Brock Biology of Microorganisms

Cover
Inside Front Cover
Title Page
Copyright Page
About the Authors
Dedications
Preface
Acknowledgments
Brief Contents
Contents
Unit 1 The Foundations of Microbiology
1 The Microbial World
microbiologynow Microorganisms, Our Constant Companions
I • Exploring the Microbial World
1.1 Microorganisms, Tiny Titans of the Earth
1.2 Structure and Activities of Microbial Cells
1.3 Microorganisms and the Biosphere
1.4 The Impact of Microorganisms on Human Society
II • Microscopy and the Origins of Microbiology
1.5 Light Microscopy and the Discovery of Microorganisms
1.6 Improving Contrast in Light Microscopy
1.7 Imaging Cells in Three Dimensions
1.8 Probing Cell Structure: Electron Microscopy
III • Microbial Cultivation Expands the Horizon of Microbiology
1.9 Pasteur and Spontaneous Generation
1.10 Koch, Infectious Diseases, and Pure Cultures
1.11 Discovery of Microbial Diversity
IV • Molecular Biology and the Unity and Diversity of Life
1.12 Molecular Basis of Life
1.13 Woese and the Tree of Life
1.14 An Introduction to Microbial Life
2 Microbial Cell Structure and Function
microbiologynow The Archaellum: Motility for the Archaea
I • Cells of Bacteria and Archaea
2.1 Cell Morphology
2.2 The Small World
II • The Cell Membrane and Wall
2.3 The Cytoplasmic Membrane
2.4 Bacterial Cell Walls: Peptidoglycan
2.5 LPS: The Outer Membrane
2.6 Archaeal Cell Walls
III • Cell Surface Structures and Inclusions
2.7 Cell Surface Structures
2.8 Cell Inclusions
2.9 Gas Vesicles
2.10 Endospores
IV • Cell Locomotion
2.11 Flagella, Archaella, and Swimming Motility
2.12 Gliding Motility
2.13 Chemotaxis and Other Taxes
V • Eukaryotic Microbial Cells
2.14 The Nucleus and Cell Division
2.15 Mitochondria, Hydrogenosomes, and Chloroplasts
2.16 Other Eukaryotic Cell Structures
Explore the Microbial World
Tiny Cells
3 Microbial Metabolism
microbiologynow Sugars and Sweets: Archaea Do It Their Way
I • Microbial Nutrients and Nutrient Uptake
3.1 Feeding the Microbe: Cell Nutrition
3.2 Transporting Nutrients into the Cell
II • Energetics, Enzymes, and Redox
3.3 Energy Classes of Microorganisms
3.4 Principles of Bioenergetics
3.5 Catalysis and Enzymes
3.6 Electron Donors and Acceptors
3.7 Energy-Rich Compounds
III • Catabolism: Fermentation and Respiration
3.8 Glycolysis and Fermentation
3.9 Respiration: Citric Acid and Glyoxylate Cycles
3.10 Respiration: Electron Carriers
3.11 Electron Transport and the Proton Motive Force
3.12 Options for Energy Conservation
IV • Biosyntheses
3.13 Sugars and Polysaccharides
3.14 Amino Acids and Nucleotides
3.15 Fatty Acids and Lipids
4 Molecular Information Flow and Protein Processing
microbiologynow Synthesis of Jumbo Proteins: Secretion of Halomucin
I • Molecular Biology and Genetic Elements
4.1 DNA and Genetic Information Flow
4.2 Genetic Elements: Chromosomes and Plasmids
II • Copying the Genetic Blueprint: DNA Replication
4.3 Templates, Enzymes, and the Replication Fork
4.4 Bidirectional Replication, the Replisome, and Proofreading
III • RNA Synthesis: Transcription
4.5 Transcription in Bacteria
4.6 Transcription in Archaea and Eukarya
IV • Protein Synthesis: Translation
4.7 Amino Acids, Polypeptides, and Proteins
4.8 Transfer RNA
4.9 Translation and the Genetic Code
4.10 The Mechanism of Protein Synthesis
V • Protein Processing, Secretion, and Targeting
4.11 Assisted Protein Folding and Chaperones
4.12 Protein Secretion: The Sec and Tat Systems
4.13 Protein Secretion: Gram-Negative Systems
Unit 2 Microbial Growth and Regulation
5 Microbial Growth and Its Control
microbiologynow Picking Apart a Microbial Consortium
I • Cell Division and Population Growth
5.1 Binary Fission, Budding, and Biofilms
5.2 Quantitative Aspects of Microbial Growth
5.3 The Microbial Growth Cycle
5.4 Continuous Culture
II • Culturing Microbes and Measuring Their Growth
5.5 Growth Media and Laboratory Culture
5.6 Microscopic Counts of Microbial Cell Numbers
5.7 Viable Counting of Microbial Cell Numbers
5.8 Turbidimetric Measures of Microbial Cell Numbers
III • Environmental Effects on Growth: Temperature
5.9 Temperature Classes of Microorganisms
5.10 Microbial Life in the Cold
5.11 Microbial Life at High Temperatures
IV • Environmental Effects on Growth: pH, Osmolarity, and Oxygen
5.12 Effects of pH on Microbial Growth
5.13 Osmolarity and Microbial Growth
5.14 Oxygen and Microbial Growth
V • Controlling Microbial Growth
5.15 General Principles and Growth Control by Heat
5.16 Other Physical Control Methods: Radiation and Filtration
5.17 Chemical Control of Microbial Growth
6 Microbial Regulatory Systems
microbiologynow Microbial Hunter: Pseudomonas aeruginosa Senses and Scavenges Nutrients from Damaged Tissues
