Note: e9780123977632v1 -- Front Cover -- Molecular Medical Microbiology, Volume 1 -- Copyright Page -- Contents -- List of Contributors -- Preface -- Preface to the First Edition -- 1 Molecular Medical Microbiology - The Expanding Concept -- A Brief History -- Molecular Medical Microbiology -- References -- 1 Bacterial Structure -- 2 Bacterial Ultrastructure -- General Morphology -- Surface Appendages -- Flagella -- Pili and Fimbriae -- Glycocalyx -- Capsules -- S-layers -- Cell Wall -- Gram-Negative Cell Walls -- Outer Membrane -- Periplasm and Peptidoglycan Gel -- Gram-Positive Cell Walls -- Peptidoglycan Layer and Periplasmic Gel -- Cell Wall Growth -- Cytoplasmic Membrane -- Nucleoid -- Cytoplasmic Inclusions -- Non-Membrane Inclusions -- Volutin Granules -- Polysaccharide Granules -- Non-Unit Membrane Inclusions -- Carboxysomes -- Lipid Bodies -- Gas Vesicles -- Photosynthetic Systems -- Cell Division -- Bacterial Conjugation -- Bacterial Sporulation -- Bacterial Germination -- Bacterial Biofilms -- Microscopy and Microbiology -- Acknowledgements -- References -- 3 Bacterial Capsules -- Introduction -- Chemistry of Capsules -- Primary Structures -- Secondary Structures -- Other Properties of CPSs -- Genetics of Capsular Biosynthesis -- Gram-Negative Bacteria -- Gram-Positive Bacteria -- Biosynthesis of Capsules -- Wzy-Dependent Polymerization -- ABC Transporter-Dependent Polymerization -- Synthase-Dependent Polymerization -- Attachment of Bacterial Capsules to the Cell Surface -- Regulation of Capsular Synthesis -- Modulation at the DNA Level -- Modulation at the Transcriptional Level -- Biological Functions of Capsules -- Capsules as a Virulence Factor -- Capsules as an Immune Evasion Factor -- Immunogenicity of CPSs as Vaccine Antigens -- Acknowledgements -- References -- 4 Genetics and Biosynthesis of Lipopolysaccharide -- Overview. , Classical Pathway of Lipid A-Kdo2 Biosynthesis -- Biosynthesis of Lipid IVA -- LpxA -- LpxC -- LpxD -- LpxBH -- LpxK -- Incorporation of Kdo Residues -- Late Acyltransferases -- Biosynthesis and Assembly of the Core Oligosaccharide -- Kdo and Ko -- Heptoses -- Isomerization -- Phosphorylation -- Phosphatase Reaction -- Synthesis of Nucleotide-Activated Heptose -- ADP-L-glycero-D-manno-Heptose-6-Epimerase -- Glycosyltransferases -- Enzymes Involved in the Completion of the Inner Core -- Assembly of the Outer Core -- Remodelling of the Lipid A-Inner Core Oligosaccharide -- Modification of the Lipid A Phosphate Groups -- Removal of Phosphate Groups -- Covalent Modifications of Phosphates -- Modification of Lipid A Acyl Chains -- Kdo Modifications -- Heptose Modifications -- Biosynthesis and Assembly of OAg -- Initiation -- Polyisoprenyl-Phosphate N-Acetylaminosugar-1-Phosphate Transferases -- Polyisoprenyl-Phosphate Hexose-1-Phosphate Transferases -- Assembly of OAg -- Wzy-Dependent O Antigen Assembly Pathway -- Und-PP-O Antigen Translocation -- Polymerization and Chain Length Regulation -- ABC Transporter-Dependent Pathway -- Synthase-Mediated Pathway -- O Antigen Ligation -- Synthesis and Recycling of Und-PP -- Export of LPS to the Outer Membrane -- Lipid A-Core Export Across the Inner Membrane -- Transport of LPS Across the Periplasm to the Cell Surface -- Acknowledgements -- References -- 5 Teichoic Acids, Lipoteichoic Acids and Other Secondary Cell Wall and Membrane Polysaccharides of Gram-Positive Bacteria -- Structure of Wall Teichoic Acids and their Attachment to the Cell Wall -- Structure and Properties of Lipoteichoic Acids -- The Cellular Roles of Teichoic Acids -- The Biological Activities of Wall Teichoic Acids -- Biological Activities of Lipoteichoic Acids -- Adhesion -- Cytokine Induction -- Nitric Oxide Induction. , Soluble Teichoic Acids In Vivo -- Genetics and Regulation of Anionic Polymer Synthesis -- Acknowledgement -- References -- 6 Peptidoglycan -- Introduction -- The Basic Chemical Structure of Peptidoglycan -- The Glycan Strands in Peptidoglycan -- The Stem Peptides in Peptidoglycan -- Peptide Cross-Links -- Variation of the Fine Structure -- Biophysical Properties of Peptidoglycan -- Thickness of Peptidoglycan -- Elasticity of Sacculi -- Pores in the Sacculus -- Architecture of Peptidoglycan -- Peptidoglycan Biosynthesis and Modifications -- Cytoplasmic Steps to UDP-MurNAc Pentapeptide -- Synthesis of the Lipid-Linked Precursor -- Variation in Lipid II Structure -- Peptidoglycan Synthases -- Peptidoglycan Hydrolases -- Secondary Modifications in the Peptidoglycan Structure -- Covalent Attachment of Secondary Cell Wall Polymers to Peptidoglycan -- Covalent Attachment of Proteins to Peptidoglycan -- Peptidoglycan Synthesis During the Cell Cycle -- Peptidoglycan Synthesis Complexes Active in Cell Elongation and Division -- Molecular Mechanism of Peptidoglycan Growth: The 3-for-1 Growth Model -- Regulation of Peptidoglycan Growth from the Inside and Outside -- Acknowledgements -- References -- 7 Flagella -- Flagellar Function -- Rate of Rotation -- Tumbling -- Energy Source -- Flagellar Structure -- Filament -- Flagellin (Hag or FliC) -- Phase Variation -- Filament Structure -- Filament Helicity -- Polymorphism -- Calladine Model -- Flagella Family -- Hook -- Universal Joint -- Hook Length Control -- Hook Protein -- Hook-Associated Proteins -- Basal Body -- The LP Ring Complex -- Rod -- The MS Ring Complex -- The C Ring -- C Rod -- Chaperones -- The Mot Proteins -- Assembly System of Flagella -- Morphogenesis -- Distal Growth -- Cap Proteins -- Export Apparatus -- Type III Secretion System -- Flil ATPase Activity -- Switching of the Export Gate. , Morphological Pathway -- In the Cytoplasm -- In the Periplasmic Space -- Outside the Cell -- Origin of Flagella -- Type III Secretion System -- F0F1-ATPase -- Conclusion -- Acknowledgement -- References -- 8 Pili and Fimbriae of Gram-Negative Bacteria -- Introduction -- Chaperone-Usher Pathway Pili -- CUP Pilus Architecture -- Subunit Structure -- Assembly Proteins and Mechanisms -- Periplasmic Chaperones -- The Chaperone Necessity -- Conserved Chaperone Surfaces and Donor Strand Complementation -- Donor Strand Exchange -- Ushers -- Functions of the Usher Domains in Pilus Assembly -- Usher Selectivity and Potential Binding Surfaces -- Current Model of Chaperone-Usher Pilus Biogenesis at the Usher -- Structural Insights into the Growing Pilus -- Pore-Gating Mechanisms of Usher -- Alternative Chaperone-Usher Pathways -- Diversity of CUP Systems in Disease -- Different Pilus Systems Involved in Adhesion and Disease -- Curli: Extracellular Nucleation/Precipitation Pathway -- Interfering With the Pilus -- References -- 9 Endospores, Sporulation and Germination -- Endospore Structure and Resistance -- Endospore Formation -- Endospore Germination -- Endospore Germination as a Therapeutic Target -- Endospore Detection -- Endospore-Based Technology -- Endospore-Borne Diseases -- Anthrax -- Bacillus cereus Syndromes -- Tetanus -- Botulism -- Clostridium sordellii and Toxic Shock Syndrome -- Clostridium difficile Infections (CDI) -- Clostridium perfringens Infections -- Opportunistic Infections -- Acknowledgements -- References -- 2 Bacterial Cell Function -- 10 Bacterial Growth, Culturability and Viability -- Introduction -- Bacterial Growth -- Patterns of Growth and Sources of Information -- Molecular Information Related to Bacterial Growth -- Ribosomal RNA -- Chromosome Replication -- Cell Division -- Global Regulatory Proteins -- Growth and Stasis. , Exponential Phase -- Exponential Phase Inocula: A Key Resource in Bacteriology -- Stress Responses -- Stationary Phase -- Dormancy and Sporulation -- Exit from Dormant or Stationary Cellular States and Re-entry into Growth -- Asymmetric Cell Division -- Culturability and Viability -- Culturability -- 'As Yet Uncultured' (AYU) Bacteria -- Cells of Culturable Organisms That Are Not Recovered in Culture -- Viability -- The VBNC Controversy -- Conclusions -- References -- 11 Bacterial Energy Metabolism -- Introduction to Energy Metabolism -- Scope of Chapter -- Chemiosmosis -- ATPase -- Na+-ATPase -- Fermentation -- Fermentations of Sugars and Polysaccharides -- Fermentation Pathways -- Ethanol Fermentations -- Lactate Fermentations -- Mixed Acid Fermentations -- Butyrate Metabolism in the Human Gut -- Utilization of Complex Carbohydrates -- Starch Utilization -- Xylan Utilization -- Cellulose Degradation -- Aerobic Respiration -- Components of Respiratory Chains -- Cytochrome Oxidases -- Cytochrome caa3 Oxidases -- Cytochrome cbb3 Oxidases -- Cytochrome bo3 Oxidase -- Cytochrome bd Oxidase -- Anaerobic Respiration -- Denitrification -- The Reductases Involved in Denitrification -- Nitrate Reductase Nar and Nitrate/Nitrite Transporter NarK -- Nitrite Reductases -- Nitric Oxide Reductases -- Nitrous Oxide Reductases -- Fumarate and Trimethylamine Oxide Reductases -- Regulation of Aerobic and Anaerobic Metabolism -- The Requirement for Regulation of Aerobic and Anaerobic Energy Metabolism -- Basic Principles of Regulatory Systems in Bacteria -- NarX-NarL Two-Component System -- Regulation at the Global Level by a Two-Component System: ArcB-ArcA -- Fnr - a One-Component System -- Diversity of Bacterial Energy Metabolism Regulators -- Regulatory Networks -- Energy Metabolism of Selected Bacterial Pathogens -- Campylobacter jejuni -- Helicobacter pylori. , Neisseria gonorrhoeae and Neisseria meningitidis.

