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    Cover
    Title Page
    Copyright Page
    Dedications
    About the Authors
    Why We Wrote This Book
    Special Features
    Key Features
    Acknowledgments
    Brief Contents
    Contents
    Chapter 1: The Microbial World
    Chapter Navigator
    Introduction
    1.1 The Microbes
    The Basis of life
    Chemical Makeup of Cells
    The Domains of Life
    Viruses
    Microbes as Research Models
    1.2 Microbial Genetics
    The Evolution of Life on Earth
    DNA and RNA: The Genetic Molecules
    Genetic Analysis
    Biotechnology and Industrial Microbiology
    1.3 Microbial Physiology and Ecology
    Photosynthesis, Respiration, and the Appearance of Atmospheric Oxygen
    Microorganisms and Biogeochemical Cycling
    Microbial Interactions
    1.4 Microbes and Disease
    The Identification of Infectious Agents
    The Effects of Infectious Diseases
    Control of Infectious Diseases
    The Rest of the Story
    Summary
    Suggested Reading
    Chapter 2: Bacteria
    Chapter Navigator
    Introduction
    2.1 Morphology of Bacterial Cells
    2.2 The Cytoplasm
    2.3 The Bacterial Cytoskeleton
    2.4 The Cell Envelope
    The Plasma Membrane
    The Bacterial Cell Wall
    Variation in the Bacterial Cell Envelope
    2.5 The Bacterial Cell Surface
    Motility from Flagella
    Non-Flagellar Motility
    Capsules
    Surface Arrays (“S-layers”)
    2.6 Diversity of Bacteria
    Classification and Nomenclature
    Phylogeny of Bacteria
    The Rest of the Story
    Summary
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    Chapter 3: Eukaryal Microorganisms
    Chapter Navigator
    Introduction
    3.1 The Morphology of Typical Eukaryal Cells
    The Nucleus: A Role in the Storage and Expression of Information
    The Secretory Pathway: A Role in Protein Trafficking
    The Mitochondria and Chloroplasts: A Role in Cell Metabolism
    The Plasma Membrane: A Role in Homeostasis
    The Cell Wall: A Role in Cell Support
    The Cytoskeleton: A Role in Cell Structure
    3.2 Diversity of Eukaryal Microorganisms
    The Phylogeny of Eukaryal Microorganisms
    Eukaryal Microorganisms: Model Organisms
    3.3 Replication of Eukaryal Microorganisms
    Mitosis
    Meiosis
    Life Cycles of Model Organisms
    3.4 The Origin of Eukaryal Cells
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    3.5 Interactions between Eukaryal Microorganisms and Animals, Plants, and the Environment
    Diseases caused by Eukaryal Microorganisms
    Beneficial Roles of Eukaryal Microorganisms
    The Rest of the Story
    Summary
    Suggested Reading
    Chapter 4: Archaea
    Chapter Navigator
    Introduction
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    The Cytoplasm
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    Thaumarchaeota
    Euryarchaeota
    Korarchaeota
    Nanoarchaeota
    The Rest of the Story
    Summary
    Suggested Reading
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    Chapter Navigator
    Introduction
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    History of Virology
    Structure of Viruses
    Replication Cycle
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    Coevolution Hypothesis
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    Progressive Hypothesis
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    Viral Quantification
    5.4 Diversity of Viruses
    Virus Names
    Virus Classification
    Virus Identification
    5.5 Virus-like Particles
    Viroids
    Satellite Viruses and RNAs
    Virophages
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    5.6 Virology Today
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    Suggested Reading
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    Chapter Navigator
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    Acquisition of Nutrients
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    Effects of Temperature on Microbial Growth
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    Temperature Manipulation
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    Chemical Methods of Controlling Microbes
    Practical Issues for Destroying Microbes or Preventing their Growth
    The Rest of the Story
    Summary
    Suggested Reading
    Chapter 7: DNA Replication and Gene Expression
    Chapter Navigator
    Introduction
    7.1 The Role of DNA
    The Griffith Experiment
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    The Hershey–Chase Experiment
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    Transcription: Termination
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    Types of Mutations
    Causes and Repair of Mutations
    The Rest of the Story
    Summary
    Suggested Reading
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    Chapter Navigator
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    Entry of Non-enveloped Viruses
    Entry of Bacteriophages
    Entry of Plant Viruses
    Viral Uncoating
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    Replication of Eukaryal DNA Viruses
    Replication of RNA Viruses
    Replication of Bacteriophages
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    Assembly
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    Suggested Reading
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    Chapter Navigator
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    Suggested Reading
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    Chapter Navigator
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    Bioinformatics
    10.2 Genomic Analysis of Gene Expression
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    Proteomes
    10.3 Comparative Genomics
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    10.4 Metagenomics and Related Analyses
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    Chapter Navigator
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    Production of Enzymes
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    11.6 Two-component Regulatory Systems
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    Study of Chemotaxis Using Mutants
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    Summary
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    Chapter Navigator
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    12.1 Microbes for Biotechnology
    Sources of Microbes
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    Industrial enzymes
    Vitamins and amino acids
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    Chapter Navigator
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    Nucleotide Synthesis
    Lipid Synthesis
    The Rest of the Story
    Summary
    Suggested Reading
    Chapter 14: Biogeochemical Cycles
    Chapter Navigator
    Introduction
    14.1 Nutrient Cycling
    Cycling of Elements
    14.2 Cycling Driven by Carbon Metabolism
    The Global Carbon Cycle
    Photosynthesis, Respiration, and Decomposition
    Methanogenesis
    Methanotrophy
    14.3 Cycling Driven by Nitrogen Metabolism
    Nitrification, Denitrification, Anammox, and Dissimilatory Reduction of Nitrate to Ammonium
    Human Impact on the Nitrogen Cycle
    14.4 Other Cycles and their Connections
    Cycling of Oxygen
    Cycling of Phosphorous and Sulfur
    Cycling of Metals
    The Rest of the Story
    Summary
    Suggested Reading
    Chapter 15: Microbial Ecosystems
    Chapter Navigator
    Introduction
    15.1 Microbes in the Environment
    Ecosystems
    Ecosystem Physiology
    Biofilms
    15.2 Microbial Community Analysis
    Cultivation-dependent Techniques
    Cultivation-independent Techniques
    Microbial Diversity
    15.3 Aquatic Ecosystems
    Marine Ecosystems
    Viruses of the Oceans
    Cultivation of Oligotrophic Microorganisms from Seawater
    Ocean Community Genomics
    Freshwater Ecosystems
    15.4 Terrestrial Ecosystems
    Soils
    Rhizosphere
    Microbial Communities in Soils
    Bioremediation
    15.5 Deep Subsurface and Geothermal Ecosystems
    Deep Subsurface Microbiology
    Hydrothermal Vents
    Terrestrial Hot Springs
    The Rest of the Story
    Summary
    Suggested Reading
    Chapter 16: The Microbiology of Food and Water
    Chapter Navigator
    Introduction
    16.1 Food Spoilage
    16.2 Food Preservation
    Reduction of the Water Activity (aw) of Food
    Control of Temperature
    Increase in Acidity of Food
    Addition of Chemical Preservatives
    Irradiation of Food
    Use of Modified Atmosphere Packaging (MAP)
    Hurdle Technology
    16.3 Food Fermentation
    Fermentation of Milk Products
    Fermentation with Mold
    Vinegar Manufacture
    16.4 Foodborne and Waterborne Illness
    16.5 Microbiological Aspects of Water Quality
    Principles of Wastewater Treatment
    Drinking Water Purification
    The Rest of the Story
    Summary
    Suggested Reading
    Chapter 17: Microbial Symbionts
    Chapter Navigator
    Introduction
    17.1 Types of Microbe-host Interactions
    17.2 Symbionts of Plants
    17.3 Symbionts of Humans
    Skin
    Vagina
    Oral Cavity
    Digestive Tract
    17.4 Symbionts of Herbivores
    Cecal Fermentation
    Rumen Fermentation
    17.5 Symbionts of Invertebrates
    Aphids
    Termites
    Shipworms
    Corals
    The Rest of the Story
    Summary
    Suggested Media Player Classic 1.8Key Genrator - Crack Key For U 18: Introduction to Infectious Diseases
    Chapter Navigator
    Introduction
    18.1 Pathogenic Microbes
    18.2 Microbial Virulence Strategies
    Attachment, Invasion, and Replication
    Evading Host Defenses
    Bacterial Defenses
    18.3 The Transmission of Infectious Diseases
    Routes of Transmission
    Epidemiology
    Patterns of Infectious Disease
    Types of Epidemics
    18.4 Proving cause and Effect in Microbial Infections
    Koch’s Postulates
    Molecular Koch’s Postulates
    18.5 The Evolution of Pathogens
    Encountering a New Population
    Microbes becoming More Virulent
    Addressing the Problem
    Summary
    Chapter 19: Innate Host Defenses Against Microbial Invasion
    Chapter Navigator
    Introduction
    19.1 Immunity
    19.2 Barriers to Infection
    Skin
    Mucosal Membranes
    Iron: The Limiting Element
    19.3 The Inflammatory Response
    19.4 The Molecules of the Innate System
    Pathogen-associated Molecular Patterns
    Complement
    Type I Interferons
    19.5 The Cells of Innate Immunity
    Phagocytes
    Eosinophils, Basophils, and Mast Cells
    Natural Killer (NK) Cells
    19.6 Invertebrate Defenses
    Invertebrate Molecules of Defense
    Invertebrate Cellular Immune Responses
    Summary
    Suggested Reading
    Chapter 20: Adaptive Immunity
    Chapter Navigator
    Introduction
    20.1 Features of Adaptive Immunity
    Immune Receptors and Antigen
    Lymphocytes and Lymphoid Tissues
    Primary and Memory Immune Responses
    Evolution of Adaptive Immunity
    20.2 T cells
    Effector T Cells and their Functions
    T-cell Activation
    20.3 Antigen Processing
    20.4 Antigen-presenting Cells
    20.5. Humoral and Cell-mediated Immune Responses
    20.6 B Cells and the Production of Antibody
    B-cell Response to Protein Antigens
    B-cell Responses to Non-protein Antigens
    Antibody Production by Plasma Cells
    Immunoglobulin Structure and Diversity
    Protection by Antibodies
    Summary
    Suggested Reading
    Chapter 21: Bacterial Pathogenesis
    Chapter Navigator
    Introduction
    21.1 Bacterial Virulence Factors
    Attachment Factors
    Capsules
    Type III and Type IV Secretion Systems
    Iron-binding Proteins
    21.2 Bacterial Virulence Factors—Toxins
    Endotoxin and Lipoteichoic Acid
    A-B Toxins
    Cytolysins
    Superantigens
    21.3 Survival in the host: Strategies and Consequences
    Pathogen Study 1: Streptococcus Pyogenes
    Pathogen Study 2: Mycobacterium Tuberculosis
    21.4 Evolution of Bacterial Pathogens
    Horizontal Gene Transfer: Evolution by Quantum Leaps
    Summary
    Suggested Reading
    Chapter 22: Viral Pathogenesis
    Chapter Navigator
    Introduction
    22.1 Recurring Themes in Viral Pathogenesis
    Types of Infections
    Types of Transmission
    22.2 Interactions with the Host: Strategies and Consequences
    Inhibiting Host Cell Transcription and Translation
    Avoiding Host Immune Responses
    22.3 Viral Infections and Cancer
    DNA Tumor-causing Viruses
    RNA Tumor-causing Viruses
    22.4 Evolution of Viral Pathogens
    Mutations
    Recombination
    Reassortment
    Evolution
    Summary
    Suggested Reading
    Chapter 23: Eukaryal Pathogenesis
    Chapter Navigator
    Introduction
    23.1 Mechanisms of Eukaryal Pathogenesis
    Transmission, Entry, and Adhesion
    Evading Host Defenses
    Obtaining Nutrients from a Host
    Toxins of Eukaryal Pathogens
    23.2 Pathogen Study: Plasmodium Falciparum
    Replication of Plasmodium Falciparum
    Effects of Plasmodium Falciparum on Humans
    Strategies for Prevention and Treatment of Plasmodium Falciparum Infections
    23.3 Macroscopic Eukaryal Pathogens
    Ascariasis
    Schistosomiasis
    23.4 Evolution of Eukaryal Pathogens
    Acquisition of Virulence Genes by Eukaryal Microorganisms
    Effects of Eukaryal Pathogens on Host Evolution
    Summary
    Suggested Reading
    Chapter 24: Control of Infectious Disease
    Chapter Navigator
    Introduction
    24.1 Historical Aspects of Infectious Disease Treatment and Control
    24.2 Antimicrobial Drugs
    Antibacterial Drugs
    Antifungal Drugs
    Antiprotozoal Drugs
    Antiviral Drugs
    24.3 Antimicrobial Drug Resistance
    Molecular Mechanisms of Resistance
    Natural Selection and Drug Resistance
    The Origin of Drug Resistance Genes
    Combating Drug Resistance
    24.4 Predicting and Controlling Epidemics
    R0 = 1, the Epidemic Threshold
    Principles of Epidemic Control
    24.5 Immunization and Vaccines
    History of Vaccination
    Vaccine Design
    Vaccine Efficacy
    Herd Immunity
    Polio—A Near Success
    Foot-and-mouth Disease: The Making of an Epidemic
    Summary
    Suggested Reading
    Appendix A: Reading and Understanding the Primary Literature
    Appendix B: Microscopy
    Appendix C: Taxonomy and Nomenclature of Microbes
    Appendix D: Origin of Blood Cells
    Glossary
    Index

    Citation preview

    Wessner_6869_FM_i-1.indd 2

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    MICROBIOLOGY DAVID R. WESSNER Davidson College

    CHRISTINE DUPONT University of Waterloo

    TREVOR C. CHARLES University of Waterloo

    JOSH D. NEUFELD University of Waterloo

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    Includes ORION

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    MICROBIOLOGY

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    MICROBIOLOGY DAVID R. WESSNER Davidson College

    CHRISTINE DUPONT University of Waterloo

    TREVOR C. CHARLES University of Waterloo

    JOSH D. NEUFELD University of Waterloo

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    VICE PRESIDENT AND DIRECTOR EXECUTIVE EDITOR EXECUTIVE MARKETING MANAGER SENIOR CONTENT MANAGER SENIOR PRODUCTION EDITOR DESIGN DIRECTOR

    Petra Recter Ryan Flahive Clay Stone Svetlana Barskaya Patricia McFadden Harry Nolan

    REPEATED DESIGN ELEMENT PHOTO CREDITS: OPENER BORDER AND ICON TAB TOOLBOX, MICROBES IN FOCUS, PERSPECTIVE, MINI-PAPER MICROBES IN FOCUS MAGNIFYING GLASS PHOTO

    TEXT AND ILLUSTRATION DEVELOPER ASSOCIATE PRODUCT DESIGNER DEVELOPMENT EDITOR ASSISTANT EDITOR EDITORIAL ASSISTANT SENIOR PHOTO EDITOR COVER ILLUSTRATION

    Kathleen Naylor Lauren Elfers Melissa Whelan Carolyn Thompson Mili Ali Mary Ann Price Janet Iwasa

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    This book was set in 10/12 BT Baskerville by Cenveo Publisher Services. Book and cover are printed and bound by Quad Graphics/Versailles. This book is printed on acid-free paper. ∞ Founded in 1807, John Wiley & Sons, Inc. has been a valued source of knowledge and understanding for more than 200 years, helping people around the world meet their needs and fulfill their aspirations. Our company is built on a foundation of principles that include responsibility to the communities we serve and where we live and work. In 2008, we launched a Corporate Citizenship Initiative, a global effort to address the environmental, social, economic, and ethical challenges we face in our business. Among the issues we are addressing are carbon impact, paper specifications and procurement, ethical conduct within our business and among our vendors, and community and charitable support. For more information, please visit our website: www.wiley.com/go/citizenship. Copyright © 2017 John Wiley & Sons, Inc. All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, recording, scanning or otherwise, except as permitted under Sections 107 or 108 of the 1976 United States Copyright Act, without either the prior written permission of the Publisher, or authorization through payment of the appropriate per-copy fee to the Copyright Clearance Center, Inc., 222 Rosewood Drive, Danvers, MA 01923 (website: www.copyright.com). Requests to the Publisher for permission should be addressed to the Permissions Department, John Wiley & Sons, Inc., 111 River Street, Hoboken, NJ 07030-5774, (201) 748-6011, fax (201) 748-6008, or online at: www.wiley.com/go/permissions. Evaluation copies are provided to qualified academics and professionals for review purposes only, for use in their courses during the next academic year. These copies are licensed and may not be sold or transferred to a third party. Upon completion of the review period, please return the evaluation copy to Wiley. Return instructions and a free-of-charge return shipping label are available at: www.wiley.com/ go/returnlabel. If you have chosen to adopt this textbook for use in your course, please accept this book as your complimentary desk copy. Outside of the United States, please contact your local representative. EVALC: 13-digit ISBN: 9781119320678 10-digit ISBN: 1119320674 BRV: 13-digit ISBN: 9781119279419 10-digit ISBN: 1119279410

    The inside back cover will contain printing identification and country of origin if omitted from this page. In addition, if the ISBN on the back cover differs from the ISBN on this page, the one on the back cover is correct

    Printed in the United States of America 10

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    D E D I C AT I O N S

    DAVID R. WESSNER

    To the wonderful students at Davidson College for making it so much fun to do what I do. Most importantly, thanks to Connie and Ian. CHRISTINE DUPONT

    To microbiologists and students everywhere, even if they never get a chance to read this textbook. TREVOR C. CHARLES

    To the students who have been an inspiration, as I have had the privilege of watching them discover and be captivated by the world of microbes. JOSH D. NEUFELD

    For my students and the love of microbiology.

