Principles of Developmental Genetics
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Table of contents
- Cover
- Contentsv
- Prefacexi
- Section I: The Impact of Genetic and Genomic Tools on Developmental Biology1
- Chapter 1: Untangling the Gordian Knot: Cell Signaling Events That Instruct Development2
- Introduction2
- I. Identification of Novel Signaling Pathway Components6
- II. Distribution/Localization of Ligand and Signal Transduction12
- III. Mechanisms of Signal Transduction15
- IV. Transcriptional Targets of Signaling Pathways18
- V. Challenges for Future Studies of Developmental Signaling20
- Summary22
- Acknowledgments22
- Glossary of Terms23
- References26
- Further Reading31
- Chapter 2: Finding Gene Expression Changes Using Microarray Technology32
- Introduction32
- I. Microarray Principles33
- II. Applications of DNA Microarray Technology38
- III. Concluding Remarks42
- Summary42
- Acknowledgments42
- Glossary of Terms43
- References43
- Chapter 3: Chemical and Functional Genomic Approaches to Study Stem Cell Biology and Regeneration45
- Introduction45
- I. Overview of Stem Cells46
- II. Genomic Approaches in Stem Cell Research48
- III. Chemical Technologies in Stem Cell Studies52
- IV. Concluding Remarks63
- Summary65
- Glossary of Terms65
- References66
- Further Reading68
- Chapter 4: Assessing Neural Stem Cell Properties Using Large-Scale Genomic Analysis69
- Introduction69
- I. The Importance of A Global Analysis and the Caveats When Comparing Cell Samples71
- II. The Use of A Reference Standard73
- III. Methods of Analysis75
- IV. Data Mining: Chromosome Mapping, Pathway Analysis, and Data Representation78
- V. General Observations about the Properties of Neural Stem Cells81
- VI. Cancer Stem Cells85
- VII. Applications of Profiling Data85
- Summary87
- Acknowledgments87
- References87
- Further Reading90
- Chapter 5: Epigenetic Influences on Gene Expression Pathways92
- Introduction92
- I. Epigenetics and Cellular Memory92
- II. Epigenetic Reprogramming During Development93
- III. Epigenetic Control of Imprinted Gene Expression94
- IV. Mechanisms of Epigenetic Regulation95
- V. Epigenetic Regulation by the Polycomb Group101
- VI. Epigenetic Control of X-Chromosome Inactivation103
- Summary109
- Glossary109
- References110
- Further Reading112
- Recommended Resources113
- Chapter 6: New Insights into Vertebrate Origins114
- Introduction114
- I. Hox Gene Cluster Organization and Expression in Deuterostomes: Anterior–Posterior Axis Developm118
- II. Pharyngeal Gills and Cartilage Development119
- III. The Postanal Tail and the Endostyle of Hemichordates: Gene Expression Dtudies121
- IV. No Genetic Expression Evidence for Stomochord Homology to Notochord122
- V. Evolutio of Placodes and Neural Crest in Chordates123
- VI. Conclusions123
- Summary124
- Acknowledgments124
- Glossary of Terms124
- References126
- Further Reading128
- Recommended Resources128
- Chapter 7: Understanding Human Birth Defects Through Model Organism Studies129
- Introduction129
- I. Developmental Malformations129
- II. Model Organisms133
- III. Perspectives144
- Summary146
- Glossary of Terms146
- References146
- Further Reading148
- Section II: Early Embryology, Fate Determination, and Patterning149
- Chapter 8: Germ Line Determinants and Oogenesis150
- Introduction150
- I. Germ Cell Specification150
- II. Conserved Genes in Organisms That Specify Germ Cells Via Germ Plasm and Inductive Mechanisms152
- III. Germ Cell Migration154
- IV. Germ Cell Sex Determination156
- V. Genomic Imprinting157
- VI. Meiosis158
- VII. Oogenesis159
- VIII. Germ Cell Development in Humans and Infertility161
- IX. Germ Cell Development In Vitro162
- Conclusions164
- Summary164
- Acknowledgments165
- Glossary of Terms165
- References166
- Recommended Resources172
- Chapter 9: Patterning the Anterior– Posterior Axis During Drosophila Embryogenesis173
- Introduction173
- I. Maternal Control of Axis Formation175
- II. Segmentation of the Fly Embryo180
- III. Conclusion192
- Summary193
- Acknowledgments194
- Glossary194
- References195
- Further Reading199
- Internet Resources on Drosophila Development200
- Chapter 10: Anterior–Posterior Patterning in Mammals201
- Introduction201
- I. A Heterogeneous Population of Cells Defines the Anterior Pole204
- II. The Anterior Visceral Endoderm Domain is Restricted by the Extra-Embryonic Ectoderm206
