance
- Chapter 19. Development of the Pre-Placodal Ectoderm and Cranial Sensory Placodes
  - Summary
  - 19.1. Introduction
  - 19.2. Cranial Sensory Placodes give Rise to Diverse Structures
  - 19.3. Specification of the Pre-Placodal Ectoderm
  - 19.4. Genes that Specify Pre-Placodal Ectoderm Fate
  - 19.5. Maintaining the Boundaries of the Pre-Placodal Ectoderm
  - 19.6. Placode Identity
  - 19.7. Regulation of Placode-Derived Sensory Neuron Differentiation
  - 19.8. Future Directions
  - 19.9. Clinical Relevance
- Chapter 20. Building the Olfactory System
  - Summary
  - 20.1. Introduction
  - 20.2. The Initial Development of the Olfactory Pathway
  - 20.3. OE Induction: Non-Axial Mesenchymal/Epithelial Interactions Drive Differentiation
  - 20.4. OB Induction: Parallel M/E Regulation of Initial Morphogenesis
  - 20.5. Stem Cells, Cell Lineages and Neuronal Specification in the OE
  - 20.6. Cell Lineages, Migration and Neuronal Specification in the Developing and Adult OB
  - 20.7. Olfactory Pathway Development Beyond Morphogenesis, Stem Cells and Neuronal Specification
  - 20.8. Perspective
  - 20.9. Clinical Relevance
- Chapter 21. Development of the Inner Ear
  - Summary
  - 21.1. Introduction
  - 21.2. Anatomy of the Inner Ear
  - 21.3. Specification of Neural and Sensory Fates: A Common Origin for Neuronal and Prosensory Cells
  - 21.4. Development of the Semicircular Canals and Cristae
  - 21.5. Development of the Cochlear Duct and Organ of Corti
  - Conclusions
  - Clinical Relevance
- Chapter 22. Molecular Genetics of Tooth Development
  - Summary
  - 22.1. Introduction
  - 22.2. Developmental Anatomy
  - 22.3. Gene Expression Pattern Databases
  - 22.4. The Disruption of Signaling Pathways Arrests Mouse Tooth Development
  - 22.5. The Genetic Basis of Human Tooth Agenesis
  - 22.6. Dental Placodes and the Pathogenesis of Ectodermal Dysplasia Syndromes
  - 22.7. Enamel Knots, Tooth Shapes, and the Fine-Tuning of Signal Pathways
  - 22.8. The Genetic Basis of Tooth Replacement
  - 22.9. The Developmental Genetics of Dentin and Enamel Formation
  - 22.10. Clinical Relevance
- Chapter 23. Early Heart Development
  - Summary
  - 23.1. Introduction
  - 23.2. Embryology of Heart Development
  - 23.3. Multiple Signaling Pathways are Involved in Early Cardiogenesis
  - 23.4. Transcriptional Regulation of Early Heart Development
  - 23.5. Programming and Reprogramming of Cells Towards a Cardiac Fate
  - 23.6. Conclusions
  - 23.7. Clinical Significance
- Chapter 24. Blood Vessel Formation
  - Summary
  - 24.1. Introduction
  - 24.2. Emergence of the Blood Vascular System
  - 24.3. Arterial-Venous Differentiation
  - 24.4. Emergence of the Lymphatic System
  - 24.5. Patterning of the Developing Vasculature
  - 24.6. Concluding Remarks
  - 24.7. Clinical Relevance
- Chapter 25. Blood Induction and Embryonic Formation
  - Summary
  - 25.1. Introduction
  - 25.2. Origin of Blood Cells during Embryogenesis
  - 25.3. Transcriptional Regulation of Blood Development
  - 25.4. Therapeutic Use of HSCs
  - 25.5. Clinical Relevance
- Chapter 26. How to Build a Kidney
  - Summary
  - 26.1. Introduction
  - 26.2. The Nephric Duct
  - 26.3. Nephron Segmentation
  - 26.4. Kidney Stem Cells?