I • DNA-Binding Proteins and Transcriptional Regulation
6.1 DNA-Binding Proteins
6.2 Negative Control: Repression and Induction
6.3 Positive Control: Activation
6.4 Global Control and the lac Operon
6.5 Transcription Controls in Archaea
II • Sensing and Signal Transduction
6.6 Two-Component Regulatory Systems
6.7 Regulation of Chemotaxis
6.8 Quorum Sensing
6.9 Stringent Response
6.10 Other Global Networks
III • RNA-Based Regulation
6.11 Regulatory RNAs
6.12 Riboswitches
6.13 Attenuation
IV • Regulation of Enzymes and Other Proteins
6.14 Feedback Inhibition
6.15 Post-Translational Regulation
7 Molecular Biology of Microbial Growth
microbiologynow Explosive Cell Death Promotes Biofilm Formation
I • Bacterial Cell Division
7.1 Visualizing Molecular Growth
7.2 Chromosome Replication and Segregation
7.3 Cell Division and Fts Proteins
7.4 MreB and Cell Morphology
7.5 Peptidoglycan Biosynthesis
II • Regulation of Development in Model Bacteria
7.6 Regulation of Endospore Formation
7.7 Caulobacter Differentiation
7.8 Heterocyst Formation in Anabaena
7.9 Biofilm Formation
III • Antibiotics and Microbial Growth
7.10 Antibiotic Targets and Antibiotic Resistance
7.11 Persistence and Dormancy
8 Viruses and Their Replication
microbiologynow Virophages: Viruses That Parasitize Other Viruses
I • The Nature of Viruses
8.1 What Is a Virus?
8.2 Structure of the Virion
8.3 Overview of the Virus Life Cycle
8.4 Culturing, Detecting, and Counting Viruses
II • The Viral Replication Cycle
8.5 Attachment and Entry of Bacteriophage T4
8.6 Replication of Bacteriophage T4
8.7 Temperate Bacteriophages and Lysogeny
8.8 An Overview of Animal Virus Infection
Unit 3 Genomics and Genetics
9 Microbial Systems Biology
microbiologynow DNA Sequencing in the Palm of Your Hand
I • Genomics
9.1 Introduction to Genomics
9.2 Sequencing and Annotating Genomes
9.3 Genome Size and Gene Content in Bacteria and Archaea
9.4 Organelle and Eukaryotic Microbial Genomes
II • The Evolution of Genomes
9.5 Gene Families, Duplications, and Deletions
9.6 Horizontal Gene Transfer and the Mobilome
9.7 Core Genome Versus Pan Genome
III • Functional Omics
9.8 Metagenomics
9.9 Gene Chips and Transcriptomics
9.10 Proteomics and the Interactome
9.11 Metabolomics
IV • The Utility of Systems Biology
9.12 Single-Cell Genomics
9.13 Integrating Mycobacterium tuberculosis Omics
9.14 Systems Biology and Human Health
10 Viral Genomics, Diversity, and Ecology
microbiologynow Viral Imaging to the Rescue: Structural Blueprint of Zika
I • Viral Genomes and Evolution
10.1 Size and Structure of Viral Genomes
10.2 Viral Evolution
II • DNA Viruses
10.3 Single-Stranded DNA Bacteriophages: ?x174 and M13
10.4 Double-Stranded DNA Bacteriophages: T7 and Mu
10.5 Viruses of Archaea
10.6 Uniquely Replicating DNA Animal Viruses
10.7 DNA Tumor Viruses
III • Viruses with RNA Genomes
10.8 Positive-Strand RNA Viruses
10.9 Negative-Strand RNA Animal Viruses
10.10 Double-Stranded RNA Viruses
10.11 Viruses That Use Reverse Transcriptase
IV • Viral Ecology
10.12 The Bacterial and Archael Virosphere
10.13 Viral Defense Mechanisms of Bacteria and Archaea
