Talaro's Foundations in Microbiology: Basic Principles

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Brief Contents
About the Author
Acknowledgments
Contents
CHAPTER 1: The Main Themes of Microbiology
	1.1 The Scope of Microbiology
	1.2 General Characteristics of Microorganisms and Their Roles in the Earth's Environments
		The Origins and Dominance of Microorganisms
		The Cellular Organization of Microorganisms
		Noncellular Pathogenic Particles—Viruses and Prions
		Microbial Dimensions: How Small Is Small?
		Microbial Involvement in Energy and Nutrient Flow
	1.3 Human Use of Microorganisms
	1.4 Microbial Roles in Infectious Diseases
	1.5 The Historical Foundations of Microbiology
		The Development of the Microscope: Seeing Is Believing
		The Scientific Method and the Search for Knowledge
		The Development of Medical Microbiology
	1.6 Taxonomy: Organizing, Classifying, and Naming Microorganisms
		The Levels of Classification
		Assigning Scientific Names
	1.7 The Origin and Evolution of Microorganisms
		All Life Is Related and Connected Through Evolution
		Systems for Presenting a Universal Tree of Life
CHAPTER 2: The Chemistry of Biology
	2.1 Atoms: Fundamental Building Blocks of All Matter in the Universe
		Different Types of Atoms: Elements and Their Properties
		The Major Elements of Life and Their Primary Characteristics
	2.2 Bonds and Molecules
		Covalent Bonds: Molecules with Shared Electrons
		Ionic Bonds: Electron Transfer Among Atoms
		Electron Transfer and Oxidation-Reduction Reactions
	2.3 Chemical Reactions, Solutions, and pH
		Formulas, Models, and Equations
		Solutions: Homogeneous Mixtures of Molecules
		Acidity, Alkalinity, and the pH Scale
	2.4 The Chemistry of Carbon and Organic Compounds
		Functional Groups of Organic Compounds
		Organic Macromolecules: Superstructures of Life
	2.5 Molecules of Life: Carbohydrates
		The Nature of Carbohydrate Bonds
		The Functions of Carbohydrates in Cells
	2.6 Molecules of Life: Lipids
		Membrane Lipids
		Miscellaneous Lipids
	2.7 Molecules of Life: Proteins
		Protein Structure and Diversity
	2.8 Nucleic Acids: A Program for Genetics
		The Double Helix of DNA
		Making New DNA: Passing on the Genetic Message
		RNA: Organizers of Protein Synthesis
		ATP: The Energy Molecule of Cells
CHAPTER 3: Tools of the Laboratory: Methods of Studying Microorganisms
	3.1 Methods of Microbial Investigation
	3.2 The Microscope: Window on an Invisible Realm
		Magnification and Microscope Design
		Variations on the Optical Microscope
		Electron Microscopy
	3.3 Preparing Specimens for Optical Microscopes
		Fresh, Living Preparations
		Fixed, Stained Smears
	3.4 Additional Features of the Six "I"s
		Inoculation, Growth, and Identification of Cultures
		Isolation Techniques
		Identification Techniques
	3.5 Media: The Foundations of Culturing
		Types of Media
		Physical States of Media
		Chemical Content of Media
		Media to Suit Every Function
CHAPTER 4: A Survey of Prokaryotic Cells and Microorganisms
	4.1 Basic Characteristics of Cells and Life Forms
		What Is Life?