- III. Origin of the Anterior Visceral Endoderm: Where do these Cells Come from?208
- IV. Evolutionary Perspective211
- V. Conclusions212
- Summary212
- Acknowledgments213
- Glossary213
- References214
- Recommended Resources215
- Chapter 11: Signaling Cascades, Gradients, and Gene Networks in Dorsal/Ventral Patterning216
- Introduction216
- I. Formation of the Developmental Axes and Subdivision of the Embryo Into Developmental Domains216
- II. Formation of the DL Nuclear Concentration Gradient220
- III. Subdivision of the Embryo Into Multiple Developmental Domains by the Dorsal Nuclear Concentrati226
- IV. Decapentaplegic/Short Gastrulation Activity Gradients are Responsible for Further Patterning of228
- V. The Dorsal-Ventral Regulatory Network231
- VI. Comparison of Dorsal–Ventral Pattering in Drosophila and Vertebrates232
- Summary235
- References236
- Further Reading239
- Internet Resources for Exploring Drosophila Development239
- Chapter 12: Early Development of Epidermis and Neural Tissue241
- Introduction241
- I. Specification of Ectoderm and Mesendoderm by Mutually Antagonistic Factors242
- II. Specification of Epidermis and Neural Tissue244
- IV. Ectodermal Cell-Type Specification and Cell Polarity250
- Summary254
- Acknowledgments255
- Glossary of Terms255
- References255
- Further Reading257
- Chapter 13: Formation of the Embryonic Mesoderm258
- Introduction258
- I. Introduction to the Embryonic Mesoderm258
- II. Mesoderm Induction: Embryology262
- III. Mesoderm Induction: Molecular Mechanisms264
- IV. The Spemann Organizer and Mesodermal Patterning275
- V. Metazoan Mesoderm Formation: Theme and Variation283
- VI. Conclusions and Perspectives285
- Summary and Future Directions285
- Acknowledgments286
- Glossary of Terms286
- References287
- Further Reading294
- Recommended Resources294
- Web Sites294
- Chapter 14: Endoderm295
- Introduction295
- I. Overview of Endoderm Development296
- II. Molecular Basis of Endoderm Formation in Vertebrates300
- III. Molecular Basis of Endoderm Development in Invertebrates307
- IV. Conserved Molecular Mechanisms309
- V. Clinical Relevance: Making Endodermal Tissue from Stem Cells310
- Summary311
- Acknowledgments312
- Glossary of Terms312
- References313
- Recommended Web Sites315
- Chapter 15: Notch Signaling: A Versatile Tool for the Fine Patterning of Cell Fate in Development316
- Introduction316
- I. Determining the Precise Fate of Single Cells321
- II. Patterning Cell Fate at Compartment Boundaries327
- III. Concluding Remarks334
- Summary335
- Glossary336
- References337
- Recommended Resources340
- Chapter 16: Multiple Roles of T-box Genes341
- Introduction341
- I. T-Box Genes: Transcription Factor Genes with Many Developmental Roles341
- II. DNA Binding and Transcriptional Regulation by T-Box Proteins343
- III. Human Syndromes and Mouse Models344
- IV. Future Directions353
- Summary354
- Acknowledgments354
- Glossary of Terms354
- References355
- Further Reading358
- Recommended Resources358
- Recommended Web Sites358
- Section III: Gastrulation in Vertebrates359
- Chapter 17: Gastrulation in Vertebrates360
- Introduction360
- I. Variable Morphology and Morphogenetic Movements of Pregastrulation Embryos361
- II. Conserved Distribution of Tissue Progenitors at the Onset of Vertebrate Gastrulation362
- III. Experimental Approaches to Study Vertebrate Gastrulation365
- IV. Epiboly367
- V. Internalization370
- VI. Convergence and Extension Movements373
- VII. Conclusion384
- Summary384
- Acknowledgments385
- References385
- Recommended Resources391
- Chapter 18: Regulation of Tissue Separation in the Amphibian Embryo392
- Introduction392
- I. The Role of Mesoderm-Inducing Growth Factors and Cadherin-Mediated Tissue Affinities394
- II. The Role of Transcription Factors in Tissue Separation395
- III. The Role of Signaling Molecules in Tissue Separation397
- Summary401
- Acknowledgments401
- Glossary of Terms401
- Reference402
- Recommended Resources403
- Chapter 19: Role of the Basement Membrane in Cell Migration404
- Introduction404
- I. Function of Extracellular Matrix Receptors in Cell Migration407
- II. Function of Basement Membrane Proteins in Cell Migration408
- III. Function of Extracellular Proteases in Cell Migration414
- IV. Perspectives418
- Summary418
- Acknowledgments419
- Glossary of Terms419
- References420
- Recommended Web Sites423
