Fish Development And Genetics: The Zebrafish And Medaka Models (Molecular Aspects of Fish and Marine Biology)

Contents......Page 6
Preface......Page 8
1. Maternal-Effect Genes......Page 10
1.2.1. Strictly maternal-effect genes......Page 11
1.2.2. Maternal-zygotic genes......Page 12
1.3. Underlying Basis for Strictly Maternal and Maternal-Zygotic Genetic Effects......Page 18
2.1. Forward Screens......Page 19
2.2.1. Viable or semi-viable mutations......Page 20
2.2.3. Non-viable mutations using germ line chimeras......Page 21
2.3.2. RNA interference......Page 23
3. Maternal Products during Egg Activation and Early Embryogenesis......Page 24
3.1.1. mRNAs evenly distributed in the mature oocyte......Page 25
3.1.2. mRNAs localized to the animal pole of the oocyte during oogenesis......Page 26
3.1.4. The mRNA for the gene vasa......Page 27
3.2. Redistribution of Components of the Germ Plasm during the Early Cleavage Stages......Page 28
3.3. Redistribution of Dorsal Determinant Signal during the Early Cleavage Stages......Page 30
3.4. The Yolk Cell and Maternal Determinants......Page 31
4.1. General Functions......Page 32
4.2.1. Local activation of Wnt/ -catenin signaling: induction of the dorsal organizer......Page 34
4.2.2. Wnt/calcium signaling: downregulation of the dorsal organizer......Page 35
4.2.3. Bmp signaling: promotion of ventral cell fates......Page 36
4.2.4. Integration of pathways regulating dorsoventral patterning......Page 37
4.4. Induction of the Mesendodermal Layer......Page 38
5. Determination of the Maternal-Zygotic Transition......Page 39
6. Conclusions......Page 41
References......Page 42
Introduction......Page 48
Epiboly......Page 50
Internalization......Page 54
Convergence and Extension......Page 56
Wnt/PCP Pathway......Page 60
Cell Adhesion Molecules......Page 65
Nodal/TGF   Signaling......Page 67
PDGF/PI3K Pathway......Page 70
Other Pathways......Page 73
‘New’ Methods......Page 76
Remaining and Arising Questions......Page 80
References......Page 82
1.1. Introduction......Page 96
Dorsal specification......Page 98
Mesendoderm induction......Page 101
1.3. Structure and Patterning of the Organizer......Page 103
1.4. Organizer Activities......Page 105
2.1. Introduction......Page 108
2.2. Differentiation of the Notochord......Page 109
2.3. Patterning of Surrounding Tissues by the Notochord......Page 111
2.4. Mechanics of Notochord Structure and Development......Page 116
References......Page 119
1. Introduction......Page 130
2.1. Formation of the Neural Tube: Neurulation......Page 132
2.2. The Floor Plate: A Transient Structure in the CNS Which Forms during Neurulation......Page 134
2.3.2. BMPs: key signaling factors in patterning the dorsal neural tube......Page 136
3.1.1. Overview of axon projections which are influenced by the floor plate......Page 138
3.1.2. Chemoattraction by the floor plate......Page 140
3.1.3. Chemorepulsion by the floor plate......Page 141
3.1.4. Guidance at the midline by the floor plate......Page 142
3.1.5. Molecular mechanisms of axon guidance by the floor plate......Page 144
3.2.2. Motor neuron differentiation by the floor plate......Page 145
4.1.1. Vertical induction of floor plate by Shh secreted from notochord......Page 148
4.1.2. Homeogenetic induction of the floor plate......Page 152
4.2.1. Node/organizer: the common source of floor plate and notochord cells......Page 153
4.2.2. When is the floor plate induced?......Page 158
4.2.3. Where are the floor plate cells induced: functional domains within Hensen’s node......Page 159
4.2.4. The different origins of medial floor plate and lateral floor plate......Page 160
The origin of the floor plate: reconciling planar, vertical and homeogenetic induction......Page 163
References......Page 164
Introduction......Page 173
Development of the Nervous System: Axon Guidance......Page 175
Mechanotransduction......Page 179
Odor Perception......Page 181
The Visual System......Page 183
The Touch Response......Page 184
References......Page 187
Introduction......Page 194