	4.2 Prokaryotic Profiles: The Bacteria and Archaea
		The Structure of a Generalized Bacterial Cell
		Cell Extensions and Surface Structures
		Biofilms
	4.3 The Cell Envelope: The Outer Boundary Layer of Bacteria
		Basic Types of Cell Envelopes
		Structure of Cell Walls
		The Cell Wall and Infections
		Mycoplasmas and Other Cell-Wall-Deficient Bacteria
		Cell Membrane Structure
	4.4 Bacterial Internal Structure
		Contents of the Cell Cytoplasm
		Bacterial Endospores: An Extremely Resistant Life Form
	4.5 Bacterial Shapes, Arrangements, and Sizes
	4.6 Classification Systems of Prokaryotic Domains: Archaea and Bacteria
		Bacterial Taxonomy: A Work in Progress
	4.7 Survey of Prokaryotic Groups with Unusual Characteristics
		Free-Living Nonpathogenic Bacteria
		Unusual Forms of Medically Significant Bacteria
		Archaea: The Other Prokaryotes
CHAPTER 5: A Survey of Eukaryotic Cells and Microorganisms
	5.1 The History of Eukaryotes
	5.2 Form and Function of the Eukaryotic Cell: External Structures
		Locomotor Appendages: Cilia and Flagella
		The Glycocalyx
		Form and Function of the Eukaryotic Cell: Boundary Structures
	5.3 Form and Function of the Eukaryotic Cell: Internal Structures
		The Nucleus: The Control Center
		Endoplasmic Reticulum: A Passageway and Production System for Eukaryotes
		Golgi Apparatus: A Packaging Machine
		Mitochondria: Energy Generators of the Cell
		Chloroplasts: Photosynthesis Machines
		Ribosomes: Protein Synthesizers
		The Cytoskeleton: A Support Network
	5.4 Eukaryotic-Prokaryotic Comparisons and Taxonomy of Eukaryotes
		Overview of Taxonomy
	5.5 The Kingdom Fungi
		Fungal Nutrition
		Organization of Microscopic Fungi
		Reproductive Strategies and Spore Formation
		Fungal Classification
		Fungal Identification and Cultivation
		Fungi in Medicine, Nature, and Industry
	5.6 Survey of Protists: Algae
		The Algae: Photosynthetic Protists
	5.7 Survey of Protists: Protozoa
		Protozoan Form and Function
		Protozoan Identification and Cultivation
		Important Protozoan Pathogens
	5.8 The Parasitic Helminths
		General Worm Morphology
		Life Cycles and Reproduction
		A Helminth Cycle: The Pinworm
		Helminth Classification and Identification
		Distribution and Importance of Parasitic Worms
CHAPTER 6: An Introduction to Viruses, Viroids, and Prions
	6.1 Overview of Viruses
		Early Searches for the Tiniest Microbes
		The Position of Viruses in the Biological Spectrum
	6.2 The General Structure of Viruses
		Size Range
		Viral Components: Capsids, Nucleic Acids, and Envelopes
	6.3 How Viruses Are Classified and Named
	6.4 Modes of Viral Multiplication
		Multiplication Cycles in Animal Viruses
		Persistent Viral Infection and Viral Integration
	6.5 The Multiplication Cycle in Bacteriophages
		Lysogeny: The Silent Virus Infection
	6.6 Techniques in Cultivating and Identifying Animal Viruses
		Using Cell (Tissue) Culture Techniques
		Using Bird Embryos
		Using Live Animal Inoculation
	6.7 Viral Infection, Detection, and Treatment
	6.8 Prions and Other Nonviral Infectious Particles
CHAPTER 7: Microbial Nutrition, Ecology, and Growth
	7.1 Microbial Nutrition
		Chemical Analysis of Cell Contents
		Forms, Sources, and Functions of Essential Nutrients
	7.2 Classification of Nutritional Types
		Autotrophs and Their Energy Sources
		Heterotrophs and Their Energy Sources
	7.3 Transport: Movement of Substances Across the Cell Membrane
		Diffusion and Molecular Motion
		The Diffusion of Water: Osmosis
		Adaptations to Osmotic Variations in the Environment
		The Movement of Solutes Across Membranes
