Keywords:
Pathogenic microorganisms.
;
Microbiology.
;
Electronic books.
Type of Medium:
Online Resource
Pages:
1 online resource (618 pages)
Edition:
1st ed.
ISBN:
9783527607518
URL:
https://ebookcentral.proquest.com/lib/geomar/detail.action?docID=481330
DDC:
579.165
Language:
English
Note:
Intro -- Pathogenomics -- Foreword -- Contents -- Preface -- List of Contributors -- Color Plates -- I Methods -- 1 Bioinformatics: Data Mining Among Genome Sequences -- 1.1 Systematic Genome Analysis of Pathogens as a Basis for Pharmacogenomic Strategies -- 1.2 Direct Sequence Annotation Tools for Functional Genomics -- 1.3 Identification of Protein Function -- 1.4 Obtaining Protein Information from a Domain Server -- 1.5 Pathway Analysis -- 1.6 Network Analysis -- 1.7 Adaptation in Time and to Stimuli -- 1.7.1 Experimental Design for Microarray Analysis -- 1.7.2 Data Analysis -- 1.8 Pathogen-Specific Challenges -- 1.9 Pathogen Adaptation Potential -- 1.10 The Fight Against Resistance -- 1.11 Drug Design and Antibiotics -- 1.12 Annotation Platforms Suitable for Pathogenomics -- 1.13 Conclusions -- 2 Transcriptome Analysis: Towards a Comprehensive Understanding of Global Transcription Activity -- 2.1 Introduction -- 2.2 Development of Transcriptomics -- 2.2.1 From Genomics to Functional Genomics -- 2.2.2 From Gene to Whole Genome -- 2.3 Introducing the Microarray -- 2.3.1 What Is a Microarray? -- 2.3.2 The Affymetrix Gene Chip -- 2.3.3 The Spotted Microarray -- 2.4 Microarray Methods -- 2.4.1 Experimental Design -- 2.4.1.1 Type of Experiment -- 2.4.1.2 Replicates -- 2.4.2 RNA Extraction -- 2.4.3 Labeling/Reverse Transcription -- 2.4.4 Hybridization -- 2.4.5 Scanning -- 2.5 Data Normalization and Analysis -- 2.5.1 Image Quantification -- 2.5.2 Data Processing -- 2.5.3 Data Analysis -- 2.5.3.1 Detection of Differential Expression -- 2.5.3.2 Pattern Recognition -- 2.5.3.3 Graphical Representations -- 2.5.6 Microarray Analysis Tools -- 2.5.7 Microarray Follow-Up -- 2.5.8 Data Storage and Reanalysis -- 2.6 Transcriptomics: Where We Are Now and What's to Come.
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3 Physiological Proteomics of Bacillus subtilis and Staphylococcus aureus: Towards a Comprehensive Understanding of Cell Physiology and Pathogenicity -- 3.1 Introduction -- 3.2 Proteomics of Bacillus subtilis: The Gram-positive Model Organism -- 3.2.1 The Vegetative Proteome -- 3.2.2 Proteomes of Nongrowing Cells: Proteomic Signatures of Stress/Starvation Stimuli -- 3.3 Physiological Proteomics of Staphylococcus aureus -- 3.3.1 The Postgenome Era of S. aureus -- 3.3.2 Proteomes of Growing and Nongrowing Cells -- 3.3.3 Extracellular Proteins and Pathogenicity Networks -- 3.4 Outlook: Second Generation Proteomics and New Fields in S. aureus Physiology and Infection Biology -- 4 Impact of Genome Sequences on Mutational Analysis of Fungal and Bacterial Pathogens -- 4.1 The Long Road from Sequence to Function -- 4.2 Classical Genetics Still at the Forefront in the Postgenome Era -- 4.2.1 Reverse Genetics -- 4.2.2 Transposon Mutagenesis -- 4.3 Genome-Scale Mutational Analyses -- 4.3.1 Saccharomyces cerevisiae -- 4.3.2 Bacterial Workhorses: E. coli and Bacillus subtilis -- 4.3.3 Bacterial Pathogens -- 4.3.3.1 Mycoplasma Species -- 4.3.3.2 Pseudomonas aeruginosa -- 4.3.3.3 Staphylococcus aureus -- 4.3.3.4 Neisseria meningitidis -- 4.4 Conclusion -- II Genomics of Pathogenic Bacteria -- 5 Pathogenomics of Escherichia coli and Shigella Species -- 5.1 Introduction -- 5.2 Comparative Genomics of Shigella -- 5.3 Comparative Genomics of Escherichia coli -- 5.3.1 Comparison of Complete Genome Sequences -- 5.3.2 Comparative Genomics Using DNA Arrays -- 5.3.3 Mobile Genetic Elements and Evolution of Pathogenic E. coli -- 5.3.4 Genomic Islands/Pathogenicity Islands -- 5.3.5 Plasmids and Bacteriophages -- 5.3.6 Genetic Diversity Among Extraintestinal Pathogenic E. coli -- 5.4 Conclusions -- 6 Pathogenomics of Salmonella Species -- 6.1 Introduction.