10.14 The Human Virome
V • Subviral Agents
10.15 Viroids
10.16 Prions
11 Genetics of Bacteria and Archaea
microbiologynow Killing and Stealing: DNA Uptake by the Predator Vibrio cholerae
I • Mutation
11.1 Mutations and Mutants
11.2 Molecular Basis of Mutation
11.3 Reversions and Mutation Rates
11.4 Mutagenesis
II • Gene Transfer in Bacteria
11.5 Genetic Recombination
11.6 Transformation
11.7 Transduction
11.8 Conjugation
11.9 The Formation of Hfr Strains and Chromosome Mobilization
III • Gene Transfer in Archaea and Other Genetic Events
11.10 Horizontal Gene Transfer in Archaea
11.11 Mobile DNA: Transposable Elements
11.12 Preserving Genomic Integrity: CRISPR Interference
12 Biotechnology and Synthetic Biology
microbiologynow Creation of a New Life Form: Design of a Minimal Cell
I • Tools of the Genetic Engineer
12.1 Manipulating DNA: PCR and Nucleic Acid Hybridization
12.2 Molecular Cloning
12.3 Expressing Foreign Genes in Bacteria
12.4 Molecular Methods for Mutagenesis
12.5 Reporter Genes and Gene Fusions
II • Making Products from Genetically Engineered Microbes: Biotechnology
12.6 Somatotropin and Other Mammalian Proteins
12.7 Transgenic Organisms in Agriculture and Aquaculture
12.8 Engineered Vaccines and Therapeutics
12.9 Mining Genomes and Engineering Pathways
12.10 Engineering Biofuels
III • Synthetic Biology and Genome Editing
12.11 From Synthetic Metabolic Pathways to Synthetic Cells
12.12 Genome Editing and CRISPRs
12.13 Biocontainment of Genetically Modified Organisms
Unit 4 Microbial Evolution and Diversity
13 Microbial Evolution and Systematics
microbiologynow Lokiarchaeota and the Origin of Eukarya
I • Early Earth and the Origin and Diversification of Life
13.1 Formation and Early History of Earth
13.2 Photosynthesis and the Oxidation of Earth
13.3 Living Fossils: DNA Records the History of Life
13.4 Endosymbiotic Origin of Eukaryotes
II • Microbial Evolution
13.5 The Evolutionary Process
13.6 The Evolution of Microbial Genomes
III • Microbial Phylogeny and Systematics
13.7 Molecular Phylogeny: Making Sense of Molecular Sequences
13.8 The Species Concept in Microbiology
13.9 Taxonomic Methods in Systematics
13.10 Classification and Nomenclature
Explore the Microbial World
The Black Queen Hypothesis
14 Metabolic Diversity of Microorganisms
microbiologynow Microbes That Plug into the Matrix
I • Phototrophy
14.1 Photosynthesis and Chlorophylls
14.2 Carotenoids and Phycobilins
14.3 Anoxygenic Photosynthesis
14.4 Oxygenic Photosynthesis
II • Autotrophy and N2 Fixation
14.5 Autotrophic Pathways
14.6 Nitrogen Fixation
III • Respiratory Processes Defined by Electron Donor
14.7 Principles of Respiration
14.8 Hydrogen (H2) Oxidation
14.9 Oxidation of Sulfur Compounds
14.10 Iron (Fe2+) Oxidation
14.11 Nitrification
14.12 Anaerobic Ammonia Oxidation (Anammox)
IV • Respiratory Processes Defined by Electron Acceptor
14.13 Nitrate Reduction and Denitrification
14.14 Sulfate and Sulfur Reduction
14.15 Other Electron Acceptors
V • One-Carbon (C1) Metabolism
14.16 Acetogenesis
14.17 Methanogenesis
14.18 Methanotrophy
