Developmental Biology (PDF)

Developmental Biology
 
Author:
Scott F. Gilbert & Michael J. F. Barresi
Release at: 2016
Pages: 940
Edition:
11th Edition
File Size: 148 MB
File Type: pdf
Language: English


Description of Developmental Biology


This Developmental Biology book 11th edition is a great & beautiful book written by Gilbert use for developmental science study to get free pdf download. It is due to talent of Chris Small and his production staff; to Jefferson Johnson and his artistic mastery of Adobe InDesign; to the expertise of the artists at Dragonfly Media Graphics; and to photo editor extraordinaire David McIntyre, who manages to find incredible photographs to complement the many wonderful images my colleagues have so generously supplied for each edition.


I have been blessed with remarkable students who have never been shy about asking me questions. Even today they continue to send me “Did you see this?” emails that make sure I’m keeping current. I also thank all those people who continue to send me emails of encouragement or who come up to me at meetings to pass on good words about the book and provide me with even more information. This book is and always has been a community endeavor.

Content of Developmental Biology



I Patterns and Processes of Becoming:  A Framework for Understanding Animal Development

CHAPTER 1   Making New Bodies:  Mechanisms of Developmental Organization  1

“How Are You?” The Questions of Developmental Biology 2

The Cycle of Life 4

An Example: A Frog’s Life 5

Gametogenesis and fertilization 6

Cleavage and gastrulation 6

Organogenesis 6

Metamorphosis and gametogenesis 8

Comparative Embryology 9

Epigenesis and preformationism 9

An Overview of Early Development 11

Patterns of cleavage 11

Gastrulation: “The most important time in your life” 14

Naming the parts: The primary germ layers and early organs 14

The four principles of Karl Ernst von Baer 15

Keeping Track of Moving Cells: Fate Maps and Cell Lineages 17

Fate maps 18

Direct observation of living embryos 19

Dye marking 19

Genetic labeling 20

Transgenic DNA chimeras 21

Evolutionary Embryology 23

Embryonic homologies 24

Medical Embryology and Teratology 26

Genetic malformations and syndromes 26

Disruptions and teratogens 26

CHAPTER 2   Specifying Identity:  Mechanisms of Developmental Patterning 29

Levels of Commitment 30

Cell differentiation 30

Commitment 30

Autonomous Specification 32

Cytoplasmic determinants and autonomous specification in the tunicate 32

Conditional Specification 35

Cell position matters: Conditional specification in the sea urchin embryo 36

Syncytial Specification 38

Opposing axial gradients define position 39

A Rainbow of Cell Identities 41

CHAPTER 3   Differential Gene Expression:  Mechanisms of Cell Differentiation 45

Defining Differential Gene Expression 45

Quick Primer on the Central Dogma 46

Evidence for Genomic Equivalence 47

Modulating Access to Genes 50

Loosening and tightening chromatin: Histones as gatekeepers 50

Maintaining a memory of methylation 52

Anatomy of the Gene 52

Exons and introns 52

Cis-regulatory elements: The on, off, and dimmer switches of a gene 55

Transcription factor function 61

The Gene Regulatory Network: Defining an Individual Cell 67

Mechanisms of Differential Gene Transcription 68

Differentiated proteins from high and low CpG-content promoters 68

DNA methylation, another key on/off switch of transcription 69

Differential RNA Processing 73

Creating families of proteins through differential nRNA splicing 73

Splicing enhancers and recognition factors 76

Control of Gene Expression at the Level of Translation 76

