Pseudomonas Methods and Protocols

ISBN-13: 9781493944163 / Angielski / Miękka / 2016 / 816 str.

Alain Filloux; Juan-Luis Ramos

Opis

In Pseudomonas aeruginosa, expert researchers in the field detail many of the methods which are now commonly used to study this fascinating microorganism. Chapters include microbiological methods to high-throughput molecular techniques that have been developed over the last decade. 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 key tips on troubleshooting and avoiding known pitfalls.Authoritative and practical, Pseudomonas aeruginosa aids in the continuing study of new and cutting edge findings.

Spis treści

Part I: BASIC PSEUDOMONAS FEATURES

1. Gene Transfer: Transduction

Emanuela Frangipani

2. Gene Transfer: Transformation/Electroporation

Frédéric Cadoret, Chantal Soscia and  Romé Voulhoux

3. Gene transfer: Conjugation

Thibault G. Sana, Aurélie Laubier and Sophie Bleves

4. Pseudomonas Bacteriophage Isolation and Production

Joana Azeredo, Sanna Sillankorva, and  Diana Priscilla Pires

5. Genotyping Methods

Burkhard Tuemmler

6. Drug Susceptibility Testing by Dilution Methods

Katy Jeannot & Patrick Plesiat

7. Plate-based Assay for Swimming Motility in Pseudomonas aeruginosa

Dae-Gon Ha, Sherry L. Kuchma & George A. O’Toole

8. Plate-based Assay for Swarming Motility in Pseudomonas aeruginosa

Dae-Gon Ha, Sherry L. Kuchma  and  George A. O’Toole

9. Motility Assay: Twitching Motility

Lynne Turnbull and Cynthia B. Whitchurch

10. Qualitative and Quantitative Assays for Flagellum-mediated Chemotaxis

José-Antonio Reyes-Darias, Cristina García-Fontana, Andrés Corral Lugo, Miriam Rico-Jiménez & Tino Krell

11. Microscopic Analysis: Morphotypes and Cellular Appendages

Olga Zaborina, John Alverdy, Megha Shah, and Yimei Chen

Part II: PROTEINS AND PROTEIN TRANSPORT

12. Determination of Lipolytic Activities

Karl-Erich Jaeger and Filip Kovacic

13. Elastinolytic and Proteolytic Enzymes

Contributors: Efrat Kessler and  Mary Safrin

14. In vitro Assays to Monitor the Activity of Pseudomonas aeruginosa Type III Secreted Proteins

Stéphanie L. Rolsma & Dara W. Frank

15. Cell Fractionation

Bérengère Ize, Véronique Viarr, and  Romé Voulhoux

16. Characterization of Molecular Interactions using Isothermal Titration Calorimetry

Tino Krell, Jesús Lacal, Cristina Garcia-Fontana, Hortencia Silva-Jimenez, Miriam Rico-Jimenez, Andrés Corral Lugo, Jose A. Reyes Darias, and  Juan Luis Ramos

17. Proteomic Analysis

Pascal Cosette and  Thierry Jouenne

18. Membrane Proteomics of Pseudomonas aeruginosa

Zofia Magnowska, Isabel Hartmann, Lothar Jänsch and Dieter Jahn

19. Construction of Pseudomonas Two-hybrid Libraries for High-throughput Assays

Sophie de Bentzmann and Christophe Bordi

Part III: SMALL MOLECULES AND POLYSACCHARIDES

20. Biosensors for Qualitative and Semi-quantitative Analysis of Quorum Sensing Signal Molecules

Matthew Fletcher, Miguel Camara, David A. Barrett, and Paul Williams

21. LC-MS/MS Quantitative Analysis of Quorum Sensing Signal Molecules

Catherine A. Ortori, Nigel Halliday, Miguel Camara, Paul Williams, and David A. Barrett