		Active Transport: Bringing in Molecules Against a Gradient
		Endocytosis: Eating and Drinking by Cells
	7.4 Environmental Factors That Influence Microbes
		Adaptations to Temperature
		Gas Requirements
		Effects of pH
		Osmotic Pressure
		Miscellaneous Environmental Factors
	7.5 Ecological Associations Among Microorganisms
	7.6 The Study of Microbial Growth
		The Basis of Population Growth: Binary Fission and the Bacterial Cell Cycle
		The Rate of Population Growth
		Determinants of Population Growth
		Other Methods of Analyzing Population Growth
CHAPTER 8: An Introduction to Microbial Metabolism: The Chemical Crossroads of Life
	8.1 An Introduction to Metabolism and Enzymes
		Enzymes: Catalyzing the Chemical
		Regulation of Enzymatic Activity and Metabolic Pathways
	8.2 The Pursuit and Utilization of Energy
		Cell Energetics
	8.3 Pathways of Bioenergetics
		Catabolism: An Overview of Nutrient Breakdown and Energy Release
		Energy Strategies in Microorganisms
		Aerobic Respiration
		Pyruvic Acid—A Central Metabolite
		The Krebs Cycle—A Carbon and Energy Wheel
		The Respiratory Chain: Electron Transport and Oxidative Phosphorylation
		Summary of Aerobic Respiration
		Anaerobic Respiration
	8.4 The Importance of Fermentation
	8.5 Biosynthesis and the Crossing Pathways of Metabolism
		The Frugality of the Cell—Waste Not, Want Not
		Assembly of the Cell
	8.6 Photosynthesis: The Earth's Lifeline
		Light-Dependent Reactions
		Light-Independent Reactions
		Other Mechanisms of Photosynthesis
CHAPTER 9: An Introduction to Microbial Genetics
	9.1 Introduction to Genetics and Genes: Unlocking the Secrets of Heredity
		The Nature of the Genetic Material
		The Structure of DNA: A Double Helix with Its Own Language
		DNA Replication: Preserving the Code and Passing It On
	9.2 Applications of the DNA Code: Transcription and Translation
		The Gene-Protein Connection
		The Major Participants in Transcription and Translation
		Transcription: The First Stage of Gene Expression
		Translation: The Second Stage of Gene Expression
		Eukaryotic Transcription and Translation: Similar yet Different
	9.3 Genetic Regulation of Protein Synthesis and Metabolism
		The Lactose Operon: A Model for Inducible Gene Regulation in Bacteria
		A Repressible Operon
		Additional Methods of Gene Expression
	9.4 Mutations: Changes in the Genetic Code
		Causes of Mutations
		Categories of Mutations
		Repair of Mutations
		The Ames Test
		Positive and Negative Effects of Mutations
	9.5 DNA Recombination Events
		Transmission of Genetic Material in Bacteria
	9.6 The Genetics of Animal Viruses
		Replication Strategies in Animal Viruses
CHAPTER 10: Genetic Engineering: A Revolution in Molecular Biology
	10.1 Basic Elements and Applications of Genetic Engineering
		Tools and Techniques of DNA Technology
	10.2 Recombinant DNA Technology: How to Imitate Nature
		Technical Aspects of Recombinant DNA and Gene Cloning
		Construction of a Recombinant, Insertion into a Cloning Host, and Genetic Expression
		Protein Products of Recombinant DNA Technology
	10.3 Genetically Modified Organisms and Other Applications
		Recombinant Microbes: Modified Bacteria and Viruses
		Recombination in Multicellular Organisms
		Medical Applications of DNA Technology
	10.4 Genome Analysis: DNA Profiling and Genetic Testing
		DNA Profiling: A Unique Picture of a Genome
CHAPTER 11: Physical and Chemical Agents for Microbial Control
	11.1 Controlling Microorganisms
		General Considerations in Microbial Control
		Relative Resistance of Microbial Forms
		Terminology and Methods of Microbial Control
		What Is Microbial Death?
