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This manual reflects practical approaches to handling bacteria in the labora tory. It is designed to recall historical methods of bacterial genetics that have had recent developments and to present new techniques that allow full genome analysis. It has been written for microbiologists who need to group their protocols at the state of the art of a new millennium and also for scientists in other fields of life sciences who need to use bacteria for their research. Teachers, graduate students, and postdocs also will benefit from having these protocols to help them understand modern bacterial genetics. I learned so much from these contributions from my colleagues that I have no doubt about the daily usefulness of this book. April 2002 Michel Blot XII Abbreviations Acyl-HSL N-acyl homoserine lactone moi multiplicity of infection Amp or Ap ampicillin N amino C carboxy NMR nuclear magnetic resonance CIO-HSL N-decanoyl-L-homoserine lactone 3-0H-C14:1-HSL N-(3-hydroxy-7 -cis-tetra- C12-HSL N-dodecanoyl-L-homoserine lac- decanoyl)homo-serine lactone tone 3-0H-C4-HSL N-3-hydroxybutanoyl-L- C14-HSL N-tetradecanoyl-L-homoserine homoserine lactone lactone ONPG o-nitrophenyl ~-D-galactopyranoside C4-HSL N-butanoyl-L-homoserine lactone ORF open reading frame C6-HSL N-hexanoyl-L-homoserine lactone OTG I-S-octyl-~-D-thioglucoside C8-HSL N-octanoyl-L-homoserine lactone 3-oxo-CIO-HSL N-3-oxodecanoyl-L-homo- Cam or Cm chloramphenicol serine lactone CBD chitin binding domain 3-oxo-C12-HSL N-3-oxododecanoyl-L CHEF contour clamped homogenous electric homoserine lactone field 3-oxo-C14-HSL N-3-oxotetradecanoyl-L CI consistency index homoserine lactone CRIM conditional-replication, integration, 3-oxo-C4-HSL N-3-oxobutanoyl-L-homoser and modular ine lactone dCTP deoxycytidine triphosphate 3-oxo-C6-HSL N-3 -oxohexanoyl-L-homoser deg.
List of contents
1 Physical Analysis of Chromosome Size Variation.- 2 Genetic Mapping in Salmonella enterica.- 3 Insertion Sequences as Genomic Markers.- 4 The Use of Noncoding Microsatellite Length Analysis for Bacterial Strain Typing.- 5 How to Amplify Easily, on the Bacterial Chromosome, a Desired DNA Sequence.- 6 Generalized Transduction.- 7 Use of Conditional-replication, Integration, and Modular CRIM Plasmids to Make Single-copy lacZ Fusions.- 8 Genetic Footprinting for Bacterial Functional Genomics.- 9 Gene Transfer to Plants through Bacterial Vectors.- 10 Quorum Sensing: Approaches to Identify Signals and Signalling Genes in Gram-negative Bacteria.- 11 Transcriptional Profiling in Bacteria Using Microarrays.- 12 Transcriptome Analysis by Macroarrays.- 13 Prokaryotic Proteomics.- 14 Intein-mediated Protein Purification.- 15 Two-hybrid Assay in Escherichia coli K12.- Guide to Protocols.
