Developmental Biology Protocols

M E T H O D S

IN M O L E C U L A R

B I O L O G Y

1

JohnM. Walker, SERIES EDITOR 149. Advanced EL1SA: Theory and Practice, ediled by John R. 117. Electron Microscopy Methods and Protocols, edited by M. A. Crowther, 2000 timer Hajibagheri. 1999 148, DNA-Protein Interactions: Principles and Protocols (2nd 116. Protein Lipidation Protocols, edited by Michael H Gelb, 1999 ed.}, edited by Tom Moss. 2000 115, Inijnunocytochemical Methods and Protocols (2nd ed,), ed147, Affinity Chromatography: Methods and Protocols, edited ited by Loretle C, Javois, 1999 by Pascal Bailon, George K. Ehrlich, Wen-Jian Fung, and 114. Caicium Signaling Protocols, edited by David C. Lambert, 1999 Wolfgang Rerthold, 2000 113. DNA Repair Protocols: Eukatyotk Systems, edited by Dary! 146. Protein and Pep tide Analysis: New Mass Spectrametric ApS Henderson. 1999 plications, edited by John R. Chapman, 2006 112.2-D Proteome Analysis Protocols, edited by Andrew J. Link, 1999 145. Bacterial Toxins: Methods and Protocols, edited by Otto 111. Plant Cell Culture Protocols, edited by Men D. Hall, 1999 Hoist. 2000 110. Lipoprotein Protocols, edited bf Jose hi. Ordovas, 199S 144. Calpain Methods and Protocols, edited by JohnS. Eke, 2000 109. Lipase and Phospholipase Protocols, edited by Mark 11 143. Protein Structure Prediction: Methods and Protocols* Doolittle and Karen Rene, 1999 edited by David Webster, 201)0 105. Free Radical and Antioxidani Protocols, edited by Donald 142. Transforming Growth Factor-Beta Protocols, edited by Armstrong. 1998 Philip H. Howe. 200(1 107. Cytochrome P450 Protocols, edited by Ian fi. Phillips and 141. Plant Hormone Protocols, edited by Jeremy A. Roberts and Elizabeth A. Shephard, 1998 Gregory A. Tucker, 2000 106. Receptor Binding Techniques, edited by Maty Keen, 1999 140. Chapernnin Protocols, edited by Christine Schneider, 2000 105. Phospholipid Signaling Protocols, edited by Ian M. Bird, 19% 139. Extracellular Matri* Protocols, edited by Charles Streuliand 104. Mycoplasma Protocols, edited by Roger J. Miles and Robin A. Michael Gram, 2000 J. Nicholas, 1998 138. Cticntokine Protocols, edited by Amanda E. I. Proudfool, Timothy 103. Pichia Protocols, edited by David R. Higgins and James M. K C. Wells, and Christine Power, 2000 Cregg, 199S 137, Developmental Biology Protocols, Volume III, edited by 102. Bioluminescence Methods and Protocols, edited by Robert A. Rocky S. Tuan and Cecilia W. Lo, 2000 LaRossa, 1998 136. Developmental Biology Protocols, Volume II, edited by 101. Mycobacteria Protocols, edited by Tanya Parish and Neil G. Rocky S. Taan and Cecilia W. Lo, 2000 Stoker. 199S 135. Developmental Biology Protocols, Volume I, edited by Rocky 100, \itric Oxide Protocols, edited by Michael A. Tithcradgc, 199& S. Tuan and Cecilia W. Lo, 2000 99. Stress Response: Methods and Protocols, ediled by Stephen 134. T Cell Protocols: Development and Activation, edited by Kelly M, Keyse, 2000 P. Kearse, 2000 98. Forensic D M Profiling Protocols, edited by Patrick J. Lin133, Gene Targeting Protocols, edited by Eric B. Kmiec, 2000 coln and James M. Thomson, 199S 132. Bioinformatics Methods and Protocols, edited by Stephen 97. Molecular Embryology: Methods and Protocols, edited by Paul Misener and Stephen A. Krawetz, 2000 T. Sharp? and Ivor Mason, 1999 131, Flavopratein Protocols, edited by S. K. Chapman and G. A. 96. Adhesion Protein Protocols, edited by Elisabetta Dejana and Reid. 1999 Monica Corada, 1999 130, Transcription Factor Protocols, edited by Martin J. Tymms, 2000 95 DNA Topoisomerases Protocols: II, Eniymolog)' and Drugs, 129. Integrin Protocols, edited by Anthony Hewlett, 1999 edited by Mary-Ann Bjornsti and Neil Osheroff, 1999 128. NMDA Protocols, ediled by Min Li, 1999 94. D\A Topoisomerases Protocols: /. DNA Topology and En127. Molecular Methods in Developmental Biology: Xenopusofld zymes, edited by Mary-Ann Bjornsti and Neil Osheroff, 1999 Zebrafish, edited by Matthew Gitilte, 1999 93. Protein Phosphatase Protocols, edited by John W. Ludlow, 1998 126. Adrenergic Receptor Protocols, edited by Curtis.4.Machida, 2000 92. PCR in Bioanalysis, edited by Stephen J. Meltzer. 1998 125, Clycoprotein Methods and Protocols: The Muciits, edited 91. Flow Cytometry Protocols, edited by Mark J. Jaroszeski. RityAnthonyP. Corfield, 2000 chard Heller, and Richard Gilbert, 1998 124, Protein Kinase Protocols, edited by Alastair D. Reith. 2000 90. Drug-DNA Interaction Protocols, edited by Keith R. Fox, 1998 123. in Situ Hybridization Protocols (2nd ed.), ediled by Ian A. 89. Retinoid Protocols, edited by Christopher Redfern, 1998 Darby, 2000 88. Protein Targeting Protocols, edited by Roger A. Clegg, 1998 122. Confocal Microscopy Methods and Protocols, edited by 87. Combinatorial Peptide Library Protocols, edited by Shmuel Stephen W. Paddock, 1999 Cabilly, 1998 121. Natural Killer Cell Protocols: Cellular and Molecular 86. RNA Isolation and Characterization Protocols, edited by Methods, edited by Kerry S. Campbell and Marco Colonna, 2000 Ralph Rapley and David L. Manning, 1998 120. Eicosanoid Protocols, edited by Elias A. Hanoi, 1999 85. Differential Display Methods and Protocols, edited by Peng 119. Chromatin Protocols, edited by Peter B. Becker, 1999 Liang and Arthur B. Pardee, 1997 118. RNA-Protein Interaction Protocols, edited by Susan R. Haynes, 1999 84. TransmembraneSignalingProtoco]s;editedbyZtynt!tox%;/»S