Different Classes of Primary Neurons Occupy Characteristic Positions in the Embryonic Nervous System......Page 195
Primary Neurons Form Distinct Domains in the Neural Plate......Page 201
External Signals in the Spatial Control of Neurogenesis......Page 203
Pre-Pattern Genes in the Neural Plate......Page 205
Primary Neurons are Selected from Pools of Precursors by Lateral Inhibition......Page 208
bHLH Genes as Regulators of Neuronal Subtype......Page 211
The Regulatory Elements Controlling Gene Expression in Primary Neurons are Conserved among Vertebrates......Page 213
References......Page 215
7 Making Scents: Development and Function of the Olfactory Sensory System Kathleen E. Whitlock......Page 225
1.1. Fish as a Model System......Page 226
1.2. Sensory Epithelium......Page 227
1.4. Terminal Nerve......Page 229
2.1. Origin......Page 231
2.3. Induction......Page 233
2.4. The Differentiating Olfactory Organ......Page 235
2.5. Mutations Disrupting Olfactory Placode Development......Page 238
2.6. Structural Elements of the Olfactory System Arise from Cranial Neural Crest......Page 239
3.1. Gene Expression in the Developing Olfactory Bulb......Page 240
3.2. Axonal Input and Olfactory Bulb Development......Page 241
4.1. Guidance Cues......Page 242
4.2. Cell Surface Molecules......Page 243
4.3. Olfactory Receptors......Page 244
4.4. Pioneer Neurons......Page 245
5.1. Main Olfactory Epithelium......Page 247
5.2. Onset of Olfactory Receptor Expression during Development......Page 248
5.3. Do Fish Have a Vomeronasal System?......Page 249
5.4. Development......Page 251
6.2. Cells Appear to Exit the Olfactory Placode......Page 252
6.3. The Neural Crest......Page 253
6.4. The Adenohypophysis......Page 254
7.1. Fishy Smells......Page 255
8.1. Is there a Unifying Placode Theme?......Page 257
8.2. Olfactory and Adenohypophysis......Page 258
8.3. Olfactory Placode Field and Neural Crest......Page 260
A World of Questions Remain......Page 261
References......Page 262
1. Introduction......Page 270
1.1. General View of Vertebrate Somite Segmentation......Page 271
1.2. Zebrafish Somite Formation and Mutants......Page 273
3. A Molecular Clock Functions in the PSM......Page 275
4. Molecular Circuit in the Clock......Page 277
5.1. Fused Somites/Tbx24 Regulate the Wavefront Activity......Page 282
5.2. Positioning the Wavefront in the Anterior PSM......Page 285
6.1. Gene Network Centered on Mesp Gene......Page 287
6.2. Rostrocaudal Patterning and Clock Mechanism......Page 289
7. Formation of Morphologically Distinct Somite Boundary......Page 291
8. Unanswered Questions......Page 293
Acknowledgment......Page 294
References......Page 295
1. Introduction......Page 303
2. The Way to a Segmentation Clock......Page 305
2.2. Cell Cycle......Page 306
2.3 Previous Models......Page 307
3.1. Cyclic Genes — Expression Level Changing with Time and Space......Page 308
3.2. Notch Signaling and Mutants......Page 309
3.3. The Clockwork of the Segmentation Clock......Page 310
3.3.1. Autoinhibitory loops — the essence of the segmentation clock......Page 311
3.3.2 Two transcription factors drive interconnected loops of segmentation clock......Page 314
3.3.3. Dual role of Notch signaling in somite segmentation......Page 315
3.3.4. Post-translational regulation in Notch signaling and others......Page 316
4.1. FGF Signaling — A Gradient Positioning the Boundary......Page 318
4.2. WNT Signaling — A Gradient Harmonizing Tail Growth with Segmentation and, Therefore, the Cellular Oscillator......Page 319
4.3. Hox Genes are Clock-Controlled......Page 320
5. Molecular Era — Compartmentation, Notch Signaling and Others......Page 321
5.2.1. Lfng......Page 322
5.2.2. Mesp......Page 324
5.2.4. fss and T-box gene......Page 325
5.3. Epithelialization and Cell Adhesion......Page 326
5.3.1. Papc......Page 327
5.3.2. Paraxis and epithelialization......Page 328
5.3.3. Eph signaling......Page 329
5.3.4. Fibronectin and Integrin......Page 330
5.3.5. Cadherins......Page 331
6. Differences among Vertebrates......Page 332
7. Perspectives......Page 334
References......Page 336
Introduction......Page 348