Note: 9780323899925v1_WEB -- Front Cover -- Molecular Medical Microbiology -- Copyright Page -- Contents -- List of contributors -- About the editors -- Preface -- 1 Molecular medical microbiology-from bench to bedside -- 1.1 The concept -- 1.2 The evolving concept -- 1.3 From bench to bedside -- References -- 1 Bacterial structure -- 2 Classification of medically important bacteria -- 2.1 Introduction -- 2.2 Basics of bacterial taxonomy -- 2.3 Gram-negative bacteria -- 2.3.1 Enterobacterales -- 2.3.1.1 Enterobacter spp -- 2.3.1.2 Klebsiella spp -- 2.3.1.3 Citrobacter spp -- 2.3.1.4 Escherichia and Shigella -- 2.3.1.5 Pseudomonas spp -- 2.3.1.6 Other glucose nonfermenting gram-negative bacilli -- 2.3.1.7 Acinetobacter spp -- 2.3.1.8 Burkholderia spp -- 2.4 Gram-positive bacteria -- 2.4.1 Mycobacterium -- 2.4.1.1 Staphylococci -- 2.4.1.2 Viridans group streptococci -- 2.5 Conclusion and summary -- References -- 3 Bacterial ultrastructure -- 3.1 Introduction -- 3.2 Overview of bacterial ultrastructures -- 3.3 Surface appendages -- 3.4 Flagella -- 3.5 Pili and fimbriae -- 3.6 Capsules and S-layers -- 3.7 Membrane vesicles -- 3.8 Bacterial cell walls -- 3.9 Gram-negative bacterial cell wall -- 3.10 Gram-positive bacterial cell walls -- 3.11 Mycobacteria -- 3.12 Cell wall-deficient bacteria -- 3.13 Cell walls of Archea and surface appendages -- 3.14 Cytoplasmic membrane -- 3.15 Nucleoid -- 3.16 Bacterial cell division -- 3.17 Cytoplasmic inclusions -- 3.18 Outlook -- References -- 4 Bacterial cell walls: peptidoglycan -- 4.1 Introduction -- 4.2 The basic chemical structure of peptidoglycan -- 4.2.1 The glycan strands in peptidoglycan -- 4.2.2 The stem peptides in peptidoglycan -- 4.2.3 Peptide cross-links -- 4.2.4 Variation of the fine structure -- 4.3 Biophysical properties of peptidoglycan -- 4.3.1 Thickness of peptidoglycan -- 4.3.2 Elasticity of sacculi. , 4.3.3 Pores in the sacculus -- 4.4 Architecture of peptidoglycan -- 4.5 Peptidoglycan biosynthesis and modifications -- 4.5.1 Cytoplasmic steps to UDP-MurNAc pentapeptide -- 4.5.2 Synthesis of the lipid-linked precursor -- 4.5.3 Variation in the lipid II structure -- 4.5.4 Peptidoglycan synthases -- 4.5.5 Peptidoglycan hydrolases -- 4.5.6 Secondary modifications in the peptidoglycan structure -- 4.6 Covalent attachment of secondary cell wall polymers to peptidoglycan -- 4.7 Covalent attachment of proteins to peptidoglycan -- 4.8 Peptidoglycan synthesis during the cell cycle -- 4.8.1 Peptidoglycan synthesis complexes active in cell elongation and division -- 4.8.2 Molecular mechanism of peptidoglycan growth: the 3-for-1 growth model -- 4.8.3 Regulation of peptidoglycan growth from the inside and outside -- Acknowledgments -- References -- 5 Bacterial capsules -- 5.1 Introduction -- 5.2 Chemical and structural properties of the capsules -- 5.2.1 Primary structures -- 5.2.2 Secondary structures -- 5.2.3 Other properties of capsular polysaccharides -- 5.3 Genetics of capsule biosynthesis -- 5.3.1 Gram-negative bacteria -- 5.3.2 Gram-positive bacteria -- 5.4 Biosynthesis of the capsules -- 5.4.1 Wzy-dependent polymerization -- 5.4.2 ABC transporter-dependent polymerization -- 5.4.3 Synthase-dependent polymerization -- 5.4.4 Attachment of bacterial capsules to the cell surface -- 5.5 Regulation of capsule production -- 5.5.1 Modulation at the DNA level -- 5.5.2 Modulation at the transcriptional level -- 5.5.3 Posttranscriptional regulation -- 5.5.4 Metabolic regulation -- 5.6 Biological functions of the capsules -- 5.6.1 Capsules as a virulence factors -- 5.6.2 Capsules as an immune evasion factor -- 5.6.3 Other functions of capsules -- 5.7 The capsules as targets for host immunity and therapeutics. , 5.7.1 Molecular recognition of bacterial capsules by host immune systems -- 5.7.2 Capsules as vaccine antigens -- 5.7.3 Capsules as therapeutic targets -- 5.8 Conclusion and prospect -- Acknowledgments -- References -- 6 Flagella -- 6.1 Flagellar function -- 6.1.1 Estimation of torque -- 6.1.2 Tumbling -- 6.1.3 Energy source -- 6.2 Flagellar structure -- 6.2.1 Filament -- 6.2.1.1 Flagellin (Hag or FliC) -- 6.3 Phase variation -- 6.4 Filament structure -- 6.5 Filament helicity -- 6.5.1 Polymorphism -- 6.6 Calladine model -- 6.6.1 Flagella family -- 6.7 Hook -- 6.7.1 Hook protein -- 6.7.2 Universal joint -- 6.7.3 Hook length control -- 6.8 Hook-associated proteins -- 6.8.1 Basal body -- 6.9 Rod -- 6.10 The LP ring complex -- 6.10.1 The MS ring complex -- 6.11 The cytoplasmic ring -- 6.12 Flagellar protein export apparatus -- 6.13 Chaperones -- 6.14 The Mot proteins -- 6.15 Assembly system of flagella -- 6.15.1 Morphogenesis -- 6.15.2 Distal growth -- 6.15.3 Cap proteins -- 6.16 Protein export apparatus -- 6.16.1 Type 3 secretion system -- 6.16.2 Substrate specificity switching -- 6.17 Morphological pathway -- 6.18 In the cytoplasm -- 6.19 In the periplasmic space -- 6.20 Outside the cell -- 6.21 Origin of flagella -- 6.21.1 Type 3 secretion system -- 6.21.2 FOF1-ATPase -- 6.22 Conclusion -- Acknowledgment -- References -- 7 Bacterial pili and fimbriae -- 7.1 Introduction -- 7.2 Chaperone-usher pathway pilus represented by type I fimbriae and P pilus of Escherichia coli -- 7.2.1 Structure of type I fimbriae and pili -- 7.2.2 Biogenesis model of type I fimbriae and P pili -- 7.2.3 Alternative chaperone/usher pathways -- 7.2.4 Regulation of type I fimbriae and P pili -- 7.2.5 Function of type I fimbriae and pili -- 7.3 Type IV fimbriae and P pilus -- 7.3.1 Structure and biogenesis of type IV fimbriae and pili. , 7.3.2 Regulation of type IV fimbriae and pili -- 7.3.3 Function of type IV fimbriae and pili -- 7.3.4 Type V pilus -- 7.3.5 Structure of type V fimbriae and pili -- 7.3.6 Biogenesis model of type V fimbriae and pili -- 7.3.7 Regulation of type V fimbriae and pili -- 7.3.8 Function of type V fimbriae and pili -- 7.4 Development of novel therapeutics via targeting the pilus biogenesis -- 7.5 Emerging themes and future directions -- Acknowledgment -- References -- 8 Endospores, sporulation, and germination -- 8.1 Introduction -- 8.2 Sporulation as a survival strategy -- 8.3 The endospore structure and resistance -- 8.4 Endospore formation -- 8.5 Spore awakening: germination -- 8.6 Endospore formers pathogens -- 8.7 Pathogenic spore formers control -- 8.8 Endospore detection -- 8.9 Endospore-based technology -- 8.9.1 Probiotics -- 8.9.2 Biocides -- 8.9.3 Biofuels and organic compounds -- 8.9.4 Bioparticles -- References -- 2 Bacterial cell function -- 9 Bacterial growth and cultivation -- 9.1 Introduction -- 9.2 Bacterial growth -- 9.2.1 Patterns of growth and sources of information -- 9.2.2 Molecular information related to bacterial growth -- 9.2.2.1 Ribosomal RNA -- 9.2.2.2 Chromosome replication -- 9.2.2.3 Cell division -- 9.2.2.4 Global regulatory proteins -- 9.2.3 Growth and stasis -- 9.2.3.1 Lag phase -- 9.2.3.2 Exponential phase -- 9.2.3.3 Stationary phase -- 9.2.3.4 Death phase -- 9.2.3.5 Exit from dormant or stationary cellular states and re-entry into growth -- 9.2.4 The Environmental factors that affect bacterial growth -- 9.2.4.1 Temperature -- 9.2.4.2 Oxygen -- 9.2.4.3 pH -- 9.2.4.4 Osmotic pressure -- 9.2.5 Unique growth forms: spores, biofilms, and persisters -- 9.3 Bacterial growth and antibiotics treatment -- 9.4 Bacterial cultivations -- 9.4.1 Historic perspective of cultivation -- 9.4.2 "As-yet-unculturable" bacteria. , 9.4.3 The renaissance of bacterial cultivation -- 9.4.3.1 Cocultivation -- 9.4.3.2 Community cultivation -- 9.4.3.3 In situ cultivation -- 9.4.3.4 Single-cell isolation and cultivation -- 9.4.3.5 High-throughput cultivation -- 9.4.3.6 Culturomics -- 9.5 Final remarks -- Acknowledgments -- References -- 10 Bacterial energy metabolism -- 10.1 Introduction -- 10.1.1 Scope of chapter -- 10.2 Fermentation -- 10.2.1 Bacterial fermentation of sugars -- 10.2.2 Bacterial ethanol fermentation -- 10.2.3 Bacterial lactate fermentation -- 10.2.4 Propionate fermentation -- 10.2.5 Bacterial organic acid fermentation -- 10.2.6 Bacterial biogas fermentation -- 10.2.7 Its role in human health -- 10.2.8 Industrial bacterial fermentation -- 10.2.8.1 Chemiosmosis -- 10.2.9 Complete steps of chemiosmosis and adenosine triphosphate synthesis -- 10.2.10 Adenosine triphosphate synthase -- 10.2.11 Evolutionary significance -- 10.2.11.1 Aerobic respiration -- 10.2.12 Glycolysis -- 10.2.13 Formation of acetyl-CoA -- 10.2.14 Tricarboxylic acid cycle -- 10.2.15 Pyruvate dehydrogenase complex -- 10.2.16 Citrate synthase -- 10.2.17 Isocitrate dehydrogenase -- 10.2.18 α-Ketoglutarate dehydrogenase complex -- 10.2.18.1 Anaerobic respiration -- 10.2.19 Nitrate respiration -- 10.2.20 Denitrification -- 10.2.21 Applications of denitrification -- 10.2.22 Sulfate respiration -- 10.2.23 Fumaric acid respiration -- 10.2.23.1 Metabolism of complex carbohydrates -- 10.2.24 Starch metabolism -- 10.2.25 Cellulose degradation -- 10.2.26 Lignin degradation -- 10.2.27 Xylan degradation -- 10.2.27.1 Energy metabolism in selected bacteria -- 10.2.28 Obligate aerobes -- 10.2.29 Obligate anaerobes -- 10.2.30 Facultative anaerobes -- 10.2.31 Microaerophile -- References -- 11 Biofilms, quorum sensing, and crosstalk -- 11.1 Communal behavior of bacteria -- 11.2 A conceptual overview of quorum sensing. , 11.3 Quorum signals and circuits.