M E T H O D S I N M O L E C U L A R B I O L O G Y™

Developmental Biology Protocols Volume I

Edited by

Rocky S. Tuan Thomas Jefferson University, Philadelphia, PA

and

Cecilia W. Lo University of Pennsylvania, Philadelphia, PA

Humana Press

Totowa, New Jersey

To Chuck and our parents

© 2000 Humana Press Inc. 999 Riverview Drive, Suite 208 Totowa, New Jersey 07512 All rights reserved. No part of this book may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, microfilming, recording, or otherwise without written permission from the Publisher. Methods in Molecular Biology™ is a trademark of The Humana Press Inc. All authored papers, comments, opinions, conclusions, or recommendations are those of the author(s), and do not necessarily reflect the views of the publisher. This publication is printed on acid-free paper. ∞ ANSI Z39.48-1984 (American Standards Institute) Permanence of Paper for Printed Library Materials. Cover design by Patricia F. Cleary Cover illustration taken from Fig. 1 in Chapter 20 and is described on page 205 of this volume. For additional copies, pricing for bulk purchases, and/or information about other Humana titles, contact Humana at the above address or at any of the following numbers: Tel.: 973-256-1699; Fax: 973-256-8341; E-mail: [email protected]; or visit our Website: http://humanapress.com Photocopy Authorization Policy: Authorization to photocopy items for internal or personal use, or the internal or personal use of specific clients, is granted by Humana Press Inc., provided that the base fee of US $10.00 per copy, plus US $00.25 per page, is paid directly to the Copyright Clearance Center at 222 Rosewood Drive, Danvers, MA 01923. For those organizations that have been granted a photocopy license from the CCC, a separate system of payment has been arranged and is acceptable to Humana Press Inc. The fee code for users of the Transactional Reporting Service is: [0-89603-574-3/00 $10.00 + $00.25]. Printed in the United States of America. 10 9 8 7 6 5 4 3 2 1 Library of Congress Cataloging in Publication Data Main entry under title: Developmental biology protocols/edited by Rocky S. Tuan and Cecilia W. Lo. Methods in molecular biology™. Developmental biology protocols, vol. I/edited by Rocky S. Tuan and Cecilia W. Lo. p. cm.—(Methods in molecular biology; v. 135, 136, 137) Includes bibliographical references and indexes. ISBN 0-89603-574-3 (v. 1: alk. paper) (hardcover), ISBN 0-89603-852-1 (paper); ISBN 0-89603575-1 (v. 2: alk. paper) (hardcover), ISBN 0-89603-853-X (paper); ISBN 0-89603-576-X (v. 3: alk. paper) (hardcover), ISBN 0-89603-854-8 (paper). 1. Developmental biology—Laboratory manuals. 2. Molecular biology—Laboratory manuals. I. Tuan, Rocky S. II. Lo, Cecilia W. III. Series. QH491.D4625 2000 571.8—dc21 99-23532 CIP

Preface

Developmental biology is one of the most exciting and fast-growing fields today. In part, this is so because the subject matter deals with the innately fascinating biological events—changes in form, structure, and function of the organism. The other reason for much of the excitement in developmental biology is that the field has truly become the unifying melting pot of biology, and provides a framework that integrates anatomy, physiology, genetics, biochemistry, and cellular and molecular biology, as well as evolutionary biology. No longer is the study of embryonic development merely "embryology." In fact, development biology has produced important paradigms for both basic and clinical biomedical sciences alike. Though modern developmental biology has its roots in "experimental embryology" and the even more classical "chemical embryology," the recent explosive and remarkable advances in developmental biology are critically linked to the advent of the "cellular and molecular biology revolution." The impressive arsenal of experimental and analytical tools derived from cell and molecular biology, which promise to continue to expand, together with the exponentially developing sophistication in functional imaging and information technologies, guarantee that the study of the developing embryo will contribute one of the most captivating areas of biological research in the next millennium. There is a demonstrated need for students of developmentai biology to be knowledgeable of the breadth and depth of the available experimental methodologies, by necessity derived from multiple disciplines, which are applicable to the study of the developing embryo, in particular, because developmental biology deals with multiple model systems, from organismal to tissue and cell levels, as well as a wide range of "change"-related biological activities, the investigator is often frustrated as to how his/her findings relate to those obtained in another model system and/or by using different reagents or functional markers. Compared to other more strictly defined fields of biological research, the number of "reference" publications that deal specifically with the practical aspects of experimental developmentai biology are, however, relatively scarce. Developmental Biology Protocols grows out of the need for a comprehensive laboratory manual that provides the readers the principles, background, rationale, as well as the practical protocols, for studying and analyzing the events of embryonic development. This three-volume set, consisting of 142 chapters, is intentionally broad in scope, because of the nature of modern developmental biology. Information is grouped into the following topics: (1) systems—production, culture, and storage; (2) developmental pattern and morphogenesis; (3) embryo structure and function; (4) cell lineage analysis; (5) chimeras; (6) experimental manipulation of embryos; (7) application of viral vectors; (8) organogenesis; (9) abnormal development and teratology;