- Chapter 20: Epithelial Morphogenesis424
- Introduction424
- I. Epithelial Architecture424
- II. Models of Epithelial Morphogenesis431
- III. Human Epithelial Diseases440
- Summary442
- Acknowledgments442
- Glossary443
- References443
- Further Reading446
- Chapter 21: Branching Morphogenesis of Mammalian Epithelia448
- Introduction448
- I. Types and Scales of Branching Morphogenesis449
- II. The Role of Genetics in Studying Mechanisms of Branching Morphogenesis451
- III. Cellular Mechanisms of Branching Morphogenesis451
- IV. Control of Branching Activities by Intracellular Signal Transduction Systems453
- V. Control of Branching Activity by External Signals456
- VI. Branching Morphogenesis is a Local Rather than a Global Activity457
- VII. The Role of Feedback in Shaping the Branching Tree460
- Summary461
- Glossary462
- References462
- Recommended Resources466
- Chapter 22: The Roles of Ephrin–Eph in Morphogenesis467
- Introduction467
- I. Conserved Ephrin/Eph Structure from Caenorhabditis Elegans to Homo Sapiens467
- II. Oocyte Maturation472
- III. Early Morphogenesis472
- IV.Cell Migration and Positioning475
- V. Eph/Ephrins in Cancer483
- Summary491
- Acknowledgments492
- Glossary492
- References493
- Further Reading497
- Recommended Resources498
- Section IV: Ectodermal Organs499
- Chapter 23: Neural Cell Fate Determination500
- Introduction500
- I. The Fundamental Process of Neurogenesis: Proneural Genes501
- II. Spatial Cell Fate Determination: Making the Right Neuron in the Right Place504
- III. Temporal Control of Cell Fate Determination: Making the Right Neuron at the Right Time508
- IV. Common Features of Cell Fate Determination in Different Regions of the Nervous System513
- V. Perspectives514
- Summary514
- Glossary515
- References515
- Further Reading523
- Recommended Resources523
- Chapter 24: Pathfinding and Patterning of Axonal Connections525
- Introduction525
- I. Transcription Factors in Cell Specification and Axon Connectivity527
- II. Axon Pathfinding at the Midline530
- III. Cell Biology Underlying Axon Pathfinding and Connectivity540
- IV. Conclusions542
- Summary543
- Acknowledgments543
- Glossary543
- References544
- Chapter 25: Retinal Development548
- Introduction548
- I. Eye Field Formation549
- II. Optic Vesicle Formation552
- III. Control of Retinal Growth555
- IV. Retinal Cell Fate Specification559
- V. Muumlller Cell Genesis565
- VI. Adult Retinal Stem Cells567
- VII. Conclusions and Future Directions569
- Summary569
- Glossary569
- References570
- Further Reading573
- Recommended Resources573
- Chapter 26: Neural Crest Determination574
- Introduction574
- I. Techniques to Identify Neural Crest Development576
- II. Specification of Neural Crest Cells577
- III. Regionalization of Neural Crest Cells584
- IV. Human Pathologies585
- Summary586
- Acknowledgments586
- Glossary of Terms586
- References587
- Further Reading588
- Recommended Resources589
- Chapter 27: Determination of Preplacodal Ectoderm and Sensory Placodes590
- Introduction590
- I. Cranial Sensory Placodes Give Rise to Diverse Structures591
- II. Initial Formation of the Preplacodal Ectoderm593
- III. Genes that Specify Preplacodal Ectoderm Fate598
- IV. Maintaining the Boundaries of the Preplacodal Ectoderm and Other Ectodermal Domains602
- V. Placode Identity and Onset of Differentiation604
- VI. Future Directions607
- Summary608
- Acknowledgments608
- Glossary609
- References609
- Recommended Resources614
- Chapter 28: Molecular Genetics of Tooth Development615
- Introduction615
- I. Developmental Anatomy616
- II. Gene Expression Pattern Database617
- III. The Disruption of Signalling Pathways Arrests Mouse Tooth Development618
- IV. The Genetic Basis of Human Tooth Agenesis620
- V. Dental Placodes and the Pathogenesis of Ectodermal Dysplasia Syndromes620
- VI. Enamel Knots, Tooth Shapes, and the Fine-Tuning of Signal Pathways623
- VII. The Genetic Basis of Tooth Replacement624
- VIII. The Developmental Genetics of Dentin and Enamel Formation626
- Summary627
- Glossary628
- References628
- Recommended Resources630
- Chapter 29: The Inner Ear631
- Introduction631
- I .Evolution of Mechanoreceptors633
- II. Neurosensory Cell Fate Specification and Differentiation636
- III. Pattern Formation in the Inner Ear643
- IV. Phylogenetic and Evolutionary Considerations647
- Summary650
- Glossary650
- References651
- Recommended Resources655
