Plant Signalling Networks: Methods and Protocols

Signal transduction is the fundamental mechanism for regulation of cellular activities by environmental cues and regulatory signals, and is particularly important for plants, whose survival requires proper physiological and developmental responses to the environmental changes. Much progress has been made recently in the plant signal transduction research field thanks to the development of diverse techniques which are covered in Plant Signalling Networks: Methods and Protocols. These include advanced research methods such as proteomics and mass spectrometry methods for studying protein modification, biochemical and cell biological tools for studying protein-protein interactions, genomic techniques for dissecting protein-DNA interaction and transcription networks, and computation methods that integrate molecular network into plant developmental processes. Written in the 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 protocols, and notes on troubleshooting and avoiding known pitfalls.   Plant Signalling Networks: Methods and Protocols presents well-honed methodologies for a wide range of research approaches including genetics, proteomics, biochemical, cell biological, and computational approaches, and seeks to serve both professionals and novices with a comprehensive understanding of complex signaling networks in plants. 

Table of Contents:
Experimental Analysis of Receptor Kinase Phosphorylation.- Quantitative Measurement of Phosphopeptides and Proteins via Stable Isotope Labeling in Arabidopsis (SILIA) and Functional Phosphoproteomic Strategies.- Identification of O-GlcNAc Modified Proteins from Arabidopsis.- Quantitative Analysis of Protein Phosphorylation Using Two-Dimensional Difference Gel Electrophoresis (2-D DIGE).- Quantitative Analysis of Plasma Proteome Using Two-Dimensional Difference Gel Electrophoresis (2-D DIGE).- Identification and Verification of Redox-Sensitive Proteins in Arabidopsis thaliana.- Small-Molecule Dissection of Brassinosteroid (BR) Signaling.- A Chemical Genetics Method to Uncover Small Molecules for Dissecting the Mechanism of ABA Responses in Arabidopsis Seed Germination.- Activation Tagging.- Rho GTPase Activity Analysis in Plant Cells.- Analysis of In Vivo ROP GTPase Activity at the Subcellular Level by Fluorescence Resonance Energy Transfer Microscopy.- In vivo Ubiquitination Assay by Agroinfiltration.- In Vitro Protein Ubiquitination Assay.- Genome-Wide Identification of Transcription Factor Binding Sites in Plants Using Chromatin Immunoprecipitation Followed by Microarray (ChIP-chip) or Sequencing (ChIP-seq).- Smart Pooling of mRNA Samples for Efficient Transcript Profiling.- Transient Expression Assays for Quantifying Signaling Output.- Genome-Wide Profiling of Uncapped mRNA.- Computational Tools for Quantitative Analysis of Cell Growth Patterns and Morphogenesis in Actively Developing Plant Stem Cell Niches.