VI • Fermentation
14.19 Energetic and Redox Considerations
14.20 Lactic and Mixed-Acid Fermentations
14.21 Clostridial and Propionate Fermentations
14.22 Fermentations That Lack Substrate-Level Phosphorylation
14.23 Syntrophy
VII • Hydrocarbon Metabolism
14.24 Aerobic Hydrocarbon Metabolism
14.25 Anaerobic Hydrocarbon Metabolism
15 Functional Diversity of Microorganisms
microbiologynow New Discoveries Have Redefined the Global Nitrogen Cycle
I • Functional Diversity as a Concept
15.1 Making Sense of Microbial Diversity
II • Diversity of Phototrophic Bacteria
15.2 Overview of Phototrophic Bacteria
15.3 Cyanobacteria
15.4 Purple Sulfur Bacteria
15.5 Purple Nonsulfur Bacteria and Aerobic Anoxygenic Phototrophs
15.6 Green Sulfur Bacteria
15.7 Green Nonsulfur Bacteria
15.8 Other Phototrophic Bacteria
III • Microbial Diversity in the Sulfur Cycle
15.9 Dissimilative Sulfate-Reducers
15.10 Dissimilative Sulfur-Reducers
15.11 Dissimilative Sulfur-Oxidizers
IV • Microbial Diversity in the Nitrogen Cycle
15.12 Diversity of Nitrogen-Fixers
15.13 Diversity of Nitrifiers and Denitrifiers
V • Other Distinctive Functional Groupings of Microorganisms
15.14 Dissimilative Iron-Reducers
15.15 Dissimilative Iron-Oxidizers
15.16 Methanotrophs and Methylotrophs
15.17 Microbial Predators
15.18 Microbial Bioluminescence
VI • Morphologically Diverse Bacteria
15.19 Spirochetes
15.20 Budding and Prosthecate/Stalked Microorganisms
15.21 Sheathed Microorganisms
15.22 Magnetic Microbes
16 Diversity of Bacteria
microbiologynow The Mystery of the Missing Peptidoglycan
I • Proteobacteria
16.1 Alphaproteobacteria
16.2 Betaproteobacteria
16.3 Gammaproteobacteria: Enterobacteriales
16.4 Gammaproteobacteria: Pseudomonadales and Vibrionales
16.5 Deltaproteobacteria and Epsilonproteobacteria
II • Firmicutes, Tenericutes, and Actinobacteria
16.6 Firmicutes: Lactobacillales
16.7 Firmicutes: Nonsporulating Bacillales and Clostridiales
16.8 Firmicutes: Sporulating Bacillales and Clostridiales
16.9 Tenericutes: The Mycoplasmas
16.10 Actinobacteria: Coryneform and Propionic Acid Bacteria
16.11 Actinobacteria: Mycobacterium
16.12 Filamentous Actinobacteria: Streptomyces and Relatives
III • Bacteroidetes
16.13 Bacteroidales
16.14 Cytophagales, Flavobacteriales, and Sphingobacteriales
IV • Chlamydiae, Planctomycetes, and Verrucomicrobia
16.15 Chlamydiae
16.16 Planctomycetes
16.17 Verrucomicrobia
V • Hyperthermophilic Bacteria
16.18 Thermotogae and Thermodesulfobacteria
16.19 Aquificae
VI • Other Bacteria
16.20 Deinococcus–Thermus
16.21 Other Notable Phyla of Bacteria
17 Diversity of Archaea
microbiologynow The Archaea Just Under Your Feet
I • Euryarchaeota
17.1 Extremely Halophilic Archaea
17.2 Methanogenic Archaea
17.3 Thermoplasmatales
17.4 Thermococcales and Archaeoglobales
II • Thaumarchaeota, Nanoarchaeota, and Korarchaeota
17.5 Thaumarchaeota and Nitrification in Archaea
17.6 Nanoarchaeota and the “Hospitable Fireball”
17.7 Korarchaeota and the “Secret Filament”
III • Crenarchaeota
17.8 Habitats and Energy Metabolism
17.9 Crenarchaeota from Terrestrial Volcanic Habitats