		How Antimicrobial Agents Work: Their Modes of Action
	11.2 Physical Methods of Control: Heat
		Effects of Temperature on Microbial Activities
		The Effects of Cold and Desiccation
	11.3 Physical Methods of Control: Radiation and Filtration
		Radiation as a Microbial Control Agent
		Modes of Action of Ionizing Versus Nonionizing Radiation
		Ionizing Radiation: Gamma Rays and X-Rays
		Nonionizing Radiation: Ultraviolet Rays
		Filtration—A Physical Removal Process
	11.4 Chemical Agents in Microbial Control
		Choosing a Microbicidal Chemical
		Factors That Affect the Germicidal Activities of Chemical Agents
		Categories of Chemical Agents
CHAPTER 12: Drugs, Microbes, Host—The Elements of Chemotherapy
	12.1 Principles of Antimicrobial Therapy
		The Origins of Antimicrobial Drugs
		Interactions Between Drugs and Microbes
	12.2 Survey of Major Antimicrobial Drug Groups
		Antibacterial Drugs That Act on the Cell Wall
		Antibiotics That Damage Bacterial Cell Membranes
		Drugs That Act on DNA or RNA
		Drugs That Interfere with Protein Synthesis
		Drugs That Block Metabolic Pathways
	12.3 Drugs to Treat Fungal, Parasitic, and Viral Infections
		Antifungal Drugs
		Antiparasitic Chemotherapy
		Antiviral Chemotherapeutic Agents
	12.4 Interactions Between Microbes and Drugs: The Acquisition of Drug Resistance
		How Does Drug Resistance Develop?
		Specific Mechanisms of Drug Resistance
		Natural Selection and Drug Resistance
	12.5 Interactions Between Drugs and Hosts
		Toxicity to Organs
		Allergic Responses to Drugs
		Suppression and Alteration of the Microbiota by Antimicrobials
	12.6 The Process of Selecting an Antimicrobial Drug
		Identifying the Agent
		Testing for the Drug Susceptibility of Microorganisms
		The MIC and the Therapeutic Index
		Patient Factors in Choosing an Antimicrobial Drug
CHAPTER 13: Microbe-Human Interactions: Infection, Disease, and Epidemiology
	13.1 We Are Not Alone
		Contact, Colonization, Infection, Disease
		Resident Microbiota: The Human as a Habitat
		Indigenous Microbiota of Specific Regions
		Colonizers of the Human Skin
		Microbial Residents of the Gastrointestinal Tract
		Inhabitants of the Respiratory Tract
		Microbiota of the Genitourinary Tract
	13.2 Major Factors in the Development of an Infection
		Becoming Established: Phase 1—Portals of Entry
		The Requirement for an Infectious Dose
		Attaching to the Host: Phase 2
		Invading the Host and Becoming Established: Phase 3
	13.3 The Outcomes of Infection and Disease
		The Stages of Clinical Infections
		Patterns of Infection
		Signs and Symptoms: Warning Signals of Disease
		The Portal of Exit: Vacating the Host
		The Persistence of Microbes and Pathologic Conditions
	13.4 Epidemiology: The Study of Disease in Populations
		Origins and Transmission Patterns of Infectious Microbes
		The Acquisition and Transmission of Infectious Agents
	13.5 The Work of Epidemiologists: Investigation and Surveillance
		Epidemiological Statistics: Frequency of Cases
		Investigative Strategies of the Epidemiologist
		Hospital Epidemiology and Healthcare-Associated Infections
		Universal Blood and Body Fluid Precautions
CHAPTER 14: An Introduction to Host Defenses and Innate Immunities
	14.1 Overview of Host Defense Mechanisms
		Barriers at the Portal of Entry: An Inborn First Line of Defense
	14.2 Structure and Function of the Organs of Defense and Immunity
		How Do White Blood Cells Carry Out Recognition and Surveillance?