Note: Cover -- Half-Title Page -- Title Page -- Copyright Page -- CONTENTS -- CONTRIBUTORS -- PREFACE -- Section I: NOVEL AND EMERGING TECHNOLOGIES -- 1. Nucleic Acid Amplification Methods Overview -- SIGNAL AMPLIFICATION TECHNIQUES -- bDNA -- Hybrid Capture -- Cleavase-Invader Technology -- TARGET AMPLIFICATION TECHNIQUES -- PCR -- Reverse Transcriptase-PCR -- Nested PCR -- Multiplex PCR -- Real-Time PCR -- dsDNA Binding Fluorescent Dyes -- Hydrolysis (TaqMan) Probes -- Dual Hybridization Probes -- Molecular Beacons -- Scorpion Probes -- Dark Quencher Probes -- Partially Double-Stranded Probes -- Melting Curve Analysis -- Digital PCR -- Transcription-Based Amplification Methods -- Strand Displacement Amplification -- Loop-Mediated Amplification -- Helicase-Dependent Amplification -- FUTURE DIRECTIONS -- REFERENCES -- 2. Application of Identification of Bacteria by DNA Target Sequencing in a Clinical Microbiology Laboratory -- METHODS: GENERAL CONSIDERATIONS -- DNA Preparation -- Amplification and Sequencing -- Controls -- Interpretation of Results -- SEQUENCING SOFTWARE -- Database Selection -- Criteria for Microorganism Identification -- Novel Organism Identification -- REPORTING RESULTS -- CONCLUSION -- REFERENCES -- 3. Microbial Whole-Genome Sequencing: Applications in Clinical Microbiology and Public Health -- THE CURRENT DIAGNOSTIC MICROBIOLOGY PARADIGM -- Culture, Identification, and Antimicrobial Susceptibility Testing of Bacterial Pathogens -- Epidemiological Typing and Detection of Virulence Determinants -- Identification of Other Pathogens -- NGS TECHNOLOGIES AND PLATFORMS -- Template Preparation -- Sequencing and Imaging -- Genome Alignment and Assembly -- CLINICAL AND RESEARCH APPLICATIONS OF NGS -- Global Evolutionary Studies -- Outbreak Investigation -- Detection and Surveillance of Antimicrobial Resistance. , Development of Novel Antibiotics -- Microbiome Analysis -- Viral WGS for Genotyping and Resistance Monitoring -- CONSIDERATIONS FOR IMPLEMENTATION OF WGS INTO CLINICAL PRACTICE -- THE FUTURE OF GENOMICS IN CLINICAL MICROBIOLOGY -- REFERENCES -- 4. Digital PCR and Its Potential Application to Microbiology -- SPECIFIC EXPERIMENTAL CONSIDERATIONS FOR dPCR -- Number of Partitions -- Reaction Volume -- Protocol Steps -- QUANTIFICATION BY dPCR -- SOURCES OF ERROR -- Variance -- Bias -- THE ABILITY OF dPCR TO PERFORM ACCURATE QUANTIFICATION -- POTENTIAL APPLICATIONS OF dPCR TO MICROBIAL RESEARCH AND DIAGNOSTICS -- CONSIDERATIONS FOR THE FUTURE -- CONCLUSION -- REFERENCES -- 5. Massively Parallel DNA Sequencing and Microbiology -- OVERVIEW OF METHODS -- METHODS BASED ON THE AMPLIFICATION OF SINGLE MOLECULES -- DNA FRAGMENT LIBRARIES -- PRE-ENRICHMENT OF PARTICULAR GENES AND "BARCODING" -- SEQUENCING CHEMISTRIES -- SINGLE-MOLECULE, LONG-READ DNA SEQUENCING TECHNOLOGY -- COMPARISON OF NGS PLATFORMS -- APPLICATION OF LONG-READ SEQUENCING TECHNOLOGY TO MICROBIOLOGY -- CONCLUDING REMARKS -- REFERENCES -- 6. Next-Generation Sequencing -- OVERVIEW OF NEXT-GENERATION SEQUENCING METHODS -- Roche 454 Pyrosequencing and SOLiD Sequencing -- Ion Torrent Sequencing -- Illumina Sequencing -- PacBio Sequencing -- Nanopore Sequencing -- DIFFERENCES BETWEEN NGS PLATFORMS -- Cost -- Read Length -- Sequencing Depth and Coverage -- Sequencing Quality -- OTHER NGS CONSIDERATIONS -- Sample Selection -- Disease and Host -- Sample Preparation Methods -- Sample Barcoding -- Library Preparation Methods -- Contamination -- NGS BIOINFORMATICS WORKFLOWS -- NGS APPLICATIONS -- Amplicon Sequencing -- Universal Bacterial Identification by 16S PCR -- UNIVERSAL EUKARYOTIC IDENTIFICATION BY 18S AND/OR ITS PCR -- Pathogen versus Commensal -- METAGENOMIC AND MICROBIOME ANALYSES. , TRANSCRIPTOME PROFILING -- INFECTIOUS DISEASE DIAGNOSTICS -- CLINICAL VALIDATION -- REGULATORY AND OTHER CONSIDERATIONS -- CONCLUSIONS AND PERSPECTIVE -- REFERENCES -- 7. Pathogen Discovery -- PATHOGEN DISCOVERY TECHNIQUES -- IMMUNOSCREENING -- REPRESENTATIONAL DIFFERENCE ANALYSIS -- TAXON-SPECIFIC CONSENSUS/ DEGENERATE PCR -- BACTERIAL IDENTIFICATION BY 16S PCR -- FUNGAL IDENTIFICATION BY CONSENSUS PCR -- VIRAL IDENTIFICATION BY CONSENSUS PCR -- RAP-PCR -- DNASE-SISPA -- DNA MICROARRAY -- VIDISCA -- DIRECT HIGH-THROUGHPUT SEQUENCING -- NGS -- 454 ROCHE -- ILLUMINA -- OTHER NGS PLATFORMS -- PARAMETERS DRIVING THE CHOICE OF NGS PLATFORM -- NGS BIOINFORMATICS WORKFLOWS -- METAGENOMICS -- CHALLENGES OF PATHOGEN DISCOVERY -- LABORATORY CONTAMINATION -- REAGENT CONTAMINATION -- METAGENOMICS LIMITATIONS -- CONCLUSIONS -- REFERENCES -- 8. Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for Microbial Identification in Clinical Microbiology -- SAMPLE PREPARATION -- MICROBIAL IDENTIFICATION -- ANTIMICROBIAL SUSCEPTIBILITY TESTING AND BACTERIAL TYPING -- MOLECULAR DIAGNOSTICS INCLUDING MS ANALYSES -- CLINICAL IMPACT -- COMPARATIVE AND TECHNICAL MULTICENTER STUDIES -- CONCLUSIONS AND FUTURE PERSPECTIVE -- REFERENCES -- 9. Multiplex Technologies -- MULTIPLEX HYBRIDIZATION -- MULTPLEX SIGNAL AMPLIFICATION -- MULTIPLEX AMPLIFICATION -- Endpoint Detection by Composition -- Endpoint Detection by Hybridization -- Real-Time Detection -- MICROARRAY TECHNOLOGIES -- Printed Microarrays -- In Situ Synthesized Microarrays -- Suspension Bead Arrays -- Diagnostic Challenges and Applications of Microarrays -- SUMMARY -- REFERENCES -- Section II: METAGENOMICS : IMPLICATIONS FOR DIAGNOSTICS -- 10. The Skin Microbiome: Insights into Potential Impact on Diagnostic Practice -- THE SKIN HABITAT -- OVERVIEW OF THE SKIN MICROBIOTA -- Bacteria -- Fungi. , Demodex Mites -- Viruses -- Acquisition and Early Colonization -- Topographical Diversity of Skin Microbiota -- Whole Metagenomic Shotgun Sequencing of Skin Microbiota -- DISORDERS CAUSED BY OR ASSOCIATED WITH SKIN MICROBIOTA -- Skin Disorders Caused by or Associated with Bacterial Microbiota -- Skin Disorders Caused by or Associated with Fungal Microbiota -- Skin Disorders Caused by or Associated with Viruses -- POTENTIAL CLINICAL DIAGNOSTIC APPLICATIONS OF THE SKIN MICROBIOME -- CONCLUSIONS -- REFERENCES -- 11. The Gastrointestinal Microbiome -- MICROBIOME CHARACTERIZATION -- LONGITUDINAL DEVELOPMENT OF THE GUT MICROBIOME -- ENTERIC PATHOGENS -- DIET, OBESITY, AND THE GUT MICROBIOME -- THE IMPACT OF ANTIBIOTIC TREATMENT ON GASTROINTESTINAL BACTERIA -- GASTROINTESTINAL DISEASE -- THE GUT-BRAIN-MICROBIOME AXIS -- THE EFFECT OF PROBIOTICS ON THE GUT MICROBIOME -- MANIPULATING THE MICROBIOME VIA FECAL MICROBIOTA TRANSPLANTATION -- THE GASTROINTESTINAL MICROBIOME AS A DIAGNOSTIC BIOMARKER -- CONCLUSIONS -- REFERENCES -- 12. The Vaginal Microbiome -- THE HEALTHY VAGINAL MICROBIOTA -- THE NORMAL VAGINAL MICROBIOTA -- BV -- The Microbiology of BV: Cultivation Studies -- The Microbiology of BV: Broad Molecular Surveys -- Diagnostics for BV -- The Potential for Molecular Diagnostics in BV -- REFERENCES -- 13. Microbial Communities of the Male Urethra -- HISTORICAL UNDERSTANDING OF THE MICROBIAL COMMUNITIES OF THE MALE URETHRA -- CULTIVATION-INDEPENDENT CHARACTERIZATION OF THE MALE URETHRAL MICROBIOME -- POTENTIAL FOR DIAGNOSTICS AND EPIDEMIOLOGIC APPLICATIONS -- CONSIDERATIONS -- SUMMARY -- REFERENCES -- 14. The Human Virome in Health and Disease -- METHODS FOR VIROME STUDIES -- THE HUMAN