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    About the Authors DAVID R. WESSNER

    Courtesy of John Lumsden

    CHRISTINE DUPONT Lecturer in the Department of Biology at the University of Waterloo in southern Ontario, Canada, Christine Dupont teaches undergraduate courses in genetics, biotechnology, virology, and bacterial pathogenesis. She earned her Ph.D. from Massey University, Faculty of Veterinary Science, New Zealand; B.Ed. from the University of Windsor, Ontario; and M.Sc. and B.Sc. in Microbiology from the University of Guelph, Ontario. Prior to her Ph.D. studies, Christine taught high nox app player for mac - Crack Key For U science for several years, developing a passion for teaching and working with students.

    Courtesy Trevor C. Charles

    A Professor in the Department of Biology, University of Waterloo, Trevor Charles teaches undergraduate courses in microbiology and synthetic biology, and runs a research program that focuses on plant-microbe interactions and functional metagenomics. Prior to joining the faculty at Waterloo, he held a faculty position at McGill University and did postdoctoral research at the University of Washington. He earned his Ph.D. from McMaster University, and his B.Sc. in Microbiology from the University of British Columbia. JOSH D. NEUFELD As a Professor in the Department of Biology at the University virtual serial port driver download - Crack Key For U Waterloo, Josh Neufeld explores microbiology with undergraduate students in the classroom and both undergraduate and graduate students in his microbial ecology research program. Josh earned his B.Sc. and M.Sc. in Microbiology from McGill University's Macdonald Campus prior to completing a Ph.D. at the University of British Columbia and postdoctoral research at the University of Warwick.

    Courtesy of Jon Schroeder

    Courtesy Bill Giduz

    Professor of Biology at Davidson College, David R. Wessner teaches introductory biology and courses on microbiology, genetics, and HIV/ AIDS. His research focuses on viral pathogenesis. He is a member of the American Society for Microbiology Committee for K–12 Education. He also is a coauthor of Vision and Change in Undergraduate Education: A Call to Action. Prior to joining the faculty at Davidson, David conducted research at the Navy Medical Center. He earned his Ph.D. in Microbiology and Molecular Genetics from Harvard University and his B.A. in Biology from Franklin and Marshall College.

    TREVOR C. CHARLES

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    Why We Wrote This Book We wrote this book for one simple reason—we have a passion for microbiology. Moreover, we want to share this passion with as many students as possible. First, we want to show students that microbiology is a dynamic discipline. The field has changed dramatically over the past 25 years, and we can only guess what remarkable changes the future will bring. Second, we want to show students that experimentation is at the very heart of microbiology. Since the development of the microscope over 300 years ago, microbiologists have asked probing questions, developed elegant experiments, and formulated testable hypotheses. This scientific exploration continues today. To achieve these two major goals, we have written this textbook as an engaging narrative that brings the story of microbiology to life. Our textbook not only provides students with a historical understanding of the field but also gives them an appreciation for the dynamic, exciting nature of today’s microbiology. Indeed, we hope that our textbook will make students as passionate as we are about the science of microbiology.

    Exploration and Experimentation To achieve our goals, we present material within the context of exploration and experimentation. Knowing myriad facts about microbiology is not sufficient. To have a true understanding of this subject, students need to understand experimentation and be able to critically analyze information. Several features within the book will help our students understand and appreciate the science behind our knowledge. First, each chapter begins with an opening vignette—a short story that frames a basic question tally erp 9 crack patch free download - Free Activators the context of both contemporary and historical issues—visually supported by a dynamic illustration. As the chapter unfolds, references back to the opening vignette are made repeatedly. At the conclusion of each chapter, an additional feature, The Rest of the Story, again refers back to this opening vignette and art. This also ties into an active learning feature, Image in Action, that includes several criticalthinking questions. Second, each chapter contains a Mini-Paper, a synopsis of a scientific journal article that includes original data and Questions for Discussion. Through the use of this feature, students will see how microbiologists ask intelligent questions, rationally design experiments, and evaluate data. Again, this feature will improve students’ critical-thinking skills and show them that our knowledge is evidence-based. Third, several chapters contain scientific methodology figures, diagrams that provide a brief overview of a specific experiment, including the original observation,

    hypothesis, experiment, results, and conclusions. Again, this feature will emphasize to our students the science behind our knowledge.

    Three Pillars: Genetics, Physiology, and Ecology Throughout the textbook, we frame information around the three pillars of genetics, physiology, and ecology. The pillars help weave concepts in evolution, structure and function, and the interactions between individual microbes, between different types of microbes, between microbes and other organisms, and between microbes and the environment. Often, the importance of these key interactions are presented from different perspectives at different places within the textbook: from that of the molecular biologist, of the ecologist, of the physician, of the engineer, or even of the microbe itself. An Emphasis on Connections Finally, we make explicit the interconnectedness of topics, both within a chapter and between chapters. This goal is achieved in several ways. Important concepts are reintroduced throughout appropriate chapters with Connection notes. Through such layering, students gradually deepen their understanding of complex topics as the semester progresses. Thus, students gain an appreciation of gene regulation by seeing how it affects different processes. Ultimately, of course, we want our students to gain a more complete understanding of and appreciation for microbiology. By presenting information within the dual contexts of experimentation and the interconnectedness of topics, we encourage students to learn important material not as discrete bits of information, but as pieces of a much larger body of knowledge. Through this approach, students will better understand and connect the basic concepts of this exciting, dynamic field. Thank you for taking the time to read these opening remarks and learn more about our book. Hopefully, our book will help you share your fascination with microbiology with your students. Who knows? Maybe an undergraduate student in today’s microbiology class will make tomorrow’s big discovery!

    Best, Dave Wessner Christine Dupont Trevor Charles Josh Neufeld ix

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    Special Features Wessner_6869_ch1_3

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    Mini‐Paper: A Fo c us o n th e R e s e a rc h THE THREE DOMAINS OF LIFE

    In every chapter, primary research articles are summarized and interpreted, helping students sharpen critical thinking skills and deepen their understanding of what microbiologists do. Mini-Papers:

    C. R. Woese, O. Kandler, and M. L. Wheelis. 1990. Towards a natural system of organisms: Proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA 87: 4576–4579.

    Context

    The sequence of this molecule changes very slowly because of the functional constraints on the molecule. Random mutations that occur within the gene encoding the small subunit rRNA often have serious negative consequences, so relatively few changes are passed on to subsequent generations. Nevertheless, there are enough differences in the roughly 1,600 nucleotide sequence to differentiate between species to map patterns of similarity. If one assumes that overall mutation rates are similar between species (which seems to be true with respect to rRNA genes), then one can quantify sequence differences between SSU rRNA genes in multiple species to infer relationships. Ultimately, Woese discovered that the methane‐producing microorganisms were no more closely related to other bacteria than they were to the eukaryotes. They were not bacteria at all! Let’s examine the scientific work that led to this conclusion.

    Aristotle categorized life into just two fundamental groups, animals and plants, and this categorization persisted until the dawn of microbiology as a science. In 1868, two centuries after van Leeuwenhoek’s discovery of microbial life, German biologist Ernst Haeckel proposed a third fundamental group, or kingdom, Media Player Classic 1.8Key Genrator - Crack Key For U, for microscopic life‐ forms. In 1938, Herbert Copeland suggested that microorganisms should actually be divided into two kingdoms, Protista and Bacteria, thereby recognizing the difference between eukaryotic and prokaryotic cells. Twenty years later, Robert Whittaker advocated further separation of eukaryotic microorganisms into kingdoms of Fungi and Experiments Protista, but kept prokaryotic cells in a single kingdom called Monera. This five‐kingdom taxonomic system—Animalia, Plantae, Fungi, ProThe 1990 Woese et al. paper actually presented no new experimental tista, and April Monera—became accepted data. Its importance was in articulating a new view of the phylogeny Wessner_6869_ch5_2 23, 2016 the 2:46 PM standard 144 for the next few decades until DNA and protein sequences became widely accessible. of life. To understand the genesis of this idea, we should step back and Carl Woese, a microbiologist at the University of Illinois, was fascinated examine the data. The biggest challenge Woese faced in the 1970s by a group of prokaryotes known at the time as “archaebacteria.” Initially, in developing ribosomal RNA sequences as a tool for phylogenetic these strange microorganisms were found primarily in marginal envianalysis was the difficulty in determining such sequences. Woese and ronments such as anoxic sediments, hypersaline ponds, and hot springs. colleagues developed a laborious method to infer the sequence of 16S Other than their curious ability to colonize extreme habitats, the feature rRNA molecules, which they described in a 1977 article, “Comparative Toolbox 5.1 of archaebacteria that generated the most interest among the wider cataloging of 16S ribosomal ribonucleic acid: A molecular approach to C E L L C U LT U R E T E C H N I Q U E S biological community was the ability of some of these organisms to procaryotic systematics,” Journal of Bacteriology, vol. 27, pp. 44–57. First, produce methane. These microorganisms remain the only organisms RNA was extracted from cells. The isolated rRNA then was cut into small known to produce this gas. chunks using a ribonuclease enzyme that yields short fragments of Because viruses only can replicate within living host cells, virologists Toare understand the phylogeny, or evolutionary history, of these nucleic acid usually 5–20 bases long. The sequence of each oligonuclepresented with an interesting problem; before researchers can effecmethane‐producing microorganisms, Woese followed the lead of otide was determined by further chemical and enzymatic analysis. In its tively study viruses in the laboratory, they must be able to growZuckerkandl approand Pauling, who had first demonstrated in the 1960s original incarnation, this method did not actually yield a complete rRNA priate host cells. Prior to the development of mammalian cellthat culture comparisons of protein sequences could reveal evolutionary sequence, but rather a catalog of short oligonucleotide sequences presmethodologies, the propagation of animal viruses occurred via serial relationships. If two organisms were closely related, these researchers ent in the rRNA. Catalogs from different species then were compared. passage of the virus in animals. A susceptible animal would be inocu- then the amino acid sequence of a common protein in the reasoned, The underlying assumption of molecular sequence comparisons is lated with a small sample of the virus of interest. At a later time, per- should be very similar. Conversely, if two organisms were organisms that the number of nucleotide differences between two sequences is haps when the infected animal became sick, virus would bedistantly isolated related, then the amino acid sequence of a common protein proportional to the time since the two species diverged from a comfrom this animal and a second susceptible animal would be inoculated, should be more divergent. Woese and colleagues began to focus not mon ancestor. Species that share a more recent common ancestor thereby allowing the virus to continue replicating. Clearly, this on method protein sequences, but on RNA sequences. Woese reasoned that will have fewer differences than species that have been separated for of viral propagation was not terribly practical; it required the researcher the ribosomal RNAs (rRNAs), because of their universal presence in all longer periods of time. Exactly how long ago two species separated to maintain appropriate animal hosts. As you can imagine, thiscells, requireToolboxes: could be excellent molecules to compare. In bacteria, the 16S depends on the rate at which mutations accumulate, which can be ment greatly reduced the study of viruses that infect humans! rRNA molecule is part of the small subunit of the ribosome. In eukaryvery difficult, if not impossible, to know. Fortunately, to determine During the 1940s and 1950s, this difficulty was overcome otes, with the the equivalent ribosomal RNA is the 18S rRNA. These molecules, phylogenetic relationships, we do not need to know exact times of development of cell culture techniques. In 1949, John Enders,collectively Thomas referred to as “small subunit (SSU) rRNA” molecules, are critdivergence. We are just interested in relative times: if organisms A and Weller, and Frederick Robbins demonstrated that poliovirus could repical in the ribosome, helping to bring together the ribosomal structure, B shared a common ancestor after they shared an ancestor with organlicate in various embryonic tissues. This discovery directly led to interacting the and with messenger RNA. Not only are ribosomal RNAs ism C, then A and B would have fewer sequence differences with each development of the poliovirus vaccine a few years later anduniversally earned distributed, but they also have the same function in all cells. other than either would have with C. The Woese method essentially the three researchers the Nobel Prize in Physiology or Medicine in The SSU rRNA gene sequence has been referred to as a “molecular took each 16S rRNA sequence and compared it against all of the other 1954. George Gey and colleagues cultured the first human chronometer, cell line ” a slowly ticking clock that measures evolutionary time. species. A method for quantifying the similarity between sequences in 1952. This cell line, derived from a human cervical carcinoma, was named HeLa, in recognition of Henrietta Lacks, the young woman from whom the cells were isolated. She died of cervical carcinoma in 1951. The HeLa cell line still is widely used by researchers throughout the world, and this contribution of Henrietta Lacks to modern biomedical research is immeasurable. A final important contribution to the budding field of virology came in 1955 when Harry Eagle and10 colleagues Chapter 1 The Microbial World developed a well‐characterized nutrient medium that could be used for the maintenance of cells in the laboratory. With the availability Figure B5.2. Propagation of mammalian cells In the laboratory, mammalian cells typically are grown at 37°C in an atmosphere containing 5 percent CO2. Here, a researcher is dislodging of defined growth media and several different cell lines, researchers cells Wessner_6869_ch01_pp02-33.indd 10 from a flask and transferring them to another flask. She is working in a laminar flow hood to prevent could propagate animal viruses easily and conduct controlled expericontamination of the cells. ments. Thus, the history of animal virology is inextricably linked to the development of in vitro cell culture methodologies. Today, researchers can use many different types of cultured cells. to as a cell line or a continuous cell line. Although these cells can be mainMammalian cells typically are incubated at 37°C (normal human tained in the laboratory indefinitely, they do differ significantly from “norbody temperature) in an atmosphere containing 5 percent CO2 mal” cells. Immortalized cells often are aneuploid, that is, they possess an incorrect chromosomal complement. For example, HeLa cells usually pos(to mimic blood gas levels and maintain an appropriate pH). Once sess 82 chromosomes, rather than the 46 chromosomes normally found attached to a substrate, the cells will begin to divide. These cells in human cells. These cells also often exhibit other aberrant properties. will continue to divide until they completely cover the substrate, or Thus, although cell lines allow researchers to conduct exquisitely detailed become confluent, at which point most animal cells cease to divide biochemical and genetic experiments, one could argue that the results (see Figure 5.15A). For the cells to continue growing, their density obtained with cell lines may differ from that which occurs in vivo. needs to be decreased. The growth medium is removed, and trypsin, a protease, usually is added to the cells to dislodge them from the surface. These dislodged cells are diluted in fresh medium and Test Your Understanding . plated, at a lower density, in new cell culture dishes, thereby allowing the cells to continue replicating (Figure B5.2). Wessner_6869_FM_i-1.indd 10 Imagine you are culturing a line of mammalian cells and

    Wessner_6869_ch5_2

    © Courtesy David Wessner

    Every chapter contains Toolboxes— in-depth descriptions of experimental techniques relevant to the chapter.

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    antigens, not carbohydrate antigens, to TH2 cells for antibody production. How then do B cells make antibody to substances such as carbohydrates? The BCR itself is not restricted to binding peptides. It can bind to non‐protein antigens too, as long as the BCR‐antigen

    Microbes in Focus 20.1 S L I P P E R Y H A E M O P H I LU S I N F LU E N Z A E Habitat: Strictly human inhabitant carried asymptomatically in the nasopharynx by approximately 40 percent of adults

    provide wtfast cracked apk - Free Activators with more detailed information about the habitats and key features of microbes mentioned in the chapter.

    Description: Gram‐negative coccobacillus, 0.3−0.8 μm in length Key Features: Pathogenic strains all possess one of six different types of capsule carbohydrate. Strains carrying type b capsule cause 95 percent of H. influenzae disease in children, predominantly meningitis and pneumonia. The capsule interferes with phagocytosis by preventing C3b opsonization of the bacterial cells (see Sections 19.4, 19.5, and 21.1). Antibody produced against the polysaccharide capsule successfully opsonizes the bacteria and SEM provides protection. Eye of Science/Science Source

    Microbes in Focus Examples: These examples

    tion into antib with TH2 cells. tion without en gens, for thym As we have carbohydrates. venting phago not readily clea against such pa against the cap tion by phagoc levels to be pro many days in a Pathogens ca immunologica Media Player Classic 1.8Key Genrator - Crack Key For U antibod can reduce thi encapsulated p pathogens tha ing by the adap T‐independen these pathogen bound, or con vaccines. Secti gate vaccines.