(10) screening and mapping of novel genes and mutations; (11) trans genes is production and gene knockout; (12) manipulation of developmental gene expression and function; (13) analysis of gene expression; (14) models of morphogenesis and development; and (15) in vitro models and analysis of differentiation and development. Throughout Developmental Biology Protocols, the authors have consistently striven for a balanced presentation of both background information and actual laboratory details. It LS believed that this highly practical format will permit readers to bring the concepts and principles we present into their personal research practices in a most efficient manner. Specifically, the wide range of model systems and multidisciplinary experimental techniques presented here should lower the "activation energy" for the student of developmental biology to become a contributing member of this exciting scientific discipline. In addition, teachers of developmental biology at all levels should also readily find relevant and useful information to enrich the experience of their students. The practice of developmental biology is currently in a state of constant change, reflecting the close relationship of the field to other rapidly developing fields of biological research, particularly cell and molecular biology, and imaging and information technology. The materials presented in this three-volume set are therefore the beginning of a project that will invoive continuous update and upgrade to reach and enhance the scientific endeavors of developmental biologists at large. The production of Developmental Biology Protocols would not have been possible without the outstanding work of the contributing authors who share here with the readers the hands-on wisdom they have earned in the laboratory. We are grateful for their intellectual contributions as well as their remarkable tolerance to our constant reminders. Tom Lanigan and his staff at Humana Press worked diligently on the project to ensure a final product of the highest quality. Chuck, our young son, persevered throughout the gestation period of the project, and constantly demonstrated to us the meaning of "developmental biology," Our final, heartfelt thanks go to Lynn Stierle, who expertly and single-handedly maintained the massive organization of the manuscripts and the correspondence (snailmail and e-mail), as well as the sanity of the editors! Michelle Levinski also provided valuable assistance in proofreading the final production. Finally, we hope that these volumes will find their place on the laboratory shelves, with their pages well soiled and their contents tried and tested, and prove their utility as an everyday resource for the students of developmental biology, the most exciting discipline of biology for many decades to come! Rocky S. Tuan, PhD Cecilia W. Lo, PhD

VI

List of Color Plates

Color plates 1-13 appear as an insert following p. 258. Plate 1 (Fig. 1 from Chapter 2). Larvae of sea urchins and sea stars. All larvae are oriented with anterior up. Plate 2 (Fig. 8 from Chapter 11). Examples of phenotypes and histological sections from various induction assays. Plate 3 (Figs. 1-6 from Chapter 14). Fig. 1, Lateral view of the cervical vertebrae (C1-C7) and cervicothoracic border in a rat fetus on gestation day 21. Fig, 2, Ventral view of a gestation day 18 mouse fetus from a dam exposed to 5 g/kg methanol on gestation day 7. Fig. 3. Cranial view of disarticulated cervical vertebrae (ventral aspect at top) of a mouse fetus on gestation day 18. Fig. 4. Lateral view of the thoracic region of a gestation day 20 rat fetus. Fig. 5. Ventral view of the lumbosacral region of a gestation day 20 rat fetus. Fig. 6. Ventral view of the lumbar region of a gestation day 21 rat fetus. Plate 4 (Fig. I from Chapter 25). A sequence of pseudocolor ratio images of one zebrafish embryo as it proceeds through the earlier stages of development. Plate 5 (Fig. 2 from Chapter 25). Example of the subtraction analysis algorithm to detect [Ca2+] transients. Plate 6 (Fig. 1 from Chapter 29). (A) Basic virus microinjection equipment, (B) Whole mount of a heart from a chick embryo. (C) Two independent groups of myocytes. Plate7 (Fig. 2 from Chapter 43). Implantation of FGM containing BMP2 protein into E2 chick embryos perturbed rib and vertebral skeletal formation. Plate 8 (Fig. 5 from Chapter 30). Creativity in the use of dynamic labeling techniques. Plate 9 (Fig. 7 from Chapter 30). Combination of in situ hybridization with immunocytochemical detection of graft cells. Plate 10 (Fig. 1 from Chapter 33). Detection of uncaged fiuorescein in zebrafish embryos. Plate 11 (Fig. 2 from Chapter 46). Example of a microcarrier bead-grafting experiment. Plate 12 (Fig. 1 from Chapter 45). Assays for cell ablation. Plate 13 (Fig. 1 from Chapter 51). Steps in microinjection of an embrvo.

VII

Contents Preface List of Color Plates Companion Tables of Contents for Volumes II and III Contributors PART I

I

INTRODUCTION

Developmental Biology Protocols: Overview I Rocky S. Tuan and Cecilia W. Lo

PART II

3 Large-Scale Culture and Preparation of Sea Urchin Embryos for Isolation of Transcriptional Regulatory Proteins James A. Coffman and Patrick $. Leahy 4 The Chick Embryo as a Model System for Analyzing Mechanisms of Development Diana K. Darnell and Gary C. Schoenwolf 5 Culture of Avian Embryos Diana K. Darnell and Gary C. Schoenwolf 6 EKO OVO Culture of Avian Embryos Tamao Ono Culture of Preimplantation Mouse Embryos Adam S, Doherty and Richard M. Schultz

8 In Vitro Culture of Rodent Embryos During the Early Postimplantation Period Masahiko Fujinaga 9 Cryopreservation of Mouse Embryos Jean Richa PART III

9

17

25 37 39 47

53 77

DEVELOPMENTAL PATTERN AND MORPHOGENESIS

10 Studying Head and Brain Development in Drosophila Robert Finkelstein I1

3

SYSTEMS: PRODUCTION, CULTURE, AND STORAGE

2 Rearing Larvae of Sea Urchins and Sea Stars for Developmental Studies Christopher J. Lowe and Gregory A. Wray

7

v ix xvii xxv

Bioassays of Inductive Interactions in Amphibian Development Takashi Ariizumi, Kazuhiro Takano, Makoto Asashima, and George M. Malacinski

ix

85

89

x

Contents

12 Gastrulation and Early Mesodermal Patterning in Vertebrates GaryC. Schoenwolf and Jodi L Smith 13 Craniofacial Development of Avian and Rodent Embryos Brian K. Hall and Tom Miyake 14 Examination of the Axial Skeleton of Fetal Rodents Michael G. Narotsky and John M. Rogers 15 Cardiac Morphogenesis and Dysmorphogenesis: An tmmunohistochemical Approach B. Rush Walter, III and Andy Wessels PART IV