		Compartments and Connections of the Immune System
	14.3 Second-Line Defenses: Inflammation
		The Inflammatory Response: A Complex Concert of Reactions to Injury
		The Stages of Inflammation
	14.4 Second-Line Defenses: Phagocytosis, Interferon, and Complement
		Phagocytosis: Ingestion and Destruction by White Blood Cells
		Interferon: Antiviral Cytokines and Immune Stimulants
		Complement: A Versatile Backup System
		An Outline of Major Host Defenses
CHAPTER 15: Adaptive, Specific Immunity, and Immunization
	15.1 Specific Immunities: The Adaptive Line of Defense
		An Overview of Specific Immune Responses
		Development of the Immune Response System
		Specific Events in T-Cell Maturation
		Specific Events in B-Cell Maturation
	15.2 The Nature of Antigens and Antigenicity
		Characteristics of Antigens and Immunogens
	15.3 Immune Reactions to Antigens and the Activities of T Cells
		The Role of Antigen Processing and Presentation
		T-Cell Responses and Cell-Mediated Immunity (CMI)
	15.4 Immune Activities of B Cells
		Events in B-Cell Responses
		Monoclonal Antibodies: Specificity in the Extreme
	15.5 A Classification Scheme for Specific, Acquired Immunities
		Defining Categories by Mode of Acquisition
	15.6 Immunization: Providing Immune Protection Through Therapy
		Artificial Passive Immunization
		Artificial Active Immunity: Vaccination
		Development of New Vaccines
		Routes of Administration and Side Effects of Vaccines
		To Vaccinate: Why, Whom, and When?
CHAPTER 16: Disorders in Immunity
	16.1 The Immune Response: A Two-Sided Coin
		Overreactions to Antigens: Allergy/Hypersensitivity
	16.2 Allergic Reactions: Atopy and Anaphylaxis
		Modes of Contact with Allergens
		The Nature of Allergens and Their Portals of Entry
		Mechanisms of Allergy: Sensitization and Provocation
		Cytokines, Target Organs, and Allergic Symptoms
		Specific Diseases Associated with IgE- and Mast-Cell-Mediated Allergy
		Anaphylaxis: A Powerful Systemic Reaction to Allergens
		Diagnosis of Allergy
		Treatment and Prevention of Allergy
	16.3 Type II Hypersensitivities: Reactions That Lyse Foreign Cells
		The Basis of Human ABO Antigens and Blood Types
		Antibodies Against A and B Antigens
		The Rh Factor and Its Clinical Importance
	16.4 Type III Hypersensitivities: Immune Complex Reactions
		Mechanisms of Immune Complex Diseases
		Types of Immune Complex Disease
	16.5 Immunopathologies Involving T Cells
		Type IV Delayed Hypersensitivity
		T Cells in Relation to Organ Transplantation
		Practical Examples of Transplantation
	16.6 Autoimmune Diseases: An Attack on Self
		Genetic and Gender Correlation in Autoimmune Disease
		The Origins of Autoimmune Disease
		Examples of Autoimmune Disease
	16.7 Immunodeficiency Diseases and Cancer: Compromised Immune Responses
		Primary Immunodeficiency Diseases
		Secondary Immunodeficiency Diseases
		The Role of the Immune System in Cancer
CHAPTER 17: Procedures for Identifying Pathogens and Diagnosing Infections
	17.1 An Overview of Clinical Microbiology
		Phenotypic Methods
		Genotypic Methods
		Immunologic Methods
		On the Track of the Infectious Agent: Specimen Collection
	17.2 Phenotypic Methods
		Immediate Direct Examination of Specimen
		Cultivation of Specimen
	17.3 Genotypic Methods
		DNA Analysis Using Genetic Probes
		Roles of the Polymerase Chain Reaction and Ribosomal RNA in Identification
	17.4 Immunologic Methods
		General Features of Immune Testing
		Agglutination and Precipitation Reactions
		The Western Blot for Detecting Proteins
		Complement Fixation
		Miscellaneous Serological Tests
		Fluorescent Antibody and Immunofluorescent Testing
	17.5 Immunoassays: Tests with High Sensitivity
		Radioimmunoassay (RIA)
		Enzyme-Linked Immunosorbent Assay (ELISA)
	17.6 Viruses as a Special Diagnostic Case
APPENDIX A Detailed Steps in the Glycolysis Pathway
APPENDIX B Tests and Guidelines
APPENDIX C General Classification Techniques and Taxonomy of Bacteria
APPENDIX D Answers to End of Chapter Questions
ONLINE APPENDICES An Introduction to Concept Mapping, Significant Events in Microbiology, Exponents, and Classification of Major Microbial Disease Agents by System Affected, Site of Infection, and Routes of Transmission
Glossary
Index