Morphogen Gradients: Methods and Protocols

Part I: Visualization of Morphogen Gradients

1. Analysis of Expression Gradients of Developmental Regulators in Arabidopsis thaliana Roots

Mar?a Florencia Ercoli, Rodrigo Vena, Camila Goldy, Javier F. Palatnik, and Ramiro E. Rodriguez

Feng He, Honggang Wu, David Cheung, and Jun Ma

3. Imaging Cytonemes in Drosophila Embryos

Lijuan Du and Sougata Roy

4. Measuring Dorsoventral Pattern and Morphogen Signaling Profiles in the Growing Neural Tube

Marcin Zagorski and Anna Kicheva

Part II: Analysis of Biophysical Properties and Functions of Morphogens

5. Fluorescence Correlation and Cross-Correlation Spectroscopy in Zebrafish

Xue Wen Ng, Karuna Sampath, and Thorsten Wohland

6. FRAP Analysis of Extracellular Diffusion in Zebrafish Embryos

Gary H. Soh and Patrick M?ller

7. Generation of Ectopic Morphogen Gradients in the Zebrafish Blastula

Maraysa de Olivera-Melo, Peng-Fei Xu, Nathalie Houssin, Bernard Thisse, and Christine Thisse

8. Polarizing Region Tissue Grafting in the Chick Embryo Limb Bud

Holly Stainton and Matthew Towers

9. Analysis of PLETHORA Gradient Formation by Secreted Peptides during Root Development

Hidefumi Shinohara and Yoshikatsu Matsubayashi

10. Live Imaging of mRNA Transcription in Drosophila Embryos

Carmina Angelica Perez-Romero, Huy Tran, Mathieu Coppey, Aleksandra M. Walczak, C?cile Fradin, and Nathalie Dostatni

11. LiveFly: A Toolbox for the Analysis of Transcription Dynamics in Live Drosophila Embryos

Huy Tran, Carmina Angelica Perez-Romero, Teresa Ferraro, Cecile Fradin, Nathalie Dostatni, Mathieu Coppey, and Aleksandra M. Walczak

Part III: Modeling of Morphogen Behaviors and Activities

12. Discrete-State Stochastic Modeling of Morphogen Gradient Formation

Hamid Teimouri and Anatoly B. Kolomeisky

13. Simulation of Morphogen and Tissue Dynamics

Michael D. Peters, L.D. Wittwer, Anna Stopka, Diana Barac, Christine Lang, and Dagmar Iber

14. Mechanisms and Measurements of Scale Invariance of Morphogen Gradients

Yan Huang and David Umulis

15. Scaling of Morphogenetic Patterns

Manan'Iarivo Rasolonjanahary and Bakhtier Vasiev

16. Modeling Time-Dependent Acquisition of Positional Information

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