Differential mRNA longevity 77

Stored oocyte mRNAs: Selective inhibition of mRNA translation 78

Ribosomal selectivity: Selective activation of mRNA translation 80

microRNAs: Specific regulation of mRNA translation and transcription 80

Control of RNA expression by cytoplasmic localization 83

Posttranslational Regulation of Gene Expression 84

The Basic Tools of Developmental Genetics 85

Characterizing gene expression 85

Testing Gene Function 88

CHAPTER 4   Cell-to-Cell Communication:  Mechanisms of Morphogenesis 95

A Primer on Cell-to-Cell Communication 96

Adhesion and Sorting: Juxtacrine Signaling and the Physics of Morphogenesis 97

Differential cell affinity 97

The thermodynamic model of cell interactions 98

Cadherins and cell adhesion 100

The Extracellular Matrix as a Source of Developmental Signals 104

Integrins: Receptors for extracellular matrix molecules 106

The Epithelial-Mesenchymal Transition 107

Cell Signaling 108

Induction and competence 108

Reciprocal induction 110

Epithelial-mesenchymal interactions 112

The insect trachea: Combining inductive signals with cadherin regulation 114

Paracrine Factors: Inducer Molecules 115

Morphogen gradients 115

Signal transduction cascades: The response to inducers 116

Fibroblast growth factors and the RTK pathway 118

FGFs and the JAK-STAT pathway 120

The Hedgehog family 121

The Wnt family 125

The TGF-b superfamily 128

Other paracrine factors 130

The Cell Biology of Paracrine Signaling 130

Focal membrane protrusions as signaling sources 134

Juxtacrine Signaling for Cell Identity 137

The Notch pathway: Juxtaposed ligands and receptors for pattern formation 137

Paracrine and juxtacrine signaling in coordination: Vulval induction in C. elegans 138

Hippo: An integrator of pathways 139

CHAPTER 5   Stem Cells:  Their Potential and Their Niches 143

The Stem Cell Concept 144

Division and self-renewal 144

Potency defines a stem cell 145

Stem Cell Regulation 146

Pluripotent Cells in the Embryo 148

Cells of the inner cell mass 148

Mechanisms promoting pluripotency of ICM cells 148

Adult Stem Cell Niches 149

Stem cells fueling germ cell development in Drosophila 150

Adult Neural Stem Cell Niche of the V-SVZ 153

The neural stem cell niche of the V-SVZ 154

Maintaining the NSC pool with cell-to-cell interactions 155

Promoting differentiation in the V-SVZ niche 156

Environmental influences on the NSC niche 156

The Adult Intestinal Stem Cell Niche 158

Clonal renewal in the crypt 159

Regulatory mechanisms in the crypt 160

Stem Cells Fueling the Diverse Cell Lineages in Adult Blood 161

The hematopoietic stem cell niche 161

Regulatory mechanisms in the endosteal niche 163

Regulatory mechanisms in the perivascular niche 163

The Mesenchymal Stem Cell: Supporting a Variety of Adult Tissues 164

Regulation of MSC development 165

Other stem cells supporting adult tissue maintenance and regeneration 165

The Human Model System to Study Development and Disease 167

Pluripotent stem cells in the lab 167

Induced pluripotent stem cells 171

Organoids: Studying human organogenesis in a culture dish 174

Stem Cells: Hope or Hype? 176

II Gametogenesis and Fertilization:  the Circle of Sex

CHAPTER 6   Sex Determination and Gametogenesis 181

Chromosomal Sex Determination 182

The Mammalian Pattern of Sex Determination 182

Primary Sex Determination in Mammals 184

The developing gonads 185

Genetic mechanisms of primary sex determination: Making decisions 187

The ovary pathway: Wnt4 and R-spondin1 188

The testis pathway: Sry and Sox9 189

The right time and the right place 193

Secondary Sex Determination in Mammals: Hormonal Regulation of the Sexual
Phenotype 194