113 127 139

151

EMBRYO STRUCTURE AND FUNCTION

16 Application of Plastic Embedding for Sectioning Whole-Mount Immunostained Early Vertebrate Embryos Kersti K. Linask and Takeshi Tsuda 165 17 Confocal Microscopy of Live Xenopus Oocytes, Eggs, and Embryos Carolyn A. Larabell 175 18 Whole-Mount immunolabeling of Embryos by Microinjection: Increased Detection Levels of Extracellular and Cell Surface Epitopes Charles D. Little and Christopher J. Drake 19 Confocal Laser Scanning Microscopy of Morphology and Apoptosis in Organogenesis-Stage Mouse Embryos Robert M. Zucker, E. Sidney Hunter III, and John M. Rogers 20 Embryo/Fetal Topographical Analysis by Fluorescence Microscopy and Confocal Laser Scanning Microscopy Robert M. Zucker and John M. Rogers 21 Magnetic Resonance Imaging Analysis of Embryos Bradley R. Smith 22 Optical Coherence Tomography Imaging in Developmental Biology Stephen A. Boppart, Mark E. Brezinski, and James G. Fujimoto 23 Ultrasound Backscatter Microscopy of Mouse Embryos Daniel H. Turnbutl... 24 Use of Doppler Echocardiography to Monitor Embryonic Mouse Heart Function Kersti K. Linask and James C. Huhta 25 Calcium Imaging and Cell—Cell Signaling Diane C. Slusarski and Victor G. Corces 26 Acquisition, Display, and Analysis of Digital ThreeDimensional and Time-Lapse (Four-Dimensional) Data Sets Using Free Software Applications Charles F. Thomas and John G. White PART V

27

183

191

203 211

217 235

245 253

263

CELL LINEAGE ANALYSIS

Cell Lineage Analysis: Applications of Green Fluorescent Protein Magdalena Zernicka-Goetz and Jonathon Pines

279

XI

28 29

30

31 32 33

34

Ceil Lineage Analysis; X-lnactivation Mosaics Seong-Seng Tan, Leanne Godinho, and Patrick P. L. Tam Retroviral Cell Lineage Analysis in the Developing Chick Heart Robert G. Gourdie, Gang Cheng, Robert P. Thompson, and Takashi Mikawa Dynamic Labeling Techniques for Fate Mapping, Testing Cell Commitment, and Following Living Cells in Avian Embryos Diana K. Darnell, Virginio Garcia-Martinez, Carmen Lopez-Sanchez, Shipeng Yuan, and Gary C. Schoenwolf Cell Lineage Analysis: Videomicroscopy Techniques Paul J. Heid and Jeff Hardin..... Cell Lineage Analysis in Xenopus Embryos Sally A. Moody Photoactivatable (Caged) Fiuorescein as a Ceil Tracer for Fate Mapping in the Zebrafish Embryo David J. Kozlowski and Eric S. Weinberg Carboxyfluorescein as a Marker at Both Light and Electron Microscope Levels to Follow Ceil Lineage in the Embryo Dazhong Sun, C. May Griffith, and Elizabeth D, Hay

PART VI

289

297

305 323 331

349

357

CHIMERAS

35 Transplantation Chimeras: Use in Analyzing Mechanisms of Avian Development Diana K. Darnell and Gary C. Schoenwolf 36 Interspecific Chimeras in Avian Embryos Nicole M. Le Douarin, Frangoise Dieterlen-Lievre, Marie-Aimee Teittet, and Catherine Ziller

373

37 Quail-Chick Transplantation in the Embryonic Limb Bud Elizabeth E. LeClairand Rocky S. Tuan

387

38 39

40

41 42

367

Mouse Chimeras and the Analysis of Development Richard L. Gardner and Timothy J. Davies 397 Cell Grafting and Fate Mapping of the Eariy-Somite-Stage Mouse Embryo Simon J. Kinder, Seong-Seng Tan, and Patrick P. L Tam 425 Interspecific Chimeras: Transplantation of Neural Crest Between Mouse and Chick Embryos Margaret L Kirby, Harriett Stadt, Donna Kumiski, and VladHerlea 439 Interspecific Mouse-Chick Chimeras Josiane Fontaine-Perus 443 Mosaic Analysis in Caenorhabditis elegans

XII

PART VII

43

44

45 46

Local Application of Bone Morphogenic Protein on Developing Chick Embryos Using a Fibrous Glass Matrix as a Carrier Akira Nifuji and Masaki Noda Laser Ablation and Fate Mapping Margaret L. Kirby, Donna Kumiski, Harriett Stadt, and Greg Hunter Photoabiation of Ceils Expressing |3-Galactosidase Sheila Nirenberg Exo utero Surgery Valerie Ngo-Muller and Ken Muneoka

PART VII!

47

48 49

EXPERIMENTAL MANIPULATION OF EMBRYOS

465

471 475 481

APPLICATION OF VIRAL VECTORS IN THE ANALYSIS OF DEVELOPMENT

Methods for Constructing and Producing Retrovirat Vectors Andrea Gambotto, Seon Hee Kim, Sunyoung Kim, and Paul D. Robbins

495

Retroviral Gene Transduction in Limb Bud Micromass Cultures N. Susan Stott and Cheng-Ming Chuong

509

Construction of Adenoviral Vectors Alan R. Davis, Nelson A. Wivel, Joseph L. Palladino, Luan Tao, and James M. Wilson

515

50 Application of Adenoviral Vectors: Analysis of Eye Development Jean Bennett, Yong Zeng, Abha R. Gupta, and Albert M. Maguire 51 The Application of Adenoviral Vectors in the Study of Mammalian Cardiovascular Development Craig S. Mickanin and H. Scott Baldwin Index

525

537 545

TABLES OF CONTENTS FROM VOLUMES II AND III VOLUME II Preface List of Color Piates Companion Tables of Contents for Volumes I and III Contributors PART I

