Genomics, proteomics and vaccines /

Preface p. xi
List of contributors p. xix
Part 1 Introduction
1 Vaccination: Past, Present and Future Maria Lattanzi and Rino Rappuoli p. 3
1.1 Introduction p. 3
1.2 Vaccination: the past p. 4
1.3 Vaccination: the present p. 6
1.4 Vaccination: the future p. 12
1.5 Conclusion: the intangible value of vaccination p. 14
References p. 15
2 Bioinformatics, DNA Microarrays and Proteomics in Vaccine Discovery: Competing or Complementary Technologies? Guido Grandi p. 23
2.1 Introduction p. 23
2.2 From genome sequence to vaccine discovery p. 25
2.3 A case study: the anti-meningococcus B vaccine p. 28
2.4 Comparison of the three approaches p. 34
2.5 Conclusions: a 'nomics' approach to vaccine discovery p. 37
References p. 40
Part 2 Technologies
3 Genome Sequencing and Analysis Herve Tettelin and Tamara Feldblyum p. 45
3.1 Introduction p. 45
3.2 Genome sequencing p. 46
3.3 Genome analysis p. 60
3.4 Conclusion p. 65
References p. 65
4 Understanding DNA Microarrays: Sources and Magnitudes of Variances in DNA Microarray Data Sets She-pin Hung and Suman Sundaresh and Pierre F. Baldi and G. Wesley Hatfield p. 75
4.1 Introduction p. 75
4.2 DNA array formats p. 76
4.3 Data analysis methods p. 79
4.4 Sources and magnitudes of noise in DNA microarray experiments p. 84
4.5 Conclusions p. 97
Acknowledgements p. 100
References p. 100
5 The Proteome, Anno Domini Two Zero Zero Three Pier Giorgio Righetti and Mahmoud Hamdan and Frederic Reymond and Joel S. Rossier p. 103
5.1 Introduction p. 103
5.2 Some definitions p. 105
5.3 What methods exist to tackle the proteome complexity? p. 107
5.4 Quantitative proteomics p. 112
5.5 Pre-fractionation in proteome analysis p. 117
5.6 Multi-dimensional chromatography p. 120
5.7 Protein chip arrays p. 123
5.8 Imaging mass spectrometry p. 126
Acknowledgements p. 127
References p. 127
6 Mass Spectrometry in Proteomics Pierre-Alain Binz p. 135
6.1 Introduction p. 135
6.2 MS technology p. 136
6.3 Principle of protein identification based on MS data p. 147
6.4 Proteomics workflows p. 155
References p. 155
7 High Throughput Cloning, Expression and Purification Technologies Andreas Kreusch and Scott A. Lesley p. 171
7.1 Introduction p. 171
7.2 Gene cloning p. 172
7.3 Protein expression p. 174
7.4 High-throughput protein purification p. 175
7.5 Validation of the pipeline and outlook p. 178
7.6 Conclusion p. 179
References p. 180
Part 3 Applications
8 Meningococcus B: from Genome to Vaccine Davide Serruto and Rino Rappuoli and Mariagrazia Pizza p. 185
8.1 Meningococcus, a major cause of bacterial meningitis p. 185
8.2 Group B meningococcus as an example of reverse vaccinology p. 190
8.3 Conclusions p. 200
References p. 201
9 Vaccines Against Pathogenic Streptococci John L. Telford and Immaculada Margarit y Ros and Domenico Maione and Vega Masignani and Herve Tettelin and Giuliano Bensi and Guido Grandi p. 205
9.1 Introduction p. 205
9.2 Comparative genomics of streptococci p. 206
9.3 A vaccine against group B streptococcus p. 208
9.4 A vaccine against group A streptococcus p. 215
9.5 Conclusions p. 218
References p. 219
10 Identification of the 'Antigenome'--a Novel Tool for Design and Development of Subunit Vaccines Against Bacterial Pathogens Eszter Nagy and Tamas Henics and Alexander von Gabain and Andreas Meinke p. 223
10.1 Introduction p. 223
10.2 Small DNA insert libraries--a tool to cover a pathogen's 'antigenome' p. 227
10.3 Proper display platforms p. 230
10.4 Selected human sera to provide imprints of pathogen encounters p. 231
10.5 Cognate antibodies reveal the 'antigenome' of a pathogen p. 234
10.6 How to retrieve from the 'antigenome' the candidate antigens for vaccine development p. 235
10.7 Summary and discussion p. 237
References p. 239
11 Searching the Chlamydia Genomes for New Vaccine Candidates Giulio Ratti and Oretta Finco and Guido Grandi p. 245
11.1 Old problems and new perspectives for chlamydial vaccines p. 245
11.2 Post-genomic approaches p. 250
11.3 Genomic screening results p. 251
11.4 Concluding considerations p. 262
References p. 263
12 Proteomics and Anti-Chlamydia Vaccine Discovery Gunna Christiansen and Svend Birkelund and Brian B. Vandahl and Allan C Shaw p. 267
12.1 Introduction p. 267
12.2 Proteome analysis p. 269
12.3 Proteomics as a complement for genomics p. 277
12.4 Benefits that proteomics provide for vaccine development p. 279
References p. 280
13 Proteome Analysis of Outer Membrane and Extracellular Proteins from Pseudomonas aeruginosa for Vaccine Discovery Stuart J. Cordwell and Amanda S. Nouwens p. 285
13.1 Introduction p. 285
13.2 Membrane proteins in P. aeruginosa p. 286
13.3 Extracellular proteins in P. aeruginosa p. 292
13.4 Immunogenic proteins and vaccine discovery p. 296
13.5 Conclusions p. 298
References p. 299
Index p. 305