VIROME: GENERAL DESCRIPTION -- GASTROINTESTINAL TRACT VIROME -- RESPIRATORY TRACT VIROME -- PLASMA VIROME -- SKIN VIROME. , METAGENOMIC STUDIES OF SEWAGE (THE SEWAGE VIROME) -- THE CANCER VIROME -- CONCLUSIONS -- REFERENCES -- Section III: HEALTH CARE-ASSOCIATED INFECTIONS -- 15. Molecular Detection of Staphylococcus aureus Colonization and Infection -- HISTORY OF SCREENING FOR S. AUREUS AND MRSA -- MEDICAL UTILITY -- Nasal Screen for MRSA Control -- Presurgical S. aureus Screening and Decolonization -- LABORATORY DETECTION OF S. AUREUS -- Premolecular Methods for Detecting S. aureus -- Development of Molecular Targets from the S. aureus Genome -- Early Molecular Assays -- Initial Commercial PCR -- Peptide Nucleic Acid Fluorescence In Situ Hybridization -- Current Commercial Assays -- IMPLICATION OF MOLECULAR TEST CHOICE -- CONCLUSIONS AND FUTURE DIRECTIONS -- REFERENCES -- 16. Molecular Diagnostics for Clostridium difficile -- GENERAL CONCEPTS -- LABORATORY METHODS FOR C. DIFFICILE TESTING -- Stool Cytotoxicity Assay -- Toxigenic Culture -- Glutamate Dehydrogenase -- EIAs for Toxins A and B -- Nucleic Acid Amplification Tests -- STRATEGIES TO OPTIMIZE LABORATORY TESTING FOR CDI -- CLINICAL AND INFECTION CONTROL CONSIDERATIONS -- Reducing Delays in Diagnosis -- Reducing Inappropriate Testing and Treatment -- False-Negative Tests Due to Empirical CDI Therapy -- Diagnostic Testing in Patients with Suspected CDI and Ileus -- Screening for Asymptomatic Carriage of C. difficile -- CONCLUSION -- REFERENCES -- 17. Overview of Molecular Diagnostics in Multiple-Drug-Resistant Organism Prevention: Focus on Multiple-Drug-Resistant Gram-Negative Bacterial Organisms -- MDRO SURVEILLANCE AND PREVENTION: A COLLABORATIVE EFFORT -- MRSA -- VRE -- MDR-GNRS -- CULTURE-BASED SCREENING FOR ESBLAND CARBAPENEMASE-PRODUCING ORGANISMS -- PHENOTYPIC CONFIRMATION OF ESBL AND CARBAPENEMASE PRODUCTION -- MOLECULAR DETECTION METHODS FOR MDR-GNR SURVEILLANCE -- Laboratory-Developed Tests. , Commercial Molecular Assays for ESBL and Carbapenemase Determinants.

Note: Front Cover -- MOLECULAR MEDICAL MICROBIOLOGY -- Copyright Page -- Content -- PART 12: RESPIRATORY INFECTIONS -- Chapter 74. Respiratory Tract Infections: A Clinical Overview -- Chapter 75. Bordetella pertussis -- Chapter 76. Streptococcus pneumoniae -- Chapter 77. Klebsiella pneumoniae -- Chapter 78. Moraxella (Branhamella) catarrhalis -- Chapter 79. Mycoplasma pneumoniae and other Mycoplasmas -- Chapter 80. Coxiella burnetii -- PART 13: MYCOBACTERIAL INFECTIONS -- Chapter 81. Mycobacterium tuberculosis -- Chapter 82. Mycobacterium leprae -- Chapter 83. The Mycobacterium avium- intracellulare Complex -- PART 14: SEXUALLY-TRANSMITTED INFECTIONS -- Chapter 84. Sexually Transmitted and Genital Infections: A Clinical Overview -- Chapter 85. Treponema pallidum -- Chapter 86. Haemophilus ducreyi -- Chapter 87. Chlamydia -- PART 15: ANAEROBIC INFECTIONS -- Chapter 88. Anaerobic Infections: A Clinical Overview -- Chapter 89. Clostridium perfringens: Wound Infections -- Chapter 90. Clostridium tetani -- Chapter 91. Bacteroides -- PART 16: CENTRAL NERVOUS SYSTEM INFECTIONS -- Chapter 92. Central Nervous System Infections: A Clinical Overview -- Chapter 93. Haemophilus influenzae -- PART 17: ANIMAL AND ECTOPARASITIC SOURCE INFECTIONS -- Chapter 94. Brucella -- Chapter 95. Bacillus anthracis and Other Bacillus species -- Chapter 96. Yersinia pestis -- Chapter 97. Borrelia burgdorferi -- Chapter 98. Relapsing Fever Borrelia -- Chapter 99. Bartonella -- Chapter 100. Leptospira -- Chapter 101. Francisella -- Chapter 102. Rickettsia and Orientia -- Chapter 103. Identification of Uncultured Pathogens -- Index -- Colour Plates.

Note: Intro -- Title -- Copyright -- Contents -- Section I Introduction to Natural Products -- 1 Major Classes of Natural Product Scaffolds and Enzymatic Biosynthetic Machinery -- 1.1 Introduction -- 1.2 Primary Metabolites vs. Secondary Metabolites -- 1.3 Polyketide Natural Products -- 1.4 Peptide Based Natural Products -- 1.5 Isoprenoid/Terpenoid Natural Products -- 1.6 Alkaloids -- 1.7 Purine and Pyrimidine Natural Products -- 1.8 Phenylpropanoid Scaffolds -- 1.9 Glycosylated Natural Products -- 1.10 Natural Product Scaffold Diversity From a Limited Set of Building Blocks and a Limited Set of Enzyme Families -- 1.11 Some Notable and Unusual Transformations in Secondary Pathways -- 1.12 Oxygenases are Pervasive in Natural Product Biosynthetic Pathways -- 1.13 Carbon-Carbon Bonds in Natural Product Biosynthesis -- 1.14 Testing Biosynthetic Hypotheses by Feeding Isotopically Labeled Building Blocks -- 1.15 Historical and Contemporary Approaches to the Detection and Characterization of Natural Products -- 1.16 Summary: Distinct Assembly Logic for Different Classes of Natural Products -- 1.17 Approach of This Volume -- References -- Section II Six Natural Product Classes -- 2 Polyketide Natural Products -- 2.1 Introduction -- 2.2 Polyketides Have Diverse Scaffolds and Therapeutic Utilities -- 2.3 Acetyl-CoA, Malonyl-CoA and Malonyl-S-Acyl Carrier Proteins as Building Blocks for Fatty Acids and Polyketides -- 2.4 The Logic and Enzymatic Machinery of Fatty Acid Synthesis is Adapted by Polyketide Synthases -- 2.5 Polyketide Synthases (PKS) -- 2.6 Biosynthesis of Major Polyketide Structural Classes -- 2.7 Polyketides with Ring-forming [4+2] Cyclizations on or After PKS Assembly Lines: Concerted or Stepwise? -- 2.8 The Polyene Subclass of Polyketides -- 2.9 Polyketide to Polyether Metabolites. , 2.10 Convergence of Polyketide and Other Natural Product Pathways -- 2.11 Post-assembly Line Tailoring Enzymes -- References -- 3 Peptide Derived Natural Products -- 3.1 Introduction -- 3.2 Ribosomal vs. Nonribosomal Amino Acid Oligomerization Characteristics -- 3.3 Posttranslational Modifications That Convert Nascent Proteins into Morphed, Compact Scaffolds: RIPPs -- 3.4 Nonribosomal Peptide Synthetase Assembly Lines: Alternative Routes to Highly Morphed Peptide Scaffolds -- 3.5 Nonproteinogenic Amino Acid Building Blocks -- 3.6 NRPS Assembly Line Logic: Priming, Initiation, Elongation, Termination -- 3.7 Different Chain Release Fates in the NRPS Termination Step -- 3.8 Structural Considerations of NRPS Assembly Lines -- 3.9 Pre-assembly Line vs. On-assembly Line vs. Post-assembly Line Tailoring of Peptidyl Chains -- 3.10 NRP-PK Hybrids: Machinery and Examples -- 3.11 Summary -- References -- 4 Isoprenoids/Terpenes -- 4.1 Isoprene-based Scaffolds Comprise the Most Abundant Class of Natural Products -- 4.2 Δ2- and Δ3-Isopentenyl Diphosphates are the Biological Isoprenyl Building Blocks for Head to Tail Alkylative Chain Elongations -- 4.3 Long Chain Prenyl-PP Scaffolds -- 4.4 Two Routes to the IPP Isomers: Classical and Nonclassical Pathways -- 4.5 Self-condensation of Two Δ2-IPPs to Chrysanthemyl Cyclopropyl Framework -- 4.6 Cation-driven Scaffold Rearrangements: and Quenching -- 4.7 Head to Head vs. Head to Tail Alkylative Couplings: C30 and C40 Terpene Compounds -- 4.8 Squalene-2,3-Oxide and Cyclized Triterpenes -- 4.9 Phytoene to Carotenes and Vitamin A -- 4.10 Reaction of Isoprenes with Other Natural Product Classes -- 4.11 Geranyl-PP to Secologanin: Entryway to Strictosidine and a Thousand Alkaloids -- References -- 5 