INTRODUCTION

1 Developmental Biology Protocols: Overview II Rocky S. Tuan and Cecilia W. Lo PART II

2 3

4 5

6

ORGANOGENESIS

Drosophila as a Genetic Tool to Define Vertebrate Pathway Players Nancy M. Bonini Bioassays for Studying the Role of the Peptide Growth Factor Activin in Early Amphibian Etnbryogenesis Makoto Asashima, Takashi Ariizumi, Shuji Takahashi, and George M. Malacinski Analysis of Mammary Gland Morphogenesis Calvin D. Roskelley, Colleen Wu, and Aruna M. Somasiri Specification of Cardiac Mesenchyme and Heart Morphogenesis In Vitro H. Joseph Yost Craniofacial Development and Patterning Harold Stavkin, Glen Nuckolls, and Lillian Shum

7 Craniofacial Skeletel Morphogenesis In Vitro Roy C. Ogle 8 Skeletal Morphogenesis Stefan Mundlos 9 Transplantation and Culture Techniques for the Analysis of Urodele Limb Regeneration David L. Stocum 10 Retroviral Infection of T-Cell Precursors in Thymic Organ Culture Lisa M. Spain, Lisa L, Lau, and Yousuke Takahama 11 Assay for the Isolation of Hepatogenic Factors: Key Molecules in Hepatocyte Formation and Liver Morphogenesis Johannes A. A. Spijkers, Theodorus B. M. Hakvoort, and Wouter H. Lamers xtn

xiv

Contents

12 Skin Morphogenesis: Embryonic Chicken Skin Explant Cultures Cheng-Ming Chuong 13 Apoptosis in Development Lin Lin and Zahra F. Zakeri 14 Methods to Detect Patterns of Cell Death in Drosophila Nancy M. Bonini PART HI ABNORMAL DEVELOPMENT AND TERATOLOGY

15 Mechanisms of Neurulation Gary C. Schoenwoif and Jodi L. Smith 16 Neurulation and Neural Tube Closure Defects Andrew Copp, Patricia Cogram, Angeleen Fleming, Dianne Gerrelli, Deborah Henderson, Andrew Hynes, Maria Kolatsi-Joannou, Jennifer Murdoch, and Patricia Ybot-Gonzales 17 Neural Tube Defects Takayuki inagaki, Jodi L. Smith, Marion L. Walker, and Gary C. Schoenwoif 18 Experimental Manipulation and Morphometric Analysis of Neural Tube Development Mary E. Desmond and Patricia A. (Sharpies) Haas 19 Isolation of Neuroepithelium and Formation of Minispheres Mary E. Desmond and Marcia E. Field 20 Examination of Normal and Abnormal Placentation in the Mouse Michael R. Blackburn 21 Palatal Dysmorphogenesis: Palate Organ Culture Barbara D. Abbott 22 Palatal Dysmorphogenesis: Quantitative RT-PCR Gary A. Held and Barbara D. Abbott 23 Trans-species Grafting as a Tool to Understand the Basis of Murine Developmental Limb Anomalies Sheila M. Bell, Claire M. Schreiner, and William J. Scott 24 Assessment of Laterality Defects in Rodent Embryos Masahiko Fujinaga 25 Cardiac Morphogenesis and Dysmorphogenesis Andy Wessels and Roger Markwald 26 Analysis of Two Aspects of Left—Right Patterning of the Vertebrate Heart: Heart Tube Position and Heart Tube Chirality Alvin Chin 27 Biologically Based Risk Assessment Models for Developmental Toxicity Christopher Lau and R. Woodrow Setzer PART IV

SCREENING AND MAPPING OF NOVEL GENES AND MUTATIONS

28 Positional Cloning Lin Xu and Yefu Li

Contents

xv

29

Gene Trapping in Embryonic Stem Cells In Vitro to identify Movei Developmental^ Regulated Genes in the Mouse Gary E, Lyons, Bradley J. Swanson, Melissa A. Haendel, and Joshua Daniels 30 PCR-Based Cloning of Cortically Localized RNAs from Xenopus Oocytes Jian Zhang and Mary Lou King 31 Analysis of mRNA Expression During Preimplantation Development Keith E. Latham, Elena De La Casa, and Richard M. Schultz 32 Differential Screens with Subtracted PCR-Generated cDNA Libraries from Subregions of Single Mouse Embryos Akihiko Shimono and Richard R. Behringer 33 HPLC-Based mRNA Differentia! Display Thomas B. Knudsen PART V

TRANSGENESIS: PRODUCTION AND GENE KNOCKOUT

34 Production of Transgenic Drosophila Miki Fujioka, James B. Jaynes, Amy Bejsovec, and Michael Weir 35 Transgenic Manipulation of the Sea Urchin Embryo Jonathan P. Rast 36 Transgenic Zebrafish Shuo Lin 37

Production of Avian Chimeras and Germline Transmission Kristin L. Woods, Scott Schau, Mary Ellen Clark, Jacqueline A. Bonseiaar, and Robert J. Etches 38 Incorporation of Genetically Modified Cells into Chicken Chimeras Laura D. Zajchowski, S. Mansoor Mohammed, Qingxia Wei, and Robert J. Etches 39 Long-Term Culture of Chicken Blastodermal Ceils (CBCs) and Selection of Transfected CBCs Using Antibiotic Resistance Qingxia Wei, Kristin L. Woods, and Robert J. Etches 40 Nuclear Transplantation and Cloning in Mammals Keith E. Latham and Mark E, Westhusin 41 Production of Transgenic Mice Jean Richa 42 Production of Transgenic Mice with Yeast Artificial Chromosome Aya Jakobovits, Bruce T. Lamb, and Kenneth R, Peterson 43 Gene-Targeting Strategies Siew-Sim Cheah and Richard R. Behringer 44 Chimeric Animals and Germline Transmission Jaspal S. Khillan 45 Conditional Gene Knockout Using Cre Recombinase Yunzheng Le and Brian Sauer 46

Application of Cre/loxP in Drosophila: Site-Specific Recombination and Transgene Coplacement Mark L. Siegal and Daniel L. Hartl

VOLUME 111

Preface List of Color Plates Companion Tables of Contents for Volumes I and II Contributors PART 1