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    694 Chapter 20 Adaptive Immunity

    Wessner_6869_ch20_pp672-709.indd 694

    In these examples, Wessner_6869_ch17_4 students see how topics may be viewed or used by different groups.

    Perspective Examples:

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    Perspective 17.2 CO W S CO N T R I B U T E TO C L I M AT E C H A N G E results in significantly less methane than cattle kept on grass pasture (Figure B17.3). However, high‐protein diets are more costly to sup-

    ply and increase the danger of bloat.

    Courtesy Christine Dupont

    In reading the previous section, you may have recognized that the major gases produced by cows—carbon dioxide and methane—are greenhouse gases. When present in the atmosphere, these gases trap radiant energy, preventing its dissipation to space. Thus, cows pose a concern for climate change because methane is a potent greenhouse gas. Cow populations have increased greatly over the past century as a result of human demand for meat and dairy products. Currently, there are an estimated 1.4 billion cattle on the planet—a source of approximately 15 percent of the total methane released into the atmosphere. When you consider the biochemistry involved in methane production in cows, it is their microbes that present the problem, although the two can hardly be separated. Researchers have been trying to find ways to reduce methane production in cows. They have found that high‐quality feeds, like alfalfa pasture,

    Figure B17.3 Cows grazing on grass Cattle fed grass produce more methane than those fed high-protein fodder, such as alfalfa.

    Special Features xi by stabbing the animal in the rumen. Surprisingly, many lived through this! Nowadays, antifoaming agents are commonly administered. Perspective 17.2 describes another consequence

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    17.4 Fact Check 1. Explain the advantage of foregut fermentation versus

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    C HAPTER

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    8 Viral Replication Strategies

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    Chapter vignette with original art:

    Every chapter begins with an opening vignette that frames a basic question. These vignettes are visually supported by original art.

    I

    n the spring of 2009, outbreaks of a novel influenza virus infection in Mexico were reported. By April 26, 2009, 38 cases (20 in the United States and 18 in Mexico) had been confirmed. By the beginning of May 2009, the World Health Organization (WHO) reported that this new virus had infected 367 people in 13 countries. On June 11, 2009, the WHO ruses. BacterioImage in Action actively destroy reported over 28,000 cases in 74 countries. Also on this date, For instance, T4 the WHO declared an influenza virus pandemic. This image depicts the replication the peptidoglyInitially referred to as swine flu, this strain of influenza cycle of influenza viruses leaving one host cell (bottom) and nveloped maminfecting another (top). virus—officially known as influenza A/California/07/2009 ns necessary for (H1N1)—quickly spread throughout the world. With its spread, 1. Describe the molecular steps that occur ssively unstable fear and uncertainty also spread. During the spring of 2009, when a virus initially interacts with a host g to the destrucmany schools were closed to avoid transmission of the virus. cell. Identify and include a description of Viruses of plants, In Mexico, soccer matches occurred in empty stadiums when the specific roles of the green‐ and red‐ ll. These viruses colored components. the Mexican government prevented fans from attending. Sevnt through the FINAL PAGES FINAL PAGES eral countries urged caution to citizens traveling to the United d to a new plant 2. Imagine that Tamiflu was administered uticle by outside States and Mexico. Common questions were hotly debated: and is present now in this situation. Describe the antiviral effects of Tamiflu and outlineCould how this virus cause widespread death throughout the world? Should schools, sporting events, and conferences be this image would look different if this drug were present. cancelled? How can we protect ourselves? proteins into the Approximately a year later, on August 10, 2010, the WHO eins on the surdeclared an end to the 2009 influenza pandemic. This declan be recognized 0.2) are immune ration did not indicate that the H1N1 strain of influenza had disappeared. Rather, the announcement that the pandemic Wessner_6869_ch8_2 April 26, 2016 12:00 PM 259 had ended simply reflected that the number of new influenza As we noted in the opening story, Tamiflu reduces the severity had receded to normal levels. Indeed, the threat of and length of the influenza disease. But how does it infections work? remains. When the 64th World Health Assembly, Media Player Classic 1.8Key Genrator - Crack Key For U Tamiflu (oseltamivir) is a neuraminidase inhibitor (NAI).influenza The neuraminidase protein (NA) is located in the influenzaannual virus meeting of the WHO, opened in May of 2011, global ly disrupt along with hemagglutinin protein (HA). When a influenza preparedness remained a primary topic. betweenenvelope, bacteriophages andthe mammalian viruses. BacterioImage inweAction virion first encounters a host cell, HA binds to sialic acid, allowing So, how can protect ourselves? During the height of the phages generally produce specific enzymes that actively destroy become the virus to enter the cell. During budding of newly replicated viral tried to protect themselves the host cell’s plasma membrane and cell wall. For instance, T4 2009 pandemic, many individuals This image depicts the replication NAan cleaves sialic acid residuesthe present on the infected from infection by purchasing hand sanitizers and protective producesparticles, lysozyme, enzyme that degrades peptidoglycycle of influenza viruses leaving one host cell (bottom) and erent for an can present cell’sinplasma membrane. So? Thenon‐enveloped cleavage of sialicmamacid residues the cell wall. Conversely, masks. Governments made plans for dealing with increased infecting another (top). by NA prevents the newlyspecific formedproteins viruses from getting for stuck to the us? Explain malian viruses rarely produce necessary demands on the health care industry. The WHO began distribinfected cell. In other words, NA increases the likelihood newDescribe the molecular steps that occur 1. egress. Rather, the host cell becomes progressively unstable that uting the antiviral drug oseltamivir, also known by the trade virus particles will move to other cells (Figure 8.24). when a virus initially interacts with a host because of the replication of the virus, leading to the destruc- name Tamiflu toand various developing countries. cell. Identify include a description of tion of the cell and release of the new virions. Viruses of plants, Numerous have Tamiflu can reduce the the specificstudies roles of the shown green‐ that and red‐ raminidase cleaves as we alluded to earlier, do not lyse the host cell. These viruses ptor, releasing severity of influenza disease and decrease the duration of the colored components. travel from to another within a plant Theone Restcell of the Story and Image in through the particle symptoms. The Food and Drug Administration (FDA) also has cytoplasmic connections cells. Spread to a new plant 2. Imagine that Tamiflu was administered Action: At the between end of each chapter, approved it for use as a preventive drug. But what does it do? Figure Tamiflu A. Neuraminidase requires the disruption of the cell wall8.24. andAction cuticleofby outside and is present now in this situation. these features revisitcleaves thesialicopening acid, allowing newly formed virions to disperse To from answer this we need an understanding influforces, such as insects. Describe thequestion, antiviral effects of Tamiflu and outline of how the infectedthem cell. B. Tamiflu functions as a neuraminidaseenza inhibitor,virus and how it replicates. vignetteInfection and art, linking this image would look different if this drug were present.

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    preventingcontent. the release of virions from infected cells and limiting the spreads explicitly to the chapter spread of the virus to other cells. CONNECTIONS The insertion of viral envelope proteins into the host cell plasma membrane exposes these viral proteins on the surxiiinfected Special face of host Features cells. These foreign proteins can be recognized by the immune system. Cytotoxic T cells (Section 20.2) are immune cells designed to destroy infected cells.

    The Rest of the Story

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    As we noted in the opening story, Tamiflu reduces the severity and length of the influenza disease. But how does it work?

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    Host organisms have evolved vario attempting to prevent, the entry an microorganisms. A more detailed natural processes may allow us to de Figure 7.2. Biochemical evidence vention Media Player Classic 1.8Key Genrator - Crack Key For U Griffith’s transforming factorand treatment strategies. T between hosts and p is DNA Avery, MacLeod,the and interactions McCarty demonstrate that the transforming factor is DNA. experimental system often is neces Live R cells were incubated with organisms the transforming often is not feasible. To be factor isolated from heat-killed S cells. Serum trees respond naturally to fungal inf that would precipitate and remove R cells was begun investigating the responses of added, and the mixture was grown on agar plates. Experimental Figures: novo‐ulmi (Mini‐Paper). T n o i t Ophiostoma a DNases, Replic but not RNases or proteases, eliminated These figures allow transformation. further improvements in resistance students toreturn better of this majestic tree.

    First infected person R cells

    +

    Precipitate R cells from mixture

    Transforming factor extracted from heat-killed S cells

    Courtesy Christine Dupont

    Observation: A highly purified extract containing DNA from heat-killed smooth (S) Streptococcus pneumoniae cells could transform living rough (R) cells into living smooth cells in vitro.

    Hypothesis: The transforming principle is DNA. Experiment: Treat the highly purified extract with various enzymes that destroy different cellular macromolecules, incubate it with living R cells, and plate on agar plates. (R cells are precipitated and do not grow.)

    Results: Treatment with DNases, but not RNases or proteases, destroyed the transforming activity of the highly purified extract.

    R cells

    +

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    First infected female Anopheles mosquito

    Courtesy Christine Dupont

    Second infected female Anopheles mosquito

    understand how an experiment proceeds, Evading host defenses from Observation to For a pathogen, simply entering a ho Hypothesispriate to Results to the host is not en cells within Conclusions. pathogen also must evade various ho

    viral pathogens achieve this goal in m pathogens are no different. Some eu pathogenic only when the host’s imm Others cause disease when the ecolo

    Second infected person S colonies

    Transforming ansforming actor extracted + DNase R cells + factor from om heat-killed S cells

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    Courtesy Christine Dupont

    Conclusion: DNA is the transforming principle and directs the phenotypes of cells.

    No colonies

    two components—protein and DNA. During the infection proexperiment opened the door for the molecular biology revocess, the capsid of bacteriophage T2 attached to,Cyst but did not lution. As Avery noted, transformation makes it “possible to Trophozoite enter, the infected cell. Biochemical studies had shown that induce predictable and hereditary changes in cells.” If we can Life-cycle Often with specific phenotypes,Courtesy Christine nucleic acids contained phosphorus Media Player Classic 1.8Key Genrator - Crack Key For U, but not sulfur (S). identify piecesFigures: of DNA associated 2 Excystation then we can insertart thatand DNA into recipient cells and alter theDupont combining releases trophozoites. characteristics of those cells. photographs, these

    figures provide a clear overview of howexperiment The Hershey–Chase microbes replicate.drawn by Avery and his colleagues Although the conclusions

    Microbes in Focus 7.1

    3 Trophozoites replicate in the small intestine.

    S T R E PTO CO CC US P N E U M O N I A E I N T H E L A B O R ATO RY A ND T H E H O S P I TA L

    easy context menu seem convincing, some biologists still questioned the pre‐ eminent role of DNA as the hereditary molecule. All linger4 Encystation occurs in the large intestine. ing doubts were put to rest by a third classic experiment, the Habitat: Commonly found in the nasopharynx of humans Hershey–Chase experiment. Shortly after Avery, MacLeod, and Description: Gram‐positive coccus, approximately 0.8 μm in McCarty published their paper, Alfred Hershey and Martha 5 Cysts are eliminated diameter, that often appears in short chains Chase, researchers at the Cold Spring Harbor Laboratory, in the4:05 feces. June PM 492 used the bacteriophage T2 toWessner_6869_ch15_4 investigate the role of DNA in 24, 2016 Key Features: Streptococcus pneumoniae played an integral role in heredity. Their approach was elegant in its simplicity. defining DNA as the genetic material. S. pneumoniae also is a sig-

    Figure 23.3. Proces of Giardia lamblia H contaminated water or eating fo excystation occurs, releasing tr organism replicates within the sm encystation occurs and the result

    CONNECTIONS Replication of bacteriophage T2 begins with a specific binding event between a viral attachment protein and a cellular receptor. Research investigating the molecular determinants of this process is presented in Section 8.1. Wessner_6869_ch23_pp788-817.indd

    792

    4 Introduction of secondary colonizers and growth of Hershey and Wise Care 365 PRO 5.6.7 Build 568 Crack With Serial Key Full Download knew that the genetic material viruses the biofilmof community. 1 Adhesion by a primary 3 Microcolony produces entered cells and directed the infected cells to produce more colonizer occurs. exopolysaccharide (EPS).

    sinus and ear infections and meningitis. oli-structure with nutrient 5 Established Its biofilm gradients, distinct distributions of species, gosaccharide capsule and dispersing cells. interferes with phagocytosis of the bacteria by immune cells, thereby enhancing its virulence.

    virus particles. They also knew that T2 was composed of just Exopolysaccharide

    206 Chapter 72 Cells DNAdivide. Replication and Gene Expression Solid surface Wessner_6869_ch07_pp202-237.indd 206

    EPS is only produced Z3x Samsung Pool Pro 43.0 cracks with Loader 2021 + Activation Code needed. How might this form of occur? It appears that cells within a growing bio-

    Process Diagrams:

    These figures lend clarity to the flow of complex processes.

    FINAL PAG

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    SECOND PAGES

    Figure 15.3. Process Diagram: Formation of biofilm Biofilms typically form through a stepwise process. First, the surface is populated by adhesion of the primary colonizers. Growth results in the formation of microcolonies that produce exopolysaccharide (EPS). Secondary colonizers are introduced as the biofilm matures. Throughout this development, intercellular communication occurs through molecular signaling known as quorum sensing.

    Wessner_6869_FM_i-1.indd 13 regulation

    © Luis M.de la Maza/ Phototake

    nificant human pathogen, causing not only pneumonia, but also 792 Chapter 23 Eukaryal Pathogenesis

    To get a better understanding of the practical concerns associated with biofilms, let’s look at the bacterium Pseudomonas

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    Special Features xiii

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    So far, we have examined the importance of biotechnology in industrial and pharmaceutical settings. Biotechnology is also critically important to modern agriculture. Green biotech 869_ch12_3 June 24, 2016 11:13 AM 361 refers to the use of biotechnology in this setting. Today, modern agriculture involves the use of large amounts of insecticides, herbicides, and synthetic fertilizers. In addition to being economically costly, this type of intensive agriculture poses human health concerns and environmental repercussions. Green CHAPTER Chapter Navigator: This feature biotech can benefit plant agriculture in several significant organizes the chapter by key NAVIGATOR ways. The soils that support the growth of plants are complex and directs students to understanding of microbialconcepts ecosystems (see Section 15.4). An the most important elements. As you study the key topics, make sure you review the the interactions of these microbes with each other and with infectious diseases following elements: the subterranean parts of the plant is crucial to our ability to tality. During World their battle wounds improve plant productivity. Additionally, bacterial systems can Microbes used for biotechnology may be obtained Little could be done from existing collections or isolated from nature. be used to introduce genes into plants that impart desired pended on the abil• Figure 12.2: Microbial culture collections properties to the plants. In this section, we will first look at the infection. Although • Perspective 12.1: Bioprospecting: Who owns the microbes? use of bacteria to alter the genetic makeup of plants. We will had been made sev• Figure 12.4: Types of bioreactors ation improved the then examine the usefulness of these transgenic traits.

    remained a serious To improve their usefulness, microbes can be genetimber 1928, a chance cally modified in numerous ways. that. CONNECTIONS In Section 17.2, we will investigate the intimate • 3D Animation: Using molecular biology tools to improve microriologist working at associations that many plants have formed with soil microorganisms bial strains t a fungus was inhibthat live as endosymbionts inside the plant. Some of these bacteria culture plates. Many • Microbes in Focus 12.2: Penicillium chrysogenum: The mold of this observation. can fix nitrogen, and the cultivation of several important crops takes that started the antibiotic revolution plore this serendipiadvantage of this bacterial capability. Because of these bacteria, • Toolbox 12.1: Site‐directed mutagenesis Penicillium, a filamenthe application of nitrogen fertilizer is not required for optimal crop • Figure 12.8: Process Diagram: Directed enzyme evolution m, which he termed agricultural inoculant industry provides cultures of endo• Figure 12.13: Process Diagram: Design and construction of a many Gram‐positive Wessner_6869_ch12_3 Juneyield. 24,The 2016 11:13 AM 366 synthetic organism on sexually transmitsymbiotic nitrogen‐fixing root nodule bacteria, as well as free‐living orrhoeae. • Mini‐Paper: Making a synthetic genome bacteria and fungi with plant growth‐promoting properties such as mal tests, that penicilphosphate solubilization. Red biotech involves the use of biotechnology in the clinical potential of pharmaceutical sector. 1930s. At that time, ard Florey and Ernst phase • of Figure 12.15: to Production recombinant insulin particular growth obtainofthe optimal production Lag Exponential Lag Exponential Connections: Throughout each Stationary phase Stationary phase t sufficient amounts phase phase phase phase of a desired product. For example, the main source of comWhite biotech involves the use of biotechnology in the able for human clinichapter, we highlight the mercial is fermentation sector. of sugars by the yeast Sacchahat the Allied forcesethanolindustrial interconnectedness of topics, romyces cerevisiae (see Figure 13.17). To maximize production • Figure 12.18: Commercial ethanol production using differentreducing mortality Cells Cells have been bred for centuries, Crop plants resulting Antibiotic in the modbothAlcohol within and between ofspurred ethanol, yeast feedstocks cells are maintained in exponential phase This success (secondary (primary metabolite) metabolite) throughout ern forms Red Giant Shooter Suite 13.2.12 Crack With Product Key Free 2020 plant‐based foods that are consumed f large‐scalewith produclow oxygen and with glucose as a carbon and energy • Perspective 12.3: Biofuels: Biodiesel and algae chapters. ions in cost of prothe world. The application of biotechnology to plant breedsource. • Figure 12.22: Structures of bacterial polyhydroxyalkanoates of the discoveryFor andyeast growing under anoxic conditions, ethanol repre(PHAs) ing broadens and extends the traits that can be introduced or nically useful antibiTime Time sents a primary metabolite, a product of metabolic processes changed. These traits includeB. Secondary taste, metabolite yield,produced nutritional content, he 1945 Nobel Prize Green biotech involves the use of biotechnology in during A. Primary metabolite produced during

    required for anaerobic growthsector. of yeast under anoxic conditions the agricultural

