Fluorescence In Situ Hybridization FISH for Microbial Cells Methods and Concepts 1st Edition by Nuno F Azevedo, Carina Almeida ISBN 1071611178 9781071611173

Fluorescence In Situ Hybridization FISH for Microbial Cells Methods and Concepts 1st Edition by Nuno F Azevedo, Carina Almeida – Ebook PDF Instant Download/Delivery: 1071611178 ,9781071611173
Full download Fluorescence In Situ Hybridization FISH for Microbial Cells Methods and Concepts 1st Edition after payment

Product details:

ISBN 10: 1071611178
ISBN 13: 9781071611173
Author: Nuno F Azevedo, Carina Almeida

Fluorescence In Situ Hybridization FISH for Microbial Cells Methods and Concepts 1st Edition Table of contents:

Chapter 1: An Introduction to Fluorescence in situ Hybridization in Microorganisms
1 Introduction
2 Parameters Involved in a FISH Method
2.1 Fixation/Permeabilization
2.2 Hybridization and Washing
2.2.1 The Target RNA
2.2.2 The Probes
2.2.3 The Hybridization Solution
2.2.4 Washing
2.3 Visualization/Detection
3 Conclusions
References
Chapter 2: FISH Variants
1 Introduction
2 FISH Variants
2.1 CARD-FISH
2.2 Gene-FISH
2.3 Phage-FISH
2.4 MAR-FISH
2.5 FISH-NanoSIMS
2.6 CLASI-FISH
2.7 DOPE-FISH
2.8 Leaf-FISH
2.9 Flow-FISH
2.10 Microfluidic-FISH
2.11 NAM-FISH
2.12 QD-FISH
3 Conclusions
References
Chapter 3: Bioinformatic Tools and Guidelines for the Design of Fluorescence In Situ Hybridization Probes
1 Introduction
2 Materials
2.1 Probe Design/Selection
2.1.1 Databases for the Selection of Sequences of Interest of Microorganisms
2.1.2 Software for Multiple Sequence Alignment
2.1.3 Web-Based Resources for the Probe Design/Selection
2.2 Theoretical Probe Evaluation
2.2.1 Databases for the Evaluation of the Theoretical Specificity and Sensitivity
2.2.2 Databases for the Melting Temperature and Gibbs Free Energy Change Determination
2.2.3 Tools for the Evaluation of Secondary Structures
2.2.4 Tools for the Evaluation of Self-Complementary Regions Within Probes
2.3 Database of Existing rRNA-Targeted Oligonucleotide Probes
3 Methods
3.1 Probe Design/Selection Using Sequence Alignment
3.2 Web-Based Resources for the Probe Design/Selection
3.3 Theoretical Probe Evaluation
3.4 Applying Nucleic Acid Mimics on Probe Design
3.4.1 PNA Probes
3.4.2 LNA and 2 ́OMe Probes
4 Notes
References
Chapter 4: FISH in Suspension or in Adherent Cells
1 Introduction
2 Materials
2.1 Reagents for Sample fixation and Dehydration
2.2 Reagents for Coating Microscope Slides
2.3 Reagents for In Situ Hybridization
2.4 Equipment
2.5 Additional Reagents and Equipment for FISH on Planktonic Communities (Membrane Filters)
2.6 Additional Reagents and Equipment for FISH on Soil Samples
3 Methods
3.1 Fixation of Cells
3.1.1 Fixation of Gram-Negative Cells
3.1.2 Fixation of Gram-Positive Cells
3.2 Coating of Microscope Slides
3.2.1 Coating with Gelatin
3.2.2 Coating with Poly-L-Lysine
3.3 Application of Samples to Slides and Dehydration of Fixed Samples
3.4 In Situ Hybridization
3.5 Mounting Slides
3.6 Viewing Slides and Quantification of Microorganisms
4 FISH on Planktonic Cells
4.1 Fixation and Dehydration of Planktonic Samples
4.2 Hybridization of Cells on Membrane Filters