INTRODUCTION

1 Developmental Biology Protocols: Overview Hi Rocky S. Tuan and Cecilia W. Lo PART II

MANIPULATION OF DEVELOPMENTAL GENE EXPRESSION AND FUNCTION

2 Ectopic Expression in Drosophila Elizabeth L. Wilder 3 Clonal Analysis in the Examination of Gene Function in Drosophila Jenny E. Rooke, Nicole A. Theodosiou, and Tian Xu 4 Application of Antisense Oligodeoxynucleotides in Developing Chick Embryos Peter G. Alexander, George L. Barnes, and Rocky S. Tuan 5 Application of Functional Blocking Antibodies: N-Cadherin and Chick Embryonic Limb Development Steven A. Oberlender and Rocky S. Tuan PART HI

ANALYSIS OF GENE EXPRESSION

6 Gene Expression Analyzed by Ribonuclease Protection Assay Vickie D. Bennett 7 Relative Reverse Transcription-Polymerase Chain Reaction Troy A. Giambernardi and Robert J. Klebe 8 Gene Expression Analysis Using Quantitative Reverse TranscriptionPolymerase Chain Reaction and a Muitispecific Internal Control David Shire and Pascale Legoux 9 In Situ PCR Detection of HtV Expression in the Human Placenta Asad U. Sheikh, Bruno M. Polliotti, and Richard K. Miller 10 Gene Expression Analysis by In Situ Hybridization: Radioactive Probes Stefan Wawersik and Jonathan A. Epstein xvii

xviii

Contents

11 Radio-isotopic In Situ Hybridization on Tissue Sections: Practical Aspects and Quantification Antoon F. M. Moorman, Piet A. J. De Boer, Jaco Hagoort, Diego Franco, and Wouter H. Lamers 12 mRNA and Protein Co-Localization on Tissue Sections by Sequential, Colorimetric In Situ Hybridization and Immunohistochemistry Rocky S. Tuan 13 Whole-Mount In Situ Hybridization to Study Gene Expression During Mouse Development Linda A. Lowe and Michael Ft. Kuehn 14 Multicolor Whole-Mount In Situ Hybridization Giselbert Hauptmann and Thomas Gerster 15

Methods for Double Detection of Gene Expression: Combined In Situ Hybridization and Immunocytochemistry or Histochemistry Ronald A. Conlon

16 Visualization of the Expression of Green Fluorescent Protein (GFP)-Unked Proteins Joseph C. Ayoob, Jean M. Sanger, and Joseph W. Sanger 17 Monoclonal Antibodies in the Analysis of Embryonic Development Vahe Bedian PART IV

MODELS OF MORPHOGENESIS AND DEVELOPMENT

18 Mesoderm induction in Xenopus: Oocyte Expression System and Animal Cap Assay Jie Yao and Daniel S. Kessler 19 Amphibian Organizer Activity Christof Niehrs 20 Improved Techniques for Avian Embryo Culture, Somite Cell Culture, and Microsurgery David S. Packard, Jr., Christopher Cox, and Thomas J. Poole 21 Neural Crest Cell Outgrowth Cultures and the Analysis of Cell Migration Donald F. Newgreen and Mark Murphy 22 The Chimeric Human/Mouse Model of Angiogenesis Eric Petitcierc, Tami von Schalscha, and Peter C. Brooks 23 Analysis of Embryonic Vascular Morphogenesis Thomas N. Sato and Sona Bartunkova 24 Epitheiial-Mesenchyme Interactions Brian K. Hall 25

Methods for Manipulating the Chick Limb Bud to Study Gene Expression, Tissue Interactions, and Patterning Maria A. Ros, B. Kay Simandl, Allen W. Clark, and John F. Fallon

26

Palate Development: In Vitro Procedures M. Michele Pisano and Robert M. Greene

Contents PART V

xix IN VITRO MODELS AND ANALYSIS DIFFERENTIATION AND DEVELOPMENT

27

In Vitro Fertilization Susan Heyner and Michael J. Tucker

28 Trophoblast Differentiation: An In Vitro Model for Trophobiast Giant Cell Development Thomas J. Peters, Belinda Nl. Chapman, and Michael J. Soares 29 Bone Marrow-Derived fvlesenchymal Progenitor Cells Brian Johnstone and Jung Yoo 30 Identification, Characterization, and Differentiation of Human Prostate Cells Parmender P. Mehta, Carlos Perez-Stable, Bernard R. Boos, and Mehrdad Nadji 31 Preparation of Chick Striated Muscle Cultures Camtlle DiLullo, Jacqueline Gerhart, and Mindy George-Weinstein 32 Study of Skeletal Myogenesis in Cultures of Unsegmented Somitic Mesoderm Anne-Gaelle Borycki and Charles P. Emerson, Jr. 33

34

35

36 37 38

Embryonic Limb Mesenchyme Micromass Culture as an In Vitro Model for Chondrogenesis and Chondrocyte Maturation Anthony M. DeLise, Emanuela Stringa, Wendy A. Woodward, Maria Alice Mello, and Rocky S, Tuan Electroporation-Mediated ONA Transfection of Embryonic Chick Limb Mesenchymal Ceils Anthony D/l. DeLise and Rocky S. Tuan Murine C3H10T1/2 Multipotentia! Cells as an In Vitro Model of Mesenchymal Chondrogenesis Andrew R. Haas and Rocky S. Tuan Skeletogenesis: In Vitro Analysis of Bone Cell Differentiation Adesola Majolagbe and Pamela G. Robey Studying Eariy Hematopoiesis Using Avian Blastoderm Cultures Carol A. Eisenberg Isolation and Culture of Mouse Germ Cells Maria P. De Miguel and Peter J. Donovan

39

Cadherin-Mediated Cell-Cei! Interactions Karen Knudsen and Alejandro Peratta Soler 40 Analysis of Hyaluronan Using Biotinylated Hyaiuronan-Binding Proteins Charles B. Underhifi and Lurong Zhang 41 Microinjection of Fluorescently Labeled Alpha-Actinin into Living Cells Jean B. Sanger, Barbara A. Danowski, and Joseph W. Sanger PART VI

