Rho GTPases: Methods and Protocols

Part I: Computational Modeling and Imaging

1. Computational Modeling of the Dynamics of Spatiotemporal Rho GTPase Signaling: A Systematic Review

            Shabnam Khatibi, Karina Islas Rios, and Lan K. Nguyen

2. Uncovering Bistability in the Rac1/RhoA Signaling Network through Integrating Computational Modeling and Experimentation

            Alex von Kriegsheim and Lan K. Nguyen

3. Modeling Rho GTPase Dynamics Using Boolean Logic

            Joseph H.R. Hetmanski, Jean-Marc Schwartz, and Patrick T. Caswell

4. EdgeProps: A Computational Platform for Correlative Analysis of Cell Dynamics and Near-Edge Protein Activity

            Anastasia Zhurikhina, Timothy Qi, Klaus M. Hahn, Timothy C. Elston, and Denis Tsygankov

5. Applying Perturbation Expectation-Maximization to Protein Trajectories of Rho GTPases

            Peter K. Koo and Simon G.J. Mochrie

6. Parallel High Resolution Imaging of Leukocyte Chemotaxis under Agarose with Rho Family GTPase Biosensors

            George R.R. Bell, Dean E. Natwick, and Sean R. Collins

7. Characterization of Genetically-Encoded FRET Biosensors for Rho Family GTPases

            Sara K. Donnelly, Veronika Miskolci, Alice M. Garrastegui, Dianne Cox, and Louis Hodgson

8. Screening for Rho GTPase Modulators in Actin-Dependent Processes Exemplified by Phagocytosis

            Daniel Schlam, Sergio Grinstein, and Spencer A. Freeman

Part II: Biochemistry and High Throughput Methods

9. An In Vitro Kinase Assay to Assess Rac1 Phosphorylation by ERK

            Daniel Brandwein, Junfeng Tong, Laiji Li, Barbara Ballermann, and Zhixiang Wang

10. Methods to Study Rho GTPases Using Bacterial Toxins

            Gudula Schmidt

11. Assessment of S-Glutathionylated Rac1 in Cells Using Biotin-Labeled Glutathione

            Hannah Edenbaum and Jingyan Han

12. High Throughput Assay for RhoGEFs Based on the Transcreener^® GDP Assay

            Robert G. Lowery and Meera Kumar

13. Small Volume Flow Cytometry-Based Multiplex Analysis of the Activity of Small GTPases

            Peter Simons, Virginie Bondu, Angela Wandinger-Ness, and Tione Buranda

Part III: Cell Types and Processes

14. Methods to Study the Roles of Rho GTPases in Platelet Function

            Francisco Rivero and Simon Calaminus

15. Methods to Investigate the Role of Rho GTPases in Osteoclast Function

            Anne Morel, Anne Blangy, and Virginie Vives

16. Methods to Study the Role of Cdc42, Rac1 and Rac2 in B Cell Cytoskeletal Responses

            Natalija Gerasimcik, Lisa S. Westerberg, and Eva Severinson

17. In Vivo Rescue Assay of RhoA Deficient Hematopoietic Stem and Progenitor Cells

            Xiongwei Cai, Xuan Zhou, and Yi Zheng

18. Cell Polarity and Division Symmetry Analyses in Transformed Blood Cells

            Benjamin Mizukawa, Eric O'Brien, James C. Mulloy, and Yi Zheng

19. C3 Transferase Gene Therapy for Continuous RhoA Inhibition

            Angel J. Santiago-Lopez, Claire-Anne Gutekunst, and Robert E. Gross

20. A Practical Protocol for the Conditional Depletion of Rho Isoforms in Human Embryonic Stem Cells

            Masatoshi Ohgushi

21. Methods to Study the Roles of Rho GTPases in Dendritic Tree Complexity

22. Assessing the Roles of Rho GTPases in Cell DNA Repair by the Nucleotide Excision Repair Pathway

            Lilian C. Russo, Pault Y. Minaya, Luiz E. Silva, and Fábio L. Forti

23. Measuring the Contributions of the Rho Pathway to the DNA Damage Response in Tumor Epithelial Cells

            Yuli T. Magalhães, Jessica O. Farias, Lucas F. Monteiro, and Fábio L. Forti

Part IV: Rho GTPases in Non-Mammalian Model Organisms

24. Using GAL4-Inducible Transgenics to Modulate Rho GTPase Activity in Zebrafish

            Nicholas J. Hanovice, Emily McMains, and Jeffrey M. Gross

25. Assaying Rho GTPase-Dependent Processes in Dictyostelium discoideum

            Maja Marinovic, Huajiang Xiong, Francisco Rivero, and Igor Weber

26. Reconstruction of ROP GTPase Domains on the Plasma Membrane in Tobacco Leaves

            Yoshihisa Oda, Yoshinobu Nagashima, and Hiroo Fukuda

27. Analyzing Rho GTPase-Dependent Processes during Cell Polarization in Brown Algae

            Whitney Hable