Tissue morphogenesis encompasses a diverse array of processes that transforms unpatterned populations of cells into the distinct tissue structures of the mature organism. The creation of complex, multicellular tissue architectures is critical for organ formation and eventual function. The study of tissue morphogenesis is a rich one, with key conceptual advances emerging from several model organisms. Recent advances have benefited from collaborations between developmental biologists and physicists and engineers, who bring sophisticated analysis techniques as well as theoretical paradigms. This volume highlights the major techniques, both experimental and computational, for the study of tissue morphogenesis, divided into several sections, with specific focus on techniques to image, manipulate, model, and analyze tissue morphogenesis.
This book comprises 22 chapters authored by 68 leading experts from institutions in the USA, Canada, Puerto Rico, France, Austria, the Netherlands, Hungary, Switzerland, Turkey, and Taiwan. This diverse group includes developmental biologists, cell biologists, engineers, and systems biologists working on a large variety of both classical and innovative model systems.
We have divided the book into five parts, based on either methodology or model system. Given that tissue morphogenesis is a dynamic process, and given the seemingly enormous advances in imaging technologies over the past 5 years, the first part (Chapters 1-9) comprises nine chapters devoted to imaging analysis of tissue morphogenesis. This part includes chapters on using imaging techniques to measure the mechanical properties of morphogenetic tissues, the forces that they either exert or experience, or the corresponding changes in cell dynamics or gene expression. The second part (Chapters 10-13) comprises four chapters focused on culture models of tissue morphogenesis, including both cell-based and organ explant models. The third part (Chapters 14-17) comprises an additional four chapters that describe techniques for manipulating cells and tissues in vivo, including classical tissue recombination experiments as well as more recently developed laser-based tissue ablation approaches. The fourth part (Chapters 18-19) contains two chapters describing novel model systems to investigate tissue morphogenesis. The fifth and final part (Chapters 20-22) comprises three chapters that describe the use of computational models in understanding tissue morphogenesis.
This book is intended to serve as a primary resource for both fundamental and practical understanding of the techniques used to uncover the basis of tissue morphogenesis. The book is intended to be a primary source for academics and professionals working in developmental biology, tissue engineering, and medicine. NJ, USA Celeste M. Nelson

Preface v

Contributors ix

Part I Imaging Morphogenesis

1 Probing Regional Mechanical Properties of Embryonic Tissue Using Microindentation and Optical Coherence Tomography 3

Benjamen A. Films, Gang Xu, and Larry A, Taber

2 Hemodynamic Flow Visualization of Early Embryonic Great Vessels Using μPIV 17

Selda Goktas, Chia-Yuan Chen, William J. Kowalski, and Kerem Pekkan

3 Using Correlative Light and Electron Microscopy to Study Zebrafish Vascular Morphogenesis 31

Jacky G. Goetz, Fabien Monduc, Yannick Schwab, and Julien Vermot

4 Micro/Nano-Computed Tomography Technology for Quantitative Dynamic, Multi-scale Imaging of Morphogenesis 47

Chelsea L. Gregg, Andrew K. Recknagel, and Jonathan T. Butcher

5 Imaging the Dorsal-Ventral Axis of Live and Fixed Drosophila melanogaster Embryos 63

Sophia N. Carrell and Gregory T. Reeves

6 Light Sheet-Based Imaging and Analysis of Early Embryogenesis in the Fruit Fly 79

Khaled Khairy, William C. Lemon, Fernando Amat, and Philipp J. Keller

7 Quantitative Image Analysis of Cell Behavior and Molecular Dynamics During Tissue Morphogenesis 99

Chun Yin Bosco Leung and Rodrigo Fernandez-Gonzalez

8 A Multiplex Fluorescent In Situ Hybridization Protocol for Clonal Analysis of Drosophila Oogenesis 115

Lily S. Cheung and Stanislav Shvartsman

9 Active Cell and ECM Movements During Development 123

Anastasiia Aleksandrova, Brenda J. Rongish, Charles D. Little, and Andras Czirok

Part II Culture Models of Morphogenesis

10 3D Culture Assays of Murine Mammary Branching Morphogenesis and Epithelial Invasion 135

Kim-Vy Nguyen-Ngoc, Eliah R Shamir, Robert J. Huebner, Jennifer N. Beck, Kevin J. Cheung, and Andrew J. Ewald

11 Culture of Mouse Embryonic Foregut Explants 163

Felicia Chen and Wellington V. Cardoso

12 Investigating Human Vascular Tube Morphogenesis and Maturation Using Endothelial Cell-Pericyte Co-cultures and a Doxycycline- Inducible Genetic System in 3D Extracellular Matrices 171

Stephanie L.K. Bowers, Chun-Xia Meng, Matthew T. Davis, and George E. Davis

13 Three Dimensional Traction Force Microscopy of Engineered Epithelial Tissues 191

Alexandra S. Piotrowski, Victor D. Varner, Nikolce Gjorevski, and Celeste M. Nelson

Part III Manipulating Cells and Tissues In Vivo

14 Probing Cell Mechanics with Subcellular Laser Dissection of Actomyosin Networks in the Early Developing Drosophila Embryo 209

M. Bauzi and P.-F. Lenne

15 UV Laser Ablation to Measure Cell and Tissue-Generated Forces in the Zebrafish Embryo In Vivo and Ex Vivo 219

Michael Smutny, Martin Behrndt, Pedro Campinho, Verena Ruprecht, and Carl-Philipp Heisenberg

16 Measurement of Intercellular Cohesion by Tissue Surface Tensiometry 237

Ramsey A. Foty

17 Quail-Chick Chimeras and Eye Development 255

Sinu Jasrapuria Agrawal and Peter Y. Lwigale

Part IV Emerging Models of Tissue Morphogenesis

18 Studying Epithelial Morphogenesis in Dictyostelium 267

Daniel J. Dickinson, W. James Nelson, and William I. Weis

19 Primary Cell Cultures of Regenerating Holothurian Tissues 283

Samir A. Bello, Ricardo J. Abreu-Irizarry, and Jose E. Garcia-Arraras

Part V Computational Models of Tissue Morphogenesis

20 Large-Scale Parameter Studies of Cell-Based Models of Tissue Morphogenesis Using Compu Cell3D or VirtualLeaf 301

MargrietM. Palm and Roeland M.H. Merks

21 Simulating Tissue Morphogenesis and Signaling 323

Dagmar Iber, Simon Tanaka, Patrick Fried, Philipp Germann, and Denis Menshykau

22 Elasticity-Based Targeted Growth Models of Morphogenesis 339

Patrick W. Alford

Index 351

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