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6.2 Salmonella Signature Genes -- 6.3 Subspecies I Signature Genes -- 6.4 Host Restriction -- 7 Pathogenomics of Enterococcus faecalis -- 7.1 Introduction -- 7.2 Enterococcal Pathogenesis -- 7.3 Genome Sequence of E. faecalis -- 7.3.1 Mobile Elements, Acquired DNA, and Antimicrobial Resistance -- 7.3.2 Environmental Adaptation and Stress Response -- 7.3.3 Survival In Vivo -- 7.3.4 Potential Virulence Factors -- 7.3.4.1 Hemolysins, Proteases, and other Enzymes -- 7.3.4.2 Cell-Wall-Associated Virulence Factors -- 7.3.5 Pathogenicity Island of E. faecalis -- 7.4 Conclusions and Future Perspectives -- 8 Genomics of Streptococci -- 8.1 Introduction -- 8.2 Bacterial Genomes -- 8.2.1 Pyogenic Group -- 8.2.1.1 Streptococcus pyogenes -- 8.2.1.1.1 Virulence Factors -- 8.2.1.1.2 Horizontal Gene Transfer -- 8.2.2.1 Streptococcus agalactiae -- 8.2.2.2 Group C (GCS) and Group G Streptococci -- 8.2.2.3 Streptococcus uberis -- 8.2.2 Bovis Group -- 8.2.2.1 Streptococcus bovis and Streptococcus suis -- 8.2.3 Mitis Group -- 8.2.3.1 Streptococcus pneumoniae -- 8.2.3.2 Streptococcus mitis, Streptococcus sanguis, and Streptococcus gordonii -- 8.2.4 Anginosus and Salivarius Group -- 8.2.4.1 Streptococcus salivarius -- 8.2.4.2 Streptococcus thermophilus -- 8.2.5 Mutans Group -- 8.2.5.1 Streptococcus mutans and Streptococcus sobrinus -- 8.2.6 Other Organisms: Enterococcus faecalis -- 8.2.7 Comparative Genomics -- 8.3 Streptococcal Genomic Bacteriophages -- 8.3.1 Prophages and Streptococcal Genomes -- 8.3.2 GAS Genome Prophages -- 8.3.2.1 Prophages and Virulence Factors -- 8.3.2.2 Prophage Attachment Sites and Host Biology -- 8.3.2.3 Prophage Diversity -- 8.3.3 Prophages Associated with other Streptococcal Species -- 9 Pathogenic Staphylococci: Lessons from Comparative Genomics -- 9.1 Introduction -- 9.2 Comparative Genomics of S. aureus -- 9.2.1 Overall Genome Structure.