1. Somitogenesis in Fish Embryos......Page 349
1.1. Notch Signaling in Somitogenesis......Page 350
1.2. FGF and Eph Signaling Pathways in Somitogenesis......Page 351
1.3. Functions of Transcription Factors Mesp and Foxc in Somitogenesis......Page 352
2. Signaling Molecules in Myoblast Specification and Differentiation......Page 353
2.1. Hedgehog Signaling in Slow Muscle Development......Page 354
2.2. BMP Signal Inhibits Slow Muscle Differentiation......Page 363
2.3. Induction of Fast and Slow Muscles by Different Signals in Zebrafish......Page 364
2.4. Heat Shock Protein and Somitogenesis......Page 366
3.1. Characterization of MRF and Mef2 Transcription Factors......Page 367
3.2. Regulation of MyoD and Myf5 Gene Expression......Page 369
3.3. Promoter Analysis of MyoD, Myf5 and Myogenin Expression in Fish......Page 370
3.4. Functional Analysis of Myf5 in Fish......Page 371
3.5. Characterization of Myogenic Regulatory Factors in Other Fish Species......Page 373
4. Myostatin and Follistatin in Regulating Muscle Development and Growth......Page 375
4.1. Characterization of Fish Myostatin Gene Expression......Page 376
4.2. Functions of Myostatin in Fish......Page 377
4.3. Regulation of Myostatin Gene Expression......Page 379
5.2. Muscle-Specific Genes and Transgenic Fish Models for Muscle Research......Page 380
References......Page 382
1. Phylogeny and Evolution......Page 401
2.1. Methodology......Page 403
2.2. Craniofacial Development......Page 405
2.3. Vertebral Column......Page 406
2.4. Median Fins......Page 408
2.5. Paired Fins......Page 409
2.6. Phylogenetic Comparisons......Page 410
3.1. Early Inductive Signals......Page 411
3.3. Bone Formation......Page 412
4. Mutational Analysis of Zebrafish Skeletal Development......Page 415
5. Molecular Identification of Zebrafish Skeletal Mutants......Page 417
6. Conclusions and Future Directions......Page 420
References......Page 421
12 Endoderm Formation in Zebrafish Nicolas B. David, Philippe Mourrain and Frederic M. Rosa......Page 433
1.1. Endoderm Progenitors are Located at the Margin of the Zebrafish Embryo at the Onset of Gastrulation......Page 434
1.2. Involution/Ingression and Convergent Extension form Endoderm......Page 436
2.1. The Xenopus Contribution......Page 440
2.2.1. The Nodal-related ligands......Page 441
2.2.2. The type I receptors Taram-A/ALK4 and the EGF-CFC co-factors Oep/Cripto......Page 442
2.2.3. The TGF- 	/leftys inhibitors......Page 443
2.2.4. Smads and Fast1 transducers......Page 444
2.2.5. An epistatic pathway leading to endoderm formation......Page 445
3.1. Endoderm Specification......Page 449
3.2. Endodermal Commitment......Page 450
3.3. Endoderm Gastrulation Movements......Page 453
3.4. Endoderm Versus Mesoderm Fate Choice......Page 454
3.5. Early Endoderm Patterning......Page 456
3.6. Convergence and Migratory Behavior of Endodermal Cells......Page 457
Conclusion......Page 458
References......Page 459
13 Gene ‘Knockdown’ Approaches Using Unconventional Antisense Oligonucleotides Eleanor Chen, Perry B. Hackett and Stephen C. Ekker......Page 463
2. Mechanisms of Unconventional Antisense Targeting......Page 464
2.1. Morpholino Phosphorodiamidate Oligonucleotides......Page 465
2.2. Translational Inhibition......Page 466
2.3. Alteration of Pre-mRNA Splicing......Page 467
2.3. Morpholino Delivery and Distribution......Page 468
3.1. Translational Blockers......Page 470
4.1. Model Systems......Page 471
5.1. Efficacy Measurements......Page 472
5.1.2. Transcriptional processing inhibition......Page 473
5.2.1. Mutant phenocopy......Page 474
5.2.3. “Rescue” with exogenous gene product......Page 475
6.2. Modeling of Biological Processes and Human Diseases......Page 476
7. Future Directions......Page 478
References......Page 479
Further Reading......Page 483
1. Introduction......Page 485
2. Transient Transgenic Expression......Page 487
2.1. Analysis of Gene Promoters/Enhancer Elements......Page 488
2.2. Analysis of Gene Function in Development and Mutants......Page 490
3. Stable Transgenic Lines......Page 491
3.1. Labeling of Cells with GFP and Recapitulation of Gene Expression Programs......Page 492