Alkaloids -- 5.1 Introduction -- 5.2 Alkaloid Family Classifications. , 5.3 Common Enzymatic Reactions in Alkaloid Biosynthetic Pathways -- 5.4 Three Aromatic Amino Acids as Alkaloid Building Blocks -- 5.5 Tryptophan as a Building Block for Alkaloids -- 5.6 Anthranilate as a Starter and Extender Unit for Fungal Peptidyl Alkaloids of Substantial Complexity -- 5.7 Tryptophan to Indolocarbazole Alkaloids -- 5.8 Tryptophan Oxidative Dimerization to Terrequinone -- 5.9 Additional Alkaloids: Steroidal Alkaloids -- 5.10 Summary -- References -- 6 Purine- and Pyrimidine-derived Natural Products -- 6.1 Introduction -- 6.2 Pairing of Specific Purines and Pyrimidines in RNA and DNA -- 6.3 Remnants of an RNA World? -- 6.4 Canonical Biosynthetic Routes to Purines and Pyrimidines -- 6.5 Caffeine, Theobromine and Theophylline -- 6.6 Plant Isopentenyl Adenine Cytokinins -- 6.7 Maturation of Ribonucleotides to Modified Purine and Pyrimidine Natural Products -- 6.8 Peptidyl Nucleosides -- 6.9 Summary -- References -- 7 Phenylpropanoid Natural Product Biosynthesis -- 7.1 Introduction -- 7.2 Phenylalanine to para-Coumaryl-CoA -- 7.3 Monolignol, Lignan and Lignin Biosynthesis -- 7.4 para-Coumaryl-CoA to All the Other Classes of Phenylpropanoids -- 7.5 Chalcone to Flavanones and Beyond -- 7.6 Cinnamate Derived Phenylpropanoids -- 7.7 A Closing Look at a Different Phenylpropanoid Route: Tyrosine as Precursor to Plastoquinines and Tocopherols -- 7.8 Summary -- References -- 8 Indole Terpenes: Alkaloids II -- 8.1 Introduction -- 8.2 Two Routes to Tricyclic Scaffolds from Trp: β-Carbolines and Pyrroloindoles -- 8.3 Trp-Xaa Diketopiperazine NRPS Assembly Line Products as Substrates for Regioselective Prenylations -- 8.4 Seven Nucleophilic Sites on the Indole Ring: A Cornucopia of Possibilities -- 8.5 Fungal Generation of Tryptophan Derived Alkaloids from DKP -- 8.6 Bacterial Generation of Pentacyclic Indolecarbazoles. , 8.7 Vinca Alkaloids: Strictosidine to Tabersonine to Vindoline -- 8.8 Lyngbyatoxin: One- and Two-electron Reaction Manifolds in Indole in a Single Biosynthetic Pathway -- 8.9 Tryptophan to Cyclopiazonic Acid -- 8.10 Summary -- References -- Section III Key Enzymes in Natural Product Biosynthetic Pathways -- 9 Carbon-based Radicals in C-C Bond Formations in Natural Products A. Oxygenases B. Oxygen-dependent Halogenases -- 9.1 Introduction -- 9.2 Oxygenases in Primary vs. Secondary Metabolism -- 9.3 Oxidases vs. Oxygenases -- 9.4 Organic vs. Inorganic Cofactors for Oxygenase Catalysis -- 9.5 Scope and Mechanism of Oxygenations Catalyzed by Iron-based vs. Flavin-based Oxygenases -- 9.6 Oxygenases in Specific Natural Product Pathways -- 9.7 Uncoupling of Carbon Radicals from OH Capture: Sidelight or Central Purpose of Natural Product Biosynthetic Iron Enzymes? -- 9.8 Oxygen-dependent Halogenases -- 9.9 Fluorination of Substrates by a Nonoxidative Route: Fluorinase -- 9.10 Summary: The Chemical Versatility of Ferryl (High Valent Oxo-iron) Reaction Intermediates -- References -- 10 S-Adenosyl Methionine: One Electron and Two Electron Reaction Manifolds in Biosyntheses -- 10.1 Introduction -- 10.2 Aerobic Radical Chemistry for SAM -- 10.3 Anaerobic Radical Chemistry for SAM -- 10.4 Scope of Reactions of Radical SAM Enzymes -- 10.5 SAM as Coenzyme -- 10.6 SAM as Consumable Substrate: No Methyl Transfers -- 10.7 Methylations at Unactivated Carbon Centers: Consumption of Two SAMs to Two Distinct Sets of Products -- 10.8 Summary on SAM reactivity and utility -- References -- 11 Natural Product Oligosaccharides and Glycosides -- 11.1 Introduction -- 11.2 Glucose is the Predominant Hexose in Primary Metabolism -- 11.3 A Gallery of Glycosylated Natural Products -- 11.4 The Chemical Logic for Converting NDP-Glucose to NDP-Modified Hexoses. , 11.5 Balance of Gtfs and Glycosidases: Cyanogenic Glycosides and Glucosinolates -- 11.6 Aminoglycosides: Oligosaccharides without an Aglycone -- 11.7 Kanamycin, Tobramycin, Neomycin -- 11.8 Streptomycin -- 11.9 Moenomycins -- 11.10 Summary -- References -- Section IV Genome-independent and Genome-dependent Detection of Natural Products -- 12 Natural Products Isolation and Characterization: Gene Independent Approaches -- 12.1 Introduction -- 12.2 Historic and Contemporary Isolation Protocols for Natural Products -- 12.3 Isolation and Characterizations of Specific Natural Products -- 12.4 Case Studies: Historical and Current -- 12.5 Five Plant Derived Natural Products -- 12.6 Three Microbial Metabolites -- 12.7 Expanding the Inventory of Natural Products -- References -- 13 Natural Products in the Post Genomic Era -- 13.1 Introduction -- 13.2 Bioinformatic and Computational Predictions of Biosynthetic Gene Clusters -- 13.3 The Phosphonate Class of Natural Products: Can Genomics Define the Complete Set? -- 13.4 Overview of Heterologous Expression Systems -- 13.5 Selected Examples of Pathway Reconstitutions -- 13.6 Bioinformatics-based Natural Product Prospecting in Bacterial Genomes -- 13.7 Heterologous expression in E. coli -- 13.8 Metabolic Engineering for Diversity Generation -- 13.9 Plug and Play Approach to Cloning Transcriptionally Silent Gene Clusters of Unknown Function from Bacteria -- 13.10 Comparative Metabolomics in the Post Genomic Era -- References -- Subject Index.

Note: Intro -- Half title -- Title -- Copyright -- Dedication -- Preface to the 2nd Edition -- Preface to the 1st Edition -- Acknowledgements -- Contents -- 1 Major Classes of Natural Product Scaffolds and Enzymatic Biosynthetic Machinery -- 1.1 Introduction -- 1.2 Primary Metabolites vs. Secondary Metabolites -- 1.3 Eight Major Classes of Natural Products -- 1.4 Nucleophiles and Electrophiles in Natural Product Biosynthesis -- 1.5 Three Enzyme Classes that Operate in Natural Product Biosynthetic Pathways -- 1.6 Genome-independent and Genome-dependent Discovery of Natural Products -- 1.7 Approach of this Volume -- References -- 2 The Chemical Logic for Major Reaction Types -- 2.1 Two Classes of Molecules that Drive Major Reaction Types in Both Primary and Secondary Metabolisms -- 2.2 Thermodynamically Activated but Kinetically Stable Metabolites that Drive Biosynthetic Equilibria -- 2.2.1 ATP and NTP Congeners -- 2.2.2 Adenosine Phosphosulfate and Phosphoadenosine Phosphosulfate -- 2.2.3 Acetyl-S-coenzyme and Related Acyl Thioesters -- 2.2.4 NADH as Hydride Transfer Agent: Two Electrons at a Time -- 2.2.5 S-Adenosylmethionine -- 2.2.6 Carbamoyl Phosphate -- 2.2.7 UDP-Glucose -- 2.2.8 Isopentenyl Pyrophosphate -- 2.2.9 Phosphoenolpyruvate (PEP) as a Trapped Carbanion Equivalent -- 2.2.10 A Diverse Range of Thermodynamically Activated, Kinetically Stable Chemical Groups Power Metabolism -- 2.2.11 Molecular Oxygen -- 2.3 Coenzyme Forms of B Vitamins as a Convergent Set of Metabolites Enabling Chemistry -- 2.4 Overview: Chemical Logic Embodied in the Two Sets of Metabolites and Coenzymes -- References -- 3 Polyketide Natural Products -- 3.1 Introduction -- 3.2 Polyketides Have Diverse Scaffolds and Therapeutic Utilities -- 3.3 Acetyl-CoA, Malonyl-CoA and Malonyl-S-Acyl Carrier Proteins as Building Blocks for Fatty Acids and Polyketides. , 3.4 The Logic and Enzymatic Machinery of Fatty Acid Synthesis is Adapted by Polyketide Synthases -- 3.4.1 Fatty Acid Synthases (FASs) -- 