- Chapter 30: Craniofacial Formation and Congenital Defects656
- Introduction656
- I. In the Beginning...656
- II. A Lexicon of Craniofacial Development657
- III. Organizing the Craniofacial Prominences657
- IV. Assembling the Pieces of the Craniofacial Complex663
- V. Differentiating the Craniofacial Complex664
- VI. Congenital Disorders666
- VII. Conclusions674
- Summary675
- Acknowledgments675
- Glossary675
- References676
- Further Readingd678
- Recommended Resources678
- Useful Web Sites678
- Section V: Mesodermal Organs679
- Chapter 31: Induction of the Cardiac Lineage680
- Introduction680
- II. Multiple Signaling Pathways are Involved in Early Cardiogenesis683
- III. Transcriptional Regulation During Heart Induction688
- IV. Transcriptional Regulation in Precardiac Tissue689
- V. Conclusions692
- Summary692
- Acknowledgments693
- Glossary693
- References693
- Recommended Resources697
- Chapter 32: Heart Patterning and Congenital Defects698
- Introduction698
- I. Genetic Epidemiology of Congenital Cardiovascular Malformations698
- II. Heart Tube704
- III. Looping705
- IV. Atrial Septation708
- V. Left Atrium and Pulmonary Veins710
- VI. Ventricular Septation711
- VII. Endocardium and Valvulogenesis712
- VIII. Common Outflow Tract714
- IX. Intracardiac Conduction System717
- Summary717
- Glossary718
- References718
- Recommended Resources720
- Chapter 33: Blood Vessel Formation721
- Introduction721
- I. Emergence of the Blood Vascular System721
- II. Arterial–Venous Differentiation729
- III. Emergence of the Lymphatic System736
- IV. Patterning of the Developing Vasculature739
- V. Concluding Remarks744
- Summary746
- Acknowledgment746
- Glossary746
- References747
- Recommended Resources754
- Chapter 34: Blood Induction and Embryonic Formation755
- Introduction755
- I .Origin of Blood Cells During Embryogenesis756
- II. Genetic Approaches to the Study of the Transcription Factors in Blood Development763
- III. Clinical Applications of Hematopoietic Stem Cells768
- Summary769
- Acknowledgments770
- Glossary770
- References770
- Further Reading777
- Recommended Resources777
- Chapter 35: Topics in Vertebrate Kidney Formation: A Comparative Perspective778
- Introduction778
- I. Vertebrate Kidney Anatomy779
- II. Early Kidney Development and Specification of the Intermediate Mesoderm783
- III. Formation of the Nephric Duct789
- IV. Formation of the Mammalian Metanephros791
- Summary and Synthesis797
- Summary799
- Acknowledgments799
- Glossary800
- References800
- Further Reading804
- Chapter 36: Development of the Genital System805
- Introduction805
- I. Genetic Sec Determination805
- II. Gonadal Differentiation810
- III. Development of the Genital Ducts816
- IV. Development of the External Genitalia821
- V. Malformations of the Genital System822
- VI. Vestigial Structures from the Embryonic Genital Ducts824
- VII. Other Abnormalities of the Genital Duct System824
- VIII. Conclusion824
- Summary825
- Glossary826
- References826
- Further Reading828
- Recommended Resources828
- Chapter 37: Diaphragmatic Embryogenesis and Human Congenital Diaphragmatic Defects829
- Introduction829
- I. Diaphragmatic Anatomy830
- II. Diaphragmatic Development833
- III. Lung Development and the Diaphragm837
- IV. Genetics of Human Congenital Diaphragmatic Defects/Congenital Diaphragmatic Hernia839
- VI. Conclusions841
- Summary841
- Acknowledgments842
- Glossary842
- References842
- Recommended Resource846
- Chapter 38: Formation of Vertebrate Limbs847
- Introduction847
- I. Limb Initiation848
- II. Limb Bud Outgrowth and Patterning850
- III. Limb Development and Diseases858
- IV. Conclusions and Perspectives860
- Summary861
- Glossary861
- References862
- Recommended Resources865
- Chapter 39: Skeletal Development866
- Introduction866
- I. The Appendicular Skeleton866
- II. Axial Skeleton878
- III. Craniofacial Skeleton Development891
- Summary896
- Acknowledgments897
- Glossary897
- References898
- Further Reading904
- Recommended Resources905
- Chondrogenesis/Endochondral Ossification905
- Somitogenesis905
- Craniofacial Development/Intramembranous Ossification905
- Section VI: Endodermal Organs907
- Chapter 40: Patterning the Embryonic Endoderm into Presumptive Organ Domains908
- Introduction908
- I. Fate Map of the Embryonic Endoderm910
- II. Gene Expression Domains Predict and Determine Endoderm Organ Primordia914