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9.2.2 Core Genome -- 9.2.2.1 Metabolism -- 9.2.2.2 Information Pathways -- 9.2.2.3 Virulence Factors -- 9.2.3 Accessory Genome -- 9.2.3.1 Pathogenicity Islands -- 9.2.3.2 Staphylococcal Cassette Chromosome -- 9.2.3.3 Bacteriophages -- 9.2.3.4 Plasmids -- 9.3 Staphylococcus epidermidis -- 9.3.1 Genomic Islands -- 9.3.2 Phage SPβ and other Bacillus Genes -- 9.3.3 Virulence Factors -- 9.3.4 Staphylococcal Cassette Chromosome -- 9.3.5 Adherence and Biofilm Formation -- 9.3.6 Insertion Sequences -- 9.4 Concluding Remarks -- 10 Pathogenomics: Insights into Tuberculosis and Related Mycobacterial Diseases -- 10.1 Introduction -- 10.2 Molecular Basis of Pathogenicity -- 10.3 Evolution of the M. tuberculosis Complex -- 10.4 Some Metabolic Insight from the Genome Sequences -- 10.5 Other Major Mycobacterial Human Pathogens -- 10.5.1 Mycobacterium leprae -- 10.5.2 Mycobacterium ulcerans -- 10.6 Concluding Remarks -- 11 Genomes of Pathogenic Neisseria Species -- 11.1 Introduction -- 11.2 Genomes of Pathogenic Neisseria Species -- 11.2.1 The Flexible Genome Pool -- 11.2.2 Repetitive DNA Sequence Elements Govern Neisserial Biology -- 11.2.2.1 DNA Uptake Sequences, Horizontal Gene Transfer, and Antigenic Diversity -- 11.2.2.2 Simple Sequence Repeats and Phase Variation -- 11.2.2.3 Insertion Sequences and the Regulation of Gene Expression -- 11.2.3 Genome-Wide Mutational Analyses -- 11.2.4 Comparative Genomics -- 11.2.5 Novel Virulence Factors of Meningococci Identified by Genomic Approaches -- 11.3 Future Perspectives -- 12 Genomics of Pathogenic Clostridia and Bacilli -- 12.1 Genomics of Pathogenic Clostridia spp. -- 12.1.1 Introduction -- 12.1.2 C. perfringens -- 12.1.3 C. tetani -- 12.1.4 C. botulinum -- 12.1.5 C. difficile -- 12.1.6 Conclusions and Perspectives -- 12.2 Genomics of Pathogenic Bacilli -- 12.2.1 Introduction.
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12.2.2 Pathogenic Properties of Bacilli not Belonging to the B. cereus Group -- 12.2.3 Pathogenicity of B. cereus -- 12.2.4 Pathogenicity of B. anthracis -- 12.2.4.1 Course of Anthrax -- 12.2.4.2 Virulence Factors of B. anthracis -- 12.2.5 Genome of B. anthracis -- 12.2.5.1 Chromosomal Genes -- 12.2.5.2 Genes Located on Plasmids pXO1 and pXO2 -- 12.2.5.3 Regulation of Virulence Genes -- 12.2.5.4 Molecular Diversity in B. anthracis Genomes -- 12.2.5.5 Genome of a Highly Virulent B. cereus Strain Resembling B. anthracis in Pathogenesis -- 12.2.6 Comparison of B. cereus Group Genomes: How Did Pathogenicity Evolve? -- 13 The Genomes of Pathogenic Bartonella Species -- 13.1 Introduction -- 13.1.1 Bartonella in a Phylogenetic Context -- 13.1.2 Hosts and Vectors for Bartonella Species -- 13.2 Bartonella Species and Pathogenicity -- 13.2.1 Infection of Reservoir and Incidental Host -- 13.2.2 Bartonella Species as Human Pathogens -- 13.3 The Bartonella Genomes -- 13.4 Genomic Islands and Phages -- 13.5 Genomic Islands and Phages in Bartonella Species -- 13.5.1 The B. henselae Prophage -- 13.5.2 B. henselae Genomic Islands and Islets -- 13.5.3 B. quintana Harbors Remnants of the B. henselae Islands -- 13.5.4 Role of Phages and Islands in the Evolution of Bartonella -- 13.6 The Chromosome II-Like Segment in Bartonella -- 13.6.1 Type IV Secretion Systems in Bartonella Species -- 13.6.2 The virB-D4 Operon -- 13.6.3 The trw Operon -- 13.7 B. quintana's Evolution into a Human Pathogen -- 13.8 Conclusions and Future Perspectives -- 14 Pathogenomics of Gastric and Enterohepatic Helicobacter Species -- 14.1 Introduction -- 14.2 Helicobacter pylori -- 14.2.1 Key Features of the H. pylori Genome Related to Pathogenesis -- 14.2.1.1 Colonization Factors: Urease and Motility -- 14.2.1.2 Phase Variation -- 14.2.1.3 The H. pylori Outer Membrane Protein Family.
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14.2.1.4 Intraspecies Variation of H. pylori Genomes.
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