3.4.2 Polyketide Synthases (PKSs) -- 3.4.3 Alternate Acyl-CoA Substrates for PKS -- 3.4.4 Organization of Multiprotein Assemblages -- 3.4.5 PKS Chain Termination Modes -- 3.5 Biosynthesis of Major Polyketide Structural Classes -- 3.5.1 Oxytetracycline Biosynthesis: Aromatic Polyketides that Initiate Cyclization at C7-C12 or C9-C14 -- 3.5.2 Fungal Aromatic Polyketides: Cyclizations that Start at C4-C9 or C6-C11 -- 3.5.3 Type II Reducing PKSs Release Polyenes as Nascent Products -- 3.5.4 Polyketide Macrolactones: Type I Assembly-line Logic and Machinery -- 3.5.5 Polyketides Formed from Concerted Pericyclic Reactions -- 3.5.6 A Stepwise Cyclization of Polyketide: Ikarugamycin -- 3.5.7 Polyene Subclass of Polyketides -- 3.5.8 Polyketide to Polyether Metabolites -- 3.6 Convergence of Polyketide and Other Natural Product Pathways -- 3.7 Post-assembly-line Tailoring Enzymes -- References -- 4 Peptide Natural Products I: RiPPs -- 4.1 RiPPs vs. NRPs -- 4.2 RiPPs: Scope of Posttranslational Modifications: One- vs. Two-electron Reaction Manifolds -- 4.3 RiPP Biosynthetic Gene Organizations -- 4.4 Lanthipeptides: RiPPs Containing Crosslinking β-Thioethers -- 4.4.1 Lysine-Dha Crosslinks -- 4.4.2 Landornamide: Protein Arginases vs. Protein Deiminase -- 4.4.3 Phomopsins and Ustiloxins -- 4.5 RiPPs with Olefins and Oxazole and Thiazole Heterocycles -- 4.5.1 Goadsporin, Microcin B17, Plantazolocin -- 4.5.2 Patellamides A and C -- 4.5.3 Pyridines, Thiazoles, Oxazoles -- 4.6 Lasso Peptides: Nature's Rotaxanes -- 4.7 One-electron Reaction Manifolds in RiPP Generation from S-Adenosylmethionine Fragmentations -- 4.7.1 Sactipeptides -- 4.7.2 Homolytic Coupling of Lys-Trp in Streptide. , 4.7.3 Six-member Aliphatic Ethers from Threonine-Glutamate Crosslinking -- 4.7.4 Polytheonamides -- 4.7.5 RiPP α-Ketoamides from Splicing Out a Tyramine Moiety -- 4.7.6 Bottromycin: Multiple PTMs -- 4.8 Other RiPP Categories -- 4.8.1 Cittilins and Protein Cyclophanes -- 4.8.2 Microviridin -- 4.8.3 Amanitin and Phalloidin -- 4.8.4 Self-N-methylation of Peptide Bonds in Borosin RiPPs -- 4.9 RiPPs from Plants -- 4.10 Summary -- 4.10.1 Multiple Macrocyclization Strategies -- 4.10.2 Rigidification by Morphing Peptide Backbone into Heterocycles -- 4.10.3 Embedding Heterocycles in Macrocycles -- 4.10.4 Rotaxane Topology Implementation -- 4.10.5 Auguries of Novel Peptide Chemical Biology from the Radical SAM Universe -- References -- 5 Peptide Natural Products II: Nonribosomal Peptides -- 5.1 NRPS Assembly-line Strategies -- 5.2 Genome Mining and Bioinformatic Analyses -- 5.3 Constituents of NRPS Assembly Lines and the Logic of Nonribosomal Peptide Chain Growth -- 5.3.1 Nonproteinogenic Amino Acid Building Blocks -- 5.3.2 Phosphopantetheinyl Arms for Tethering Growing Peptidyl Thioester Chains -- 5.3.3 NRPS Domains and Modules -- 5.4 Representative NRPS Assembly Lines -- 5.4.1 The ACV Synthetase Assembly Line -- 5.4.2 The Enterobactin Synthetase Assembly Line -- 5.4.3 Obafluorin an Amino β-lactone from a Two-module NRPS -- 5.4.4 Azabicyclene Scaffolds from Pseudomonas aeruginosa -- 5.4.5 Vancomycin and Teicoplanin Glycopeptide Antibiotics -- 5.4.6 Echinocandins: Antifungal Cyclic Hexapeptides -- 5.4.7 Syringomycins and Syringopeptins: The Outer Limit of NRPs -- 5.4.8 Structural Biology of NRPS Domains and Modules -- 5.5 Hybrid Nonribosomal Peptide-polyketide Assembly Lines -- 5.5.1 Statine, Isostatine and Vinyl-arginine Revisited -- 5.5.2 α-Cyclopiazonic Acid: a Dieckmann Condensation in Mid-pathway. , 5.5.3 Bleomycin and Yersiniabactin: Hybrid Assembly Lines that are Mostly NRPS -- 5.5.4 Epothilone D and Rapamycin: Hybrid NRP-PK Scaffolds where the PK Units Dominate -- 5.5.5 Colibactin: a Genotoxic Human Gut Hybrid Scaffold with a Reactive Cyclopropane -- 5.6 Tailoring Enzymes and Morphed Scaffolds: RiPPs vs. NRPs vs. NRP-PK Hybrids -- References -- 6 Isoprenoids/Terpenes -- 6.1 Isoprene-based Scaffolds Comprise the Most Abundant Class of Natural Products -- 6.2 Δ2- and Δ3-Isopentenyl Diphosphates are the Biological Isoprenyl Building Blocks for Head-to-tail Alkylative Chain Elongations -- 6.3 Long-chain Prenyl Scaffolds -- 6.4 Two Routes to the IPP Isomers: Classical and Nonclassical Pathways -- 6.5 Self-condensation of Two Δ2-IPPs to the Chrysanthemyl Cyclopropyl Framework -- 6.6 Cation-driven Scaffold Rearrangements and Quenching -- 6.6.1 Monoterpenes: Geranyl-PP to α-terpinyl Cation and Its Partitioning to Products -- 6.6.2 Sesquiterpenes: Six Regiospecific Cyclizations from C15 Farnesyl-PP -- 6.6.3 How Good Are Terpene Synthases at Directing Flux of the Sequential Series of Cations in Their Active Sites? -- 6.6.4 Abscisic Acid -- 6.7 Diterpene Cyclization and Scaffold Complexity Generation -- 6.7.1 Geranylgeranyl-PP to ent-kaurene -- 6.7.2 Geranylgeranyl-PP to Taxadiene -- 6.7.3 Pleuromutilin -- 6.7.4 Momilactone B and Forskolin -- 6.8 Head-to-head vs. Head-to-tail Alkylative Couplings: C30 and C40 Hydrocarbons -- 6.9 Squalene-2,3-oxide and Cyclized Triterpenes -- 6.9.1 Formation of Squalene-2,3-oxide -- 6.9.2 Squalene Cyclases: Squalene to Hopene Framework -- 6.9.3 Oxidosqualene to Lanosterol, Cycloartenol, β-amyrin -- 6.9.4 Structural Biology Insights -- 6.9.5 Promiscuity of Oxidosqualene Cyclases: How Good Are the Oxidocyclases at Directing Flux Down One Reaction Manifold? -- 6.9.6 Lanosterol to Cholesterol and Beyond: A Bevy of Oxygenases. , 6.9.7 Regiospecific Furanosteroids -- 6.10 Phytoene to Carotenes and Vitamin A -- 6.11 Reaction of Isoprenes with Other Natural Product Classes -- 6.11.1 Meroterpenoids -- 6.11.2 Hyperforin is a Tetraprenylated Polyketide -- 6.11.3 Tetrahydrocannabinol -- 6.11.4 Paxilline -- 6.11.5 Merosterolic Acid -- 6.11.6 Xenovulene -- 6.12 Geranyl-PP to Secologanin: Entryway to Strictosidine and a Thousand Alkaloids -- References -- 7 Alkaloids I -- 7.1 Introduction -- 7.2 Amino Acid Building Blocks -- 7.3 Common Enzymatic Reactions in Alkaloid Biosynthetic Pathways -- 7.3.1 Reactions Involving Amino Acid Building Blocks -- 7.3.2 Ornithine as Building Block for Cocaine and Retronecine -- 7.3.3 Lysine to Pelletierine and Pseudopelletierine and Sparteine -- 7.3.4 Lysine to the 6,5-Indolizidine Bicyclic Framework -- 7.4 Three Aromatic Amino Acids as Alkaloid Building Blocks -- 7.4.1 Phenylalanine to Hyoscyamine to Scopolamine: Radical Rearrangement -- 7.4.2 Tyrosine is the Entry Point for Several Complex Alkaloid Scaffolds -- 7.4.3 Tyrosine to S-reticuline to Berberine -- 7.4.4 Tyrosine to R-reticuline to Morphine -- 7.5 Phenylalanine and Tyrosine Scaffolds Morphed to the 6-7-7 Tricyclic Framework of Colchicine -- 7.6 Tryptophan as a Building Block to Alkaloids -- 7.6.1 Tryptophan to Harmine: β-Carbolines -- 7.6.2 Tryptophan to Strictosidine and Beyond: Ajmalicine, Camptothecin, Quinine -- 7.6.3 Tryptophan to Lysergic Acid and Ergotamine -- 7.7 Tryptophan to Indolocarbazole Alkaloids -- 7.7.1 Rebeccamycin and Staurosporine -- 7.7.2 Prenylated Carbazole Metabolites -- 7.8 Tryptophan Oxidative Dimerization to Terrequinone -- 7.9 Additional Alkaloids: Steroidal Alkaloids -- 7.10 Summary -- References -- 8 Purine- and Pyrimidine-derived Natural Products -- 8.1 Introduction -- 8.2 Pairing of Specific Purines and Pyrimidines in RNA and DNA. , 8.3 Remnants of an RNA World?.

