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Chapter 1： History and Basic Concepts3

The origins of developmental biology3

1-1 Aristotle first defined the problem of epigenesis and preformation3

Box 1A Basic stages of Xenopus laevis development4

1-2 Cell theory changed the conception of embryonic development and heredity5

1-3 Mosaic and regulative development6

1-4 The discovery of induction8

1-5 The coming together of genetics and development8

A conceptual tool kit9

1-6 Development involves cell division， the emergence of pattern，change in form，cell differentiation，and growth9

Box 1 B Germ layers11

1-7 Cell behavior provides the link between gene action and developmental processes12

1-8 Genes control cell behavior by controlling which proteins are made by a cell13

1-9 Differential gene activity controls development14

1-10 Development is progressive and the fate of cells becomes determined at different times15

1-11 Inductive interactions can make cells different from each other17

1-12 The response to inductive signals depends on the state of the cell18

1-13 Patterning can involve the interpretation of positional information19

1-14 Lateral inhibition can generate spacing patterns20

1-15 Localization of cytoplasmic determinants and asymmetric cell division can make cells different from each other20

1-16 The embryo contains a generative rather than a descriptive program21

Chapter 2：Model Systems25

Model organisms：vertebrates25

2-1 Amphibians：Xenopus laevis26

Box 2A Polar body formation27

2-2 Birds：the chicken31

2-3 Mammals：the mouse37

2-4 Fishes：the zebrafish41

Model organisms：invertebrates43

2-5 The fruit fly Drosophila melanogaster43

2-6 The nematode Caenorhabditis elegans47

Model systems：plants49

2-7 Arabidopsis thaliana50

Identifying developmental genes52

2-8 Developmental genes can be identified by rare spontaneous mutation53

2-9 Identification of developmental genes by induced mutation and screening54

Box 2B Mutagenesis and genetic screening for identifying developmental mutants in Drosophila56

Chapter 3： Patterning the Vertebrate Body PlanI： Axes and Germ Layers63

Setting up the body axes63

3-1 The animal-vegetal axis of Xenopus is maternally determined63

Box 3A Protein intercellular signaling molecules64

Box 3B In situ detection of gene expression65

3-2 The dorso-ventral axis of amphibian embryos is determined by the site of sperm entry66

3-3 The Nieuwkoop center is specified by cortical rotation68

3-4 Maternal proteins with dorsalizing and ventralizing effects have been identified69

3-5 The dorso-ventral axis of the chick blastoderm is specified in relation to the yolk and the ante ro-posterior axis is set by gravity70

3-6 The axes of the mouse embryo are specified by cell—cell interactions71

3-7 Specification of left-right handedness of internal organs requires special mechanisms73

3-8 Organ handedness in vertebrates is under genetic control73

The origin and specification of the germ layers75

3-9 A fate map of the amphibian blastula is constructed by following the fate of labeled cells75

3-10 The fate maps of vertebrates are variations on a basic plan77

3-11 Cells of early vertebrate embryos do not yet have their fates determined79

Box 3C Transgenic mice81

3-12 In Xenopus the mesoderm is induced by signals from the vegetal region81

3-13 The mesoderm is induced by a diffusible signal during a limited period of competence83

3-14 An intrinsic timing mechanism controls the time of expression of mesoderm-specific genes84

3-15 Several signals induce and pattern the mesoderm in the Xenopus blastula85

3-16 Sources of the mesoderm-inducing signals86

3-17 Candidate mesoderm inducers have been identified in Xenopus87

3-18 Mesoderm patterning factors are produced within the mesoderm88

3-19 Zygotic gene expression begins at the mid-blastula transition in Xenopus90

3-20 Mesoderm induction activates genes that pattern the mesoderm91

3-21 Gradients in protein signaling factors and threshold responses could pattern the mesoderm92

Chapter 4： Patterning the Vertebrate Body PlanⅡ： The Mesoderm and Early Nervous System98

Somite formation and patterning98

4-1 Somites are formed in a well-defined order along the ante ro-posterior axis99

4-2 The fate of somite cells is determined by signals from the adjacent tissues100