5 FISH on Soil Samples
5.1 Sample Fixation
5.2 Cell Extraction from Soil Samples
6 Notes
References
Chapter 5: Application of Nucleic Acid Mimics in Fluorescence In Situ Hybridization
1 Introduction
2 Materials
3 Methods
3.1 Reconstitution and Storage of Probes
3.2 Preparation of Samples for the FISH Procedure on a Surface
3.2.1 Pure or Enriched Samples
3.2.2 Histological Samples
3.3 Fixation and Permeabilization
3.3.1 Cells Adhered to Surfaces
3.3.2 Procedure in Suspension
3.4 Hybridization
3.4.1 Cells Adhered to Surfaces
3.4.2 Cells in Suspension
3.5 Analysis of the Samples by Epifluorescence Microscopy
3.6 Analysis of the Samples by Flow Cytometry
4 Notes
References
Chapter 6: Delivery of Oligonucleotides into Bacteria by Fusogenic Liposomes
1 Introduction
2 Materials
2.1 Lipoplexes
2.2 Fluorescence In Situ Hybridization (FISH)
3 Methods
3.1 Preparation of Liposomes and Lipoplexes
3.2 PEGylation of Lipoplexes
3.3 Fluorescence In Situ Hybridization (FISH)
4 Notes
References
Chapter 7: Characterization of Social Interactions and Spatial Arrangement of Individual Bacteria in MultiStrain or Multispeci…
1 Introduction
2 Materials
2.1 Biofilm Formation
2.2 Biofilm Fixation and Permeabilization
2.3 Hybridization
2.4 Microscopy Analysis
3 Methods
3.1 Coupon Preparation
3.2 Biofilm Formation
3.3 Biofilm fixation and Permeabilization
3.4 Hybridization
3.5 Confocal Laser Scanning Microscopy
3.6 Image Analysis
4 Notes
References
Chapter 8: Leaf-FISH: In Situ Hybridization Method for Visualizing Bacterial Taxa on Plant Surfaces
1 Introduction
2 Materials
2.1 Plant Material
2.2 Fixation
2.3 Pigment Removal
2.4 Hybridization
3 Methods
3.1 Plant Tissue Preparation
3.2 Fixation
3.3 Pigment Removal
3.4 Hybridization
3.5 Image Acquisition and Analysis
3.6 Linear Unmixing
3.7 Image Composition
3.8 Quantification of Bacterial Losses During Leaf Fixation Method
4 Notes
5 Conclusions
References
Chapter 9: CAtalyzed Reporter Deposition Fluorescence In Situ Hybridization (CARD-FISH) for Complex Environmental Samples
1 Introduction
2 Materials
2.1 Sample Preparation, Fixation, and Permeabilization
2.2 Hybridization and Washing
2.3 Tyramide Signal Amplification
2.4 Counterstaining and Microscopic Visualization
2.5 Other General Equipment/Materials
3 Methods
3.1 Fixation
3.2 Filtration
3.3 Embedding
3.4 Prehybridization (Optional)
3.5 Permeabilization
3.6 Endogenous Peroxidase Inactivation
3.7 Hybridization
3.8 Washing
3.9 Tyramide Signal Amplification
3.10 Final Washing
3.11 DAPI Counterstaining
3.12 Microscope Visualization and Quantification
4 Notes
References
Chapter 10: Fluorescence In Situ Hybridization with Quantum Dot Labels in E. coli Cells
1 Introduction
2 Materials
2.1 Reagents and Buffers
2.2 Special Equipment
3 Methods
3.1 Conjugation of Streptavidin to Dibenzylcyclooctyne
3.2 Conjugation of Streptavidin to Quantum Dots
3.3 Gel Electrophoresis of Streptavidin-Quantum Dot Conjugates
3.4 Grow, Fix, and Permeabilize E. coli Cells
3.5 Stain E. coli Cells through QD-FISH
3.6 Imaging and Data Analysis
3.7 Photostability Analysis
4 Notes
References
