Genomics, Proteomics and Vaccines

Cover -- Contents -- Preface -- List of contributors -- PART 1: INTRODUCTION -- 1 Vaccination: Past, Present and Future -- 1.1 Introduction -- 1.2 Vaccination: the past -- 1.3 Vaccination: the present -- 1.4 Vaccination: the future -- 1.5 Conclusion: the intangible value of vaccination -- References -- 2 Bioinformatics, DNA Microarrays and Proteomics in Vaccine Discovery: Competing or Complementary Technologies? -- 2.1 Introduction -- 2.2 From genome sequence to vaccine discovery -- 2.3 A case study: the anti-meningococcus B vaccine -- 2.4 Comparison of the three approaches -- 2.5 Conclusions: a nomics' approach to vaccine discovery -- References -- PART 2: TECHNOLOGIES -- 3 Genome Sequencing and Analysis -- 3.1 Introduction -- 3.2 Genome sequencing -- 3.3 Genome analysis -- 3.4 Conclusion -- References -- 4 Understanding DNA Microarrays: Sources and Magnitudes of Variances in DNA Microarray Data Sets -- 4.1 Introduction -- 4.2 DNA array formats -- 4.3 Data analysis methods -- 4.4 Sources and magnitudes of noise in DNA microarray experiments -- 4.5 Conclusions -- Acknowledgements -- References -- 5 The Proteome, Anno Domini Two Zero Zero Three -- 5.1 Introduction -- 5.2 Some definitions -- 5.3 What methods exist to tackle the proteome complexity? -- 5.4 Quantitative proteomics -- 5.5 Pre-fractionation in proteome analysis -- 5.6 Multi-dimensional chromatography -- 5.7 Protein chip arrays -- 5.8 Imaging mass spectrometry -- Acknowledgements -- References -- 6 Mass Spectrometry in Proteomics -- 6.1 Introduction -- 6.2 MS technology -- 6.3 Principle of protein identification based on MS data -- 6.4 Proteomics workflows -- References -- 7 High Throughput Cloning, Expression and Purification Technologies -- 7.1 Introduction -- 7.2 Gene cloning -- 7.3 Protein expression -- 7.4 High-throughput protein purification -- 7.5 Validation of the pipeline and outlook -- 7.6 Conclusion -- References -- PART 3: APPLICATIONS -- 8 Meningococcus B: from Genome to Vaccine -- 8.1 Meningococcus, a major cause of bacterial meningitis -- 8.2 Group B meningococcus as an example of reverse vaccinology -- 8.3 Conclusions -- References -- 9 Vaccines Against Pathogenic Streptococci -- 9.1 Introduction -- 9.2 Comparative genomics of streptococci -- 9.3 A vaccine against group B streptococcus -- 9.4 A vaccine against group A streptococcus -- 9.5 Conclusions -- References -- 10 Identification of the Antigenome' ... a Novel Tool for Design and Development of Subunit Vaccines Against Bacterial Pathogens -- 10.1 Introduction -- 10.2 Small DNA insert libraries ... a tool to cover a pathogen's antigenome' -- 10.3 Proper display platforms -- 10.4 Selected human sera to provide imprints of pathogen encounters -- 10.5 Cognate antibodies reveal the antigenome' of a pathogen -- 10.6 How to retrieve from the antigenome' the candidate antigens for vaccine development -- 10.7 Summary and discussion -- References -- 11 Searching the Chlamydia Genomes for New Vaccine Candidates -- 11.1 Old problems and new perspectives for chlamydial vaccines -- 11.2 Post-genomic