Note: Intro -- Title Page -- Copyright Page -- Preface -- Acknowledgements -- Contents -- Section I: Overview -- 1 Human Vitamins: Discovery and Characterization -- 1.1 What Are Human Vitamins? -- 1.2 Vitamin Discovery: A Golden Age from 1910-1948 -- 1.3 Vitamin Deficiencies: Primary and Secondary Symptoms -- 1.4 Water-soluble Versus Fat-soluble Vitamins -- 1.5 Key Functional Groups in Vitamin Biochemistry: Heterocycles -- 1.6 Vitamins Active as Ingested Versus Those Requiring Metabolic Processing to Active Forms -- 1.7 How Vulnerable Are Humans with Dependence on These 13 Vitamins -- 1.8 Vitamin Nomenclature -- 1.9 Why Study Vitamins Now? -- 1.10 Why Do Americans Take So Many Vitamins? -- 1.11 Scope and Approach of This Volume -- 1.12 A Molecular View of Vitamin Action -- References -- 2 Metabolic Logic through the Lens of Coenzyme Forms of Human Vitamins -- 2.1 Metabolites, Metabolism, Metabolomics and How Vitamins Fit in the Picture -- 2.2 All Eight B Vitamins Function as Coenzymes -- 2.3 NADH, Acetyl-CoA, ATP as Thermodynamically Activated Kinetically Stable Molecules that are the Products of Catabolic Pathways -- 2.4 The Logic of Anabolic Metabolism -- 2.5 Central Metabolic Pathways in Humans Depend on the Coenzyme Forms of Vitamins at Key Nodal Points -- References -- Section II: The Metabolic Roles of the Water-soluble Vitamins -- 3 Vitamin B1 Converted to the Coenzyme Thiamin Pyrophosphate -- 3.1 Discovery of Thiamin -- 3.2 Pyrophosphorylation of Thiamin Yields the Coenzymatically Active Thiamin Pyrophosphate (TPP) -- 3.3 C2-hydrogen Exchange of Thiamin and Thiamin-PP is the Key to their Chemical Biology -- 3.4 The Metabolic Niches for Thiamin-PP in Humans -- 3.5 α-Keto Acid versus β-Keto Acid Decarboxylation Mechanisms -- 3.6 Enzymatic Machinery to Convert α-Keto Acids from Nonoxidative to Oxidative Outcomes. , 3.7 Transketolase: Ketol Transfers between Aldose Sugar Cosubstrates -- 3.8 Peroxisomal Fatty Acyl Thioester Lyase -- 3.9 Summary on Thiamin Chemical Biology and Metabolic Roles -- References -- 4 Vitamin B2 Riboflavin -- 4.1 Discovery of Riboflavin -- 4.2 Logic for Biosynthesis in Microbes and Commercial Production Strategies -- 4.3 Conversion of Vitamin B2 to the Coenzyme Forms FMN and FAD -- 4.4 Why Should We Care About Electron Transfer Coenzymes in Metabolism? -- 4.5 The Chemical Biology of Riboflavin as Two Electron/One Electron Step Down Redox Transformer in Cell Metabolism -- 4.6 Flavoenzyme Reoxidative Half Reactions with O2 as Cosubstrate in Obligate One Electron Transfers -- 4.7 Distinct Roles for Flavin and Nicotinamide Coenzymes Based in Differential O2 Reactivities -- 4.8 Glutathione as Cellular Guardian: The Key Role of Glutathione Reductase -- 4.9 Summary on Metabolic Redox Niches for Riboflavin-based Coenzymes -- References -- 5 Vitamin B3 Niacin and the Nicotinamide Coenzymes -- 5.1 Discovery of Vitamin B3 -- 5.2 Biosynthesis of Nicotinic Acid and of NAD+ -- 5.3 Conversion of Ingested Niacin to NAD+ and NADP+ -- 5.4 Hydride Transfers to and from NAD+ and NADP+ -- 5.5 Stereochemical Outcomes in NAD(P)H Redox Enzymatic Reactions -- 5.6 Scope of Substrate Functional Groups Oxidized or Reduced by Nicotinamide-utilizing Enzymes -- 5.7 Why Should We Care About Redox Reactions in Cells: A Brief Nicotinamide-centered Reprise -- 5.8 Functional Distinctions Between NADH and NADPH -- 5.9 Nonredox Roles for NAD+ -- 5.10 Summary of the Metabolic Functions of the Coenzyme Forms of Vitamin B3 -- References -- 6 Vitamin B5: Pantothenate -- 6.1 Discovery and Characterization of Pantothenate as Vitamin B5 -- 6.2 Biosynthesis of Pantothenate -- 6.3 Conversion of Vitamin B5 to Coenzyme A. , 6.4 The Thiol Group of Coenzyme A Is the Key to All Its Biologic Functions -- 6.5 Acyl-CoA Thioesters Are Thermodynamically Activated and Kinetically Stable Metabolites -- 6.6 Acyl-CoAs: Diffusible Cellular Packets of Acyl Group Transfer Currency -- 6.7 Acetyl-CoA as a Kinetically Accessible C2 Carbanion Equivalent for C-C Bond Formations -- 6.8 Summary -- References -- 7 Coenzyme Forms of Vitamin B6 -- 7.1 Discovery and Characterization of Vitamin B6 -- 7.2 Metabolism of Pyridoxine to the Coenzymatically Active Aldehyde Pyridoxal-Phosphate (pyridoxal-P, PLP) -- 7.3 The Resting State of PLP-dependent Enzymes Contain PLP in Aldimine Linkage to an Active Site Lysine Side Chain -- 7.4 Each Catalytic Cycle for PLP-enzymes Starts with Transaldimination between Resting PLP-Enzyme and Substrate Amino Group -- 7.5 PLP-substrate Aldimines: Carbanion Chemistry at Cα, Cβ, Cγ of the Amino Acid Scaffolds -- 7.6 PLP-Enzymes Catalyzing Transformation at Amino Acid Cα -- 7.7 Cβ-Elimination and Replacement Reactions -- 7.8 Cγ Elimination and Replacement Reactions -- 7.9 PLP-Enzymes That Make C-C Bonds with Decarboxylation -- 7.10 Glycogen Phosphorylase: PLP as Specific Acid Catalyst -- 7.11 Overview of Metabolic Roles of Coenzyme Forms of Vitamin B6 -- References -- 8 Vitamin B7: Biotin -- 8.1 Discovery and Characterization -- 8.2 Biotin Biosynthesis in Microbes and Plants but Not Vertebrates -- 8.3 Biotin Structure and Function -- 8.4 Posttranslational Incorporation of Biotin in a Small Family of Carboxylases -- 8.5 Acyl-CoA Carboxylases -- 8.6 Pyruvate Carboxylase: Mechanism and Physiologic Role -- 8.7 Tandem Action of Acetyl-CoA Carboxylase and the β-Ketoacyl Thioester Synthase in Fatty Acid Chain Elongation Steps. The Logic of Transient Carboxylations -- 8.8 Other Biotin-independent Carboxylations -- 8.9 Overview of Vitamin B7 Human Metabolism -- References. , 9 Vitamin B9: Folic Acid -- 9.1 Isolation and Characterization of Vitamin B9 -- 9.2 Biosynthesis and Chemistry of the Bicyclic Pterin Ring System -- 9.3 Conversion of Vitamin B9 to the Active Coenzyme Forms -- 9.4 Folate Deficiency -- 9.5 One-carbon Oxidation States in Metabolism -- 9.6 Serine Transhydroxymethylase, Nascent Formaldehyde, and FH4 as Formaldehyde Sponge -- 9.7 Redox Changes of the Attached C1 Unit -- 9.8 One-carbon Units Transferred Out At All Three Oxidation States -- 9.9 Biopterins versus Folates -- 9.10 Overview -- References -- 10 Vitamin B12: Two Coenzyme Forms -- 10.1 Isolation and Characterization -- 10.2 Vitamin B12 Properties -- 10.3 Biosynthetic Logic -- 10.4 Conversion to Coenzymatically Active Forms -- 10.5 Adenosyl-B12 as Radical Generator in 1,2-Rearrangements: Methylmalonyl-CoA Mutase -- 10.6 Methyl-B12 as Donor of [CH3+] in Methionine Synthase -- 10.7 How B12 Deficiency Traps Tetrahydrofolate and Blocks DNA Synthesis -- 10.8 Similarity Between Adenosyl-B12 and S-Adenosylmethionine as 5-Deoxyadenosine Radical Generators -- 10.9 Overview -- References -- 11 Vitamin C: Ascorbic Acid -- 11.1 Discovery and Characterization of Ascorbic Acid as Vitamin C -- 11.2 Vitamin C Biosynthesis and the Missing Step in Humans -- 11.3 Chemistry of Vitamin C: One and Two Electron Reductions -- 11.4 Two Biological Redox Functions for Vitamin C -- 11.5 Cofactor Role for Eight Nonheme Iron and Two Copper Oxygenases -- 11.6 Mechanism and Role of Prolyl Hydroxylation in Collagen Triple Helix Formation and Maturation -- 11.7 Dopamine-β-Hydroxylase and Peptidylglycine α-Amidating Monooxygenase -- 11.8 Nonspecific Role in Scavenging Reactive Oxidant Flux -- 11.9 Overview of Vitamin C Metabolic Functions -- References -- Section III: The Metabolic Roles of Lipid-soluble Vitamins. , 12 Vitamin A: Three Vitamer Forms: Retinol, Retinal, and Retinoic Acid -- 12.1 Discovery and Characterization of Vitamin A -- 12.2 Three Vitamer Forms, Two with Distinct Biologic Activities. Metabolic Conversions in Humans -- 12.3 Retinal Biosynthesis from β-Carotene Follows Isoprenoid Lineage -- 12.4 Vitamin A Deficiency -- 12.5 Uptake, Extracellular, and Intracellular Transport of Vitamin A Forms -- 12.6 Role of Retinyl Esters and Retinal in the Visual Cycle -- 12.7 Retinoic Acid Effects in Development, Immune System Function, Reproduction and Gene Transcription -- 12.8 Retinoic Acid as Ligand for the RAR Subset of Nuclear Hormone Receptors -- 12.9 Therapeutic Intervention in Acne and in Acute Promyelocytic Leukemia -- 12.10 Overview: Vitamin or Hormone -- References -- 13 Vitamin D -- 13.1 Vitamin D Is a Steroid-derived Metabolite -- 13.2 Discovery and Characterization of Vitamin D as Antirachitic Factor -- 13.3 Biosynthesis of Vitamin D3 in Skin -- 13.4 Enzymatic Conversion of Vitamin D3 to Calcitriol -- 13.5 Regulation of Calcium and Phosphate Metabolism -- 13.6 Calcitriol as Ligand for Vitamin D Receptor as Transcriptional Regulator -- 13.7 Vitamin D Receptors in Many Other Tissues -- 13.8 VDR-independent Effects of 1,25-Dihydroxy Vitamin D3 -- 13.9 Summary -- References -- 14 Vitamin E -- 14.1 Discovery and Structure of Vitamin E -- 14.2 Biosynthetic Logic for Vitamin E -- 14.3 Redox Chemistry of Tocopherols and Tocotrienols -- 14.4 Uptake and Transport of Vitamin E to Tissues -- 14.5 Antioxidant to Interrupt Lipid Peroxide Radical Chains -- 14.6 Cellular Antioxidant Pyramid: The Full Arsenal -- 14.7 Overview -- References -- 15 Vitamin K -- 15.1 Discovery of Vitamin K1 and K2 -- 15.2 Vitamin K Deficiency and Hemophilia A versus B -- 15.3 Proteins of the Blood Coagulation Cascade -- 15.4 Biosynthesis of Vitamin K1 and K2. , 15.5 Role of Phylloquinones and Plastoquinones in Plant Chloroplasts.

