Programmed Morphogenesis

1. Front Matter

   Pages i-xii

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2. Understanding Signaling Events and Patterns

   1. Front Matter

      Pages 1-1

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   2. TASBE Image Analytics : A Processing Pipeline for Quantifying Cell Organization from Fluorescent Microscopy

      • Nicholas Walczak, Jacob Beal, Jesse Tordoff, Ron Weiss

      Pages 3-15

   3. Neighborhood Impact Factor to Study Cell-Fate Decision-Making in Cellular Communities

      • Shaylina R. Carter, Joshua Hislop, Joshua Hsu, Jeremy J. Velazquez, Mo R. Ebrahimkhani

      Pages 17-28

   4. A Quantitative Lineage-Tracing Approach to Understand Morphogenesis in Gut

      • Svetlana Ulyanchenko, Jordi Guiu

      Pages 29-40

3. Programming Signaling Events and Patterns

   1. Front Matter

      Pages 41-41

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   2. Reconstitution of Morphogen Signaling Gradients in Cultured Cells

      • Julia S. Kim, Michael Pineda, Pulin Li

      Pages 43-56

   3. Engineering Shape-Controlled Microtissues on Compliant Hydrogels with Tunable Rigidity and Extracellular Matrix Ligands

      • Megan L. Rexius-Hall, Nethika R. Ariyasinghe, Megan L. McCain

      Pages 57-72

   4. Engineering Biophysical Cues for Controlled 3D Differentiation of Endoderm Derivatives

      • Thomas Richardson, Shibin Mathew, Connor Wiegand, Kevin Pietz, Joseph Candiello, K. Ravikumar et al.

      Pages 73-92

   5. Rewiring Endogenous Bioelectric Circuits in the Xenopus laevis Embryo Model

      • Vasilios Nanos, Michael Levin

      Pages 93-103

   6. Engineering the Spatiotemporal Mosaic Self-Patterning of Pluripotent Stem Cells

      • Ashley R. G. Libby, David A. Joy, Todd C. McDevitt

      Pages 105-116

4. Early Developmental Engineering

   1. Front Matter

      Pages 117-117

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   2. Fate-Patterning of 2D Gastruloids and Ectodermal Colonies Using Micropatterned Human Pluripotent Stem Cells

      • George Britton, Sapna Chhabra, Joseph Massey, Aryeh Warmflash

      Pages 119-130

   3. Gastruloids: Embryonic Organoids from Mouse Embryonic Stem Cells to Study Patterning and Development in Early Mammalian Embryos

      • Kerim Anlas, Peter Baillie-Benson, Krisztina Arató, David A. Turner, Vikas Trivedi

      Pages 131-147

5. Organoids, Tissue Barriers, and Disease Models

   1. Front Matter

      Pages 149-149

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   2. A Synergistic Engineering Approach to Build Human Brain Spheroids

      • Djuna von Maydell, Mehdi Jorfi

      Pages 151-169

   3. Directed Differentiation of Human Pluripotent Stem Cells for the Generation of High-Order Kidney Organoids

      • Idoia Lucía Selfa, Maria Gallo, Nuria Montserrat, Elena Garreta

      Pages 171-192

   4. Methods for Controlled Induction of Singular Rosette Cytoarchitecture Within Human Pluripotent Stem Cell-Derived Neural Multicellular Assemblies

      • Alireza Aghayee, Randolph Ashton

      Pages 193-203

   5. 3D Self-Organized Human Blood–Brain Barrier in a Microfluidic Chip

      • Marco Campisi, Sei Hien Lim, Valeria Chiono, Roger Dale Kamm

      Pages 205-219

   6. Modeling the Complexity of the Metastatic Niche Ex Vivo

      • Amanda M. Clark

      Pages 221-239

This detailed book explores techniques for understanding and engineering programs that naturally control and drive formation of tissues and organs in order to open powerful opportunities to produce physiologically relevant tissues of interest, generate models to study human disease, and set the path for the manufacturing of advanced tissue and organs. Beginning with chapters to help understand signaling events and patterns in morphogenetic systems, the volume continues by covering programming signaling events and patterns to drive morphogenesis, techniques for engineering organoids, tissue barriers, and disease models, as well as in vivo therapeutic applications. Written for the highly successful Methods in Molecular Biology series, 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. 

Authoritative and cutting-edge, Programmed Morphogenesis: Methods and Protocols aims not only to communicate knowledge but also to inspire approaches to new challenges and to empower readers with the capability to approach those challenges.

• Morphogenetic cues
• Cellular engineering
• Tissue development
• Developmental engineering
• Signaling events
• Organoids
• Therapeutic applications

• Department of Pathology, Division of Experimental Pathology, School of Medicine, University of Pittsburgh, Pittsburgh Liver Research Center, University of Pittsburgh, Department of Bioengineering Swanson School of Engineering, University of Pittsburgh, McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, USA

  Mo R. Ebrahimkhani

• Department of Bioengineering Swanson School of Engineering, Pittsburgh Liver Research Center, Department of Pathology, Division of Experimental Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, USA

  Joshua Hislop

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