- III. Signaling Processes Involved in the Patterning and Formation of the Fetal Gut917
- IV. Impact of Genomics On Our Understanding of Early Endoderm Organogenesis925
- V. Clinical Applications for Studies in Endoderm Organogenesis926
- Summary927
- Acknowledgments927
- Glossary928
- References928
- Recommended Resources931
- Chapter 41: Developmental Genetics of the Pulmonary System932
- Introduction932
- I. Lung Specification and Symmetry933
- II. Branching Morphogenesis934
- III. Sacculation and Epithelial Cell Differentiation935
- IV. Mesenchymal Differentiation and Vascular Development936
- V. Secondary Crest Elongation and Alveogenesis937
- VI. Transition to Air Breathing939
- VII. Conclusion940
- Summary941
- Acknowledgments941
- Glossary941
- References942
- Recommended Resources945
- Chapter 42: Pancreas Development and Stem Cells946
- Introduction946
- I. The Initial Stages of Pancreatic Bud Formation947
- II. Inductive Interactions During Pancreas Development950
- III. Genes that Affect Pancreatic Bud Development952
- IV. Genes that Affect the Differentiation of Particular Pancreatic Cell Types955
- V. Pancreas/beta-Cell Regeneration and Neogenesis961
- VI. Conclusion969
- Summary969
- Acknowledgments970
- Glossary970
- References971
- Further Reading980
- Recommended Resources980
- Chapter 43: Early Liver Development and Hepatic Progenitor Cells982
- Introduction982
- I. Two Endodermal Origins of Embryonic Liver Cells983
- II. Developmental Competence of the Ventral Foregut Endoderm, The Specification of Hepatoblasts, and984
- III. Hepatoblast Differentiation Into Hepatocytes and Cholangiocytes (Biliary Cells)989
- IV. Adult Liver Stem Cells991
- V. Differentiation of Liver-Like Cells from Embryonic Stem Cells995
- Summary996
- Glossary996
- References997
- Recommended Reading1003
- Liver Development1003
- Adult Liver Progenitor Cells1003
- Chapter 44: Intestinal Stem Cells in Physiologic Regeneration and Disease1004
- Introduction1004
- I. Overview of Intestinal Anatomy and Functional Histology1004
- II. Intestinal Stem Cells1006
- III. Stem Cell/Niche Interactions1007
- IV. Signaling Mechanisms Controlling Intestinal Stem Cell Self-Renewal, Proliferation, and Different1008
- V. Intestinal Stem Cells in Human Disease1014
- VI. Closing Remarks1017
- Summary1018
- Glossary1018
- References1019
- Recommended Resources1022
- Index1023
- Color Plates1056
Unlike anything currently available in the market, Dr. Sally A. Moody and a team of world-renowned experts provide a groundbreaking view of developmental genetics that will influence scientific approaches in embryology, comparative biology, as well as the newly emerging fields of stem cell biology and regenerative medicine. Principles of Developmental Genetics highlights the intersection of developmental biology with new revolutionary genomic technologies, and details how these advances have accelerated our understanding of the molecular genetic processes that regulates development. This definitive resource provides researchers with the opportunity to gain important insights into the clinical applicability of emerging new technologies and animal model data. This book is a must-have for all researchers in genetics, developmental biology, regenerative medicine, and stem cell biology.
• Includes new research not previously published in any other book on the molecular genetic
processes that regulates development
• Chapters present a broad understanding on the application of animal model systems, allowing
researchers to better treat clinical disorders and comprehend human development
• Relates the application of new technologies to the manipulation of stem cells, causes of
human birth defects, and several human disease conditions
• Each chapter includes a bulleted summary highlighting clinical aspects of animal models
• Includes new research not previously published in any other book on the molecular genetic
processes that regulates development
• Chapters present a broad understanding on the application of animal model systems, allowing
researchers to better treat clinical disorders and comprehend human development
• Relates the application of new technologies to the manipulation of stem cells, causes of
human birth defects, and several human disease conditions
• Each chapter includes a bulleted summary highlighting clinical aspects of animal models