4-3 Positional identity of somites along the antero-posterior axis is specified by Hox gene expression102

Box 4A Homeobox genes104

4-4 Deletion or overexpression of Hox genes causes changes in axial patterning106

4-5 Retinoic acid can alter positional values107

Box 4B Gene targeting： insertional mutagenesis and gene knock-out108

The role of the organizer region and neural induction110

4-6 The organizer can specify a new antero-posterior axis110

4-7 The neural plate is induced by mesoderm113

4-8 The nervous system can be patterned by signals from the mesoderm114

4-9 Signals that pattern the neural plate may travel within the neural plate itself116

4-10 The hindbrain is segmented into rhombomeres by boundaries of cell lineage restriction117

4-11 Neural crest cells have positional values119

4-12 Hox genes provide positional identity in the hindbrain region119

4-13 The embryo is patterned by the neurula stage into organ-forming regions that can still regulate121

Chapter 5： Development of the Drosophila Body Plan127

Maternal genes set up the body axes127

5-1 Three classes of maternal genes specify the ante ro-posterior axis128

5-2 The bicoid gene provides an ante ro-posterior morphogen gradient129

5-3 The posterior pattern is controlled by the gradients of nanos and caudal proteins131

5-4 The anterior and posterior extremities of the embryo are specified by cell-surface receptor activation132

5-5 The dorso-ventral polarity of the egg is specified by localization of maternal proteins in the vitelline envelope133

5-6 Positional information along the dorso-ventral axis is provided by the dorsal protein134

Polarization of the body axes during oogenesis136

5-7 Antero-posterior and dorso-ventral axes of the oocyte are specified by interactions with follicle cells136

Zygotic genes pattern the early embryo139

5-8 The expression of zygotic genes along the dorso-ventral axis is controlled by dorsal protein139

5-9 The decapentaplegic protein acts as a morphogen to pattern the dorsal region141

5-10 The ante ro-posterior axis is divided up into broad regions by gap gene expression142

5-11 bicoid protein provides a positional signal for the anterior expression of hunchback143

Box 5A Transgenic flies144

5-12 The gradient in hunchback protein activates and represses other gap genes144

Segmentation： activation of the pair-rule genes146

5-13 Parasegments are delimited by expression of pair-rule genes in a periodic pattern146

5-14 Gap gene activity positions stripes of pair-rule gene expression148

Segment polarity genes and compartments150

5-15 Expression of the engrailed gene delimits a cell lineage boundary and defines a compartment151

Box 5B Genetic mosaics and mitotic recombination153

5-16 Segment polarity genes pattern the segments and stabilize parasegment and segment boundaries155

5-17 Compartment boundaries are involved in patterning and polarizing segments157

5-18 Some insects use different mechanisms for patterning the body plan158

Segmentation： selector and homeotic genes161

5-19 Homeotic selector genes of the bithorax complex are responsible for diversification of the posterior segments162

5-20 The Antennapedia complex controls specification of anterior regions164

5-21 The order of HOM gene expression corresponds to the order of genes along the chromosome164

5-22 HOM gene expression in visceral mesoderm controls the structure of the adjacent gut165

Chapter 6：Development of Invertebrates，Ascidians，and Slime Molds173

Nematodes173

6-1 The developmental axes are determined by asymmetric cell division and cell—cell interactions173

6-2 Cell—cell interactions specify cell fate in the early nematode embryo176

6-3 A small cluster of homeobox genes specify cell fate along the antero-posterior axis177

6-4 Genes control graded temporal information in nematode development178

Molluscs180

6-5 The handedness of spiral cleavage is specified maternally181

6-6 Body axes in molluscs are related to early cleavages181

Annelids183

6-7 The teloblasts are specified by localization of cytoplasmic factors183

6-8 Antero-posterior patterning and segmentation in the leech is linked to a lineage mechanism184

Echinoderms186

6-9 The sea urchin egg is polarized along the animal-vegetal axis187

6-10 The dorso-ventral axis in sea urchins is related to the plane of the first cleavage188