DEVELOPMENTAL MODELS OF DISEASES

42 Pax-3 and Vertebrate Development Jonathan Epstein

xx

Contents

43 Genetic-Engineered Models of Skeletal Diseases t: Collagen Type X Olena Jacenko 44 Genetic-Engineered Models of Skeletal Diseases II: Targeting Mutations into Transgenic Mice Chondrocytes Silvio Garofalo and William A. Norton 45 Transgenic Mouse Models of Craniofacial Disorders Yi-Hsin Liu, Malcolm L. Snead, and Robert E. Maxson, Jr. Index

Contributors

• CREST, Japan Science and Technology Corp., The University of Tokyo, Tokyo, Japan MA KOTO As ASH IMA * Department of Life Sciences (Biology), Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan H. SCOTT BALDWIN * Department ofPediatric Cardiology, Children's Hospital of Philadelphia, Philadelphia, PA JEAN BENNETT • Department of Department of Ophthalmology, Scheie Eye Institute, University of Pennsylvania School of Medicine, Philadelphia, PA STEPHEN A. BOPPART • Department of Electrical Engineering and Computer Science and Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA MARK E. BREZFNSKI • Cardiac Unit and Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA ELIZABETH A. BUCHER • Department of Cell and Developmental Biology, School of Medicine, University of Pennsylvania, Philadelphia, PA GANG CHENG • Department of Cell Biology and Anatomy, Medical University of South Carolina, Charleston, SC CHENG-MING CHUONG * Department of Pathology, School of Medicine, University of Southern California, Los Angeles, CA JAMES A. COFFMAN • Division of Biology, Stowers Institute for Medical Research, California Institute of Technology, Pasadena, CA VICTOR G. CORCES • Department of Biology, Johns Hopkins University, Baltimore, MD DIANA K. DARNELL • Department of Neurobiology and Anatomy, University of Utah School of Medicine, Salt Lake City, UT TIMOTHY J. DAVIES • Department of Zoology, University of Oxford, Oxford, UK ALAN R. DAVIS • Shell Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX FRANCOISE DIETERLEN-LIEVRE • Institut d'Embryologie Cellulaire et Moleculaire du CNRS et du College de France, Nogent/Marnec Cedex, France ADAM S. DOHERTY • Department of Biology, University of Pennsylvania, Philadelphia, PA CHRISTOPHER J. DRAKE • Department of Cell Biology and Anatomy, Medical University of South Carolina, Charleston, SC TAKASHI ARUZUMI

xxi

xxii ROBERT FINKELSTEIN

Contributors • Department ofNeuroscience, University of Pennsylvania,

Philadelphia, PA • Faculte des Sciences et des Techniques, Universite de Nantes, Nantes Cedex, France JAMES G. FUJIMOTO • Department of Electrical Engineering and Computer Science and Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA MASAHIKO FUJINAOA • Department of Anesthesia, Stanford University School of Medicine, Palo Alto, CA ANDREA GAMBOTTO • Department of Molecular Genetics and Biochemistry, University of Pittsburgh School of Medicine, Pittsburgh, PA VIRCINIO GARCIA-MARTINE? • Department of Anatomy and Neurobiology, University of Utah School of Medicine, Salt Lake City, UT RICHARD L. GARDNER • Department of Zoology, University of Oxford, Oxford, UK LEANNE GODINHO • Howard Florey Institute of Experimental Physiology and Medicine, University of Melbourne, Parkville, Victoria, Australia ROBERT G, GOURDIE • Department of Cell Biology and Anatomy,Medical University of South Carolina, Charleston, SC C. MAY GRIFFITH • Department of Cell Biology, Harvard Medical School, Boston, MA ARHA R. GUPTA • Department of Ophthalmology, Scheie Eye Institute, University of Pennsylvania School of Medicine, Philadelphia, PA BRIAN K. HALL • Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada ELIZAHETH D. HAY • Department of Cell Biology, Harvard Medical School, Boston, MA JEFF HARDIN • Department of Zoology, University of Wisconsin, Madison, WI PAUL J. HEID • Department oj Zoology, University of Wisconsin, Madison, WI VLAD HERLEA • Laboratory of Anatomy and Pathology, Bucharest, Romania JAMES C. HUHTA • Department of Cell Biology, University of Medicine and Dentistry of New Jersey, Stratford, NJ E. SIDNEY HUNTER, III • Reproductive Toxicology Division, National Health and Environmental Effects Research Laboratory, US Environmental Protection Agency, Research Triangle Park, NC GREG HUNTER • Developmental Biology Program, Institute of Molecular Medicine and Genetics, Medical College of Georgia, Augusta, GA SEON HEE KIM • Department of Department of Molecular Genetics and Biochemistry, University of Pittsburgh School of Medicine, Pittsburgh, PA, and Institute for Molecular Biology and Genetics, Seoul National University, Seoul, Korea SUNYOUNG KIM • Institute for Molecular Biology and Genetics, Seoul National University, Seoul, Korea SIMON J. KIN&ER » Embryology Unit, Children's Medical Research Institute, Wenworthville, New South Wales, Australia MARGARET L. KIRBY • Developmental Biology Program, Institute of Molecular Medicine and Genetics, Medical College of Georgia, Augusta, GA JOSIANE FONTAINE-PERLS