Chapter 11: Monitoring Bacteriophage Infection on Bacterial Cells Using FISH
1 Introduction
2 Materials
2.1 Design and Theoretical Evaluation of the Phage Probes
2.2 Bacteria Growth and Phage Infection
2.3 Fixation and Hybridization Procedures
2.4 Sample Analysis
3 Methods
3.1 Design and Theoretical Evaluation of the Phage Probes
3.2 Theoretical Adaptation for LNA Probes
3.3 Bacteria Growth and Phage Infection
3.3.1 Fixation and Hybridization of a Sample in Suspension
3.3.2 Fixation and Hybridization of a Sample in a Support
3.4 Specificity and Sensitivity of LNA Probes
3.5 LNA-FISH Validation in Infected Cells
4 Notes
References
Chapter 12: Linking Microbes to Their Genes at Single Cell Level with Direct-geneFISH
1 Introduction and General Considerations
1.1 Probe Design
1.2 Determination of Hybridization Parameters
1.3 Probe Synthesis
1.4 The “Core ́ ́ Direct-geneFISH Protocol
1.5 Microscopy and Data Analysis
2 Materials
2.1 Stock Solutions and Chemicals
2.2 Working Solutions
2.3 Glass and Plasticware
2.4 Laboratory Equipment
2.5 Software
3 Methods
3.1 Gene Probe Design
3.1.1 Design of Multiple Polynucleotides Along a Single Gene or Gene Region
3.1.2 Design of Polynucleotides Targeting Multiple Alleles of the Same Gene
3.2 Determination of Hybridization Parameters
3.2.1 Oligonucleotide Probes
3.2.2 Polynucleotide Probes
3.2.3 Simultaneous Hybridization with rRNA-Targeting Oligonucleotide Probes and Gene-Targeting Polynucleotide Probes
3.3 Gene Probe Synthesis
3.3.1 Synthesis of Double-Stranded DNA Polynucleotides by PCR
3.3.2 Chemical Synthesis of Double-Stranded DNA Polynucleotides
3.3.3 Chemical Labeling
3.3.4 Calculation of the Probe Concentration and Labeling Ratio
3.4 The “Core ́ ́ Direct-geneFISH Protocol: For Filters
3.4.1 Fixation and Immobilization on Filters
3.4.2 Permeabilization
3.4.3 Denaturation and Hybridization
3.4.4 Counterstaining and Embedding
3.5 The “Core ́ ́ Direct-geneFISH Protocol: For Microscopy Slides
3.5.1 Fixation and Immobilization on Microscopy Slides
3.5.2 Permeabilization
3.5.3 Denaturation and Hybridization
3.5.4 Counterstaining and Embedding
3.6 Microscopy and Image Analysis
3.6.1 Image Acquisition
3.6.2 Image Processing: Cell Counts and Calculation of Relative Abundances
3.6.3 Image Processing: Quantification of the Number of Target Genes per Cell
4 Notes
References
Chapter 13: Assigning Function to Phylogeny: FISH-nanoSIMS
1 Introduction
2 Materials
2.1 Chemicals and Solutions
2.2 Laboratory Equipment
2.3 Other General Materials
3 Methods
3.1 Cell Fixation and Filtration
3.2 CARD-FISH
3.3 Laser Microdissection (LMD) Marking and Epifluorescence Microscopy
3.4 nanoSIMS
4 Notes
References
Chapter 14: Assigning Function to Phylogeny: MAR-FISH
1 Introduction
2 Materials
2.1 Sample Collection, Incubation, Washing, and Immobilization on Slides
2.2 Darkroom Materials
3 Methods
3.1 Sample Collection
3.2 Incubation Considerations
3.3 Incubations
3.4 Microscopic Visualization
4 Notes
References
Chapter 15: Counting mRNA Copies in Intact Bacterial Cells by Fluctuation Localization Imaging-Based Fluorescence In Situ Hybr…
1 Introduction
2 Materials
2.1 FISH Probe Preparation
2.2 Cell Fixation