6-11 The sea urchin fate map is very finely specified，yet considerable regulation is possible189

6-12 The vegetal region of the sea urchin embryo acts as an organizer190

6-13 The regulatory regions of sea urchin develop-mental genes are complex and modular191

Ascidians193

6-14 Muscle may be specified by localized cytoplasmic factors193

6-15 Notochord development in ascidians requires induction195

Cellular slime molds196

6-16 Patterning of the slug involves cell sorting and positional signaling197

6-17 Chemical signals direct cell differentiation in the slime mold199

Chapter 7： Plant Development204

Embryonic development204

7-1 Electrical currents are involved in polarizing the Fucus zygote205

7-2 Cell fate in early Fucus development is determined by the cell wall206

7-3 Differences in cell size resulting from unequal divisions could specify cell type in the Volvox embryo207

7-4 Both asymmetric cell divisions and cell position pattern the early embryos of flowering plants208

Box 7A Angiosperm embryogenesis209

7-5 The patterning of particular regions of the Arabidopsis embryo can be altered by mutation210

7-6 Plant somatic cells can give rise to embryos and seedlings211

Meristems213

7-7 The fate of a cell in the shoot meristem is dependent on its position214

7-8 Meristem development is dependent on signals from the plant217

Box 7B Transgenic plants218

7-9 Leaf positioning and phyllotaxy involves lateral inhibition218

7-10 Root tissues are produced from root apical meristems by a highly stereotyped pattern of cell divisions219

Flower development221

7-11 Homeotic genes control organ identity in the flower221

7-12 The transition to a floral meristem is under environmental and genetic control226

7-13 The Antirrhinum flower is patterned dorso-ventrally as well as radially226

7-14 The internal meristem layer can specify floral meristem patterning227

Chapter 8： Morphogenesis： Change in Form in the Early Embryo232

Cell adhesion232

8-1 Sorting out of dissociated cells demonstrates differences in cell adhesiveness in different tissues232

Box 8A Cell adhesion molecules233

8-2 Cadherins can provide adhesive specificity234

Cleavage and formation of the blastula235

8-3 The asters of the mitotic apparatus determine the plane of cleavage at cell division237

8-4 Cells become polarized in early mouse and sea urchin blastulas238

8-5 Ion transport is involved in fluid accumulation in the blastocoel240

8-6 Internal cavities can be created by cell death241

Gastrulation242

8-7 Gastrulation in the sea urchin involves cell migration and invagination243

Box 8B Change in cell shape and cell movement244

8-8 Mesoderm invagination in Drosophila is due to changes in cell shape，controlled by genes that pattern the dorso-ventral axis246

8-9 Xenopus gastrulation involves several different types of tissue movement247

8-10 Convergent extension and epiboly are due to cell intercalation250

8-11 Notochord elongation is caused by cell intercalation252

Neural tube formation254

8-12 Neural tube formation is driven by both internal and external forces254

8-13 Changes in the pattern of expression of cell adhesion molecules accompany neural tube formation255

Cell migration256

8-14 The directed migration of sea urchin primary mesenchyme cells is determined by the contacts of their filopodia to the blastocoel wall257

8-15 Neural crest migration is controlled by environ-mental cues and adhesive differences258

8-16 Slime mold aggregation involves chemotaxis and signal propagation260

Directed dilation262

8-17 Circumferential contraction of hypodermal cells elongates the nematode embryo263

8-18 The direction of cell enlargement can determine the form of a plant leaf263

Chapter 9： Cell Differentiation271

The reversibility and inheritance of patterns of gene activity271

9-1 Nuclei of differentiated cells can support develop-ment of the egg272

9-2 Patterns of gene activity in differentiated cells can be changed by cell fusion273

9-3 The differentiated state of a cell can change by transdifferentiation274

9-4 Differentiation of cells that make antibodies is due to irreversible changes in their DNA276

9-5 Maintenance and inheritance of patterns of gene activity may depend on regulatory proteins，as well as chemical and structural modifications of DNA277

Control of specific gene expression281

9-6 Control of transcription involves both general and tissue-specific transcriptional regulators282

