c-di-GMP Signaling

c-di-GMP Signaling : Methods and Protocols

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Description

This volume provides a collection of protocols for the common experimental approaches used in the in the burgeoning field of c-di-GMP-dependent signaling. The chapters, divided into eight major parts, guide readers through methods on synthesis, detection, quantitation, modulation of the levels of c-di-GMP present in cells, procedures to detect and evaluate the interaction of c-di-GMP, and up and coming approaches focusing on the inhibition of c-di-GMP signaling.Written in the highly 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 laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, c-di-GMP Signaling: Methods and Protocols aims to inspire researchers to try new approaches.show more

Product details

  • Hardback | 486 pages
  • 178 x 254 x 26.92mm | 1,124g
  • Humana Press Inc.
  • Totowa, NJ, United States
  • English
  • 1st ed. 2017
  • 64 Illustrations, color; 32 Illustrations, black and white; XIV, 486 p. 96 illus., 64 illus. in color.
  • 1493972391
  • 9781493972395
  • 1,565,316

Back cover copy

This volume provides a collection of protocols for the common experimental approaches used in the in the burgeoning field of c-di-GMP-dependent signaling. The chapters, divided into eight major parts, guide readers through methods on synthesis, detection, quantitation, modulation of the levels of c-di-GMP present in cells, procedures to detect and evaluate the interaction of c-di-GMP, and up and coming approaches focusing on the inhibition of c-di-GMP signaling.Written in the highly 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 laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, c-di-GMP Signaling: Methods and Protocols aims to inspire researchers to try new approaches.show more

