Fluorescence In-Situ Hybridization (FISH) for Microbial Cells Methods and Concepts

This volume provides a comprehensive review of concepts and protocols related to fluorescence in situ hybridization (FISH) applied to microbial cells. Chapters will serve guide for the design of new probes and the development of novel FISH-based protocols.  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,  Fluorescence In Situ Hybridization (FISH) for Microbial Cells: Methods and Concepts aims to ensure successful results in the further study of this vital field.

1. An Introduction to Fluorescence in situ Hybridization in Microorganisms

Carina Almeida and Nuno F. Azevedo

2. FISH Variants

Nuno M. Guimarães, Nuno F. Azevedo, and Carina Almeida

3. Bioinformatic Tools and Guidelines for the Design of Fluorescence in situ Hybridization Probes

Helena Teixeira, Ana L. Sousa, and Andreia S. Azevedo

4. FISH in Suspension or in Adherent Cells

Francesca Di Pippo, Diogo Queirós, Joana Pereira, Paulo C. Lemos, Luísa S. Serafim, and Simona Rossetti

5. Application of Nucleic Acid Mimics in Fluorescence in situ Hybridization

Ricardo Oliveira, Andreia S. Azevedo, and Luzia Mendes

6. Delivery of Oligonucleotides into Bacteria by Fusogenic Liposomes

Sara Pereira, Rita S. Santos, Luís Moreira, Nuno M. Guimarães, Kevin Braeckmans, Stefaan C. De Smedt, and Nuno F. Azevedo

7. Characterisation of Social Interactions and Spatial Arrangement of Individual Bacteria in Multi-Strain or Multispecies Biofilm Systems using Nucleic acid mimics-Fluorescence in situ Hybridization

Jontana Allkja and Andreia S. Azevedo

8. Leaf-FISH: In Situ Hybridization Method for Visualizing Bacterial Taxa on Plant Surfaces

Elena L. Peredo, and Sheri Simmons

9. CAtalyzed Reporter Deposition Fluorescence In Situ Hybridization (CARD-FISH) for Complex Environmental Samples

Bruna Matturro, Simona Rossetti, and Patrícia Leitão

10. Fluorescence in Situ Hybridization with Quantum Dot Labels in E. coli Cells

Yang Liu, Zhiyuan Han, Suresh Sarkar, and Andrew M. Smith

11. Monitoring Bacteriophage Infection on Bacterial Cells using FISH

Diana Vilas-Boas and Luís D. R. Melo

Jimena Barrero-Canosa and Cristina Moraru  

Katharina Kitzinger, Daniela Tienken, Sten Littmann, Abiel T. Kidane, Marcel M. M. Kuypers, and Jana Milucka

14. Assigning Function to Phylogeny: MAR-FISH

Jeppe L. Nielsen

15. Counting mRNA Copies in Intact Bacterial Cells by Fluctuation Localization Imaging-based Fluorescence in situ hybridization (fliFISH)

Dehong Hu, Yi Cui, Lye M. Markillie, William B. Chrisler, Qian Wang, Roland Hatzenpichler, and Galya Orr

16. Integration of FISH and Microfluidics

Célia F. Rodrigues, Nuno F. Azevedo, and João M. Miranda

17. Flow-FISH using Nucleic Acid Mimic Probes for the Detection of Bacteria

Andreia S. Azevedo, Rui Rocha, and Nicolina Dias

18. FISH in Food Samples

Rui Rocha, Carina Almeida, and Nuno F. Azevedo

19. Extraction of Microbial Cells from Environmental Samples for FISH Approaches

20. Quality Control in Diagnostic Fluorescence In Situ Hybridization (FISH) in Microbiology

21. Computational Resources and Strategies to Construct Single-Molecule Models of FISH

Beatriz T. Magalhães, Rita S. Santos, Nuno F. Azevedo, and Anália Lourenço