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c-di-GMP Signaling

Overview of attention for book
Cover of 'c-di-GMP Signaling'

Table of Contents

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    Book Overview
  2. Altmetric Badge
    Chapter 1 Discovery of the Second Messenger Cyclic di-GMP.
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    Chapter 2 Enzymatic Production of c-di-GMP Using a Thermophilic Diguanylate Cyclase.
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    Chapter 3 Synthesis of [(32)P]-c-di-GMP for Diguanylate Cyclase and Phosphodiesterase Activity Determinations.
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    Chapter 4 High-Performance Liquid Chromatography (HPLC)-Based Detection and Quantitation of Cellular c-di-GMP.
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    Chapter 5 Identification and Quantification of Cyclic Di-Guanosine Monophosphate and Its Linear Metabolites by Reversed-Phase LC-MS/MS.
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    Chapter 6 Detection of Cyclic Dinucleotides by STING
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    Chapter 7 Spectrophotometric and Mass Spectroscopic Methods for the Quantification and Kinetic Evaluation of In Vitro c-di-GMP Synthesis
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    Chapter 8 Gauging and Visualizing c-di-GMP Levels in Pseudomonas aeruginosa Using Fluorescence-Based Biosensors.
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    Chapter 9 Cyclic di-GMP-Responsive Transcriptional Reporter Bioassays in Pseudomonas aeruginosa.
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    Chapter 10 Live Flow Cytometry Analysis of c-di-GMP Levels in Single Cell Populations
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    Chapter 11 Experimental Detection and Visualization of the Extracellular Matrix in Macrocolony Biofilms.
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    Chapter 12 Congo Red Stain Identifies Matrix Overproduction and Is an Indirect Measurement for c-di-GMP in Many Species of Bacteria.
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    Chapter 13 Type IV Pili-Dependent Motility as a Tool to Determine the Activity of c-di-GMP Modulating Enzymes in Myxococcus xanthus.
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    Chapter 14 Using Light-Activated Enzymes for Modulating Intracellular c-di-GMP Levels in Bacteria
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    Chapter 15 Analysis of c-di-GMP Levels Synthesized by a Photoreceptor Protein in Response to Different Light Qualities Using an In Vitro Enzymatic Assay
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    Chapter 16 Probing the Role of Cyclic di-GMP Signaling Systems in Disease Using Chinese Radish.
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    Chapter 17 Contribution of Cyclic di-GMP in the Control of Type III and Type VI Secretion in Pseudomonas aeruginosa.
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    Chapter 18 Semiquantitative Analysis of the Red, Dry, and Rough Colony Morphology of Salmonella enterica Serovar Typhimurium and Escherichia coli Using Congo Red
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    Chapter 19 Fluorescent 2-Aminopurine c-di-GMP and GpG Analogs as PDE Probes
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    Chapter 20 Measuring Cyclic Diguanylate (c-di-GMP)-Specific Phosphodiesterase Activity Using the MANT-c-di-GMP Assay.
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    Chapter 21 Determining Phosphodiesterase Activity (Radioactive Assay).
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    Chapter 22 Determining Diguanylate Cyclase Activity (Radioactive Assay).
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    Chapter 23 Detection of c-di-GMP-Responsive DNA Binding.
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    Chapter 24 Use of Nonradiochemical DNAse Footprinting to Analyze c-di-GMP Modulation of DNA-Binding Proteins.
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    Chapter 25 Detection of Cyclic di-GMP Binding Proteins Utilizing a Biotinylated Cyclic di-GMP Pull-Down Assay.
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    Chapter 26 Probing Protein-Protein Interactions with Genetically Encoded Photoactivatable Cross-Linkers.
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    Chapter 27 Identification of c-di-AMP-Binding Proteins Using Magnetic Beads
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    Chapter 28 Pull-Down with a c-di-GMP-Specific Capture Compound Coupled to Mass Spectrometry as a Powerful Tool to Identify Novel Effector Proteins.
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    Chapter 29 Identification of c-di-GMP-Responsive Riboswitches.
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    Chapter 30 Isothermal Titration Calorimetry to Determine Apparent Dissociation Constants (K d) and Stoichiometry of Interaction (n) of C-di-GMP Binding Proteins
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    Chapter 31 Targeting c-di-GMP Signaling, Biofilm Formation, and Bacterial Motility with Small Molecules.
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    Chapter 32 Discovering Selective Diguanylate Cyclase Inhibitors: From PleD to Discrimination of the Active Site of Cyclic-di-GMP Phosphodiesterases.
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    Chapter 33 High-Throughput Screening for Compounds that Modulate the Cellular c-di-GMP Level in Bacteria
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    Chapter 34 Genetic Tools to Study c-di-GMP-Dependent Signaling in Pseudomonas aeruginosa.
Attention for Chapter 29: Identification of c-di-GMP-Responsive Riboswitches.
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Chapter title
Identification of c-di-GMP-Responsive Riboswitches.
Chapter number 29
Book title
c-di-GMP Signaling
Published in
Methods in molecular biology, January 2017
DOI 10.1007/978-1-4939-7240-1_29
Pubmed ID
Book ISBNs
978-1-4939-7239-5, 978-1-4939-7240-1
Authors

Peltier, Johann, Soutourina, Olga, Johann Peltier, Olga Soutourina

Abstract

Bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP) is an important signaling molecule for community behavior control, cell morphogenesis, and virulence in bacteria. In addition to protein effectors, this second messenger binds RNA molecules that act as riboswitches to control target gene expression. In this chapter, we describe a method for experimental validation of the functionality of c-di-GMP-responsive riboswitches and the analysis of c-di-GMP control of target gene expression by qRT-PCR and Northern blot. This procedure can be used for the studies of in silico-predicted riboswitch candidates, as well as a targeted experimental approach for exploring the data from next-generation sequencing. The examples on the analysis of type I and type II c-di-GMP-responsive riboswitches in Clostridium difficile are provided to illustrate the application of the method.

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Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 15 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 15 100%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 3 20%
Student > Bachelor 2 13%
Student > Master 2 13%
Researcher 2 13%
Student > Postgraduate 1 7%
Other 0 0%
Unknown 5 33%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 4 27%
Agricultural and Biological Sciences 4 27%
Immunology and Microbiology 2 13%
Unknown 5 33%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 2. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 12 May 2018.
All research outputs
#14,954,297
of 23,001,641 outputs
Outputs from Methods in molecular biology
#4,724
of 13,154 outputs
Outputs of similar age
#243,390
of 421,214 outputs
Outputs of similar age from Methods in molecular biology
#416
of 1,074 outputs
Altmetric has tracked 23,001,641 research outputs across all sources so far. This one is in the 32nd percentile – i.e., 32% of other outputs scored the same or lower than it.
So far Altmetric has tracked 13,154 research outputs from this source. They receive a mean Attention Score of 3.4. This one has gotten more attention than average, scoring higher than 59% of its peers.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 421,214 tracked outputs that were published within six weeks on either side of this one in any source. This one is in the 39th percentile – i.e., 39% of its contemporaries scored the same or lower than it.
We're also able to compare this research output to 1,074 others from the same source and published within six weeks on either side of this one. This one has gotten more attention than average, scoring higher than 56% of its contemporaries.