17.10 Crenarchaeota from Submarine Volcanic Habitats
IV • Evolution and Life at High Temperature
17.11 An Upper Temperature Limit for Microbial Life
17.12 Molecular Adaptations to Life at High Temperature
17.13 Hyperthermophilic Archaea, H2, and Microbial Evolution
18 Diversity of Microbial Eukarya
microbiologynow Arbuscular Mycorrhizal Fungi: Intimate, Unseen, and Powerful
I • Organelles and Phylogeny of Microbial Eukarya
18.1 Endosymbioses and the Eukaryotic Cell
18.2 Phylogenetic Lineages of Eukarya
II • Protists
18.3 Excavata
18.4 Alveolata
18.5 Stramenopiles
18.6 Rhizaria
18.7 Amoebozoa
III • Fungi
18.8 Fungal Physiology, Structure, and Symbioses
18.9 Fungal Reproduction and Phylogeny
18.10 Microsporidia and Chytridiomycota
18.11 Zygomycota and Glomeromycota
18.12 Ascomycota
18.13 Basidiomycota
IV • Archaeplastida
18.14 Red Algae
18.15 Green Algae
Unit 5 Microbial Ecology and Environmental Microbiology
19 Taking the Measure of Microbial Systems
microbiologynow The Vineyard Microbiome Revealed by Next-Generation Sequencing Technology
I • Culture-Dependent Analyses of Microbial Communities
19.1 Enrichment Culture Microbiology
19.2 Classical Procedures for Isolating Microbes
19.3 Selective Single-Cell Isolation: Laser Tweezers, Flow Cytometry, Microfluidics, and High-Throughput Methods
II • Culture-Independent Microscopic Analyses of Microbial Communities
19.4 General Staining Methods
19.5 Fluorescence In Situ Hybridization (FISH)
III • Culture-Independent Genetic Analyses of Microbial Communities
19.6 PCR Methods of Microbial Community Analysis
19.7 Microarrays for Analysis of Microbial Phylogenetic and Functional Diversity
19.8 Environmental Genomics and Related Methods
IV • Measuring Microbial Activities in Nature
19.9 Chemical Assays, Radioisotopic Methods, and Microsensors
19.10 Stable Isotopes and Stable Isotope Probing
19.11 Linking Functions to Specific Organisms
19.12 Linking Genes and Cellular Properties to Individual Cells
20 Microbial Ecosystems
microbiologynow Microbes of the Abyss
I • Microbial Ecology
20.1 General Ecological Concepts
20.2 Ecosystem Service: Biogeochemistry and Nutrient Cycles
II • The Microbial Environment
20.3 Environments and Microenvironments
20.4 Surfaces and Biofilms
20.5 Microbial Mats
III • Terrestrial Environments
20.6 Soils
20.7 The Terrestrial Subsurface
IV • Aquatic Environments
20.8 Freshwaters
20.9 The Marine Environment: Phototrophs and Oxygen Relationships
20.10 Major Marine Phototrophs
20.11 Pelagic Bacteria, Archaea, and Viruses
20.12 The Deep Sea
20.13 Deep-Sea Sediments
20.14 Hydrothermal Vents
21 Nutrient Cycles
microbiologynow The Big Thaw and the Microbiology of Climate Change
I • Carbon, Nitrogen, and Sulfur Cycles
21.1 The Carbon Cycle
21.2 Syntrophy and Methanogenesis
21.3 The Nitrogen Cycle
21.4 The Sulfur Cycle
II • Other Nutrient Cycles
21.5 The Iron and Manganese Cycles
21.6 The Phosphorus, Calcium, and Silica Cycles
III • Humans and Nutrient Cycling
21.7 Mercury Transformations
21.8 Human Impacts on the Carbon and Nitrogen Cycles
Explore the Microbial World
Microbially Wired