  - 26.5. Summary and Future Directions
  - Clinical Relevance
- Chapter 27. Development of the Genital System
  - Summary
  - 27.1. Introduction
  - 27.2. Genetic Sex Determination
  - 27.3. Gonadal Differentiation
  - 27.4. Development of the Genital Ducts
  - 27.5. Development of the External Genitalia
  - 27.6. Malformations of the Genital System
  - 27.7. Conclusion
- Chapter 28. Skeletal Development
  - Summary
  - 28.1. Introduction
  - 28.2. The Appendicular Skeleton
  - 28.3. Axial Skeleton
  - 28.4. Conclusion
  - 28.5. Clinical Relevance
- Chapter 29. Formation of Vertebrate Limbs
  - Summary
  - 29.1. Introduction
  - 29.2. Limb Initiation
  - 29.3. Limb Bud Outgrowth and Patterning
  - 29.4. Limb Development and Diseases
  - 29.5. Conclusions and Perspectives
  - 29.6. Clinical Relevance
- Chapter 30. Patterning the Embryonic Endoderm into Presumptive Organ Domains
  - Summary
  - 30.1. Introduction
  - 30.2. Fate Map of the Embryonic Endoderm
  - 30.3. Gene Expression Domains Predict and Determine Endoderm Organ Primordia
  - 30.4. Translational Embryology: The Impact of Embryonic Studies on Human Health
  - Clinical Relevance
- Chapter 31. Pancreas Development and Regeneration
  - Summary
  - 31.1. Introduction
  - 31.2. The Initial Stages of Pancreatic Bud Formation
  - 31.3. Inductive Interactions During Pancreas Development
  - 31.4. Genes that Affect Pancreatic Bud Development
  - 31.5. Genes that Affect the Differentiation of Particular Pancreatic Cell Types
  - 31.6. Generating Islets/β-Cells from Stem or Progenitor Cells
  - 31.7. Clinical Relevance
Section IV. Selected Clinical Problems
- Chapter 32. Diaphragmatic Embryogenesis and Human Congenital Diaphragmatic Defects
  - Summary
  - 32.1. Introduction
  - 32.2. Diaphragmatic Anatomy
  - 32.3. Diaphragmatic Development
  - 32.4. Genetics of Human Congenital Diaphragmatic Defects
  - 32.5. Cardiopulmonary Development and the Diaphragm
  - Conclusions
  - Clinical Relevance
- Chapter 33. Genetic and Developmental Basis of Congenital Cardiovascular Malformations
  - Summary
  - 33.1. Understanding Congenital Heart Defects in the Context of Normal Cardiac Development
  - 33.2. Heart Tube and Cardiac Looping
  - 33.3. Formation of the Atrioventricular Canal
  - 33.4. Targeted Growth of the Pulmonary Veins
  - 33.5. Atrial and Ventricular Septation
  - 33.6. Valvulogenesis and Outflow Tract Development
  - 33.7. Intracardiac Conduction System
  - 33.8. Clinical Relevance
- Chapter 34. T-Box Genes and Developmental Anomalies
  - Summary
  - 34.1. T-Box Genes: Transcription Factor Genes with Many Developmental Roles
  - 34.2. DNA Binding and Transcriptional Regulation by T-Box Proteins
  - 34.3. Human Syndromes and Mouse Models
  - 34.4. Future Directions
  - Clinical Relevance
- Chapter 35. Craniofacial Syndromes: Etiology, Impact and Treatment
  - Summary
  - 35.1. Introduction
  - 35.2. First Arch Derived Structures
  - 35.3. Midface
  - 35.4. Cranial Vault
  - 35.5. Conclusions
  - 35.6. Clinical Relevance
- Chapter 36. 22q11 Deletion Syndrome: Copy Number Variations and Development
  - Summary
  - 36.1. 22q11DS is a Genomic Disorder with Widespread Consequences for Development
  - 36.2. 22q11DS as Viewed from a Developmental Perspective
  - 36.3. Genes and Phenotypes: 22q11DS as a Prototype Genomic Disease
  - 36.4. Clinical Relevance
- Chapter 37. Neural Tube Defects
  - Summary
  - 37.1. Introduction
  - 37.2. Discussion
  - 37.3. Future Directions
  - 37.4. Clinical Relevance
Glossary
Index