Talaro’s Foundations in Microbiology – Basic Principles

Description:

Talaro’s Foundations in Microbiology: Basic Principles is an allied health microbiology text with a taxonomic approach to the disease chapters. It offers an engaging and accessible writing style through the use of case studies and analogies to thoroughly explain difficult microbiology concepts.

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About the Author

Barry Chess has taught microbiology at Pasadena City College (PCC) for more than 20 years. Prior to that, while studying at the California State University and the University of California, he conducted research into the expression of genes involved in the development of muscle and bone.

At PCC, beyond his usual presence in the microbiology laboratory and lecture hall, Barry has taught majors and non-majors biology, developed a course in human genetics, helped to found a biotechnology program on campus, and regularly supervises students completing independent research projects in the life sciences. Of late, his interests focus on innovative methods of teaching that lead to greater student success. He has written and reviewed cases for the National Center for Case Study Teaching in Science and contributed to the book Science Stories You Can Count On: 51 Case Studies with Quantitative Reasoning in Biology. Barry has presented papers and talks on the effective use of case studies in the classroom, the use of digital tools to enhance learning, and for several years served as a scientific advisor for the American Film Institute.

In addition to Foundations in Microbiology, Barry is the author of Laboratory Applications in Microbiology, A Case Study Approach, now in its fourth edition. He is a member of the American Association for the Advancement of Science, the American Society for Microbiology, and the Skeptics Society. When not teaching or writing, he spends as much time as possible skiing, diving, or hiking with Toby, his 110 pound pandemic puppy. Barry was profiled in the book What Scientists Actually Do, where he was illustrated as a young girl with pigtails, about to stick a fork into an electrical outlet.

Acknowledgments

The idea of “writing a book” has changed considerably over the last several years. It used to be ink on paper, very straightforward. Now it’s ink on paper, online content, clickable links, and the whole thing downloads to your phone. Two things I’m grateful for. First, I’m not responsible for most of that, and second, I have a whole bunch of help.

Those who do know about online content and clickable links— and typefaces, paper types, permissions, and everything else that goes into a book—are the remarkable people at McGraw Hill. It is impossible for me to thank them adequately, so I will thank them inadequately: Portfolio Manager Lauren Vondra, Lead Product Developer Krystal Faust, Sales Manager Tami Hodge, Project Manager Jeni McAtee, Content Licensing Specialist Lorraine Buczek, Designer David Hash, and Copy Editor Kevin Campbell. These are the hosts of the reality show Let’s Write a Textbook, where they bring their considerable powers to bear on, well, me, I suppose. Without them, Foundations in Microbiology would not exist, and it is my great good fortune to work with them once again.

Despite the careful work of all these people, typos, errors, and oversights may make it to the printed page. These errors belong solely to me. If you find an error or wish to make other comments, feel free to contact the publisher, sales representative, or myself (barry.chess.micro@gmail.com). Enjoy.

—Barry Chess

To the Student

In this space I usually write something about microbiology being an invisible science, and despite our close and constant interactions with microorganisms of all sorts, the subject is the very definition of “out of sight, out of mind.”
Not anymore.

The last 3 years have been dominated by one thing, and without setting foot in a micro classroom or reading a single textbook page, you’ve taken a crash course in at least some aspects of microbiology. You know about viral spikes, ivermectin, and herd immunity, and you’ve had more than one conversation with a stranger over the side effects of the Moderna versus Pfizer vaccines. You’ve received a scattershot course on microbiology, focused on a single organism (and most will say it’s not an organism at all, but let us put off that discussion for six chapters) and driven in countless cases by people with an agenda that has nothing to do with facts. My hope is that we can improve upon that.

For most of you, this course is a required prerequisite for your chosen career, but microbiology is so much more. From before we’re born until after we die, we have an intimate association with all manner of microorganisms, and the goal of this book is to make these relationships more familiar. Which organisms are dangerous? Beneficial? Useful? Along the way, there will be Greek terminology, a little chemistry, and some math. Sorry.

As you use this book, please, use this book; it was designed solely with you in mind. Study the photographs, look up unfamiliar words, answer the questions, and make the information yours. Without even being aware of it, you’ll gain a greater understanding of not only the world around you, but the world within you. Not a bad way to spend some time.

—Barry Chess

Table of contents :

Cover
Title
Copyright
Brief Contents
About the Author
Acknowledgments
To the Student
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
The Changing Specter of Infectious Diseases
Microbial Roles in Noninfectious 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 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
Prokaryotic 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 Reactions of Life
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
RNA and 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 and Genetic Analysis
10.1 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
Standard 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
Science Photo Library/ Alamy Stock Photo
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?
Vaccine Protection: Magical but Not Magic
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
Point-of-Care and Rapid Diagnostic Tests
Miscellaneous Serological Tests
Fluorescent Antibody and Immunofluorescent Testing
John Watney/Science Source
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
Glossary