Table of contents

1. Discovery of the Intracellular Signaling Molecule Cyclic di-GMP Ute Romling and Michael Y. Galperin PARt I: Synthesis of c-di-GMP 2. Enzymatic Production of C-di-GMP Using a Thermophilic Diguanylate Cyclase Prabhadevi Venkataramani and Zhao-Xun Liang 3. Synthesis of [32P]-c-di-GMP for Diguanylate Cyclase and Phosphodiesterase Activity Determinations Barbara I. Kazmierczak Part II: Detection and Quantitation of c-di-GMP 4. High-performance Liquid Chromatography (HPLC)-based Detection and Quantitation of Cellular c-di-GMP Olga E Petrova and Karin Sauer 5. Identification and Quantification of Cyclic Di-Guanosine Monophosphate and its Linear Metabolites by Reversed-Phase LC-MS/MS Heike Bahre and Volkhard Kaever 6. Detection of Cyclic Dinucleotides by STING Xiao-Xia Du and Xiao-Dong Su 7. Spectrophotometric and Mass Spectroscopic Methods for the Quantification and Kinetic Evaluation of In Vitro c-di-GMP Synthesis Geoffrey B. Severin and Christopher M. Waters Part III: Visualizing c-di-GMP levels using biosensors 8. Gauging and Visualizing c-di-GMP Levels in Pseudomonas aeruginosa using Fluorescence-based Biosensors Morten Rybtke, Song Lin Chua, Joey Kuok Hoong Yam, Michael Givskov, Liang Yang, and Tim Tolker-Nielsen 9. Cyclic di-GMP-responsive Transcriptional Reporter Bioassays in Pseudomonas aeruginosa Bradley R. Borlee, Grace I. Borlee, Kevin H. Martin, and Yasuhiko Irie 10. Live Flow Cytometry Analysis of c-di-GMP levels in Single Cell Populations Jongchan Yeo, Xin C. Wang, and Ming C. Hammond Part IV: Indirect detection of c-di-GMP levels < 11. Experimental Detection and Visualization of the Extracellular Matrix in Macrocolony Biofilms Diego O. Serra and Regine Hengge 12. Congo Red Stain Identifies Matrix Overproduction and is an Indirect Measurement for c-di-GMP in many Species of Bacteria Christopher J. Jones and Daniel J. Wozniak 13. Type IV Pili-dependent Motility as a Tool to Determine the Activity of c-di-GMP Modulating Enzymes in Myxococcus xanthus Dorota Skotnicka and Lotte Sogaard-Andersen PART V: Modulation of c-di-GMP levels And bacterial responses 14. Using Light-Activated Enzymes for Modulating Intracellular c-di-GMP Levels in Bacteria Min-Hyung Ryu, Anastasia Fomicheva, Lindsey O'Neal, Gladys Alexandre, and Mark Gomelsky 15. Analysis of c-di-GMP Levels Synthesized by a Photoreceptor Protein in Response to Different Light Qualities using an in vitro Enzymatic Assay Veronika Angerer, Lars-Oliver Essen, and Annegret Wilde 16. Probing the Role of Cyclic di-GMP Signalling Systems in Disease using Chinese Radish Shi-Qi An, Ji-Liang Tang, and J. Maxwell Dow 17. Contribution of Cyclic di-GMP in the Control of Type III and Type VI Secretion in Pseudomonas aeruginosa Ronan R McCarthy, Martina Valentini, and Alain Filloux 18. Semi-quantitative Analysis of the Red, Dry, and Rough Colony Morphology of Salmonella enterica serovar Typhimurium and Escherichia coli using Congo Red Annika Cimdins and Roger Simm Part VI: Measuring c-di-GMP modulating activities 19. Fluorescent 2-aminopurine c-di-GMP and GpG analogs as PDE Probes Jie Zhou, Clement Opoku-Temeng, and Herman O. Sintim 20. Measuring Cyclic Diguanylate (c-di-GMP)-specific Phosphodiesterase Activity using the MANT-c-di-GMP Assay Dorit Eli, Trevor E. Randall, Henrik Almblad, Joe J. Harrison, and Ehud Banin 21. Determining Phosphodiesterase Activity (Radioactive Assay) Barbara I. Kazmierczak 22. Determining Diguanylate Cyclase Activity (Radioactive Assay) Barbara I. Kazmierczak PART VII: c-di-GMP binding proteins 23. Detection of c-di-GMP-responsive DNA Binding Jacob R. Chambers and Karin Sauer 24. Use of Nonradiochemical DNAse Footprinting to Analyze c-di-GMP Modulation of DNA-binding Proteins Claudine Baraquet and Caroline S. Harwood 25. Detection of Cyclic di-GMP Binding Proteins Utilizing a Biotinylated Cyclic di-GMP Pulldown Assay Jacob R. Chambers and Karin Sauer 26. Probing Protein-protein Interactions with Genetically Encoded Photo-activatable Crosslinkers Richard B. Cooley and Holger Sondermann 27. Identification of c-di-AMP-Binding Proteins Using Magnetic Beads Jan Kampf, Jan Gundlach, Christina Herzberg, Katrin Treffon, and Jorg Stulke < 28. Pulldown with a c-di-GMP-specific Capture Compound Coupled to Mass Spectrometry as a Powerful Tool to Identify Novel Effector Proteins Benoit-Joseph Laventie, Timo Glatter, and Urs Jenal 29. Identification of c-di-GMP-responsive Riboswitches Johann Peltier and Olga Soutourina 30. Isothermal Titration Calorimetry to Determine Apparent Dissociation Constants (Kd) and Stoichiometry of Interaction (n) of c-di-GMP Binding Proteins Bruno Y. Matsuyama, Petya V. Krasteva, and Marcos V. A. S. Navarro PART VIII: Targeting c-di-GMP signaling 31. Targeting c-di-GMP Signaling, Biofilm Formation and Bacterial Motility With Small Molecules Clement Opoku-Temeng and Herman O. Sintim 32. Discovering Selective Diguanylatecyclases Inhibitors: From PleD to Discrimination of the Active Site of cyclic-di-GMP Phosphodiesterases S. Rinaldo, G. Giardina, F. Mantoni, A. Paiardini, and A. Paone, F. Cutruzzola 33. High throughput Screening for Compounds that Modulate the Cellular c-di-GMP Level in Bacteria Julie Groizeleau, Jens Bo Andersen, Michael Givskov, Jens Berthelsen, and Tim Tolker-Nielsen 34. Genetic Tools to Study c-di-GMP-dependent Signaling in Pseudomonas aeruginosa Livia Leoni, Sarika Vishnu Pawar, and Giordano Rampionishow more