    Amount of cells or product

    Amount of cells or product

    Agrobacterium—Nature’s genetic engineer

    exponential phase Fact Check: stationary Each section with pest and pathogen resistance, andphase shelf life. ends The introduction

    12.5). Secondary metabolites, such as antibiotics, are opment as (Figure an antibiaand few questions to test students’ of traits depends thesecondary ability tometabolite introduce DNA intoA.the • 3D Animation: Agrobacterium in agricultural biotechnology Figure 12.5. Primaryon production The plant breakthrough the notinrequired for growth and are often produced during the stagenome and thenunderstanding The different methods ofculture, the content. • Toolbox 12.3: Plant transformation using bacteria production of primary metabolites, suchhave as ethanolitin aexpressed. yeast anaerobic mirrors the increase in biomass. ough, though, is notphase of tionary the growth curve. Concentrations of primary The production of secondarythis metabolites, such as antibiotics, is“transformation,” usually induced in stationary phase.but should used to achieve are all called • Figure 12.33: Process Diagram: Bacillus thuringiensis crystals B. ed to the design and metabolites may be difficult to increase in a culture. Because and mode of action arge‐scale growth of not be confused with the same term used in bacterial genetics, they are intrinsically linked to energy‐production pathways, tions. This advance which refers to the uptake of exogenous DNA by cells. One of high that concentrations of primary metabolites frequently interology products the most efficient ways to introduce DNA into plants is transfere with growth by producing toxicity or feedback inhibition. ted to the improve-

    12.1 Fact Check

    Even production strains of S. cerevisiae that have been selected CONNECTIONS thiscan chapter: for resistance to higher ethanol for levels tolerate only about Using metagenomics to find potential for biotechnology 15 percent ethanol before the culture ceases genes to grow. On the applications in uncultured microbes 10.4) other hand, secondary metabolites can often(Section be overproduced Use of GFP fusion proteins (Section 3.1) without affecting the growth of the culture. Effects of endotoxin on humans (Section 19.3)

    formation by Agrobacterium. 1. Describe what is meant by red, white, and green At the beginning of the twentieth century, the researchers biotechnology. Erwin Smith and C. O. Townsend demonstrated that a bacte2. How are culture collections used in biotechnology? rium they called Bacterium tumefaciens caused crown gall disease 3. What is bioprospecting? (Figure 12.30A), which produces tumors in many dicot plants. Sci4. Explain how bioreactors are used for biotechnology entists later changed the name of this plant pathogen to Agrobacfermentation processes. terium tumefaciens. Active research over the years demonstrated

    between plants(Section and soil microbes (Section 17.2) CONNECTIONSInteractions Feedback inhibition 13.3) occurs when the product of an enzyme or series of enzyme reactions accumulates 361 5. Distinguish between fed‐batch bioreactors and chemostats. in the cell and inhibits the action of an enzyme. Typically, bind390 Chapter 12 Microbial Biotechnology 6. Distinguish between a primary and a secondary ing of the product causes a conformational change in the enzyme that diminishes its ability to bind or act on the substrate, inhibiting metabolite. 24/06/16 11:43 am production.

    that the bacterium However, the bacte tion without interfe tumors continued Researchers be tumor formation in tumorigenic bacter necessary for tumo bacteria prevented for “tumor‐inducin strains of A. tumefac induced by opines duced by Agrobacter the tumor formatio that part of pTi, ca Figure 12.30B, was t into the plant’s ge clear that the expre resulted in the pro (also referred to as These materials res bacteria are natura with the genetic a bacteria then resid amounts of opines the presence of opi The mechanism cinating. It represe of trans‐kingdom of the vir genes th T‐DNA (Figure 12.3 naturally contain genome, presuma tion events that oc this was known, e and phytohormon the bacteria could could still be tran it these foreign ge immediately realiz plants through T‐D gators quickly dev plant transformati plants, genetically be generated. Suc North America. W rium transformatio Even though Ag introduce foreign cells of other plan nately, plants in thi tant crops such as not naturally susce

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    Summary Section 23.1: How do pathogenic eukarya cause disease?



    Eukaryal pathogens can be transmitted between hosts in various ways. Insect vectors passively transport spores between hosts for eukaryal pathogens like Ophiostoma novo‐ulmi. ■ Some eukaryal pathogens have a complex life cycle in which they undergo sexual reproduction in the definitive host and asexual reproduction and differentiation in the intermediate host. ■ The eukaryal pathogen Plasmodium falciparum must replicate and develop within the mosquito to be transmitted. ■ The eukaryal pathogen Giardia lamblia undergoes a simple life cycle. It is transmitted via the ingestion of cysts, which then give rise to trophozoites. ■ Upon entering an appropriate host, eukaryal pathogens must evade the host defenses. ■ Some opportunistic pathogens, like Pneumocystis jirovecii, only cause disease in immunocompromised individuals, such as people with HIV disease or people on immunosuppressive drugs. ■ Other opportunistic pathogens, like Candida albicans, cause disease when the normal microbial inhabitants of the host change. ■ Some pathogens, like Trypanosoma brucei subspecies, actively subvert the host defenses through antigenic variation. These organisms, characterized by a kinetoplast, exhibit cyclic variations in parasitemia. ■ Eukaryal pathogens exhibit various means of obtaining nutrients Summary: Organized section, from their hosts andby causing disease.the Summary lists the introductory questions, ■ Some phytopathogenic fungi produce enzymes like xylanase. Others use appressoria to penetrate host cells physically. In some along with short descriptions of the key species, mitogens promote appressoria development. points.■ Key terms also are incorporated and A number of eukaryal pathogens produce toxins. Cochliobolus highlighted. carbonum, a fungus of maize, produces HC‐toxin, which is an inhibitor of histone deactylases (HDACs), disrupting the expression of host defense genes. ■ Certain species of fungi produce mushrooms containing toxins such as α‐amanitin, which can lead to intoxication. ■ Certain dinoflagellates associated with harmful algal blooms (HABs) produce saxitoxin. ■



    ■ ■











    DRmare M4V Converter 4.1.1.21 Crack - Free Activators can be transmitted to a human when an infected mosquito Media Player Classic 1.8Key Genrator - Crack Key For U. In the human, these sporozoites initially infect liver cells, where they replicate, releasing diploid merozoites, which then infect erythrocytes. In an infected human, P. falciparum replication leads to malaria. To facilitate attachment to red blood cells, the merozoites express a series of merozoite surface proteins (MSPs). Once inside an erythrocyte, the merozoites obtain hemoglobin from the host cell through cytostomes. Digestion of hemoglobin by the pathogen releases heme, which P. falciparum then converts to hemozoin. Replication of merozoites within erythrocytes leads to the destruction of these cells, resulting in anemia. Although malaria remains a huge global problem, methods of preventing malaria and treating it do exist. Insecticide‐treated mosquito sleeping nets can prevent the transmission of P. falciparum. The antimalarial drug chloroquine blocks the formation of hemozoin.

    Section 23.3: What do we know about macroscopic eukaryal pathogens? Macroscopic eukaryal pathogens, like microbial pathogens, obtain resources from their hosts and, in the process, cause disease. ■





    Parasitic worms, or helminths, cause a number of severe human diseases throughout the world. The parasitic worm Ascaris lumbricoides is transmitted from human to human via contaminated water and causes ascariasis. Other parasitic worms, like Schistosoma spp., are transmitted via an intermediate host—freshwater snails—and cause schistosomiasis.

    Section 23.4: How do some eukaryal organisms become pathogens?

    Application Questions: Each chapter ends Some eukaryal organisms become more virulent by acquiring viruwith a series of thought-provoking questions lence genes. test the students’ factual understanding Eukaryal pathogens acquire virulence genes through Wessner_6869_ch22_1 June 9,that 2016 11:19 AM may787 Section 23.2: How does Plasmodium falciparum gene transfer. of horizontal the chapter and their ability to apply cause malaria? Pyrenophora tritici‐repentis became more pathogenic after acquiring Plasmodium falciparum exhibits a complex life cycle, replicating in their knowledge. the gene for ToxA. ■



    mosquitoes and humans, ultimately leading to the destruction of erythrocytes in humans. Within humans, the intermediate host, gametocytes (gamonts) are released from infected erythrocytes and ingested by feeding mosquitoes. From a virus’s perspective, explain the potential advantages of ■ Within the female Anopheles mosquito, the definitive host, the acutegametocytes and persistent infections. differentiate into gametes, which fuse, forming a Whydiploid might stress cause theookinete reactivation a latent virus? ookinete. The formsofan oocysthuman and undergoes meiosis, sporozoites. Explain why producing apoptosis haploid of infected cells may be beneficial to an ■

    Application Questions 1. 2. 3.

    organism. 4. We mentioned that cancer may be an unintended outcome of certain virus replication strategies. Explain. 5. Define antigenic drift and antigenic shift. How are these two events similar? How are they different? 6. Explain how bacteriophage lysogeny occurs. 7. What is an endogenous retrovirus? 8. An HIV‐infected cell can fuse with adjoining, non‐infected cells, forming a syncytium. Explain how this process might occur. Wessner_6869_ch23_pp788-817.indd 815

    Eukaryal pathogens may affect the evolution of their hosts. The prevalence of sickle‐cell disease is due, in large part, to the resistance to malaria conferred by the mutant β‐globin allele associated with sickle‐cell disease. 9. ■ Some researchers are concerned thatflies the have current H1N1 human Certain mycophagous species of fruit evolved resistance to α‐amanitin. influenza virus and the H5N1 avian influenza virus may give rise to ■ ■

    a more deadly human virus. How could this occur? 10. For a virus, which is more advantageous: evolving to become highly virulent or evolving to become less virulent? Explain your answer and provide examples. 11. For a respiratory virus like rhinovirus, transmission often occurs through the air. Viral particles exit an infected individual when the host coughs or sneezes and then are inhaled by another susceptible host. The viral particles must remain infectious during this exposure to the outside environment. Devise an experiment that Summary 815 would allow you to measure infectivity of a virus after exposure to various environmental conditions.

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    Special Features xv

    Suggested Reading Wessner_6869_FM_i-1.indd 15 Christie,

    A., G. J. Davies‐Wayne, T. Cordier‐Lasalie, et al. 2015. Possible

    Lau, S. K. P., P. C. Y. Woo, K. S. M. Li, Y. Huang, H.‐W. Tsoi, B. H. L.

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    Key Features • CHAPTER VIGNETTE WITH ORIGINAL ART Every chapter begins with an opening vignette that frames a basic question within the context of both contemporary and historical issues. Each vignette is visually supported by original art created by Janet Iwasa, University of Utah. • CHAPTER NAVIGATOR Organizes the chapter by key concepts and directs students to the most important elements (such as examples, animations, tables) within the chapter to support each concept. • MINI-PAPERS: A FOCUS ON THE RESEARCH & MINIPAPER PROJECT ACTIVITIES In every chapter, primary research articles are summarized and the original data is presented and interpreted, helping students sharpen critical thinking skills and deepen their understanding of microbiological research. The Mini-Paper examples are brief, edited versions of actual scientific papers designed to expose students to highly relevant and current research. Each Mini-paper article is accompanied by critical-thinking questions, and questions for discussion to help students learn to ask intelligent questions and design and evaluate experiments rationally. • TOOLBOXES IN MICROBIOLOGY Every chapter contains Toolboxes, which are in-depth descriptions of experimental techniques relevant to the chapter. These examples present and explain important techniques and/or experiments and are accompanied by Test Your Understanding questions.

    material was covered previously or that related material will be introduced again in a subsequent chapter. • PROCESS DIAGRAMS Each chapter includes selected, numbered Process Diagrams to lend clarity to the flow of complex processes. • EXPERIMENTAL FIGURES These figures allow students to better understand how an experiment proceeds, from Observation to Hypothesis to Results to Conclusions. • LIFE-CYCLE FIGURES Often combining art and photographs, these figures provide a clear overview of how microbes replicate. • THE REST OF THE STORY At the end of each chapter, this feature revisits the opening vignette, linking them explicitly to the chapter content. • IMAGE IN ACTION Here we revisit the chapter opener art and ask students questions about how the art and the chapter content are connected. • SUMMARY Organized by section, introductory questions are included along with short narrative descriptions of the key points, allowing students to gauge their understanding of the topics. Key terms are also incorporated as appropriate throughout the Summary. • APPLICATION QUESTIONS Each chapter ends with 10 to 15 thought-provoking questions that not only test students’ factual understanding of the chapter but also test their ability to apply their knowledge.

    • PERSPECTIVES IN MICROBIOLOGY EXAMPLES Perspectives In Microbiology Examples show students how topics may be viewed or used by different groups. They examine how someone, such as an ecologist or geneticist, would study or use the information presented in the chapter.

    Additional Resources for Instructors and Students

    • MICROBES IN FOCUS EXAMPLES Microbes in Focus Examples provide students with more detailed information about the habitats and key features of the microbes that are mentioned in each chapter. Detailed photomicrographs throughout this textbook magnify the microbial world for your eyes. Look to the bottom corner for information about how each image was obtained. Notice the many differences in magnification and information provided by light microscopy (LM), fluorescence microscopy (FM), scanning electron microscopy (SEM), and transmission electron microscopy (TEM). Appendix B explores these different forms of microscopy in more detail.

    ANIMATIONS 55 animations, many of which have been developed using 3D animation techniques by Janet Iwasa, University of Utah. Following the unique style of the chapter opener illustrations and developed to support learning objectives in the text, these animations help students visualize and master the most challenging topics in microbiology. A series of system-gradable assessments specific to the animations can be assigned by the instructor in WileyPLUS Learning Space.

    • FACT CHECKS Each section of the chapter ends with 3 to 5 questions to test students’ understanding of the content covered in that section. • CONNECTIONS Emphasize the interconnectedness of topics, both within a chapter and between chapters. These notes serve as reminders to the students that related

    Student Resources Available in WileyPLUS Learning Space:

    VIDEOS Each chapter contains a chapter opening and closing video featuring the authors of this text. The authors first present a remarkable example of microbiology in action or provide historical perspective pertaining to the upcoming chapter content. In the chapter summary section, the author videos revisit the opening vignette, explicitly linking them to the material they have read, helping students make important connections.

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    READING AND UNDERSTANDING THE PRIMARY LITERATURE

    STUDENT AND INSTRUCTOR RESOURCES

    As students prepare lab reports or science research papers, it is important to know what types of information are relevant, appropriate, and available to assist in developing a meaningful connection with the material through the incorporation of primary literature. The goal of this resource is to assist students in navigating this wealth of information.

    AVAILABLE IN THE TEXT:

    ILLUSTRATION AUDIO TUTORIALS A set of downloadable

    audio tutorials walk students through the detail in many of the chapter opener illustrations throughout the text. ORION ADAPTIVE PRACTICE ORION assesses student under-

    standing at the learning objective level and identifies areas where further studying is needed. Dvdfab passkey crack dvdfab passkey keygen - Free Activators practice meets students at just above their level in order to keep them challenged, but not frustrated. Adaptive practice includes extensive actionable reports that focus student study in key areas individual to each learner. INTERACTIVE GRAPHICS 120 static text illustrations have been

    visualized as interactive figures allowing students to engage with the art in dynamic ways enhancing their connection to the content. CONCEPT CHECK QUESTIONS Each reading section is fol-

    lowed by a series of questions for low-stakes student practice to measure their understanding of the reading content. Students are allowed multiple attempts and receive instant feedback on their performance.

    Instructor Resources Available in Debut video capture registration code 2018 - Free Activators Learning Space: ASSESSMENT: An expansive selection of system-gradable

    Assessment content with prebuilt Assignments are available to instructors using WileyPLUS Learning Space, including the following banks of questions for each chapter: • Image in Action Questions based on the chapter opener art for every chapter • Animation Questions based on many of the animations available • Pre Lecture Quiz and Post Lecture Quiz 70 questions per chapter provide opportunities for students to prepare prior to class and to assess post lecture understanding. • Application Questions Each chapter ends with a series of thought-provoking questions that test the students’ factual understanding of the chapter and their ability to apply their knowledge. • Test Bank (also available in Respondus and RTF formats) • INSTRUCTOR’S MANUAL • LECTURE POWERPOINT • IMAGES AND TABLES IN POWERPOINT • CLICKER QUESTIONS

    Mini-Papers: A Focus On The Research & Mini-Paper Project Activities The following is a list of each Mini-Paper per chapter. Links to additional topics can be found throughout WileyPLUS Learning Space.