The genetic analysis of secondary sex determination 195

Chromosomal Sex Determination in Drosophila 197

The Sex-lethal gene 198

Doublesex: The switch gene for sex determination 200

Environmental Sex Determination 201

Mammalian Gametogenesis 202

Meiosis: The intertwining of life cycles 205

Gametogenesis in mammals: Spermatogenesis 207

Gametogenesis in mammals: Oogenesis 211

Coda 212

CHAPTER 7   Fertilization:  Beginning a New Organism 217

Structure of the Gametes 218

Sperm 218

The egg 220

Recognition of egg and sperm 223

External Fertilization in Sea Urchins 223

Sperm attraction: Action at a distance 224

The acrosome reaction 225

Recognition of the egg’s extracellular coat 226

Fusion of the egg and sperm cell membranes 228

One egg, one sperm 228

The fast block to polyspermy 230

The slow block to polyspermy 230

Calcium as the initiator of the cortical granule reaction 231

Activation of Egg Metabolism in Sea Urchins 233

Release of intracellular calcium ions 234

Effects of calcium release 236

Fusion of Genetic Material in Sea Urchins 238

Internal Fertilization in Mammals 239

Getting the gametes into the oviduct: Translocation and capacitation 240

In the vicinity of the oocyte: Hyperactivation, thermotaxis, and chemotaxis 242

The acrosome reaction and recognition at the zona pellucida 243

Gamete fusion and the prevention of polyspermy 245

Fusion of genetic material 246

Activation of the mammalian egg 247

Coda 248

III Early Development:  Cleavage, Gastrulation, and Axis Formation

CHAPTER 8   Rapid Specification in Snails and Nematodes 251

Developmental Patterns among the Metazoa 252

Basal phyla 252

The triploblastic animals: Protostomes and deuterostomes 252

Early Development in Snails 254

Cleavage in Snail Embryos 255

Maternal regulation of snail cleavage 256

The snail fate map 258

Cell specification and the polar lobe 259

Altering evolution by altering cleavage patterns: An example from a bivalve mollusk 263