Note: Intro -- Advanced Techniquesin Diagnostic Microbiology -- Preface -- Contents -- Contributors -- Part I: Methods -- Chapter 1: Automated Blood Cultures -- Introduction -- Principles -- Automated Culturing Systems -- Blood Culture and CMBCS for Mycobacteria -- Concluding Remarks -- References -- Chapter 2: Breath Tests for Detection of Helicobacter pylori and Aspergillus fumigatus -- Introduction -- Helicobacter pylori -- Aspergillus spp. -- Conventional Diagnostic Tests -- Detection of H. pylori -- Detection of Aspergillus spp. -- Breath Tests -- Introduction -- Sample Collection -- Urea Breath Test for H. pylori -- Breath Test for Aspergillosis -- Conclusions -- References -- Chapter 3: Rapid Antigen Tests -- Introduction -- Principles of the Techniques -- Agglutination -- Immuno uorescence -- Enzyme Immunoassay -- Chemiluminescent Methods -- Lateral Flow Immunochromatography and Fluoroimmunoassay -- Characteristics of the Techniques -- Applications of the Techniques -- Bacteria -- Fungi -- Parasites -- Viruses -- References -- Chapter 4: Antibody Detection: Principles and Applications -- Introduction -- Principles and Characteristics of Techniques -- Colorimetric or Chromogenic Substrate -- Radioimmunoassay -- Chemiluminescence-Immunoassay -- Electrochemiluminescent -- Fluorescent Immunoassays -- Multi-Analyte Pro le Technology -- Contrast of These Techniques -- Application of the Techniques in the Diagnostic Microbiology -- Clinical Applications -- Automation -- Summary -- References -- Chapter 5: Cytometry-Based Antimicrobial Resistance Techniques -- Introduction -- Flow Cytometry Setup -- Antimicrobial Resistance Measurements -- Assay Turnaround Time -- Comparator Methods -- Flow Cytometry Challenges -- Conclusions and Future Prospects -- References -- Chapter 6: Biochemical Pro le-Based Microbial Identi cation Systems. , Introduction -- Conventional Microbial Identi cation Systems -- Single Enzyme Rapid Tests -- Catalase Test -- Oxidase Test -- Spot Indole Test -- Slide Coagulase Test -- Microdase -- Bile Solubility Test -- PYR -- Leucine Aminopeptidase Test -- MUG Test -- Indoxyl Butyrate Disk -- Chromogenic Enzyme Substrate Test -- Gonocheck II -- Bacticard Neisseria -- Hippurate -- Lysostaphin -- CLO Test -- Overnight Biochemical Tests -- Tube Coagulase Test -- DNA Hydrolysis -- Vancomycin Disk Test -- Bacitracin Inhibition Test (Taxo A Disk) -- Bacitracin and STX Susceptibility Test -- Taxo P Disks (Optochin) -- CAMP Test -- Reverse CAMP Test -- Bile Esculin Agar Slant -- 6.5 % Salt Broth -- Indole Test -- Nitrite Test -- ALA ( Haemophilus in uenzae Porphyrin Test) -- Motility Indole Lysine Sul de (MILS) Medium -- O -Nitrophenyl-b- d -Galactopyranoside Test -- Methyl Red Test -- Voges-Proskauer Test -- Pseudosel Agar Slant -- Urea Agar Slant -- Citrate Agar Slant -- Cetrimide Agar -- Gelatin -- Acetate Utilization -- Lead Acetate for Hydrogen Sul de Detection -- Lysine Iron Agar -- Triple Sugar Iron Agar Slant -- Phenylalanine Deaminase -- Decarboxylase (Moeller's Method) -- OF Glucose Medium -- OF Sugars -- Commercial Microbial Identi cation System -- API Identi cation System -- API Gram-Negative Identi cation -- API Gram-Positive Identi cation -- API Anaerobe Identi cation -- BBL™ Crystal™ Identi cation System -- BBL Phoenix Identi cation and Susceptibility System -- VITEK and VITEK 2 Identi cation System -- MicroScan WalkAway -- Sensititre ® Microbiology Systems -- MIDI Sherlock -- BioLog ID System -- References -- Chapter 7: Infectious Disease Biomarkers: Non-Antibody-Based Host Responses -- Introduction -- Procalcitonin -- The Roles of PCT and Other Biomarkers in Sepsis -- The Roles of PCT in Sepsis -- The Roles of CRP in Sepsis. , The Roles of CRP and PCT in Infectious States Other than Sepsis -- The Roles of Miscellaneous and Novel Biomarkers in Infectious States -- Serum Amyloid A -- Lipopolysaccharide-Binding Protein -- Coagulation Markers -- Angiopoietins -- Neopterin -- Toll-Like Receptor-2 -- Triggering Receptor Expressed on Myeloid Cells-1 -- Soluble Urokinase-Type Plasminogen Activator Receptor -- Soluble Receptor for Advanced Glycation End Products -- CD64 -- HLA-DR -- Presepsin -- Cytokines -- Proadrenomedullin -- Alpha-1 Antitrypsin and Other Hepatitis Biomarkers -- Gelsolin -- Interferon-Gamma-Inducible Protein-10 -- Neutrophil Distribution Width -- Regulatory T Lymphocytes (Treg) -- Summary of Miscellaneous Biomarkers -- Newer Platforms for Measurement of Biomarkers -- Conclusions and Future Directions -- References -- Chapter 8: Functional Assessment of Microbial and Viral Infections by Real-Time Cellular Analysis System -- Introduction -- RTCA and Its Principle of Detection Using Impedance Microelectrode Sensor Arrays -- Analysis of Host Cell Responses to Bacterial Infections on RTCA System -- Detection of Clostridium dif cile Toxin -- Detection of Clostridium botulinum Toxin -- Detection of Meningococcal Infection -- Virus-Induced CPE and Neutralizing Antibody Detection on RTCA System -- West Nile Virus and St. Louis Encephalitis Virus CEP and Neutralizing Antibody Detection -- In uenza Virus and Neutralizing Antibody Detection -- Hand-Foot-Mouth Virus Detection -- Helminth Motility and Egg Hatching Activity on RTCA System -- Host Immune Function Assessment on RTCA: Nature Killer Cells and T Cells -- Natural Killer Cell Function Assessment -- T Cell Surface Receptor Detection -- Perspectives -- References -- Chapter 9: Cellular Fatty Acid-Based Microbial Identi cation and Antimicrobial Susceptibility Testing -- Introduction. , General Principles and Methods of Cellular Fatty Acid Analysis -- CFA Testing Platforms for Bacterial Identi cation -- Library Expansion and Fatty Acid Polymorphisms -- Identi cation of Agents of Bioterrorism and Other Select Agents -- Mycolic Acid Analysis for Identi cation of Mycobacteria -- HPLC and Susceptibility Testing -- Advantages and Disadvantages of Fatty Acid-Based Identi cation Methods -- References -- Chapter 10: MALDI-TOF Mass Spectrometry-Based Microbial Identi cation -- Introduction -- General Remarks on Mass Spectrometry -- MALDI and ESI MS -- Species Identi cation Using MALDI-TOF MS -- Limitations and Shortcomings of MALDI-TOF MS -- Further Challenges Approaching MALDI-TOF MS for Species Diagnosis -- Conclusion -- References -- Chapter 11: Nucleic Acid Extraction Techniques -- Introduction -- Nucleic Acid Extraction Techniques -- Cesium Chloride/Ethidium Bromide Density Gradient Centrifugation -- Phenol-Chloroform Extraction -- Solid-Phase Extraction -- Magnetic Bead Method -- Applications to Clinical Specimens -- Cellular Component -- Serum, Plasma, and Whole Blood -- In uence of Speci c Pathogen -- PCR Inhibitors -- Measurement of DNA Quality -- Comparison of Nucleic Acid Extraction Methods -- Manual Method -- Automatic Methods -- Conclusion -- References -- Chapter 12: Nonampli ed Probe-Based Microbial Detection and Identi cation -- Introduction -- Probe-Based Assay Design -- Target Selection -- Probe Selection -- Nucleic Acid Hybridization Formats -- Clinical Application of Nonampli ed Probe-Based Assays -- Gen-Probe Nucleic Acid Detection Methods -- Hybrid Capture Assay -- Af rm DNA Assay -- Line Probe Assay -- In Situ Hybridization Assays -- Peptide Nucleic Acid FISH Assays -- Future Considerations -- References -- Chapter 13: Molecular Typing Techniques: State of the Art -- Introduction. , What Does "State of the Art" Mean? -- The Ultimate Foundation for Epidemiological Comparison: The Bacterial Genome -- Methods with Electrophoretic Output -- Pulsed-Field Gel Electrophoresis -- Optical Mapping -- PCR-Based -- Repetitive Sequence-Based PCR -- PCR Ribotyping -- Staphylococcal Cassette Chromosome mec Typing -- Multiple-Locus VNTR Analysis -- DNA Sequence-Based Methods -- Single-Locus Sequence Typing -- S. aureus Protein A Typing -- Strepcococcus pyogenes M Protein ( emm) Typing -- mec -Associated Direct Repeat Unit Typing -- Multi-Locus Sequence Typing -- Other Multi-Locus Approaches: Hybridization-Based Typing -- Whole Genome Sequence Typing -- Non-Sequence-Based Whole Cell Typing -- Strain Typing in the Context of the Epidemiological Window -- References -- Chapter 14: An Introduction to In Vitro Nucleic Acid Ampli cation Techniques -- Target Ampli cation Systems -- Probe Ampli cation Systems -- Signal Ampli cation Systems -- References -- Chapter 15: PCR and Its Variations -- PCR: The Quintessential Nucleic Acid Ampli cation Method -- Principles of PCR -- Enzymatic Ampli cation of DNA: Components of the PCR -- The PCR Cycle -- Denaturation -- Annealing -- Extension -- Detection and Analysis of the PCR Product -- Conventional PCR -- Real-Time PCR -- PCR Variations -- Allele-Speci c PCR -- Hot-Start PCR -- Touchdown PCR -- Degenerate PCR -- Nested and Heminested PCR -- Multiplex PCR -- Reverse Transcription-PCR -- Quantitative PCR -- Real-Time PCR -- PCR-Based Strain Typing Techniques -- Arbitrarily Primed-PCR and Random Ampli ed Polymorphic DNA -- Ampli ed Fragment-Length Polymorphism -- ERIC-, Rep-, BOX-, IS-, and VNTR-PCR -- Appendix -- Primer Design Resources -- References -- Chapter 16: Non-PCR Target Ampli cation Techniques -- Introduction -- Isothermal Transcription-Based Ampli cation. , Strand Displacement Ampli cation.