xxiii

J. KINDER * Embjyology Unit, Children's Medical Research Institute, Wenworthville, New South Wales, Australia MARGARET L. KlRBY * Developmental Biology Program, Institute of Molecular Medicine and Genetics, Medical College of Georgia, Augusta, GA DAVID J. KOZLOWSKI • Department of Biology, University of Pennsylvania, Philadelphia, PA DONNA KUMISKI * Developmental. Biology Program, Institute of Molecular Medicine and Genetics, Medical College of Georgia, Augusta, GA CAROLYN A. LARABELL • Life Sciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, CA PATRICK S. LEAHY • Division of Biology. California Institute of Technology, Pasadena, CA ELIZABETH E. LECLAIR • Department of Orthopaedic Surgery, Thomas Jefferson University, Philadelphia, PA NICOLE M. LE DOUARIN • Institut d'Embryologie Cellulaire et Moleculaire du CNRS et du College de France, Nogent/Marnec Cedex, France KERSTI K.. LiNASK • Department of Cell Biology, University of Medicine and Dentistry of New Jersey, Stratford, NJ CHARLES D. LITTLE • Department of Cell Biology and Anatomy, Medical University of South Carolina, Charleston, SC CECILIA W. LO • Department of Biology, University of Pennsylvania, Philadelphia, PA CARMEN LOPEZ-SANCHEZ • Department of Neurobiology and Anatomy, University of Utah School of Medicine, Salt Lake City, UT CHRISTOPHER J. Lowe • Department of Molecular and Cellular Biology, University of California—Berkeley, Berkeley, CA ALBERT M. MAGUIRE • Department of Ophthalmology, Scheie Eye Institute, University of Pennsylvania Medical School, Philadelphia, PA GEORGE M. MALACINSKI • Department of Biology, Indiana University, Bloomington, IN CRASG S. MICK AN IN • Department of'Pediatric Cardiology, Children's Hospital of Philadelphia, Philadelphia, PA TAKASHI MIKAWA • Department of Cell Biology and Anatomy, Medical University of South Carolina, Charleston, SC TOM MIYAKE • Department of Biology, Dalhousie University, Halifax, Canada SALLY A. MOODY • Department of Anatomy and Cell Biology, The George Washington University Medical Center, Washington, DC KEN MUNEOKA • Department of Cell and Molecular Biology, Tulane University, New Orleans, LA MICHAEL G. NAROTSKY • Reproductive Toxicology Division, National Health and Environmental Effects Laboratory, US Department of Environmental Protection, Research Triangle Park, NC VALERIE NGO-MULLER • Universite Pierre et Marie Curie, Paris Cedex, France SIMON

xxiv

Contributors

L. PALLADTNO • Institute for Human Gene Therapy, University of Pennsylvania, Philadelphia, PA JONATHON PINES • Department of Zoology, Wellcome/CRC Institute, Cambridge, UK JEAN RICHA • Department ofGenetics, University of Pennsylvania, Philadelphia, PA PAUL D. ROBBINS • Departments of Molecular Genetics and Biochemistry, University of Pittsburgh School of Medicine, Pittsburgh, PA JOHN M. ROGERS • Reproductive Toxicology Division, National Health and Environmental Effects Laboratory, US Department of Environmental Protection, Research Triangle Park, NC GARY C. SCHOENWOLF • Department ofNeurobiology and Anatomy, University of Utah School of Medicine, Salt Lake City, UT RICHARD M. SCHULTZ • Department of Biology, University of Pennsylvania, Philadelphia, PA DIANE C. SLUSARSKI • Department of Biological Sciences, University of Iowa, Iowa City, IA BRADLEY R. SMITH • Department of Radiology, Duke University Medical Center, Durham, NC JOD! L. SMITH • Department ofhleurosurgery, University of Utah Medical Center, Salt Lake City, UT HARRIETT STADT • Developmental Biology Program, Institute of Molecular Medicine and Genetics, Medical College of Georgia, Augusta, GA N. SUSAN STOTT • Department of Surgery, Auckland Hospital, Auckland, NZ DAZHONO SUN • Department of Cell Biology, Harvard Medical School, Boston, MA MEERA SUMDARAM • Department of Genetics, School of Medicine, University of Pennsylvania, Philadelphia, PA KAZUHIRO TAKANO • Department of Life Sciences (Biology), Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan PATRICK P. L. TAM • Embryology Unit, Children 's Medical Research Institute, Wenworthville, New South Wales, Australia SEONG-SENG TAN * Howard Florey Institute of Experimental Physiology and Medicine, University of Melbourne, Parkville, Australia LUAN TAO * Institute for Human Gene Therapy, University of Pennsylvania, Philadelphia, PA MARIE-AIMEE TEILLET • Institut d 'Embryologie Cellulaire et Moleculaire du CNRS et du College de France, Nogent/Marnec Cedex, France CHARLES F. THOMAS • Department of Integrated Microscopy Resource, University of Wisconsin—Madison, Madison, WI ROBERT P. THOMPSON * Department of Cell Biology and Anatomy, Medical University of South Carolina, Charleston, SC JOSEPH

Contributors

xxv

• Department of Ceil Biology, University of Medicine and Dentistry of New Jersey, Stratford, NJ ROCKY S. TUAN • Department of Orthopaedic Surgery, Thomas Jefferson University, Philadelphia, PA DANIEL R. TURNBULL • Skirbali Institute ofBiomolecular Medicine, New York University Medical Center, New York, NY B. RUSH WALLER, III • Department of Cell Biology and Anatomy, Cardiovascular Developmental Biology Center, and Department of Pediatrics, Medical University of South Carolina, Charleston, SC ERIC S. WEINBERG • Department of Biology, University of Pennsylvania, Philadelphia, PA ANDY WESSELS • Department of Cell Biology and Anatomy, Medical University of South Carolina, Charleston, SC JOHN G. WHITE • Department of Integrated Microscopy Resource, University of Wisconsin—Madison, Madison, WI JAMES M, WILSON • Institute for Human Gene Therapy, University of Pennsylvania, Philadelphia, PA NELSON A. WIVEL * Institute for Human Gene Therapy, University of Pennsylvania, Philadelphia, PA GREGORY A. WRAY • Department of Medicine, State University of New Yorli, Stony Brook, NY JOHN YOCHEM • Department of Genetics and Cell Biology, University oj Minnesota, St. Paul, MN SHIPENG YUAN • Department of Neurobiology and Anatomy, University of Utah School of Medicine, Salt Lake City, UT YONG ZENG • Department of Ophthalmology, Scheie Eye Institute, University of Pennsylvania School of Medicine, Philadelphia, PA MAGDALENA ZERNICKA-GOETZ • Department of Genetics, Wellcome/CRC Institute, University of Cambridge, Cambridge, UK CATHERINE ZILLER • Institut d'Embryologie, Cellulaire et Moleculaire du CNRS et du College de France, Nogent/Marnec Cedex, France ROBERT M. ZUCKER • Reproductive Toxicology Division, National Health and Environmental Effects Research Laboratory, US Environmental Protection Agency, Research Triangle Park, NC TAKESHI TSUDA

Developmental Biology Protocols