22. LC/MS/MS-Based Quantitative Assay for the Secondary Messenger Molecule, c-di-GMP

Yasuhiko Irie  and Matthew R. Parsek

23. Metabolic Footprinting: Extracellular Metabolomic Analysis

Volker Behrends, Huw D. Williams, and  Jaco G. Bundy

24. Pyoverdine and Pyochelin Measurements

Françoise Hoegy, Gaetan L. A. Mislin & Isabelle J. Schalk

25. Measurement of Phenazines in Bacterial Cultures

Suzanne E. Kern, and Dianne K. Newman

26. Extraction and Measurement of NAD(P)⁺ and NAD(P)H

Suzanne E. Kern, Alexa Price-Whelan, and Dianne K. Newman

27. Cyanide Measurements in Bacterial Culture and Sputum

 Chandrika Goh Nair, Ben Ryall, and Huw D. Williams

28. Monitoring Iron Uptake by Siderophores

Françoise Hoegy, and Isabelle J. Schalk

29. Exopolysaccharide Quantification

Irina Sadovskaya

30. Liquid Chromatography/Mass Spectrometry for the Identification and Quantification of Rhamnolipids

Ahmad Mohammad Abdel-Mawgoud, François Lépine & Eric Déziel

31. LPS quantitation Procedures

Joseph S. Lam, Erin M. Anderson, and Youai Hao

32. Monitoring Lectin Interaction with Carbohydrates

Sophie de Bentzmann, Annabelle Varrot, and Anne Imberty

Part IV: PSEUDOMONAS GENES and GENE EXPRESSION

33. Mining the Pseudomonas Genome

Geoffrey L. Winsor and  Fiona S. L. Brinkman

34. Identification of Bacterial Small RNAs by RNA Sequencing

Maria Gomez-Lozano, Rasmus Lykke Marvig, Soeren Molin, and  Katherine S. Long

35. Gene Amplification and qRT-PCR

Cerith Jones and Alain Filloux

36. The Standard European Vector architecture (SEVA) plasmid toolkit

Gonzalo Durante-Rodriguez, Victor de Lorenzo and Esteban Martinez-Garcia

37. Chromosomal integration of transcriptional fusions

Rafael Silva-Rocha and Victor de Lorenzo

38. A Method to Capture Large DNA Fragments from Genomic DNA

Geneviève Ball, Alain Filloux, and  Romé Voulhoux

39. Transposon Mutagenesis

Hemantha D. Kulasekara and Bridget R. Kulasekara

40. Site-directed Mutagenesis and Gene Deletion using Reverse Genetics

Contributors: Daniela Muhl and  Alain Filloux

41. Signature Tagged Mutagenesis

 Irena-Kukavika-Ibrulj & Roger Levesque

42. Construction of a Pseudomonas aeruginosa Genomic Bank

Christophe Bordi

43. Strategy for Genome Sequencing Analysis and Assembly for Comparative Genomics of Pseudomonas Genomes

Julie Jeukens, Brian Boyle, Nicholas P. Tucker, and Roger Levesque

44. Promoter Fusions with Optical Outputs in Individual Cells and in Populations

Ilaria Benedetti and  Victor de Lorenzo

45. Chromatin Immunoprecipitation for ChIP-chip and ChIP-Seq

Contributors: Sebastian Schulz  and Susanne Haussler

46. Transcriptional Analysis of Pseudomonas aeruginosa Infected C.aenorhabditis elegans

Ashleigh MacKenzie, Lewis Stewart, Paul A. Hoskisson and Nicholas P. Tucker

Part V: LIFESTYLES AND INFECTION MODELS

47. Methods for Studying Biofilm Formation: Flow Cells and Confocal Laser Scanning Microscopy

Tim Tolker-Nielsen and Claus Sternberg

48. Biofilm Formation in the 96-well Microtiter Plate

Barbara M. Coffey and  Gregory G. Anderson

49. Methods for Studying Biofilm Dispersal in Pseudomonas aeruginosa

Contributors: Nicolas Barraud, Joana A. Moscoso, Jean Marc Ghigo, and  Alain Filloux

50. Pseudomonas aeruginosa PA14 Pathogenesis in Caenorhabditis Elegans

Natasha V. Kirienko, Brent O. Cezairliyan, Frederick M. Ausubel and  Jennifer R. Powell

51. Assessing Pseudomonas Virulence using a Non-mammalian Host Model: Dictyostelium Discoideum

Geneviève Filion and  Steve Charette

52. Assessing Pseudomonas virulence with non-mammalian host: Galleria mellonella

Gudrun Koch, Pol Nadal Jimenez, Robbert H. Cool &Wim J. Quax

53. Assessing Pseudomonas Virulence with the Non-mammalian Host: Arabidopsis Thaliana

Regina L. Baldini, Melissa Starkey, and Laurence G. Rahme

54. Assessing Pseudomonas aeruginosa Persister/Antibiotic Tolerant Cells

Ronen Hazan, Damien Maura, Yok-Ai Que & Laurence G. Rahme

55. Assessing Pseudomonas Virulence with Non-mammalian Host: Zebrafish

Maria A. Llamas and  Astrid M. van der Sar

56. Assessing Pseudomonas Virulence with a Non-mammalian Host: Drosophila Melanogaster

Samantha Haller, Stefanie Limmer, and Dominique Ferrandon

57. Assessing Pseudomonas Virulence using Host Cells

Iwona Bucior, Cindy Tran, and  Joanne Engel

58. Assessing Pseudomonas aeruginosa  Virulence and the Host Response using Murine Models of Acute and Chronic Lung Infection

Irena Kukavica-Ibrulj, Marcella Facchini, Cristina Cigina, Roger Levesque & Alessandra Bragonzi

59. Assessing Pseudomonas Virulence using Mammalian Models: Acute Infection Model

Antje Munder and  Burkhard Tuemmler

60. Burn Mouse Models

Henrik Calum, Niels Hoiby and Claus Moser