22 Microbiology of the Built Environment
microbiologynow After the Toilet Flushes
I • Mineral Recovery and Acid Mine Drainage
22.1 Mining with Microorganisms
22.2 Acid Mine Drainage
II • Bioremediation
22.3 Bioremediation of Uranium-Contaminated Environments
22.4 Bioremediation of Organic Pollutants: Hydrocarbons
22.5 Bioremediation of Organic Pollutants: Pesticides and Plastics
III • Wastewater and Drinking Water Treatment
22.6 Primary and Secondary Wastewater Treatment
22.7 Advanced Wastewater Treatment
22.8 Drinking Water Purification and Stabilization
22.9 Water Distribution Systems
IV • Indoor Microbiology and Microbially Influenced Corrosion
22.10 The Microbiology of Homes and Public Spaces
22.11 Microbially Influenced Corrosion of Metals
22.12 Biodeterioration of Stone and Concrete
23 Microbial Symbioses with Microbes, Plants, and Animals
microbiologynow The Inner Life of Bees
I • Symbioses between Microorganisms
23.1 Lichens
23.2 “Chlorochromatium aggregatum”
II • Plants as Microbial Habitats
23.3 The Legume–Root Nodule Symbiosis
23.4 Mycorrhizae
23.5 Agrobacterium and Crown Gall Disease
III • Insects as Microbial Habitats
23.6 Heritable Symbionts of Insects
23.7 Termites
IV • Other Invertebrates as Microbial Habitats
23.8 Hawaiian Bobtail Squid
23.9 Marine Invertebrates at Hydrothermal Vents and Cold Seeps
23.10 Entomopathogenic Nematodes
23.11 Reef-Building Corals
V • Mammalian Gut Systems as Microbial Habitats
23.12 Alternative Mammalian Gut Systems
23.13 The Rumen and Ruminant Animals
Explore the Microbial World
The Multiple Microbial Symbionts of Fungus-Cultivating Ants
Unit 6 Microbe–Human Interactions and the Immune System
24 Microbial Symbioses with Humans
microbiologynow Frozen in Time: The Iceman Microbiome
I • Structure and Function of the Healthy Adult Human Microbiome
24.1 Overview of the Human Microbiome
24.2 Gastrointestinal Microbiota
24.3 Oral Cavity and Airways
24.4 Urogenital Tracts and Their Microbes
24.5 The Skin and Its Microbes
II • From Birth to Death: Development of the Human Microbiome
24.6 Human Study Groups and Animal Models
24.7 Colonization, Succession, and Stability of the Gut Microbiota
III • Disorders Attributed to the Human Microbiome
24.8 Disorders Attributed to the Gut Microbiota
24.9 Disorders Attributed to the Oral, Skin, and Vaginal Microbiota
IV • Modulation of the Human Microbiome
24.10 Antibiotics and the Human Microbiome
24.11 Probiotics and Prebiotics
Explore the Microbial World
The Gut–Brain Axis
25 Microbial Infection and Pathogenesis
microbiologynow The Microbial Community That Thrives on Your Teeth
I • Human–Microbial Interactions
25.1 Microbial Adherence
25.2 Colonization and Invasion
25.3 Pathogenicity, Virulence, and Attenuation
25.4 Genetics of Virulence and the Compromised Host
II • Enzymes and Toxins of Pathogenesis
25.5 Enzymes as Virulence Factors
25.6 AB-Type Exotoxins
25.7 Cytolytic and Superantigen Exotoxins
25.8 Endotoxins
26 Innate Immunity: Broadly Specific Host Defenses
microbiologynow Rehabilitating a Much-Maligned Peptide: Amyloid-b
I • Fundamentals of Host Defense