3.2. Expression of GFP Fusion Protein......Page 497
3.4. Cell Lineage and Cell Migration......Page 498
3.5. Analysis of Upstream Regulatory Genes......Page 499
3.6. Monitoring of Signaling Molecules......Page 500
3.7. Cell Sorting for in vitro Culture and Cell Type Specific cDNA Library Construction......Page 501
3.9. Chi-Recombination and Artificial Chromosome Transgenesis......Page 502
4. Conditional Gene Activation in Transgenic Systems......Page 503
4.1. Inducible Systems......Page 504
4.2. GAL4-UAS System......Page 505
4.3. Cre-loxP System......Page 506
5. Cell Lineage Ablation and Genetic Ablation......Page 507
6. Transgenic Insertional Mutagenesis......Page 508
7. Gene Targeting......Page 510
8. Concluding Remarks......Page 512
Acknowledgments......Page 513
References......Page 514
1. Introduction......Page 526
2.1. Cyprinids......Page 527
2.2. Loach......Page 528
2.3. Medaka......Page 529
2.4. Cloning the Zebrafish......Page 530
3.1. Production of Transgenic Fish Through Cloning......Page 536
3.4. Study of Effects of Cloning on Animal Development......Page 537
References......Page 538
16 Applications of Transposable Elements in Fish for Transgenesis and Functional Genomics Perry B. Hackett, Karl J. Clark, Stephen C. Ekker and Jeffrey J. Essner......Page 541
1.1. Transgenesis in Fish......Page 542
1.2. Retroviruses and Transposons for Gene Delivery in Fish......Page 543
2.1. Structures and Mechanisms of Transposition of DNA-Type Transposons......Page 546
2.2. Advantages of Transposon-Mediated Gene Transfer......Page 551
3. Applications of Transposons in Fish......Page 553
3.1.1. Microinjection......Page 554
3.1.3. Sperm-mediated DNA delivery......Page 555
3.1.5. Lipofection......Page 556
3.1.6. Remobilization of transposons......Page 557
3.2. Analysis for Integration of Transgenes into Chromosomes......Page 558
3.3. Transposition of Transgenes into Chromosomes of Fish......Page 559
3.3.1. Transposition in fish using the SB transposon system......Page 560
3.3.2. Transposition of trap vectors in fish using the SB transposon system......Page 562
4. Future Directions......Page 565
4.1. Parameters Affecting Transposition......Page 566
4.2. Identification of Host Factors Associated with Transposition......Page 567
4.3. Regulation of the Ratio of Transposase to Transposons......Page 568
4.5. Site-Specific Integration......Page 569
References......Page 570
1. Introduction......Page 590
3. Gene Maps......Page 591
4.1. Levels of Conservation......Page 592
3. Conserved chromosome segments......Page 593
2. Conserved gene orders......Page 595
4. Chromosome mosaics......Page 596
5. Gene duplication......Page 597
6. Translocations......Page 598
5. Genome Duplication......Page 600
6. Evolution of a Duplicated Chromosome Segment......Page 603
2. Local inversions......Page 605
4. Non-conserved syntenies......Page 606
8. Chromosome Fission and Fusion......Page 607
9. Retention of “Ohnologs”......Page 609
10. A Model for the Evolution of the Zebrafish Genome......Page 610
References......Page 612
18 Medaka Genome Mapping for Functional Genomics Hiroshi Mitani, Akihiro Shima, Kiyoshi Naruse and Minoru Tanaka......Page 621
1. Introduction......Page 622
2.1. Phylogenic Position......Page 623
2.3. Polymorphisms and Inbred Strains......Page 624
2.4. Spontaneous and Induced Mutants......Page 626
3. Genome Mapping......Page 627
4.1. Colorless Melanophore......Page 630
4.2. Eyeless Mutation......Page 631
4.3. Reduced Scales-3, rs-3......Page 632
4.4. Sex-Determining Gene......Page 633
5. Genome Duplication......Page 634
6. Future Aspects......Page 638
References......Page 639
19 Medaka Embryonic Stem Cells Hong Yunhan and Manfred Schartl......Page 646
Introduction......Page 647
ES Cells......Page 648
ES Cells in Fishes......Page 650
Gene Targeting in Medaka ES-Like Cells......Page 656
Chimera Formation in Fish......Page 658
Alternatives to ES Cells......Page 661
Alternatives to Germline Chimeras......Page 662
Perspectives......Page 665
References......Page 666
Subject Index......Page 674