9-7 External signals can activate genes284

Models of cell differentiation287

9-8 A family of genes can activate muscle-specific transcription287

9-9 The differentiation of muscle cells involves withdrawal from the cell cycle288

9-10 Complex combinations of transcription factors control cell differentiation289

9-11 All blood cells are derived from pluripotent stem cells290

9-12 Colony-stimulating factors and intrinsic changes control differentiation of the hematopoietic lineages291

9-13 Globin gene expression is controlled by distant upstream regulatory sequences293

9-14 Neural crest cells differentiate into several cell types295

9-15 Steroid hormones and polypeptide growth factors specify chromaffin cells and sympathetic neurons297

9-16 Neural crest diversification involves signals for both specification of cell fate and selection for cell survival297

9-17 Programmed cell death is under genetic control298

Chapter 10：Organogenesis304

The development of the chick limb304

10-1 The vertebrate limb develops from a limb bud305

10-2 Patterning of the limb involves positional information305

10-3 The apical ectodermal ridge induces the progress zone307

10-4 The polarizing region specifies position along the ante ro-posterior axis308

10-5 Position along the proximo-distal axis may be specified by a timing mechanism311

10-6 The dorso-ventral axis is controlled by the ectoderm312

10-7 Different interpretations of the same positional signals give different limbs312

10-8 Homeobox genes are involved in patterning the limbs and specifying their position313

10-9 Self-organization may be involved in pattern formation in the limb bud315

10-10 Limb muscle is patterned by the connective tissue316

Box 10A Reaction-diffusion mechanisms317

10-11 The initial development of cartilage， muscles，and tendons is autonomous318

10-12 Separation of the digits is the result of programmed cell death318

Insect imaginal discs320

10-13 Signals from the ante ro-posterior compartment boundary pattern the wing imaginal disc321

10-14 The dorso-ventral boundary of the wing acts as a pattern-organizing center322

10-15 The leg disc is patterned in a similar manner to the wing disc，except for the proximo-distal axis323

10-16 Butterfly wing markings are organized by additional positional fields324

10-17 The segmental identity of imaginal discs is determined by the homeotic selector genes325

The insect compound eye328

10-18 Signals maintain progress of the morpho-genetic furrow and the ommatidia are spaced by lateral inhibition329

10-19 The patterning of the cells in the ommatidium depends on intercellular interactions329

10-20 The development of R7 depends on a signal from R8330

10-21 Activation of the gene eyeless can initiate eye development331

The nematode vulva332

10-22 The anchor cell induces primary and secondary fates333

Development of the kidney334

10-23 The development of the ureteric bud and mesen-chymal tubules involves induction334

Chapter 11： Development of the Nervous System340

Specification of cell identity in the nervous system340

11-1 Neurons in Drosophila arise from proneural clusters340

11-2 Lateral inhibition allocates neuronal precursors342

11-3 Asymmetric cell divisions are involved in Drosophila sensory organ development343

11-4 The vertebrate nervous system is derived from the neural plate344

11-5 Specification of vertebrate neuronal precursors involves lateral inhibition345

11-6 The pattern of differentiation of cells along the dorso-ventral axis of the spinal cord depends on ventral and dorsal signals346

11-7 Neurons in the mammalian central nervous system arise from asymmetric cell divisions，then migrate away from the proliferative zone348

Axonalguidance352

11-8 Motor neurons from the spinal cord make muscle-specific connections353

11-9 The growth cone controls the path taken by the growing axon354

11-10 Choice of axon pathway depends on environmental cues and neuronal identity355

11-11 Neurons from the retina make ordered connections on the tectum to form a retino-tectal map356

11-12 Axons may be guided by gradients of diffusible agents358

Neuronal survival， synapse formation， and refinement360

11-13 Many motor neurons die during limb innervation361

11-14 Neuronal survival depends on competition for neurotrophic factors361

11-15 Reciprocal interactions between nerve and muscle are involved in formation of the neuromuscular junction362