26.1 Basic Properties of the Immune System
26.2 Barriers to Pathogen Invasion
II • Cells and Organs of the Immune System
26.3 The Blood and Lymphatic Systems
26.4 Leukocyte Production and Diversity
III • Phagocyte Response Mechanisms
26.5 Pathogen Challenge and Phagocyte Recruitment
26.6 Pathogen Recognition and Phagocyte Signal Transduction
26.7 Phagocytosis and Phagocyte Inhibition
IV • Other Innate Host Defenses
26.8 Inflammation and Fever
26.9 The Complement System
26.10 Innate Defenses against Viruses
Explore the Microbial World
Drosophila Toll Receptors—An Ancient Response to Infections
27 Adaptive Immunity: Highly Specific Host Defenses
microbiologynow Got (Raw) Milk? The Role of Unprocessed Cow’s Milk in Protecting against Allergy and Asthma
I • Principles of Adaptive Immunity
27.1 Specificity, Memory, Selection Processes, and Tolerance
27.2 Immunogens and Classes of Immunity
II • Antibodies
27.3 Antibody Production and Structural Diversity
27.4 Antigen Binding and the Genetics of Antibody Diversity
III • The Major Histocompatibility Complex (MHC)
27.5 MHC Proteins and Their Functions
27.6 MHC Polymorphism, Polygeny, and Peptide Binding
IV • T Cells and Their Receptors
27.7 T Cell Receptors: Proteins, Genes, and Diversity
27.8 T Cell Diversity
V • Immune Disorders and Deficiencies
27.9 Allergy, Hypersensitivity, and Autoimmunity
27.10 Superantigens and Immunodeficiency
28 Clinical Microbiology and Immunology
microbiologynow Bacteriophages: Tiny Allies in the Fight against Antibiotic-Resistant Bacteria
I • The Clinical Microbiology Setting
28.1 Safety in the Microbiology Laboratory
28.2 Healthcare-Associated Infections
II • Isolating and Characterizing Infectious Microorganisms
28.3 Workflow in the Clinical Laboratory
28.4 Choosing the Right Treatment
III • Immunological and Molecular Tools for Disease Diagnosis
28.5 Immunoassays and Disease
28.6 Precipitation, Agglutination, and Immunofluorescence
28.7 Enzyme Immunoassays, Rapid Tests, and Immunoblots
28.8 Nucleic Acid–Based Clinical Assays
IV • Prevention and Treatment of Infectious Diseases
28.9 Vaccination
28.10 Antibacterial Drugs
28.11 Antimicrobial Drugs That Target Nonbacterial Pathogens
28.12 Antimicrobial Drug Resistance and New Treatment Strategies
Explore the Microbial World
MRSA—A Formidable Clinical Challenge
Unit 7 Infectious Diseases and Their Transmission
29 Epidemiology
microbiologynow A Mysterious New Disease Outbreak
I • Principles of Epidemiology
29.1 The Language of Epidemiology
29.2 The Host Community
29.3 Infectious Disease Transmission and Reservoirs
29.4 Characteristics of Disease Epidemics
II • Epidemiology and Public Health
29.5 Public Health and Infectious Disease
29.6 Global Health Comparisons
III • Emerging Infectious Diseases, Pandemics, and Other Threats
29.7 Emerging and Reemerging Infectious Diseases
29.8 Examples of Pandemics: HIV/AIDS, Cholera, and Influenza
29.9 Public Health Threats from Microbial Weapons
Explore the Microbial World
Textbook Epidemiology: The SARS Epidemic
30 Person-to-Person Bacterial and Viral Diseases
microbiologynow A New Weapon against AIDS?