Gastrulation in Snails 265

The Nematode C. Elegans 265

Cleavage and Axis Formation in C. elegans 267

Rotational cleavage of the egg 268

Anterior-posterior axis formation 268

Dorsal-ventral and right-left axis formation 269

Control of blastomere identity 269

Gastrulation in C. elegans 272

CHAPTER 9   The Genetics of Axis Specification in Drosophila 277

Early Drosophila Development 278

Fertilization 279

Cleavage 279

The mid-blastula transition 281

Gastrulation 283

The Genetic Mechanisms Patterning the Drosophila Body 284

Segmentation and the Anterior-Posterior Body Plan 284

Anterior-posterior polarity in the oocyte 285

Maternal gradients: Polarity regulation by oocyte cytoplasm 286

The anterior organizing center: The Bicoid and Hunchback gradients 292

The terminal gene group 293

Segmentation Genes 294

Segments and parasegments 294

The gap genes 295

The pair-rule genes 297

The segment polarity genes 298

The Homeotic Selector Genes 301

Generating the Dorsal-Ventral Axis 303

Dorsal-ventral patterning in the oocyte 303

Generating the dorsal-ventral axis within the embryo 305

Establishing a nuclear Dorsal gradient 305

Axes and Organ Primordia: The Cartesian Coordinate Model 306

Coda 307

CHAPTER 10   Sea Urchins and Tunicates:  Deuterostome Invertebrates 311

Early Development in Sea Urchins 311

Early cleavage 312

Blastula formation 314

Fate maps and the determination of sea urchin blastomeres 314

Gene regulatory networks and skeletogenic mesenchyme specification 316

Specification of the vegetal cells 319

Sea Urchin Gastrulation 320

Ingression of the skeletogenic mesenchyme 320

Invagination of the archenteron 324

Early Development in Tunicates 326

Cleavage 327

The tunicate fate map 327

Autonomous and conditional specification of tunicate blastomeres 328

CHAPTER 11   Amphibians and Fish 333

Early Amphibian Development 333

Fertilization, Cortical Rotation, and Cleavage 334

Unequal radial holoblastic cleavage 335

The mid-blastula transition: Preparing for gastrulation 337

Amphibian Gastrulation 337

Vegetal rotation and the invagination of the bottle cells 337

Epiboly of the prospective ectoderm 342

Progressive Determination of the Amphibian Axes 343

Specification of the germ layers 343

The dorsal-ventral and anterior-posterior axes 344

The Work of Hans Spemann and Hilde Mangold 344

Autonomous specification versus inductive interactions 344

Primary embryonic induction 347

Molecular Mechanisms of Amphibian Axis Formation 348

How does the organizer form? 349

Functions of the organizer 355

Induction of neural ectoderm and dorsal mesoderm: BMP inhibitors 355

Regional Specificity of Neural Induction along the Anterior-Posterior Axis 359

The head inducer: Wnt antagonists 361

Trunk patterning: Wnt signals and retinoic acid 363

Specifying the Left-Right Axis 364

Early Zebrafish Development 365

Cleavage 368

Gastrulation and Formation of the Germ Layers 370

Dorsal-ventral axis formation 374

Anterior-posterior axis formation 376

Left-right axis formation 376

CHAPTER 12   Birds and Mammals 379

Early Development in Birds 381

Avian Cleavage 381

Gastrulation of the Avian Embryo 382

The hypoblast 382

The primitive streak 382

Molecular mechanisms of migration through the primitive streak 386

Regression of the primitive streak and epiboly of the ectoderm 387

Axis Specification and the Avian “Organizer” 389

The role of gravity and the PMZ 389

Left-right axis formation 390

Early Development in Mammals 391

Cleavage 391

The unique nature of mammalian cleavage 391

Compaction 393

Trophoblast or ICM? The first decision of the rest of your life 394

Escape from the zona pellucida and implantation 395

Mammalian Gastrulation 396

Modifications for development inside another organism 396

Mammalian Axis Formation 399

The anterior-posterior axis: Two signaling centers 400

Anterior-posterior patterning by FGF and RA gradients 401

Anterior-posterior patterning: The Hox code hypothesis 402

The left-right axis 404

Twins 406

Coda 408

IV Building with Ectoderm:  the Vertebrate Nervous System and Epidermis

CHAPTER 13   Neural Tube Formation and Patterning 413

Transforming the Neural Plate into a Tube: The Birth of the Central Nervous System 415

Primary neurulation 416

Secondary neurulation 427

Patterning the Central Nervous System 428

The anterior-posterior axis 428

The dorsal-ventral axis 430

Opposing morphogens 431

Transcriptional cross-repression 434

All Axes Come Together 435

CHAPTER 14   Brain Growth 439

Neuroanatomy of the Developing Central Nervous System 440

The cells of the developing central nervous system 440

Tissues of the developing central nervous system 443

Developmental Mechanisms Regulating Brain Growth 447

Neural stem cell behaviors during division 447

Neurogenesis: Building from the bottom up (or from the inside out) 448

Glia as scaffold for the layering of the cerebellum and neocortex 450

Signaling mechanisms regulating development of the neocortex 451

Development of the Human Brain 455

Fetal neuronal growth rate after birth 455

Hills raise the horizon for learning 456

Genes for neuronal growth 459

High transcriptional activity 460

Teenage brains: Wired and unchained 460

CHAPTER 15   Neural Crest Cells and Axonal Specificity 463

The Neural Crest 463

Regionalization of the Neural Crest 465

Neural Crest: Multipotent Stem Cells? 466

Specification of Neural Crest Cells 468

Neural Crest Cell Migration: Epithelial to Mesenchymal and Beyond 470

Delamination 471

The driving force of contact inhibition 473

Collective migration 473

Migration Pathways of Trunk Neural Crest Cells 474

The ventral pathway 475

The dorsolateral pathway 479

Cranial Neural Crest 481

The “Chase and Run” Model 483

Neural Crest-Derived Head Skeleton 484

Coordination of face and brain growth 485

Cardiac Neural Crest 486

Establishing Axonal Pathways in the Nervous System 488

The Growth Cone: Driver and Engine of Axon Pathfinding 488

“Plus tips” and actin-microtubule interactions 490

Rho, Rho, Rho your actin filaments down the signaling stream 491

Axon Guidance 493

The Intrinsic Navigational Programming of Motor Neurons 494

Cell adhesion: A mechanism to grab the road 495

Local and long-range guidance molecules: The street signs of the embryo 496

Repulsion patterns: Ephrins and semaphorins 496

How Did the Axon Cross the Road? 498

The Travels of Retinal Ganglion Axons 502

Growth of the retinal ganglion axon to the optic nerve 502

Growth of the retinal ganglion axon through the optic chiasm 503

Target Selection: “Are We There Yet?” 504

Chemotactic proteins 504

Target selection by retinal axons: “Seeing is believing” 505

Adhesive specificities in different regions of the optic tectum: Ephrins and Ephs 506

