Note: Front Cover -- Automation: Genomic and Functional Analyses -- Copyright Page -- Contents -- Contributors -- Foreword -- Introduction -- Chapter 1. Automation in Clinical Microbiology -- Chapter 2. Vision Systems for Automated Colony and Plaque Picking -- Chapter 3. Library Picking, Presentation and Analysis -- Chapter 4. The PREPSEQ Robot: An Integrated Environment for Fully Automated -- Chapter 5. Building Realistic Automated Production Lines for Genetic Analysis -- Chapter 6. Examples of Automated Genetic Analysis Developments -- Chapter 7. Deciphering Genomes Through Automated Large-scale Sequencing -- Chapter 8. DNA Arrays for Transcriptional Profiling -- Chapter 9. Large-scale Phenotypic Analysis in Microtitre Plates of Mutants with Deleted Open Reading Frames from Yeast Chromosome III: Key-step Between Genomic Sequencing and Protein Function -- Chapter 10. Automatic Analysis of Large-scale Pairwise Alignments of ProteinSequences -- Chapter 11. Towards Automated Prediction of Protein Function from Microbial Genomic Sequences -- Index.

Note: Intro -- Contents -- Contributors -- Foreword -- Preface -- 1 Mechanisms of Antigenic Variation: an Overview -- Random 'unprogrammed' variation -- Programmed antigenic variation: general principles -- Recombinational mechanisms of antigenic variation -- In situe activation of surface antigen genes by altering the size of simple DNA repeats or by DNA modification -- Gene families controlled without detectable DNA alternations -- As a survival strategy, programmed antigenic variation is not as simple as it looks -- Unsolved problems and challenges -- 2 HIV Variation - a Question of Signal-to-Noise -- The HIV lentiviruses -- Mutation, recombination and fixation rates -- A touch of 'flu -- An inside look at HIV replication -- Tempo of HIV replication -- Gulliver and HIVland -- Rampant recombination -- If not by mutation, how does HIV persist? -- In vivo most viral variation is basically noise -- 3 Calicivirus -- Clinical, antigenic and genetic variability -- Antigenic structure of the capsid -- Virus evolution -- Conclusion -- 4 Influenza - the Chameleon Virus -- X-ray crystallography of influenza haemagglutinin -- Genetic variation of the haemagglutinin -- X-ray crystalography of influenza neuraminidase -- The biological properties of antibody to influenza HA -- Are T cells responses important in the immune response to influen za HA? -- The practical consequences of antigenic change in HA and NA: pandemics and epidemics -- The conflicting theories of the origin of pandemic influenza -- The 1918/19 great pandemic of influenza A and subsequent outbreaks in humans caused by influenza A/swine (H1N1) virus -- The 1957 'Asian' influenza pandemic -- The vanishing pandemic virus -- The 'Hong Kong' virus pandemic and the period 1968-2003 -- A curiosity and a warning: reappearance of a influenza A (H1N1) virus in 1977. , Nucleotide sequence analysis of the influenza HA gene from samples from the great 1918 pandemic -- Could the human infections in Hong Kong in 1997 with avian influenza A viruses warn of a new pandemic? -- Biological factors which drive antigenic drift of HA -- Would influenza vaccine viruses replicated in MDCK cells ratehr than eggs be more immunogenic? -- Conclusions -- 5 Rotavirus -- Virus classification and structure -- Antigens and epidemiological markers -- Pathogensis and immunity -- 6 Haemophilus i nfluenzae -- Capsule phase variation -- Phase variation mediated by simple nucleotide repeats -- Phase variation by modulation of transcription -- Phase variation mediated by tetranucleotide repeats -- Factors influencing the rate of phase variation -- 7 Phase Variation in Helicobacter Pylori l ipopolysaccaride -- H pylori LPS expresses blood group antigens -- Phase variation in H pylori LPS Lewis antigens -- Biological role of LPS phase variation -- Lewis antigen mimicry and immune evasion -- H pylori LPS phase variation and bacterial adhesion -- 8 Genetic Variation in Pathogenic Neisseria Species -- Genetic diversity and evolutionary adaptability of Neisseria species -- Rapid micro-environmental adaptation -- Molecular models for pilE variation -- Genetic variation via the illegitimate route -- Functional significance of genetic variation -- 9 Candida albicans -- The discovery of switching in C albicans -- The white-opaque transition -- The white-opaque transition affects the budding yeast cell morphology -- Antigenic chagnes in the white-opaque transition -- Switching involves differential gene expression -- A contextual framework for investigating the mechamisms of gene regulation during switching -- Phase-specific trans-acting factors -- Possible switching mechanisms -- Gross chromosomal rearrangements are not the basis of switching. , The deacetylases play a role in the suppression of switching -- Heat-induced mass conversion and a model for switching -- The role of C albicans switching in pathogenesis -- Switching in C glabrata -- Phase varation in the fungi: general lessons and summary -- 10 The MSG Gene Family and Antigenic Variation in the Fucus Pneumocystis carinii -- P carinii is one species in a large fungal genus -- P carinii and laboratory rats -- P carinii has a gene family that confers the potential for antigenic variation -- The MSG gene family is expressed in a way that could cause antigenic variation -- Translation and transport of MSG probably involves the UCS -- A protease family appears to have co-evolved with the MSG family -- A third gene family closely related to MSG -- Expression of a specific MSG is correlated with the presence of its cognate gene at the UCS locus -- MSG and antigenic variation -- On the possibility that the MSG gene family does not cause antigenic variation -- Conclusion -- 11 Trypanosome Antigenic Variation - a Heavy Investment in the Evasion of Immunity -- Biology of antigenic variation -- VSG genes and the genome -- DNA recombination as the main driver of antigenic variation -- Transcription control of metacyclic VSGS -- Secondary phenotypes associated with antigenic variation -- Conclusion -- 12 Antigenic Variation in Anaplasma marginale and Ehrlichia (Cowdria) ruminatium -- Phylogentic re-classification of A marginale and C ruminantium -- Disease pathogenesis -- Anaplasma marginale -- Ehrlichia (Cowdria) ruminantium -- Discussion and conclusion -- 13 Antigenic Variation and its Significance to Babesia -- The phenotype of antigenic variation in Babesia bovis -- Probable mechanism of antigenic variation in B bovis -- Association of antigenic variation with pathology -- Future directions. , 14 Antigenic Variation in Plasmodium falciparum and Other Plasmodium Species -- Antigenic variation of infected red blood cells -- Phenotypic/antigenic variation of merozoites -- Antigenic diversity, another way of increasing the repertoire of genes -- Conclusions -- 15 Antigenic Variation in Borrelia: Relapsing Fever and Lyme Borreliosis -- Ecology and epidemiology -- Clinical manifestations and pathology -- Morphology and physiology -- Phylogeny and genetics -- Pathogenesis -- Immunity -- Variable antigens -- Evolution of variable antigens -- Mechanisms of antigenic variation -- 16 Surface Antigenic Variation in Giardia lamblia -- Characteristics of antigenic variation in vitro -- Characteristics of variant-specific surface proteins -- Biology of variant-specific proteins -- Role of immune and biological selection -- Molecular mechanisms -- 17 Free-living and Parasitic Ciliates -- Paramecium variable surface antigens -- I-antigens in the context of infection and immunity -- 18 The Impact of Antigenic Variation on Pathogen Population Structure, Fitness and Dynamics -- Influence of antigenic variation on pathogen fitness -- Inter-strain competition and epidemiological constraints on diversity -- Control of antigenically variable pathogens -- Conclusions -- Appendix: model details -- Index.