I • Airborne Bacterial Diseases
30.1 Airborne Pathogens
30.2 Streptococcal Syndromes
30.3 Diphtheria and Pertussis
30.4 Tuberculosis and Leprosy
30.5 Meningitis and Meningococcemia
II • Airborne Viral Diseases
30.6 MMR and Varicella-Zoster Infections
30.7 The Common Cold
30.8 Influenza
III • Direct-Contact Bacterial and Viral Diseases
30.9 Staphylococcus aureus Infections
30.10 Helicobacter pylori and Gastric Diseases
30.11 Hepatitis
30.12 Ebola: A Deadly Threat
IV • Sexually Transmitted Infections
30.13 Gonorrhea and Syphilis
30.14 Chlamydia, Herpes, and Human Papillomavirus
30.15 HIV/AIDS
31 Vectorborne and Soilborne Bacterial and Viral Diseases
microbiologynow A New Look at Rabies Vaccines
I • Animal-Transmitted Viral Diseases
31.1 Rabies Virus and Rabies
31.2 Hantavirus and Hantavirus Syndromes
II • Arthropod-Transmitted Bacterial and Viral Diseases
31.3 Rickettsial Diseases
31.4 Lyme Disease and Borrelia
31.5 Yellow Fever, Dengue Fever, Chikungunya, and Zika
31.6 West Nile Fever
31.7 Plague
III • Soilborne Bacterial Diseases
31.8 Anthrax
31.9 Tetanus and Gas Gangrene
32 Waterborne and Foodborne Bacterial and Viral Diseases
microbiologynow The Classic Botulism Scenario
I • Water as a Disease Vehicle
32.1 Agents and Sources of Waterborne Diseases
32.2 Public Health and Water Quality
II • Waterborne Diseases
32.3 Vibrio cholerae and Cholera
32.4 Legionellosis
32.5 Typhoid Fever and Norovirus Illness
III • Food as a Disease Vehicle
32.6 Food Spoilage and Food Preservation
32.7 Foodborne Disease and Food Epidemiology
IV • Food Poisoning
32.8 Staphylococcal Food Poisoning
32.9 Clostridial Food Poisoning
V • Food Infection
32.10 Salmonellosis
32.11 Pathogenic Escherichia coli
32.12 Campylobacter
32.13 Listeriosis
32.14 Other Foodborne Infectious Diseases
33 Eukaryotic Pathogens: Fungi, Protozoa, and Helminths
microbiologynow Environmental Change and Parasitic Diseases in the Amazon
I • Fungal Infections
33.1 Pathogenic Fungi and Classes of Infection
33.2 Fungal Diseases: Mycoses
II • Visceral Parasitic Infections
33.3 Amoebae and Ciliates: Entamoeba, Naegleria, and Balantidium
33.4 Other Visceral Parasites: Giardia, Trichomonas, Cryptosporidium, Toxoplasma, and Cyclospora
III • Blood and Tissue Parasitic Infections
33.5 Plasmodium and Malaria
33.6 Leishmaniasis, Trypanosomiasis, and Chagas Disease
33.7 Parasitic Helminths: Schistosomiasis and Filariases
Photo Credits
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