    Key Features xvii

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    Toolboxes in Microbiology

    Perspectives in Microbiology Examples

    The following is a list of each Toolbox in Microbiology per chapter.

    The following is a list of each Perspective Example per chapter. Perspective 1.1 Creating Life in the Laboratory: The Miller– Urey Experiment

    Toolbox 1.1

    Polymerase Chain Reaction Amplification of rRNA Genes

    Toolbox 2.1

    The Gram Stain

    Perspective 2.2 The Protective Shells of Endospores

    Toolbox 3.1

    Using Microscopy to Examine Cell Structure

    Perspective 3.1 Hijacking the Cytoskeleton

    Toolbox 4.1

    Vaccine Delivery Strategies

    Toolbox 5.1

    Cell Culture Techniques

    Perspective 3.2 Secondary Endosymbiosis: The Origins of an Organelle with Four Membranes

    Toolbox 5.2

    Reverse Transcriptase Polymerase Chain Reaction (RT-PCR)

    Toolbox 6.1

    Phenotype Microarrays for Examining Microbial Growth

    Toolbox 6.2

    FISHing for Uncultivated Microorganisms

    Perspective 6.1 The Discovery of Heliobacter pylori

    Toolbox 7.1

    Using a Gel Shift Assay to Identify DNA-binding Proteins

    Perspective 6.2 Mycobacterium leprae, An Extraordinarily Slow-growing Pathogen

    Toolbox 8.1

    The Western Blot

    Toolbox 9.1

    Isolating Nutritional Mutants

    Perspective 6.3 The Human Intestine—A Continuous Culture

    Perspective 2.1 Marvelous Magnetosomes!

    Perspective 4.1 Extremophiles and Biotechnology Perspective 5.1 Ribozymes: Evidence for an RNA-based world Perspective 5.2 Measurement of HIV Viral Load

    Toolbox 10.1 Genome Databases

    Perspective 7.1 Using Mutations to Control Viral Infections

    Toolbox 11.1 Using RNA Molecules to Decrease Gene Expression

    Perspective 8.1 DNA Microarrays and the SARS Virus

    Toolbox 12.1 Site-directed Mutagenesis

    Perspective 9.1 Plasmids That Produce Pathogens

    Toolbox 12.2 Fusion Protein Purification

    Perspective 10.1 Rate of DNA Sequencing

    Toolbox 12.3 Plant Transformation Using Bacteria

    Perspective 10.2 The Minimal Genome

    Toolbox 13.1 Metabolism and Rapid Bacterial Identification Systems

    Perspective 11.1 The Use of Lactose Analogs in Gene Expression Studies

    Toolbox 14.1 Using Microarrays to Examine Microbial Communities: The GeoChip

    Perspective 12.1 Bioprospecting: Who Owns the Microbes?

    Perspective 8.2 Phage Therapy: Biocontrol for Infections

    Toolbox 14.2 Biogeochemistry in a Bottle: The Winogradsky Column

    Perspective 12.2 The International Genetically Engineered Machine (IGEM) Competition, Standard Biological Parts, and Synthetic Biology

    Toolbox 15.1 Flow Cytometry

    Perspective 12.3 Biofuels: Biodiesel and Algae

    Toolbox 16.1 Measuring Biochemical Oxygen Demand (BOD)

    Perspective 13.1 Who Needs Vitamins?

    Toolbox 16.2 Most Probable Number (MPN) Method Toolbox 17.1 Germfree and Gnotobiotic Animals

    Perspective 13.2 Electricigenic Bacteria and Microbial Fuel Cells

    Toolbox 18.1 Measuring the Virulence of Pathogens

    Perspective 14.1 CO2 as a Greenhouse Gas and Its Influence on Climate Change

    Toolbox 19.1 The Complement Fixation Test

    Perspective 14.2 Life in a World without Microbes

    Toolbox 19.2 The Limulus Amoebocyte Assay for LPS

    Perspective 14.3 The Microbiology of Environmentally Toxic Acid Mine Drainage

    Toolbox 20.1 Monoclonal Antibody (mAb) Production Toolbox 20.2 Enzyme-linked Immunosorbent Assay (ELISA) Toolbox 21.1 Serotyping Toolbox 21.2 The Tuberculin Test for Tuberculosis Toolbox 22.1 Immunoprecipitation Toolbox 23.1 Testing for Malaria Toolbox 24.1 Drug Susceptibility Testing and MIC

    Perspective 15.1 Naming the Uncultured and Uncharacterized Perspective 15.2 Dead Zones Perspective 16.1 Implication of Sludge Bulking Perspective 17.1 Food Probiotics—Do They Work? Perspective 17.2 Cows Contribute to Climate Change Perspective 17.3 Midichlorians—Not Just for Jedi Perspective 17.4 Death of Coral Reefs

    xviii

    Key Features

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    Perspective 18.1 Genome Editing: A Powerful and Controversial New Technique

    Microbes in Focus 4.3 The Salty Life of Halobacterium salinarum

    Perspective 18.2 The Armadillo—An Ideal Animal Model?

    Microbes in Focus 4.4 Methanobrevibacter smithii

    Perspective 19.1 Messy Mucus Perspective 20.1 Too Much of a Good Thing?

    Microbes in Focus 5.1 The Many Contributions of Bacteriophage T2

    Perspective 20.2 Vaccines Against T-independent Antigens

    Microbes in Focus 5.2 Poliovirus and the Race for a Vaccine

    Perspective 20.3 Turning Antibody Upside Down

    Microbes in Focus 6.1 The Metabolic Diversity of Pseudomonas aeruginosa

    Perspective 21.1 Iron, Vampires, Fashion, and the White Plague

    Microbes in Focus 6.2 A Picky Eater—Bordetella pertussis

    Perspective 21.2 The Good, the Bad, and the Ugly Side of Botulinum Toxin

    Microbes in Focus 7.1 Streptococcus pneumoniae in the Laboratory and the Hospital

    Perspective 21.3 Superabsorbent Tampons and Superantigens

    Microbes in Focus 7.2 The Extreme Life of Sulfolobus solfataricus

    Perspective 21.4 Antibiotics Trigger Toxins?

    Microbes in Focus 8.1 Mouse Hepatitis Virus (MHV)

    Perspective 22.1 Vertical Transmission of HIV

    Microbes in Focus 8.2 Human Papillomaviruses (HPVs) and Cervical Cancer

    Perspective 22.2 Viral Induction of Apoptosis Perspective 22.3 SV40 and Human Cancers Perspective 22.4 Ethical Concerns about Avian Flu Research Perspective 23.1 Pneumocystis jirovecii or carinii: The Evolving Field of Taxonomy

    Microbes in Focus 9.1 Escherichia coli Microbes in Focus 9.2 Bacillus subtilis Microbes in Focus 10.1 Mycoplasma genitalium Microbes in Focus 10.2 Yersinia pestis

    Perspective 23.2 Magic Mushrooms

    Microbes in Focus 11.1 Aliivibrio fischeri

    Perspective 23.3 Chytrid Fungus: An Emerging Fungal Pathogen

    Microbes in Focus 12.1 Streptomyces: A Gold Mine of Natural Products

    Perspective 24.1 The Pursuit of New Antibiotics: Why Bother?

    Microbes in Focus 12.2 Penicillium chrysogenum: The Mold That Started the Antibiotic Revolution

    Perspective 24.2 Health Care-Associated Infections: A Recipe for Resistance Perspective 24.3 Variolation: Deliberate Infection with Smallpox Virus Perspective 24.4 The War Against Vaccines

    Microbes in Focus Examples The following is a list of each Microbes in Focus per chapter. Microbes in Focus 1.1 Bacillus anthracis Microbes in Focus 2.1 Epulopiscium fishelsoni: Remarkable for More Than Its Size Microbes in Focus 2.2 Proteus mirabilis: A Swarming Bacterium Microbes in Focus 3.1 Chlamydomonas reinhardtii and the Study of Cell Motility Microbes in Focus 3.2 Entamoeba histolytica: The Cause of Amoebic Dysentery Microbes in Focus 3.3 Phytophthora infestans and the Irish Potato Famine

    Microbes in Focus 12.3 Bacillus thuringiensis: The Natural, Safe Insecticide Microbes in Focus 13.1 Chlorobium tepidum: The Bacterium That Does It All Microbes in Focus 13.2 Sinorhizobium meliloti Microbes in Focus 14.1 Methanococcus maripaludis: A Methane Producer Microbes in Focus 14.2 Methylosinus trichosporium: A Methane Eater Microbes in Focus 14.3 Nitrobacter winogradskyi Microbes in Focus 15.1 Synechocystis sp. PCC6803—From Unpleasant Cyanobacterial Blooms to Science and Biotechnology Workhorse Microbes in Focus 16.1 Winzip driver updater crack download - Crack Key For U lactis Microbes in Focus 16.2 Cryptosporidium parvum Microbes in Focus 17.1 Malassezia

    Microbes in Focus 4.1 Haloquadratum walsbyi: The Square Microbe

    Microbes in Focus 17.2 Streptococcus mutans, A Sweet Tooth and Cavities

    Microbes in Focus 4.2 Living in “Hot Vinegar”: Thermoplasma acidophilum

    Microbes in Focus 17.3 Candidatus Carsonella ruddii: Is It a Cell or an Organelle?

    Key Features xix

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    Microbes in Focus 18.1 Measles: A Highly Contagious Disease Microbes in Focus 18.2 Salmonella Typhi: The Cause of Typhoid Fever Microbes in Focus 18.3 Chikungunya virus: An Emerging Pathogen Microbes in Focus 18.4 Life in the Stomach: Helicobacter pylori Microbes in Focus 18.5 Borrelia burgdorferi and Lyme Disease Microbes in Focus 19.1 Covert Operations of Human Cytomegalovirus Microbes in Focus 20.1 Slippery Haemophilus influenzae Microbes in Focus 21.1 Neisseria gonorrhoeae Microbes in Focus 21.2 Clostridium botulinum

    Microbes in Focus 22.1 Human Rhinoviruses and the Common Cold Microbes in Focus 22.2 Lifelong Infections: Herpes Simplex Viruses 1 and 2 Microbes in Focus 22.3 Ebola Virus: The Cause of a Zoonotic Disease Microbes in Focus 22.4 Tomato Spotted Wilt Virus: A Major Agricultural Pest Microbes in Focus 23.1 An AIDS-defining Opportunistic Infection: Toxoplasma gondii Microbes in Focus 23.2 Trypanosoma brucei: The Cause of African Sleeping Sickness

    Microbes in Focus 21.3 Corynebacterium diphtheriae

    Microbes in Focus 23.3 The Rice Blast Pathogen: Magnaporthe grisea

    Microbes in Focus 21.4 Clostridium perfringens and Gas Gangrene

    Microbes in Focus 23.4 Getting Through the Cell Wall: Lessons from Cochliobolus carbonum

    Microbes in Focus 21.5 Streptococcus pyogenes

    Microbes in Focus 23.5 Ascaris lumbricoides: A Roundworm Parasite of Humans

    Microbes in Focus 21.6 Mycobacterium tuberculosis Microbes in Focus 21.7 Vibrio cholerae Microbes in Focus 21.8 Legionella pneumophila: The Accidental Pathogen

    xx

    Microbes in Focus 23.6 Pyrenophora tritici-repentis: The Cause of Tan Spot in Wheat Microbes in Focus 24.1 Foot-and-Mouth Disease Virus

    Key Features

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    Acknowledgments We acknowledge the invaluable contributions of our colleagues: Barbara Butler, Brian Driscoll, Heidi Elmendorf, Craig Stephens, and Dave Westenberg. We also thank the editorial and production team at Wiley: Executive Editor Ryan Flahive, Freelance Developmental Editors Kathy Naylor and Deborah Allen, Production Editor Trish McFadden, Executive Marketing Manager Clay Stone, Associate Product Designer Lauren Elfers, Development Editor Melissa Whelan, and Senior Photo Editor Mary Ann Price for their guidance and support. We would like to thank Sarah J. VanVickle-Chavez, Ph.D., of Washington University in St. Louis who wrote Appendix A, Reading and Understanding the Primary Literature. We also would like to extend a very warm thanks to Kelly Prior for her efforts in writing the in-text questions and to Janet Iwasa for her amazing cover and chapter opener illustrations. Her art has helped us bring microbiology to life. A very special thank you to the members of our advisory board and to all the instructors who helped along the way as we wrote our book.

    Microbiology 2e Reviewers, Class Testers, Focus Group Participants Derrick Brazil Alison Buchan Dale Casmatta Janet Donaldson Terri Ellis Kathleen A. Feldman Roger S. Greenwell Jr. Sheela S. Huddle Ed Ishiguro Sanghoon Kang Georgia Pirino Ines Rauschenbauch Carlos Rios-Velasquez Matthew M. Schmidt James Leif Smith Joseph A. Sorg Jance Speshock John Steiert Craig Stephens Monica Tischler

    Hunter College University of Tennessee University of North Florida Mississippi State University University of North Florida University of Connecticut Worcester State University Harrisburg Area Community College University of Victoria Baylor University University of California Los Angeles Rutgers University University of Puerto Rico at Mayaguez Stony Brook University Texas A&M University Texas A&M University Tarleton State University Missouri State University Santa Clara University Benedictine University

    Microbiology 2e Advisory Board Dwayne Boucaud Joanna Brooke Ann Buchmann Silvia Cardona Wendy Dustman Kathleen Feldman Sandra Gibbons Janice Haggart Michael Ibba Ross Johnson William Navarre Rebecca Sparks-Thissen John Steiert

    Quinnipiac University DePaul University Chadron State University University of Manitoba University of Georgia University of Connecticut, Storrs University of Illinois, Chicago North Dakota State University Ohio State University Chicago State University University of Toronto Wabash College Missouri State University

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    Brief Contents PART I THE MICROBES

    1 2 3 4 5 6

    The Microbial World

    2

    Bacteria

    34

    Eukaryal Microorganisms

    72

    Archaea

    106

    Viruses

    130

    Cultivating Microorganisms

    164

    PART II MICROBIAL GENETICS

    7 8 9 10 11 12

    DNA Replication and Gene Expression

    202

    Viral Replication Strategies

    238

    Bacterial Genetic Analysis and Manipulation

    264

    Microbial Genomics

    300

    Regulation of Gene Expression

    328

    Microbial Biotechnology

    360

    PART III MICROBIAL PHYSIOLOGY AND ECOLOGY

    13 14 15 16 17

    Metabolism

    400

    Biogeochemical Cycles

    456

    Microbial Ecosystems

    486

    The Microbiology of Food and Water

    524

    Microbial Symbionts

    562

    PART IV Internet explorer for windows 10 - Crack Key For U AND DISEASE

    18 19 20 21 22 23 24

    Introduction to Infectious Diseases

    600

    Innate Host Defenses Against Microbial Invasion

    638

    Adaptive Immunity

    672

    Bacterial Pathogenesis

    710

    Viral Pathogenesis

    756

    Eukaryal Pathogenesis

    788

    Control of Infectious Diseases

    818

    xxii

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    Contents PART I THE MICROBES Perspective 2.1 MARVELOUS MAGNETOSOMES! 44 Toolbox 2.1 THE GRAM STAIN 53 Perspective 2.2 THE PROTECTIVE SHELLS OF ENDOSPORES 54 Mini-Paper: A Focus on the Research NEW MICROSCOPY

    1

    METHODS REVEAL A PERIPLASM IN GRAM-POSITIVE BACTERIAL CELLS 58

    The Microbial World

    2

    2.5 The Bacterial Cell Surface 59 2.6 Diversity of Bacteria 66

    1.1 The Microbes 4 Mini-Paper: A Focus on the Research THE THREE DOMAINS OF LIFE 10 Toolbox 1.1 POLYMERASE CHAIN REACTION AMPLIFICATION OF rRNA GENES 12

    1.2 Microbial Genetics 15 Perspective 1.1 CREATING LIFE IN THE LABORATORY: THE MILLER–UREY EXPERIMENT 18

    1.3 Microbial Physiology and Ecology 23 1.4 Microbes and Disease 26

    3

    Eukaryal Microorganisms

    72

    3.1 The Morphology of Typical Eukaryal Cells 74 Mini-Paper: A Focus on the Research LIPID RAFTS: ORGANIZED CLUSTERING OF LIPIDS WITHIN A MEMBRANE 80 Toolbox 3.1 USING MICROSCOPY TO EXAMINE CELL STRUCTURE 82 Perspective 3.1 HIJACKING THE CYTOSKELETON 86

    2

    Bacteria 2.1 2.2 2.3 2.4

    34

    Morphology of Bacterial Cells 36 The Cytoplasm 38 The Bacterial Cytoskeleton 41 The Cell Envelope 43