11-16 The map from eye to brain is refined by neural activity365

11-17 The ability of mature vertebrate axons to regenerate is restricted to peripheral nerves367

Chapter 12：Germ Cells and Sex372

Determination of the sexual phenotype372

12-1 The primary sex-determining gene in mammals is on the Y chromosome372

12-2 Mammalian sexual phenotype is regulated by gonadal hormones373

12-3 In Drosophila， the primary sex-determining signal is the number of X chromosomes and is cell autonomous374

12-4 Somatic sexual development in Caenorhabditis is determined by the number of X chromosomes376

12-5 Most flowering plants are hermaphrodites，but some produce unisexual flowers377

12-6 Germ cell sex determination may depend both on cell signals and genetic constitution378

12-7 Various strategies are used for dosage compen-sation of X-linked genes379

The development of germ cells382

12-8 Germ cell fate can be specified by a distinct germ plasm in the egg382

12-9 Pole plasm becomes localized at the posterior end of the Drosophila egg384

12-10 Germ cells migrate from their site of origin to the gonad384

12-11 Germ cell differentiation involves a reduction in chromosome number385

12-12 Oocyte development can involve gene amplifi-cation and contributions from other cells387

12-13 Genes controlling embryonic growth are imprinted387

Fertilization390

12-14 Fertilization involves cell-surface interactions between egg and sperm391

12-15 Changes in the egg membrane at fertilization block polyspermy392

12-16 A calcium wave initiated at fertilization results in egg activation393

Chapter 13：Regeneration401

Morphallaxis401

13-1 Hydra grows continuously， with loss of cells from its ends and by budding401

13-2 Regeneration in Hydra is polarized and does not depend on growth402

13-3 The head region of Hydra acts both as an organizing region and as an inhibitor of inappropriate head formation402

13-4 Head regeneration in Hydra can be accounted for in terms of two gradients403

Epimorphosis405

13-5 Vertebrate limb regeneration involves cell dedifferentiation and growth406

13-6 The limb blastema gives rise to structures with positional values distal to the site of amputation408

13-7 Retinoic acid can change proximo-distal positional values in regenerating limbs410

13-8 Insect limbs intercalate positional values by both proximo-distal and circumferential growth412

13-9 Polarized regeneration in plants is due to the polarized transport of auxin413

Chapter 14： Growth and Post-Embryonic Development418

Growth418

14-1 Tissues can grow by cell proliferation，cell enlargement，or accretion418

14-2 Cell proliferation can be controlled by an intrinsic program and by external signals419

14-3 Growth of mammals is dependent on growth hormones421

14-4 Developing organs can have their own intrinsic growth programs423

14-5 Growth of the long bones occurs in the growth plates424

14-6 Growth of vertebrate striated muscle is dependent on tension426

14-7 The epithelia of adult mammalian skin and gut are continually replaced by derivatives of stem cells426

14-8 Cancer can result from mutations in genes controlling cell multiplication and differentiation430

14-9 Hormones control many features of plant growth430

14-10 Cell enlargement is central to plant growth431

Molting and metamorphosis432

14-11 Arthropods have to molt in order to grow433

14-12 Metamorphosis is under environmental and hormonal control434

Aging and senescence437

14-13 Genes can alter the timing of senescence438

14-14 Cells senesce in culture439

Chapter 15： Evolution and Development444

Modification of development in evolution444

15-1 Embryonic structures have acquired new functions during evolution445

15-2 Limbs evolved from fins446

15-3 Development of vertebrate and insect wings makes use of evolutionarily conserved mechanisms449

15-4 Hox gene complexes have evolved through gene duplication450

15-5 Changes in specification and interpretation of positional identity have generated the elaboration of vertebrate and arthropod body plans451

15-6 The position and number of paired appendages in insects is dependent on Hox gene expression453

15-7 The body plan of arthropods and vertebrates is similar，but the dorso-ventral axis is inverted454

Changes in the timing of developmental processes during evolution456

15-8 Changes in relative growth rates can alter the shapes of organisms456

15-9 Evolution of life histories has implications for development457

15-10 The timing of developmental events has changed during evolution458