Cover -- Title Page -- Copyright -- Dedication -- Preface: Preface -- Chapter 1: A Brief Introduction to Ascidians -- 1.1 What are Ascidians? -- 1.2 A Brief History of Research on Ascidian Embryos -- Selected References -- Chapter 2: The Development of Tadpole Larvae and Sessile Juveniles -- 2.1 Embryogenesis and Tadpole Larvae -- 2.2 Metamorphosis and Making a Sessile Juvenile -- Selected References -- Chapter 3: Genomics, Transcriptomics, and Proteomics -- 3.1 The Genome of Ciona intestinalis -- 3.2 Transcriptomics -- 3.3 Proteomics -- Selected References -- Chapter 4: Research Tools -- 4.1 Experimental Manipulation of Embryonic Cells -- 4.2 Tracing of Cell Divisions -- 4.3 Analyses of Gene Function -- 4.4 Analyses of Regulatory Mechanisms of Specific Gene Expression -- 4.5 Microarray -- 4.6 Genetics, Mutagenesis, and Transgenesis -- Selected References -- Cold Spring Harbor Laboratory Protocols for Embryogenesis Studies -- Chapter 5: The Function and Regulation of Maternal Transcripts -- 5.1 Gene Expression Profiles Observed During the Ciona Life Cycle -- 5.2 Oocyte Maturation, Fertilization, Ooplasmic Segregation, and Embryonic Axis Formation -- 5.3 Contribution of Maternal Information -- 5.4 Postplasmic/PEM RNAs -- Selected References -- Chapter 6: Larval Tail Muscle -- 6.1 Primary (B-Line) Muscle Cells: Autonomous Specification and Gene Regulatory Networks -- 6.2 Secondary (A- and -Line) Muscle Cells: Evolutionary Alteration of Gene Regulatory Networks -- Selected References -- Chapter 7: Endoderm -- 7.1 Lineage -- 7.2 Specification Mechanisms -- 7.3 Differentiation Mechanisms -- Selected References -- Chapter 8: Epidermis -- 8.1 Lineage and Specification Mechanisms -- 8.2 Adhesive Organ -- 8.3 Cellulose Biosynthesis -- Selected References -- Chapter 9: Notochord -- 9.1 Notochord Lineage, Cell-Fate Determination, and Morphogenesis.

9.2 Specification Mechanisms and the Gene Regulatory Network -- 9.3 Genes Involved in Notochord Formation -- Selected References -- Chapter 10: The Larval and Adult Nervous Systems -- 10.1 Larval CNS -- 10.2 Sensory Systems in the Larval CNS -- 10.3 Peripheral Nervous System -- 10.4 Remodeling of the Central Nervous System During Metamorphosis -- 10.5 The Adult Nervous System -- Selected References -- Chapter 11: Mesenchyme -- 11.1 Embryonic Lineages and Their Adult Progeny -- 11.2 Molecular Cascades Involved in Mesenchymal Specification -- Selected References -- Chapter 12: Making Blueprint of Chordate Body: Dynamic Activities of Regulatory Genes -- 12.1 The Embryonic Axes Formation -- 12.2 The Fate Map -- 12.3 From Maternal Factors to Zygotic Activities of Regulatory Genes -- 12.4 The Antagonistic Actions of FGF and Ephrin Pathways to form Germ Layers -- 12.5 The Nodal and Delta2 Signaling Relay -- 12.6 The ANISEED Database as an Interface for Elucidation of Ciona Developmental Program -- 12.7 Strategy of Body Plan Formation in Ascidians -- 12.8 Gene Regulatory Network in Early Ciona Embryos -- 12.9 Chromosomal-Level Regulation of Gene Expression -- 12.10 Hox Genes and Retinoic Acid -- 12.11 Left-Right Asymmetry -- 12.12 Genomic DNA Methylation and Chromatin-Level Modification of Regulatory Genes -- 12.13 Micro RNAs -- Selected References -- Chapter 13: Development of the Juvenile Heart -- 13.1 The Ascidian Heart -- 13.2 Lineage of Cells Involved in Heart Development -- 13.3 The Gene Regulatory Network -- 13.4 Changes in Chordate Heart Morphology Through Evolution -- Selected References -- Chapter 14: Germ-Cell Line, Gametes, Fertilization, and Metamorphosis -- 14.1 Germ Cell Formation in Ciona -- 14.2 Spermatogenesis -- 14.3 Oogenesis -- 14.4 Fertilization -- 14.5 Metamorphosis -- Selected References.

Chapter 15: Innate Immune System and Blood Cells -- 15.1 Innate Immunity in Ciona -- 15.2 Blood Cells -- 15.3 Vanadium Concentration -- Selected References -- Chapter 16: Colonial Ascidians: Asexual Reproduction and Colony Specificity -- 16.1 Asexual Reproduction of Colonial Ascidians and Stem Cells in the Budding -- 16.2 Germ Cell Formation in Colonial Ascidians -- 16.3 The Development of Colony Specificity -- Selected References -- Chapter 17: Evolutionary Developmental Genomics -- 17.1 The Origin and Evolution of Chordates -- 17.2 Evolution of Urochordates -- 17.3 Evolution Among Ascidians -- Selected References -- Index.