    3.2 Diversity of Eukaryal Microorganisms 86 3.3 Replication of Eukaryal Microorganisms 91 3.4 The Origin of Eukaryal Cells 94 Perspective 3.2 SECONDARY ENDOSYMBIOSIS: THE ORIGINS OF AN ORGANELLE WITH FOUR MEMBRANES 97

    3.5 Interactions Between Eukaryal Microorganisms and Animals, Plants, and the Environment 98

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    Toolbox 5.2 REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION (RT-PCR) 154

    5.5 Virus-Like Particles 155 5.6 Virology Today 158

    4

    Mini-Paper: A Focus on the Research NEW FINDINGS IN THE PACKAGING OF DNA BY THE MODEL BACTERIOPHAGE T4 160

    Archaea

    106

    4.1 Evolution of Archaea 108 4.2 Archaeal Cell Structure 110 Toolbox 4.1 VACCINE DELIVERY STRATEGIES 115

    4.3 Diversity of Archaea 118 Perspective 4.1 EXTREMOPHILES AND BIOTECHNOLOGY 120 Mini-Paper: A Focus on the Research THE ROLE OF ARCHAEA IN OUR DIGESTIVE SYSTEM 124

    6

    Cultivating Microorganisms

    164

    6.1 Nutritional Requirements of Microorganisms 166 6.2 Factors Affecting Microbial Growth 168 Streaming video capture software - Crack Key For U 6.1 PHENOTYPE MICROARRAYS FOR EXAMINING MICROBIAL GROWTH 169

    6.3 Growing Microorganisms in the Laboratory 173

    5

    Viruses

    130

    5.1 A Basic Overview of Viruses 132 5.2 Origins of Viruses 140 Perspective 5.1 RIBOZYMES: EVIDENCE FOR AN RNA-BASED WORLD 141

    5.3 Cultivation, Purification, and Quantification of Viruses 143 Toolbox 5.1 CELL CULTURE TECHNIQUES 144 Perspective 5.2 MEASUREMENT OF HIV VIRAL LOAD 147

    5.4 Diversity of Viruses 150

    Perspective 6.1 THE DISCOVERY OF HELICOBACTER PYLORI 178 Toolbox 6.2 FISHING FOR UNCULTIVATED MICROORGANISMS 180

    6.4 Measuring Microbial Population Growth 181 Mini-Paper: A Focus on the Research BRINGING TO LIFE THE PREVIOUSLY UNCULTURABLE USING THE SOIL SUBSTRATE MEMBRANE SYSTEM (SSMS) 182 Perspective 6.2 MYCOBACTERIUM LEPRAE, AN EXTRAORDINARILY SLOW-GROWING PATHOGEN 189 Perspective 6.3 THE HUMAN INTESTINE—A CONTINUOUS CULTURE 191

    6.5 Eliminating Microbes and Preventing Their Growth 192

    PART II MICROBIAL GENETICS 7.2 DNA Replication 210 7.3 Transcription 217 Toolbox 7.1 USING A GEL SHIFT ASSAY TO IDENTIFY DNA-BINDING PROTEINS 219

    7

    7.4 Translation 222 7.5 The Effects of Mutations 229

    DNA Replication and Gene Expression 202 7.1 The Role of DNA 204 xxiv

    Mini-Paper: A Focus on the Research TELOMERES WITH PROMOTER ACTIVITY 232 Perspective 7.1 USING MUTATIONS TO CONTROL VIRAL INFECTIONS 234

    Contents

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    Perspective 10.1 RATE OF DNA SEQUENCING 306 Toolbox 10.1 GENOME DATABASES 310

    10.2 Genomic Analysis of Gene Expression 312 10.3 Comparative Genomics 318

    8

    Perspective 10.2 THE MINIMAL GENOME 318 Mini-Paper: A Focus on the Research GENOME SEQUENCE

    Viral Replication Strategies

    238

    OF A KILLER BUG 320

    10.4 Metagenomics and Related Analyses 323

    8.1 Recognition of Host Cells 240 Perspective 8.1 DNA MICROARRAYS AND THE SARS VIRUS 242 Toolbox 8.1 THE WESTERN BLOT 244

    8.2 Viral Entry and Uncoating 246 8.3 Viral Replication 249 Perspective 8.2 PHAGE THERAPY: BIOCONTROL FOR INFECTIONS 256

    8.4 Viral Assembly and Egress 258 Mini-Paper: A Focus on the Research THE DISCOVERY OF REVERSE TRANSCRIPTASE 260

    11

    Regulation of Gene Expression

    328

    11.1 Differential Gene Expression 330 11.2 The Operon 332 11.3 Global Gene Regulation 337 Mini-Paper: A Focus on the Research TUNING PROMOTERS FOR USE IN SYNTHETIC BIOLOGY 338 Perspective 11.1 THE USE OF LACTOSE ANALOGS IN GENE

    9

    EXPRESSION STUDIES 342

    Bacterial Genetic Analysis and Manipulation 264 9.1 Bacteria as Subjects of Genetic Research 266 9.2 Mutations, Mutants, and Strains 269 Toolbox 9.1 ISOLATING NUTRITIONAL MUTANTS 271

    11.4 Post-initiation Control of Gene Expression 345 Toolbox 11.1 USING RNA MOLECULES TO DECREASE GENE EXPRESSION 347

    11.5 Quorum Sensing 348 11.6 Two-Component Regulatory Systems 351 11.7 Chemotaxis 354

    9.3 Restriction Enzymes, Vectors, and Cloning 276 9.4 Recombination and DNA Transfer 283 Perspective 9.1 PLASMIDS THAT PRODUCE PATHOGENS 287 Mini-Paper: A Focus on the Research THE DISCOVERY

    12

    OF TRANSDUCTION 294

    Microbial Biotechnology

    360

    12.1 Microbes for Biotechnology 362

    10

    Microbial Genomics

    Perspective 12.1 BIOPROSPECTING: WHO OWNS THE MICROBES? 364

    12.2 Molecular Genetic Modification 366

    300

    10.1 Genome Sequencing 302

    Toolbox 12.1 SITE-DIRECTED MUTAGENESIS 368 Toolbox 12.2 FUSION PROTEIN PURIFICATION 374

    Contents xxv

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    Mini-Paper: A Focus on the Research MAKING A SYNTHETIC GENOME 376

    12.4 White Biotechnology 381 Perspective 12.3 BIOFUELS: BIODIESEL AND ALGAE 384

    Perspective 12.2 THE INTERNATIONAL GENETICALLY ENGINEERED MACHINE (IGEM) COMPETITION, STANDARD BIOLOGICAL PARTS, AND SYNTHETIC BIOLOGY 378

    12.5 Green Biotechnology 390 Toolbox 12.3 PLANT TRANSFORMATION USING BACTERIA 392

    12.3 Red Biotechnology 379

    PART III MICROBIAL PHYSIOLOGY AND ECOLOGY Toolbox 14.1 USING MICROARRAYS TO EXAMINE MICROBIAL COMMUNITIES: The GeoChip 461

    14.2 Cycling Driven by Carbon Metabolism 462 Perspective 14.1 CO2 AS A GREENHOUSE GAS AND ITS

    13

    Metabolism

    INFLUENCE ON CLIMATE CHANGE 464

    14.3 Cycling Driven by Nitrogen Metabolism 471

    400

    Mini-Paper: A Focus on the Research THE FIRST ISOLATION AND

    13.1 Energy, Enzymes, and ATP 402 Perspective 13.1 WHO NEEDS VITAMINS? 405

    13.2 Central Processes in ATP Synthesis 406 13.3 Carbon Utilization in Microorganisms 412 13.4 Respiration and the Electron Transport System 421

    CULTIVATION OF A MARINE ARCHAEON 476

    14.4 Other Cycles and their Connections 476 Perspective 14.2 LIFE IN A WORLD WITHOUT MICROBES 478 Perspective 14.3 THE MICROBIOLOGY OF ENVIRONMENTALLY TOXIC ACID MINE DRAINAGE 479 Toolbox 14.2 BIOGEOCHEMISTRY IN A BOTTLE: THE WINOGRADSKY COLUMN 481

    Perspective 13.2 ELECTRICIGENIC BACTERIA AND MICROBIAL FUEL CELLS 425

    13.5 Metabolism of Non-glucose Carbon Sources 429 Toolbox 13.1 METABOLISM AND RAPID BACTERIAL IDENTIFICATION SYSTEMS 431

    13.6 Phototrophy and Photosynthesis 433 13.7 Nitrogen and Sulfur Metabolism 442 Mini-Paper: A Focus on the Research GENOME SEQUENCE OF A DEEP SEA SYMBIONT 443

    13.8 Biosynthesis of Cellular Components 448

    15

    Microbial Ecosystems

    486

    15.1 Microbes in the Environment 488 15.2 Microbial Community Analysis 493 Toolbox 15.1 FLOW CYTOMETRY 498 Mini-Paper: A Focus on the Research INSIGHTS INTO THE PHYLOGENY AND CODING POTENTIAL OF MICROBIAL DARK MATTER 500

    14

    Biogeochemical Cycles 14.1 Nutrient Cycling 459

    xxvi

    Perspective 15.1 NAMING THE UNCULTURED AND UNCHARACTERIZED 502

    15.3 Aquatic Ecosystems 502

    456

    Perspective 15.2 DEAD ZONES 503

    15.4 Terrestrial Ecosystems 509 15.5 Ca antivirus - Crack Key For U Subsurface and Geothermal Ecosystems 515

    Contents

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    16

    The Microbiology of Food and Water 524 16.1 16.2 16.3 16.4 16.5

    Food Spoilage 526 Food Preservation 530 Food Fermentation 535 Foodborne and Waterborne Illness 542 Microbiological Aspects of Water Quality 545

    17

    Microbial Symbionts

    562

    17.1 Types of Microbe-Host Interactions 564 17.2 Symbionts of Plants 566 17.3 Symbionts of Humans 571 Toolbox 17.1 GERM-FREE AND GNOTOBIOTIC ANIMALS 575 Perspective 17.1 FOOD PROBIOTICS—DO THEY WORK? 577 Mini-Paper: A Focus on the Research FECAL BACTERIOTHERAPY: “REPOOPULATION” OF THE GUT 580

    Perspective 16.1 IMPLICATIONS OF SLUDGE BULKING 550

    17.4 Symbionts of Herbivores 582

    Toolbox 16.1 MEASURING BIOCHEMICAL OXYGEN DEMAND

    Perspective 17.2 COWS CONTRIBUTE TO CLIMATE CHANGE 588

    (BOD) 551

    17.5 Symbionts of Invertebrates 588

    Mini-Paper: A Focus on the Research ENHANCED BIOLOGICAL

    Perspective 17.3 MIDICHLORIANS—NOT JUST FOR JEDI 592

    REMOVAL OF PHOSPHORUS 553

    Perspective 17.4 DEATH OF CORAL REEFS 595

    Toolbox 16.2 MOST PROBABLE NUMBER (MPN) METHOD 556

    PART IV MICROBES AND DISEASE Perspective 18.2 THE ARMADILLO—AN IDEAL ANIMAL MODEL? 628

    18.5 The Evolution of Pathogens 629

    18

    Introduction to Infectious Diseases 600 18.1 Pathogenic Microbes 603 Toolbox 18.1 MEASURING THE VIRULENCE OF PATHOGENS 605

    18.2 Microbial Virulence Strategies 607 Perspective 18.1 GENOME EDITING: A POWERFUL AND CONTROVERSIAL NEW TECHNIQUE 613

    18.3 The Transmission of Infectious Diseases 614 Mini-Paper: A Focus on the Research EPIDEMIOLOGY OF AN INFECTIOUS DISEASE 622

    19

    Innate Host Defenses Against Microbial Invasion 638 19.1 Immunity 640 19.2 Barriers to Infection 641 Perspective 19.1 MESSY MUCUS 644

    19.3 The Inflammatory Response 645 19.4 The Molecules of the Innate System 646

    18.4 Proving Cause and Effect in Microbial Infections 624 Contents xxvii

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    Mini-Paper: A Focus on the Research MAMMALIAN CELLS CAN

    Toolbox 21.1 SEROTYPING 724

    RECOGNIZE BACTERIAL DNA 650

    Perspective 21.2 THE GOOD, THE BAD, AND THE UGLY SIDE

    Toolbox 19.1 THE COMPLEMENT FIXATION TEST 654

    OF BOTULINUM TOXIN 732

    19.5 The Cells of Innate Immunity 657 19.6 Invertebrate Defenses 665

    Perspective 21.3 SUPERABSORBENT TAMPONS AND

    Toolbox 19.2 THE LIMULUS AMOEBOCYTE ASSAY FOR LPS 667

    SUPERANTIGENS 737

    21.3 Survival in the Host: Strategies and Consequences 738 Toolbox 21.2 THE TUBERCULIN TEST FOR TUBERCULOSIS 746

    21.4 Evolution of Bacterial Pathogens 746 Perspective 21.4 ANTIBIOTICS TRIGGER TOXINS? 750

    20

    Adaptive Immunity 20.1 20.2 20.3 20.4 20.5

    672

    Features of Adaptive Immunity 674 T Cells 677 Antigen Processing 682 Antigen-Presenting Cells 684 Humoral and Cell-Mediated Immune Responses 688

    22

    Viral Pathogenesis

    756

    22.1 Recurring Easeus partition manager in Viral Pathogenesis 758 Perspective 22.1 VERTICAL TRANSMISSION OF HIV 763

    A VIRUS TO IMPROVE IMMUNOCONTRACEPTION 690

    22.2 Interactions with the Host: Strategies and Consequences 765

    Perspective 20.1 TOO MUCH OF A GOOD THING? 691

    Perspective 22.2 VIRAL INDUCTION OF APOPTOSIS 767

    20.6 B Cells and the Production of Antibody 692

    22.3 Viral Infections and Cancer 770

    Perspective 20.2 VACCINES AGAINST T-INDEPENDENT

    Toolbox 22.1 IMMUNOPRECIPITATION 773

    ANTIGENS 696

    Mini-Paper: A Focus on the Research VIRUSES THAT CAUSE CAN-

    Toolbox 20.1 MONOCLONAL ANTIBODY (mAb) PRODUCTION 698

    CER BY AFFECTING CELLULAR PROLIFERATION 774

    Perspective 20.3 TURNING ANTIBODY UPSIDE DOWN 703

    Perspective 22.3 SV40 AND HUMAN CANCERS 776

    Toolbox 20.2 ENZYME-LINKED IMMUNOSORBENT

    22.4 Evolution of Viral Pathogens 780

    ASSAY (ELISA) 704

    Perspective 22.4 ETHICAL CONCERNS ABOUT AVIAN FLU

    Mini-Paper: A Focus on the Research ATTEMPTING TO ENGINEER

    RESEARCH 784

    21

    Bacterial Pathogenesis

    710

    21.1 Bacterial Virulence Factors 712

    23

    Eukaryal Pathogenesis

    788

    Mini-Paper: A Focus on the Research ESCHERICHIA COLI INJECTS

    23.1 Mechanisms of Eukaryal Pathogenesis 790

    ITS OWN RECEPTOR 718

    Mini-Paper: A Focus on the Research AN EXPERIMENTAL

    Perspective 21.1 IRON, VAMPIRES, FASHION, AND THE WHITE

    SYSTEM FOR THE GENOMIC STUDY OF DUTCH ELM DISEASE 794

    PLAGUE 722

    Perspective 23.1 PNEUMOCYSTIS JIROVECII OR CARINII :

    21.2 Bacterial Virulence Factors—Toxins 723

    THE EVOLVING FIELD OF TAXONOMY 797

    xxviii

    Contents

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    Perspective 23.2 MAGIC MUSHROOMS 802

    Perspective 24.1 THE PURSUIT OF NEW ANTIBIOTICS: WHY

    23.2 Pathogen Study: Plasmodium Falciparum 803 23.3 Macroscopic Eukaryal Pathogens 807

    BOTHER? 844 Perspective 24.2 HEALTH CARE-ASSOCIATED INFECTIONS: A RECIPE FOR RESISTANCE 845

    23.4 Evolution of Eukaryal Pathogens 811

    24.4 Predicting and Controlling Epidemics 846 24.5 Immunization and Vaccines 848

    Perspective 23.3 CHYTRID FUNGUS: AN EMERGING FUNGAL

    Perspective 24.3 VARIOLATION: DELIBERATE INFECTION WITH

    PATHOGEN 812

    SMALLPOX VIRUS 849

    Toolbox 23.1 TESTING FOR MALARIA 808

    Perspective 24.4 THE WAR AGAINST VACCINES 854

    Appendix A

    24

    Control of Infectious Diseases

    Reading and Understanding the Primary Literature A1 Appendix B Microscopy A9 Appendix C Taxonomys A13 Appendix D Origin of Blood Cells A15

    818

    24.1 Historical Aspects of Infectious Disease Treatment and Control 820 24.2 Antimicrobial Drugs 821 24.3 Antimicrobial Drug Resistance 834 Toolbox 24.1 DRUG SUSCEPTIBILITY TESTING AND MIC 838 Mini-Paper: A Focus on the Research SOIL MICROORGANISMS

    GLOSSARY INDEX I-1

    GL-1

    ONLINE APPENDICES Appendix E Classification of Archaea Appendix F Classification of Viruses Appendix G Origin of Blood Cells

    POSSESS EXTENSIVE RESISTANCE TO ANTIBIOTICS 840

    Contents xxix

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    MICROBIOLOGY

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    C HAPTER

    1 The Microbial World

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    CHAPTER NAVIGATOR

    A

    nton van Leeuwenhoek was a successful textile merchant in the city of Delft, in the Netherlands, in the late seventeenth century. He used magnifying lenses in his trade to examine cloth, but in 1665, after reading Robert Hooke’s book Micrographia, van Leeuwenhoek became fascinated with using microscopes to explore the natural world. Hooke, an Englishman of about the same age as van Leeuwenhoek, had laboriously constructed microscopes that magnified objects roughly 30 times and used them to examine the fine structure of materials both living and dead. His greatest contribution to biology was the discovery of cells, which he first observed in cork slices, as the units from which living organisms are assembled. Hooke’s writings inspired van Leeuwenhoek, who enjoyed blowing glass and grinding tiny lenses, to fabricate simple but remarkably powerful microscopes. Some of the 400 or so microscopes that van Leeuwenhoek built magnified images almost 300‐fold, and could be used to observe objects one‐tenth the size that Hooke had seen. If we consider that the best modern light microscopes of today are limited to around 1000‐fold magnification, van Leeuwenhoek’s accomplishments are even more astounding! With his extraordinary lenses, van Leeuwenhoek pushed the frontiers of human knowledge to ever‐smaller dimensions. No one had imagined living creatures so small they could not be seen by the human eye, yet van Leeuwenhoek saw them all around us, on us, even inside us. In a letter to the Royal Society of London in 1684, he related that: The number of these Animals in the scurf of a man’s Teeth, are so many, that I believe they exceed the number of Men in a kingdom. For upon the examination of a small parcel of it, no thicker than a Horse‐hair, I found too many living Anima’s therein, that I guess there might have been 1000 in a quantity of matter no bigger then the 1/100 part of a sand.

