Avian and Reptilian Developmental Biology Methods and Protocols

About this book

Avian and Reptilian Developmental Biology discusses recent advances in avian and reptilian biology that have caused this diverse field to re-emerge. The chapters in this book are divided into 4 parts: genomics and transcriptomics, genetic manipulation, stem cells, and new model systems. Part I details how to perform genomic and transcriptomic analyses in birds and reptiles; Part II highlights technological advancements in avian genetic manipulation; Part III focuses on methods to handle pluripotent cells; and part IV looks at the emerging models in avian and reptilian developmental biology. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

Cutting-edge and comprehensive, Avian and Reptilian Developmental Biology: Methods and Protocols explores a variety of approaches and different sauropsid models that will help facilitate communication and collaboration among researchers, which in turn will progress this field forward.

Contents

Preface
Contributing Authors

1 Some Thoughts on Experimental Design Claudio D. Stern

Part I Genomics and Transcriptomics
2 Comparative Genomics as a Foundation for Evo-Devo Studies in Birds Phil Grayson, Simon Y.W. Sin, Timothy B. Sackton, and Scott V. Edwards
3 A Step-by-Step Guide to Assemble a Reptilian Genome Asier Ullate-Agote, Yingguang Frank Chan, Michel C. Milinkovitch, and Athanasia C. Tzika
4 Genomic and Transcriptomic Analyses of Avian Sex Chromosomes and Sex-Linked Genes Jilin Zhang, Jing Li, and Qi Zhou
5 Systems Biology Analyses in Chicken: Workflow for Transcriptome and ChIP-Seq Analyses using the Chicken Skin Paradigm Yung-Chih Lai, Randall B. Widelitz and, and Cheng-Ming Chuong
6 Application of a CAGE Method to an Avian Development Study Ruslan Deviatiiarov, Marina Lizio, and Oleg Gusev

Part II Genetic Manipulation
7 CRISPR/Cas9 in the Chicken Embryo Valerie Morin, Nadege Veron, and Christophe Marcelle
8 Fluorescent Quail: A Transgenic Model System for the Dynamic Study of Avian Development David Huss and Rusty Lansford
9 Lentiviral-Mediated Transgenesis in Songbirds Wan-chun Liu, Marian Hruska-Plochan, and Atsushi Miyanohara
10 In Ovo Electroporation Methods in Chick Embryos Hidekiyo Harada, Minoru Omi, and Harukazu Nakamura
11 Genetic Manipulation of the Avian Urogenital System using In Ovo Electroporation Claire E. Hirst, Olivier Serralbo, Katie L. Ayers, Kelly N. Roeszler and Craig A. Smith
12 Enhancer Analyses using Chicken Embryo Electroporation Masanori Uchikawa, Naoko Nishimura, Makiko Iwafuchi-Doi, and Hisato Kondoh
13 Transgene Introduction into the Chick Limb Bud by Electroporation Shogo Ueda, Takayuki Suzuki, and Mikiko Tanaka

Part III Stem Cells
14 Chicken Induced Pluripotent Stem Cells: Establishment and Characterization Aurelie Fuet and Bertrand Pain
15 Isolation and Characterization of Chicken Primordial Germ Cells and their Application in Transgenesis Jae Yong Han and Bo Ram Lee
16 Handling of Gametes for In Vitro Insemination in Birds Shusei Mizushima, Mei Matsuzaki, and Tomohiro Sasanami
17 In Vitro and Ex Ovo Culture of Reptilian and Avian Neural Progenitor Cells Wataru Yamashita, Toyo Shimizu and Tadashi Nomura

Part IV New Model Systems
18 Lifting the Veil on Reptile Embryology: The Veiled Chameleon (Chamaeleo calyptratus) as a Model System to Study Reptilian Development Raul E. Diaz, Jr., Federica Bertocchini, and Paul A. Trainor
19 Model Clades versus Model Species: Anolis Lizards as an Integrative Model of Anatomical Evolution Thomas J. Sanger and Bonnie K. Kircher
20 The Feather Model for Chemo- and Radiation Therapy-Induced Tissue Damage Zhicao Yue and Benhua Xu
21 An Early Chick Embryo Culture Device for Extended Continuous Observation Hans-Georg Sydow, Tobias Pieper, Christoph Viebahn, and Nikoloz Tsikolia
22 A Sensitive and Versatile In Situ Hybridization Protocol for Gene Expression Analysis in Developing Amniote Brains Pei-Shan Hou, Takuma Kumamoto, and Carina Hanashima
23 Somitogenesis and Axial Development in Reptiles Cindy Xu, Mariana B. Grizante, and Kenro Kusumi
24 Micro-CT Imaging on Living Alligator Teeth Reveals Natural Tooth Cycling Randall B. Widelitz, Alaa Abdelhamid, M. Khalil Khan, A. Elkarargy, Cheng-Ming Chuong , and Ping Wu

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