2.3 Hybridization and Imaging
2.4 Microscope
3 Methods
3.1 FISH Probe Preparation
3.2 Bacterial Cell Fixation
3.3 Cell Hybridization with FISH Probes
3.4 Fluorescence Imaging
3.5 fliFISH Analysis
4 Notes
References
Chapter 16: Integration of FISH and Microfluidics
1 Introduction
1.1 Modern Microfluidics Fabrication
1.2 Microfluidics in Diagnostics: Microorganism Detection and Disease Management
2 Materials
3 Methods
3.1 Cell Culture and FISH
3.2 Device Design, Microfabrication, and Testing
3.3 PNA-FISH Within the Microchannel
3.4 Conclusion
4 Notes
References
Chapter 17: Flow-FISH Using Nucleic Acid Mimic Probes for the Detection of Bacteria
1 Introduction
2 Materials
3 Methods
3.1 Reconstitution and Storage of Probes
3.2 Procedure in Suspension
3.3 Flow cytometry Analysis
4 Notes
References
Chapter 18: FISH in Food Samples
1 Introduction
2 Materials
2.1 Sampling
2.2 Sample Pre-Enrichment
2.3 Sample Pre-Treatment (Optional-See Note 5)
2.4 FISH Procedure
2.5 Sample Analysis
3 Methods
3.1 Sampling
3.2 Sample Pre-Enrichment
3.3 Sample Pre-Treatment
3.3.1 Standard Pre-Treatment
3.3.2 Pre-Treatment for Matrices with High-Lipid Content
3.3.3 Pre-Treatment for Matrices with High-Protein Content
3.3.4 Pre-Treatment for Matrices with High Protein and Lipid Content
3.4 FISH Procedure
3.5 Sample Analysis
4 Notes
References
Chapter 19: Extraction of Microbial Cells from Environmental Samples for FISH Approaches
1 Introduction
2 Materials
3 Methods
3.1 Environmental Samples
3.2 Sample Homogenization
3.2.1 Sample Homogenization Using Shaking/Vortexing
3.2.2 Sample Homogenization Using Sonication
3.2.3 Sample Homogenization Using a Waring Blender
3.3 Histodenz Density Gradient Centrifugation
3.4 Sample Storage
3.5 Preparation of Stored Cells for FISH
3.5.1 Optional: Ethanol Dehydration Series
4 Notes
References
Chapter 20: Quality Control in Diagnostic Fluorescence In Situ Hybridization (FISH) in Microbiology
1 Introduction
1.1 Pre-Analysis for FISH
2 Sample Preparation for FISH
2.1 Sample Fixation and Embedding
2.2 FISH Probe Selection
2.3 FISH Probe Labeling
2.4 FISH Probe Optimization
3 FISH Analysis
4 Epifluorescence Microscopy
5 Interpretation of FISH Results
6 Documentation of FISH Assay, Results, and Assessment
7 Summary
8 Outlook
References
Chapter 21: Computational Resources and Strategies to Construct Single-Molecule Models of FISH
1 Introduction
2 Methods
2.1 Literature Search
2.1.1 Defining the Simulation Environment
2.1.2 Defining the Agents
2.1.3 Defining the Interactions Between Agents
2.2 Simulation
2.3 Model Validation
3 Practical Example on the Construction of an ABM on FISH
4 Notes
References
Index

People also search for Fluorescence In Situ Hybridization FISH for Microbial Cells Methods and Concepts 1st Edition:

fluorescence in situ hybridization fish for microbial cells
    
what is fish fluorescence in situ hybridization
    
fluorescence in situ hybridization (fish) analysis
    
fluorescence in situ hybridization applications
    
fluorescence in situ hybridization and microarrays

Tags: Nuno F Azevedo, Carina Almeida, Fluorescence, Situ Hybridization FISH, Microbial Cells