    As you study the key topics, make sure you review the following elements: Microbiology involves the study of bacteria, archaea, eukaryal microorganisms, and viruses. • • • •

    Table 1.1: Macromolecules in microbial cells Animation: Classification systems Toolbox 1.1: Polymerase chain reaction amplification of rRNA genes Mini‐Paper: The three domains of life

    Studies of microbes have provided insight into the evolution of life and genetics. • • • •

    Perspective 1.1: Creating life in the laboratory: The Miller–Urey experiment Animation: Endosymbiosis Figure 1.20: Effects of mutations Figure 1.22: Recombinant DNA techniques

    The metabolic properties of microorganisms are related to their habitats. • •

    Figure 1.24: Glycolysis, fermentation, and aerobic respiration Figure 1.25: Role of microbes in the global nitrogen cycle

    Microbes remain important causes of disease throughout the world. • • •

    Microbes in Focus 1.1: Bacillus anthracis Figure 1.30: Infectious disease deaths in the United States during the twentieth century Figure 1.32: Impact of malaria in sub‐Saharan Africa

    In another letter, he confided with amazement that: I then most always saw, with great wonder, that in the said matter there were many very little living animalcules, very prettily a‐moving. Thus, this modest Dutch merchant revealed a whole new “microscopic” world to humanity. Van Leeuwenhoek discovered microorganisms.

    CONNECTIONS

    for this chapter:

    Development of antimicrobial and antiviral drugs (Section 24.2) Evolution of eukaryal cells through an endosymbiotic process (Section 3.4) Oxygenic and anoxygenic photosynthesis (Section 13.6) Epidemiology: The study of how infectious diseases spread within populations (Section 18.3)

    3

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    Introduction With wonder in his voice, Anton van Leeuwenhoek shared his observations of microbial life with a skeptical public. In the three centuries since van Leeuwenhoek first viewed these “animalcules,” the scientific community and the general public have become much more appreciative of the importance of microbes. We now know that microscopic life on Earth is enormously abundant and diverse, that microbes appeared billions of years before humans, and that the health of the entire biosphere depends on its tiniest microbial inhabitants. We also know that microbes interact with each other and with multicellular organisms, including humans, in many ways. Because of our increased understanding of microbes, we now can use them to help us in many agricultural and industrial settings. Additionally, we now better understand how our own bodies work. We also have learned to fear microbes; some of them cause diseases that have resulted in the suffering and death of untold millions of people through the ages. Throughout this book, we will explore all of these aspects of microbiology. While we will use specific examples to illustrate our points, we will focus on the general principles. We will emphasize the relationships between microbes and the evolutionary history of biological processes. We also will learn how the study of microbes relates to various other disciplines,

    like genetics, chemistry, and environmental science. Finally, we will see that microbiology itself is a dynamic, evolving science. Our knowledge of postbox mac crack - Crack Key For U is predicated on thoughtful, interesting, and exciting experiments. Much more still awaits our discovery. As we will note throughout this book, we do not know all the answers. We probably do not even know all the questions! The field of microbiology is ever changing. Today’s basic research will lead to tomorrow’s revelations. So, let’s start our exploration of this dynamic field. In this chapter and in the book as a whole, we first will learn about the microbes. Then, we will examine the genetics of microbes. Next, we will look at the metabolism of microorganisms and how microbes interact with their environment. Finally, we will explore the role of microbes in disease. We will frame our initial discussion around these questions: What is microbiology? (1.1) What do we know about the evolution of life and the genetics of microbes? (1.2) How do microbes get energy and interact with the world around them? (1.3) How are microbes associated with disease? (1.4)

    1.1 The microbes What is microbiology? Microorganisms are microscopic forms of life—organisms that are too small to see with the unaided eye. They usually consist of a single cell and include bacteria, archaea, fungi, protozoa, and algae. We will include viruses in many of our discussions as well. Viruses are not living, but they are microscopic; they use biological molecules and cellular machinery (borrowed from their host) to replicate, and they can cause infectious diseases like some microorganisms. Although viruses are not microorganisms, we can refer to them as microbes, a more general term that includes microorganisms and viruses. Microbiology, then, is the study of microbes. Our relationship with the microbial world is complex and dynamic. On one hand, harmful bacteria, viruses, fungi, and protozoa kill millions of people each year and sicken billions. On the other hand, beneficial microbes associated with our bodies help us digest food and protect us from potentially harmful microbial invaders (Figure 1.1). Some microbes cause crops to fail, while others provide essential nitrogen to plant roots through symbiotic relationships. Some microbes cause food to rot, but others carry out fermentations that produce yogurt, wine, beer, and other foods and beverages (Figure 1.2). In the past few decades, we have learned so much about the molecular machinery of life through the study of microbes, like the bacterium Escherichia coli. Indeed, scientists now routinely

    CONNECTIONS Throughout this book, we will show you many micrographs, photographs or digital images obtained through a microscope. For each one, an icon will tell you what type of microscopy was used. Specifically, LM indicates light microscopy, SEM refers to scanning electron microscopy, TEM signifies transmission electron microscopy, and FM represents fluorescence microscopy. A detailed examination of microscopy is provided in Appendix B.

    alter microbial cells to produce high‐value, lifesaving medical products (Figure 1.3). Whether helpful or harmful, the microbial world is deeply intertwined with our lives, and with the very fabric of life on Earth. Let’s begin our exploration of microbiology, then, by asking a very fundamental question. What is life?

    The basis of life So, what is life? This question has fascinated humans for millennia—perhaps since our ancestors first developed conscious, introspective thought. As biologists, we will focus on a practical definition of “life” that distinguishes living organisms from non‐living objects.

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    © Eye of Science/Science Source Images

    © Science Source/Science Source Images

    TEM

    Figure 1.1. Microbes and humans A. Some microbes cause horrific infectious diseases, like smallpox. Man with smallpox (left); color-enhanced smallpox viruses (right). B. Other microbes, particularly those that reside in our gut, do not usually cause disease and help us digest the food that we eat (left). Food debris (yellow) and bacteria (purple) in the small intestine (right).

    SEM

    © SPL/Science Source Images

    © Jose Luis Pelaez/Getty Images

    A. Microbes and disease

    © Nigel Cattlin/Alamy

    © Inga Spence/Science Source Images

    B. Microbes and digestion

    B. Other microbes provide nutrients to plants.

    © Courtesy of Dave Wessner

    © Julien Bastide/iStockphoto

    A. Some microbes infect important agricultural plants.

    C. Many microbes cause food to spoil.

    Wessner_6869_ch01_pp02-33.indd 5

    D. Other microbes aid in food and beverage preparation.

    Figure 1.2. Microbes and food A. Soybean rust, a disease caused by a fungus, causes significant crop losses every year. B. Nitrogen-fixing bacteria interact with the roots of certain plants, forming nodules. The bacteria provide essential nutrients to plants, thereby aiding in their growth. C. These rotting tomatoes show growth of fungi. D. For centuries, humans have used microbes to help us produce cheese, yogurt, wine, and beer.

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    © Maximilian Stock Ltd/Phototake

    Figure 1.3. Microbes and medicine Using recombinant DNA techniques, researchers can alter genes of microbes such that the microbes produce large quantities of medically important compounds. As we will see later in this chapter, human insulin today is produced by the bacterium Escherichia coli. Here, researchers monitor conditions in a large-scale bioreactor used to grow recombinant bacteria.

    First, living organisms are composed of cells, the smallest units of life as we know it. Second, living organisms are capable of: • Metabolism: A controlled set of chemical reactions that extract energy and nutrients from the environment, and transform them into new biological materials. • Growth: An increase in the mass of biological material. • Reproduction: The production of new copies of the organism. To accomplish these tasks, organisms contain a biological instruction set to guide their actions. These instructions need to be reproduced as the organism itself reproduces. Other features that living organisms share include: • Genetic variation, allowing the possibility of evolution, or inherited change within a population, through natural selection over the course of multiple generations. • Response to external stimuli and adaptation to the local environment (within genetic and physiological constraints). • Homeostasis: Active regulation of their internal environment to maintain relative constancy. Does this list represent a complete description of what it means to be alive? Probably not. It’s easy to come up with situations that challenge these criteria. Consider the curious case of bacterial endospores, specialized, metabolically inert cells produced by some bacterial species under highly stressful conditions. After shutting down metabolism, growth, and reproduction, endospores can remain dormant for long periods of time, even thousands of years, awaiting a favorable environment to germinate. Is an endospore alive during this state of suspended animation? These spores have all the components of living cells and, when conditions are appropriate,

    they will again develop into cells that meet the criteria listed above. As we will see later in this section, viruses—subcellular microbes—represent an even more interesting anomaly to the standard definition of life. As a result, our definition of life should be applied holistically; an organism may not exhibit all of these traits at all times. Most microorganisms live and function as single, autonomous cells. A free‐living unicellular, or single‐celled, organism can carry out all the necessary functions of metabolism, growth, and reproduction without physical connection to any other cells. In contrast, multicellular organisms are composed of many physically connected and genetically identical cells. The constituent cells that contribute to a multicellular organism can have distinct, specialized functions. A complex organism like a human can have hundreds of cell types organized into tissues and organs. Although the distinction between unicellular and multicellular organisms seems obvious, you might rethink this issue later as we learn more about the microbial world. Some unicellular organisms, for instance, only can survive in close association with cells of another species. Other unicellular microorganisms can communicate, behave socially, form three‐dimensional structures containing millions of cells with different functions, and enter into dependent relationships with other cells. These behaviors blur the boundaries between unicellular and multicellular lifestyles. The slime mold Dictyostelium discoideum, for instance, exists as a rather typical unicellular organism when food is readily available. However, individual cells aggregate and form a complex structure during periods of nutrient depletion, with cells differentiating to assume specialized tasks (Figure 1.4). Before we investigate these more unusual arrangements, though, let’s learn more about the chemical makeup of cells.

    Chemical makeup of cells As we shall see in this section, all cells share some basic features. Notably, all cells are built from macromolecules, large, complex molecules composed of simpler subunits (Table 1.1). Typically, macromolecules make up over 90 percent of a cell’s dry weight, or the weight obtained after the removal of all water. In this section, we will explore the four major types of macromolecules found in cells: polypeptides, nucleic acids, lipids, and polysaccharides. For each, we will look briefly at their structure and functions. Polypeptides, polymers of amino acids, constitute the most abundant class of macromolecules. Polypeptides, also often referred to as proteins, fold into elaborate structures and can execute a vast array of important jobs. Some proteins function as enzymes, macromolecules that catalyze chemical reactions within the cell (Figure 1.5). Other proteins may facilitate the movement of material into or out of the cell. Still other proteins comprise critical structures such as microfilaments that facilitate cell movement (Table 1.2). Nucleic acids, polymers of nucleotides, make up most of the remainder of the macromolecules within a cell. This category includes deoxyribonucleic acid (DNA), a polymer of deoxyribonucleotides, and ribonucleic acid (RNA), a polymer of ribonucleotides. Individual nucleotides are composed

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    A. Unicellular form

    Substrate

    Active site

    © Courtesy T. A. Steitz, Yale University

    LM

    © Courtesy Richard A. Firtel

    Enzyme

    LM

    © Carolina Biological Supply Company/Phototake

    Figure 1.5. Structure and function of enzymes In cells, many polypeptides function as enzymes, macromolecules that can catalyze chemical reactions. The function of the enzyme depends on its structure. The three-dimensional shape creates an active site with which the substrate interacts.

    B. Aggregation and differentiation

    Figure 1.4. Developmental stages of Dictyostelium discoideum A. The slime mold Dictyostelium discoideum exists as a unicellular organism when food is plentiful. B. When its food supply becomes limited, cells aggregate in response to a cellular signal forming a multicellular slug. Cells then begin to differentiate, eventually forming a stalk and fruiting body.

    of a sugar molecule (deoxyribose in DNA, ribose in RNA), a phosphate moiety, and one of four nitrogen‐containing bases (abbreviated A, T, C, and G in DNA; A, U, C, and G in RNA). In all cells, DNA constitutes the main informational molecule, containing instructions for the production of RNA molecules. These RNA molecules fulfill numerous functions within the cell, most of which are associated with protein production. Lipids, hydrophobic hydrocarbon molecules, represent another important class of macromolecules. The primary role of lipids in most cells is to form the foundation of the plasma membrane, a barrier surrounding the cell that, quite simply, separates inside from outside. This membrane restricts the movement of materials into and out of the cell, thereby

    TA B L E 1 .1 M ac ro m o l ecul es i n m i c rob i a l ce lls Macromolecule Subunits Functions

    Dry weight of cell (%)

    Polypeptides

    Amino acids

    Enzymes catalyze the vast majority of biochemical reactions in the cell. Other proteins are structural components of cells.

    50–55

    Nucleic acids

    Deoxyribonucleotides

    Informational: DNA provides the instructions for assembly and reproduction of the cell.

    2–5

    Ribonucleotides

    Many functions, most of which are involved in the production of polypeptides. Some serve structural or catalytic functions.

    Lipids

    Diverse structures

    Structural: Make up cellular membranes that form physical boundaries between the inside of a cell and its surroundings and membranes of internal organelles.

    10

    Polysaccharides

    Sugars

    Structural (such as cellulose and chitin) and energy storage (such as glycogen and starch).

    6–7

    15–20

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    TA B L E 1. 2 Polypeptide

    Fun c t i o n s o f s el ec ted p oly p e p t i d e s Location Function

    RNA polymerase

    Cytoplasm of bacteria and archaea, nucleus of eukarya

    Produces RNA molecules from DNA template

    Glycogen phosphorylase

    Cytoplasm

    Conversion of glycogen into glucose monomers

    K+ channel

    Plasma membrane

    Passive transport of K+ across the membrane, from an area of high concentration to an area of low concentration

    Na+/K+ ATPase

    Plasma membrane

    Active transport of Na+ and K+ across the membrane, from areas of low concentration to areas of high concentration

    Flagellin

    Bacterial flagellum

    Monomers polymerize to form flagellum, which aids in bacterial motility

    FtsZ

    Associated Key component of cell division with plasma machinery membrane of bacteria

    allowing the cell to capture and concentrate nutrients for metabolism and growth and prevent the products of metabolism from escaping (Figure 1.6). Polysaccharides are polymers of monosaccharides, or sugars. These molecules are composed entirely of carbon, hydrogen, and oxygen, with the general formula of Cm(H2O)n. Some polysaccharides serve as energy storage molecules. Starch and glycogen, for instance, are both polymers of the monosaccharide glucose (C6H12O6). Other polysaccharides serve as structural molecules. Cellulose, the primary structural component

    Figure 1.6. Plasma membrane All cells are enclosed within a lipid-based membrane that compartmentalizes the cell, allowing the composition of the inside and outside to differ. In most organisms, the membrane consists of a lipid bilayer. However, this membrane is not impervious. Various polypeptides and polysaccharides are associated with the membrane. These macromolecules help the cell control the movement of materials into and out of the cell.