Synapse Formation 508

A Program of Cell Death 509

Activity-dependent neuronal survival 511

Differential survival after innervation: The role of neurotrophins 511

CHAPTER 16   Ectodermal Placodes and the Epidermis 517

Cranial Placodes: The Senses of Our Heads 517

The Dynamics of Optic Development: The Vertebrate Eye 520

Formation of the Eye Field: The Beginnings of the Retina 521

The Lens-Retina Induction Cascade 523

Lens and cornea differentiation 525

Neural retina differentiation 526

The Epidermis and It's Cutaneous Appendages 528

Origin of the Epidermis 528

The Ectodermal Appendages 529

Recombination experiments: The roles of epithelium and mesenchyme 530

Signaling pathways 531

Ectodermal appendage stem cells 533

Coda 537

V Building with Mesoderm and Endoderm:  Organogenesis

CHAPTER 17   Paraxial Mesoderm:  The Somites and Their Derivatives 539

Cell Types of the Somite 542

Establishing the Paraxial Mesoderm and Cell Fates Along the Anterior-Posterior Axis 543

Specification of the paraxial mesoderm 543

Spatiotemporal collinearity of Hox genes determine identity along the trunk 545
Somitogenesis 548

Axis elongation: A caudal progenitor zone and tissue-to-tissue forces 549

The clock-wavefront model 552

Linking the clock-wavefront to Hox-mediated axial identity and the end of somitogenesis 558

Sclerotome Development 560

Vertebrae formation 562

Tendon formation: The syndetome 565

Formation of the dorsal aorta 566

Dermomyotome Development 566

Determination of the central dermomyotome 568

Determination of the myotome 568

An emerging model of neural crest-regulated myogenesis 570

Osteogenesis: The Development of Bones 572

Endochondral ossification 572

Mechanotransduction and vertebrate bone development 574

Maturation of Muscle 575

Myoblasts and myofibers 575

Satellite cells: Unfused muscle progenitor cells 577

Mechanotransduction in the musculoskeletal system 578

CHAPTER 18   Intermediate and Lateral Plate Mesoderm:  Heart, Blood, and Kidneys 581

Intermediate Mesoderm: The Kidney 582

Specification of the Intermediate Mesoderm: Pax8 and Lim1 584

Reciprocal Interactions of Developing Kidney Tissues 585

Mechanisms of reciprocal induction 586

Lateral Plate Mesoderm: Heart and Circulatory System 591

Heart Development 592

A minimalist heart 592

Formation of the heart fields 593

Specification of the cardiogenic mesoderm 595

Migration of the cardiac precursor cells 596

Initial heart cell differentiation 599

Blood Vessel Formation 601

Vasculogenesis: The initial formation of blood vessels 601

Angiogenesis: Sprouting of blood vessels and remodeling of vascular beds 604

Anti-angiogenesis in normal and abnormal development 605

Hematopoiesis: Stem Cells and Long-Lived Progenitor Cells 605

Sites of hematopoiesis 606

The bone marrow HSC niche 608

Hematopoietic inductive microenvironments 609

Coda 610

CHAPTER 19   Development of the Tetrapod Limb 613

Limb Anatomy 613

The Limb Bud 614

Hox Gene Specification of Limb Skeleton Identity 616

From proximal to distal: Hox genes in the limb 616

From fins to fingers: Hox genes and limb evolution 617

Determining What Kind of Limb to Form and Where to Put It 619

Specifying the limb fields 619

Induction of the early limb bud 620

Outgrowth: Generating the Proximal-Distal Axis of the Limb 625

The apical ectodermal ridge 625

Specifying the limb mesoderm: Determining the proximal-distal polarity 627

Turing’s model: A reaction-diffusion mechanism of proximal-distal limb development 631

Specifying the Anterior-Posterior Axis 635

Sonic hedgehog defines a zone of polarizing activity 635

Specifying digit identity by Sonic hedgehog 636

Sonic hedgehog and FGFs: Another positive feedback loop 639

Hox specification of the digits 640

A Turing model for self-organizing digit skeletogenesis 642

Generating the Dorsal-Ventral Axis 644

Cell Death and the Formation of Digits and Joints 645

Sculpting the autopod 645

Forming the joints 646

Continued limb growth: Epiphyseal plates 647

Fibroblast growth factor receptors: Dwarfism 648

Evolution by Altering Limb Signaling Centers 649

CHAPTER 20   The Endoderm:  Tubes and Organs for Digestion and Respiration 653

The Pharynx 655

The Digestive Tube and Its Derivatives 657

Specification of the gut tissue 658

Accessory organs: The liver, pancreas, and gallbladder 660

The Respiratory Tube 666

VI Postembryonic Development

CHAPTER 21   Metamorphosis:  The Hormonal Reactivation of Development 671

Amphibian Metamorphosis 672

Morphological changes associated with amphibian metamorphosis 673

Hormonal control of amphibian metamorphosis 675

Regionally specific developmental programs 678

Metamorphosis in Insects 679

Imaginal discs 680

Hormonal control of insect metamorphosis 683

The molecular biology of 20-hydroxyecdysone activity 685

Determination of the wing imaginal discs 688

Metamorphosis of the Pluteus Larva 690

CHAPTER 22   Regeneration 693

Many Ways to Rebuild 694

Hydra: Stem Cell-Mediated Regeneration, Morphallaxis, and Epimorphosis 695

Routine cell replacement by three types of stem cells 696

The head activator 697

The head inhibition gradients 699

Stem Cell-Mediated Regeneration in Flatworms 701

Salamanders: Epimorphic Limb Regeneration 707

Formation of the apical epidermal cap and regeneration blastema 708

Proliferation of the blastema cells: The requirement for nerves and the apical epidermal cap 711

Luring the Mechanisms of Regeneration from Zebrafish Organs 714

Regeneration in Mammals 718

CHAPTER 23   Aging and Senescence 723

Genes and Aging 723

DNA repair enzymes 724

Aging and the insulin signaling cascade 726

The mTORC1 pathway 728

Chromatin modification 728

Random Epigenetic Drift 729

Stem Cells and Aging 730

Exceptions to the Aging Rule 731

VII Development in Wider Contexts

CHAPTER 24   Development in Health and Disease:  Birth Defects, Endocrine Disruptors, and Cancer 735

The Role of Chance 736

Genetic Errors of Human Development 736

The nature of human syndromes 736

Genetic and phenotypic heterogeneity 738

Teratogenesis: Environmental Assaults on Animal Development 738

Alcohol as a teratogen 741

Retinoic acid as a teratogen 744

Endocrine Disruptors: The Embryonic Origins of Adult Disease 746

Diethylstilbestrol (DES) 747

Bisphenol A (BPA) 749

Atrazine: Endocrine disruption through hormone synthesis 751

Fracking: A potential new source of endocrine disruption 752

Transgenerational Inheritance of Developmental Disorders 753

Cancer as a Disease of Development 754

Developmental therapies for cancer 758

Coda 759

CHAPTER 25   Development and the Environment:  Biotic, Abiotic, and Symbiotic Regulation of Development 763

The Environment as a Normal Agent in Producing Phenotypes 764

Diet-induced polyphenisms 764

Predator-induced polyphenisms 768

Temperature as an environmental agent 771

Polyphenic Life Cycles 773

Larval settlement 773

The hard life of spadefoot toads 774

Developmental Symbioses 775

Mechanisms of developmental symbiosis: Getting the partners together 776

The Euprymna-Vibrio symbiosis 777

Obligate developmental mutualism 778

Developmental symbiosis in the mammalian intestine 779

Coda 782

CHAPTER 26   Development and Evolution:  Developmental Mechanisms of Evolutionary Change 785

Descent with Modification: Why Animals Are Alike and Different 786

Preconditions for Evolution: The Developmental Structure of the Genome 786

Modularity: Divergence through dissociation 787

Molecular parsimony: Gene duplication and divergence 789

Deep Homology 792

Mechanisms of Evolutionary Change 793

Heterotopy 794

Heterochrony 795

Heterometry 796

Heterotypy 798

Developmental Constraints on Evolution 799

Selectable Epigenetic Variation 801

Genetic assimilation 804

Fixation of environmentally induced phenotypes 806

Coda 807

Glossary G-1

Author Index AI-1

Subject Index SI-1

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