    Polysaccharide

    of plant cell walls, also is a polymer of glucose monomers. Chitin, the primary structural component of fungal cell walls, consists of a derivative of glucose: N‐acetylglucosamine. Many bacterial and archaeal cells use other polysaccharides for their cell walls.

    The domains of life Although polypeptides, nucleic acids, lipids, and polysaccharides exist in all living organisms, major groups of organisms also differ in substantial ways. Today, we categorize all living organisms and, by extension, their cells, into three domains: Bacteria, Archaea, and Eukarya. Until the late 1900s, however, biologists divided cells into only two types: prokaryotes and eukaryotes (Figure 1.7). The term “eukaryote” is derived from Greek roots meaning “true kernel,” in contrast to the term “prokaryote,” which translates as “before kernel.” The “kernel” refers to the membrane‐enclosed nucleus of eukaryal cells. The nucleus contains the genetic material of the eukaryal cell during most of the cell cycle and was clearly visible to microscopists in the 1800s. Its function as the organizer of the hereditary material was not understood until well into the 1900s. Biologists noted other differences between these cell types. Additional membrane‐enclosed organelles exist within eukaryal cells, with each organelle serving a unique and important function. Prokaryotes and eukaryotes also differ strikingly in the organization of their genetic material. Prokaryotes usually contain a single circular chromosomal DNA molecule. In contrast, eukaryotes usually contain multiple linear DNA molecules. At some point in their life cycle, most eukaryal organisms have two copies, or a 2n complement, of their genetic material. Most prokaryotes, in contrast, possess a single copy of their genetic material. Conventional wisdom through the better part of the twentieth century stated that prokaryotes represented a fairly uniform group, until scientists started looking in more detail at the molecular machinery for the most ancient, important, and conserved processes in cells—the synthesis of DNA, RNA,

    Polypeptide

    Plasma membrane (lipid bilayer)

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    © David M. Phillips / Science Source Images

    © Dr. Klaus Boller/Science Source Images

    TEM A. Prokaryotic cell

    B. Eukaryotic cell

    and polypeptides. In the 1970s, microbiologists studying some prokaryotes noted that their molecular machinery resembled that of eukaryotes more than it did other prokaryotes. Leading the way in these studies was Dr. Carl Woese of the University of Illinois. Woese focused his attention on the structure and sequence of one of the RNA molecules that serves as a scaffold for assembly of the ribosome—the small subunit (SSU) ribosomal RNA. This molecule is a critical component of the ribosome in all living organisms and interacts with the messenger RNA during translation (see Section 7.4). His work paved the way for a revolution in thinking about the phylogeny, or evolutionary history, of organisms (Figure 1.8). His studies also led to a major revision in the taxonomy, or the classification, of living organisms. Because of Woese’s W W Classification systems work, we now categorize all ANIMATION living organisms into one of three domains: Bacteria, Archaea, or Eukarya (Mini‐Paper). Thanks largely to the development of the polymerase chain reaction (PCR), a technique that allows researchers to W

    @

    Bacteria

    Archaea

    Eukarya

    Figure 1.8 Phylogenetic tree of life By comparing the sequences of small subunit (SSU) ribosomal RNA gene sequences, researchers now classify all living organisms into one of three domains: Bacteria, Archaea, or Eukarya. In this phylogenetic tree, bacteria are shown in green, archaea are shown in blue, and eukarya are shown in red. The linear distance between the endpoints of any two lines is proportional to the sequence similarity of the SSU rRNA gene sequences from the organisms corresponding to the endpoints. Sequence similarity reflects VSDC Free Video Editor 6.3.6.18 Crack keygen - Crack Key For U distance.

    Figure 1.7. Prokaryotic and eukaryotic cells A. Prokaryotic cells, as seen in this colorized micrograph of Escherichia coli, lack a membrane-bound nucleus. They include organisms in the domains Bacteria and Archaea. B. Eukaryotic cells contain a membrane-bound nucleus, as seen in purple in this artist’s rendition of a plant cell. Until the latter decades of the twentieth century, biologists divided all cells into these two main types: prokaryotes and eukaryotes. Today, we recognize that all living organisms really should be divided into three categories, or domains: Bacteria, Archaea, and Eukarya. Eukarya contain nuclei. Bacteria and archaea do not.

    quickly amplify specific pieces of DNA (Toolbox 1.1), we now have a richer and more accurate phylogenetic tree. This tree is consistent with the idea that the archaeal and eukaryal domains shared a common ancestor after they split from the bacterial domain. It probably is impossible, though, to determine when the divergence of these lineages actually occurred; microorganisms do not fossilize well. That said, fossilized stromatolites, mineralized mats built up by layer upon layer of photosynthetic bacteria and other microbes in shallow marine Avast Cleanup Premium 21.7.2475 Crack + Free Activation Code, have been observed in rock formations nearly 3.5 billion years old (see Figure 1.13). If such elaborate microbial communities, including bacteria capable of photosynthesis (see Section 2.4), existed 3.5 billion years ago, then the split between Bacteria and the Archaea/Eukarya domains probably occurred much earlier. Although all cells share many features, studies have demonstrated clearly that bacteria, archaea, and eukarya are evolutionarily distinct. Some of their differences are listed in Table 1.3. We will discuss each of these types of cells in much more detail in Chapters 2–4.

    Viruses Are viruses alive? They are not cellular, but they certainly replicate and evolve. Viruses, however, require host cells for replication. Outside of a host cell, virus particles are essentially inert. An isolated virus has no metabolism—it takes up no nutrients and extracts no energy from its environment. Viruses also lack most of the basic machinery needed for the synthesis of macromolecules. Viruses do not respond to stimuli, except perhaps when they bind to receptors on a new host cell, and they do not maintain internal homeostasis. When a virus enters a host cell, it does not grow and reproduce in the same sense that cellular organisms do. Virus particles are more or less completely disassembled in the host cell, and new virus particles are only assembled after the genetic material has been replicated and the host cell has synthesized new viral proteins. Cellular organisms have no comparable state of disassembly during their growth and reproduction. 1.1 The Microbes 9

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    Mini‐Paper: A Foc u s on t h e R e se arch THE THREE DOMAINS OF LIFE C. R. Woese, O. Kandler, and M. L. Wheelis. 1990. Towards a natural system of organisms: Proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA 87: 4576–4579.

    Context Aristotle categorized life into just two fundamental groups, animals and plants, and this categorization persisted until the dawn of microbiology as a science. In 1868, two centuries after van Leeuwenhoek’s discovery of microbial life, German biologist Ernst Haeckel proposed a third fundamental group, or kingdom, Protista, for microscopic life‐ forms. In 1938, Herbert Copeland suggested that microorganisms should actually be divided into two kingdoms, Protista and Bacteria, thereby recognizing the difference between eukaryotic and prokaryotic cells. Twenty years later, Robert Whittaker advocated further separation of eukaryotic microorganisms into kingdoms of Fungi and Protista, but kept prokaryotic cells in a single kingdom called Monera. This five‐kingdom taxonomic system—Animalia, Plantae, Fungi, Protista, and Monera—became the accepted standard for the next few decades until DNA and protein sequences became widely accessible. Carl Woese, a microbiologist at the University of Illinois, was fascinated by a group of prokaryotes known at the time as “archaebacteria.” Initially, these strange microorganisms were found primarily in marginal environments such as anoxic sediments, hypersaline ponds, and hot springs. Other than their curious ability to colonize extreme habitats, the feature of archaebacteria that generated the most interest among the wider biological community was the ability of some of these organisms to produce methane. These microorganisms remain the only organisms known to produce this gas. To understand the phylogeny, or evolutionary history, of these methane‐producing microorganisms, Woese followed the lead of Zuckerkandl and Pauling, who had first demonstrated in the 1960s that comparisons of protein sequences could reveal evolutionary relationships. If two organisms were closely related, these researchers reasoned, then the amino acid sequence of a common protein in the organisms should be very similar. Conversely, if two organisms were distantly related, then the amino acid sequence of a common protein should be more divergent. Woese and colleagues began to focus not on protein sequences, but on RNA sequences. Woese reasoned that the ribosomal RNAs (rRNAs), because of their universal presence in all cells, could be excellent molecules to compare. In bacteria, the 16S rRNA molecule is part of the small subunit of the ribosome. In eukaryotes, the equivalent ribosomal RNA is the 18S rRNA. These molecules, collectively referred to as “small subunit (SSU) rRNA” molecules, are critical in the ribosome, helping to bring together the ribosomal structure, and interacting with messenger RNA. Not only are ribosomal RNAs universally distributed, but they also have the same function in all cells. The SSU rRNA gene sequence has been Media Player Classic 1.8Key Genrator - Crack Key For U to as a “molecular chronometer,” a slowly ticking clock that measures evolutionary time.

    The sequence of this molecule changes very slowly because of the functional constraints on the molecule. Random mutations that occur within the gene encoding the small subunit rRNA often have serious negative consequences, so relatively few changes are passed on to subsequent generations. Nevertheless, there are enough differences in the roughly 1,600 nucleotide sequence to differentiate between species to map patterns of similarity. If one assumes that overall mutation rates are similar between species (which seems to be true with respect to rRNA genes), then one can quantify sequence differences between SSU rRNA genes in multiple species to infer relationships. Ultimately, Woese discovered that the methane‐producing microorganisms were no more closely related to other bacteria than they were to the eukaryotes. They were not bacteria at all! Let’s examine the scientific work that led to this conclusion.

    Experiments The 1990 Woese et al. paper actually presented no new experimental data. Its importance was in articulating a new view of the phylogeny of life. To understand the genesis of this idea, we should step back and examine the data. The biggest challenge Woese faced in the 1970s in developing ribosomal RNA sequences as a tool for phylogenetic analysis was the difficulty in determining such sequences. Woese and colleagues developed a laborious method to infer the sequence of 16S rRNA molecules, which they described in a 1977 article, “Comparative cataloging of 16S ribosomal ribonucleic acid: A molecular approach to procaryotic systematics,” Journal of Bacteriology, vol. 27, pp. 44–57. First, RNA was extracted from cells. The isolated rRNA then was cut into small chunks using a ribonuclease enzyme that yields short fragments of nucleic acid usually 5–20 bases long. The sequence of each oligonucleotide was determined by further chemical and enzymatic analysis. In its original incarnation, this method did not actually yield a complete rRNA sequence, but rather a catalog of short oligonucleotide sequences present in the rRNA. Catalogs from different species then were compared. The underlying assumption of molecular sequence comparisons is that the number of nucleotide differences between two sequences is proportional to the time since the two species diverged from a common ancestor. Species that share a more recent common ancestor will have fewer differences than species that have been separated for longer periods of time. Exactly how long ago two species separated depends on the rate at which mutations accumulate, which can be very difficult, if not impossible, to know. Fortunately, to determine phylogenetic relationships, we do not need to know exact times of divergence. We are just interested in relative times: if organisms A and B shared a common ancestor after they shared an ancestor with organism C, then A and B would have fewer sequence differences with each other than either would have with C. The Woese method essentially took each 16S rRNA sequence and compared it against all of the other species. A method for quantifying the similarity between sequences

    10 Chapter 1 The Microbial World

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    was developed to yield an association coefficient between 0 and 1. A perfect match between sequences would result in an association coefficient of 1, whereas no matches would give a score of 0. From these scores, a computer algorithm was used to plot the most likely phylogenetic tree. Starting with papers in 1977 and continuing through the 1980s, Woese and colleagues built a “universal phylogenetic tree” through comparison of SSU rRNA sequences from diverse organisms, including members of each of the five kingdoms of life, as defined at that time. The great strength of this universal tree is that it compares all organisms using a common standard, a molecule they all possess. Woese noted that this universal tree supports three primary branches of life, not the five kingdoms previously accepted. In the 1990 paper, Woese and his coauthors propose that these very ancient branches— Bacteria, Eukarya (or Eucarya, as it is spelled in the 1990 paper), and Archaea—be referred to as domains (see Figure 1.8). The domain Archaea is composed of species previously known as archaebacteria. Though archaea lack a nucleus, they turned out to be no more similar to bacteria than they are to eukaryotic organisms, or eukarya. In fact, Woese’s tree suggests that the domains Archaea and Eukarya share a more recent common ancestor than either does with the domain Bacteria. As we will see in Chapter 4, archaea are similar in size and shape to bacteria. Many of the enzymes used by archaea for DNA replication, transcription, and translation, however, more closely resemble the corresponding enzymes found in eukarya. Perhaps most interestingly, the plasma membrane of archaea differs chemically from the plasma membranes of bacteria or eukarya. The exact evolutionary history of these organisms is yet to be determined. In this three‐domain phylogenetic tree, Monera and Protista disappear as kingdoms. In fact, if kingdoms are to be defined by equivalent depth of branching—which implies roughly equivalent evolutionary times since divergence—rRNA gene sequence comparisons support many more kingdoms than were previously known, most of which are populated by microorganisms. As we will see in Chapter 4, Woese and coauthors proposed two kingdoms within the domain Archaea: Crenarchaeota and Euryarchaeota. The authors also noted the presence of heat‐loving microorganisms in several other branches of life. It is quite possible, then, that the organism at the root of the tree (the last common ancestor of all life on Earth) was thermophilic, or heat‐ loving. We will return to this point in Section 1.2.

    Impact For the first time, biologists could create a natural taxonomic system in which all organisms are compared by the same criteria. The realization that the prokaryotes could not be united as a phylogenetic group raised many questions regarding the validity of the five‐kingdom

    system. Not surprisingly, there was initial resistance. Many scientists challenged the validity of this approach and the computational methods on which it was based. Since Woese first conducted his experiments, there have been methodological improvements, specifically in the ability to amplify entire rRNA genes using the polymerase chain reaction (PCR; see Toolbox 1.1), followed by rapid and straightforward DNA sequencing. The basic concept of using rRNA gene sequence comparisons to derive phylogenetic relationships is now accepted as an essential method of phylogenetic analysis. Sequence‐based phylogenies have had more impact on microbiology than any other branch of science. Since this paper was published in 1990, databases containing ribosomal RNA gene sequences have grown explosively. The universal phylogenetic tree is now much richer and more complex, but the three‐domain organization remains unchallenged. Using PCR, microbiologists can characterize organisms using rRNA gene sequences even if the microorganisms cannot be grown in culture. Because the majority of microbes apparently will not grow in laboratory culture (see Section 6.3), this approach is enormously important for understanding the true diversity of life on Earth and its evolutionary history. Proposals for new bacterial and archaeal kingdoms, based on rRNA gene analysis of uncultured organisms, have appeared regularly since 1990. Classification of eukaryal microorganisms also is affected by rRNA‐based phylogenetics. Ribosomal RNA sequences do not tell the entire evolutionary story of an organism. In the last decade, the DNA sequences of hundreds of entire genomes have been determined, most of them from microorganisms. It is clear that microbes are rampant sharers of genes, which we will discuss more in Chapters 9, 10, and 21. Although it is likely that rRNA genes are rarely shared and do accurately reflect the evolutionary history of the “core” genome, large fractions of genetic material in many organisms may have distinct histories, a finding that Carl Woese could scarcely have imagined when he began his revolutionary efforts to clarify microbial taxonomy.

    Questions for Discussion 1. What features make SSU rRNA gene sequences ideal for phylogenetic studies? 2. What drawbacks do you see with the use of rRNA for these studies? 3. If we discover forms of life on another planet, would studies of rRNA gene sequences be useful for categorizing these life‐forms?

    1.1 The Microbes

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    Toolbox 1.1 P O LY M E R A S E C H A I N R E AC T I O N A M P L I F I C AT I O N O F r R N A G E N E S Target DNA

    Template

    Repeat the process

    Figure B1.1. The polymerase chain reaction (PCR) After heating the DNA to denature, or separate, the two strands, the mixture is cooled, allowing the short, single-stranded DNA primers to anneal to their complementary regions. The DNA polymerase then extends these primers, using the opposite strand as a template. This process is repeated multiple times, resulting in the generation of many copies of the segment of DNA bounded by the primers. In this fashion, a small amount of input DNA can be amplified sufficiently to perform routine chemical analyses.

    DNA is heated, causing it to denature or become single-stranded.

    After the DNA cools, primers anneal to complementary regions.

    DNA polymerase extends the DNA from the primers.

    Products

    The method of ribosomal RNA sequencing developed by Carl Woese was extremely laborious. Fortunately, techniques just being developed in the 1970s and 1980s, as Woese and colleagues were initially developing the universal phylogenetic tree, made nucleic acid sequencing much simpler. W W Polymerase chain reaction The most important of ANIMATION these techniques was the polymerase chain reaction (PCR). With this technique, researchers can create millions of copies of a specific piece of DNA. Kary Mullis, then a scientist at Cetus Corporation, a biotechnology company in Emeryville, California, invented PCR in 1983 and was awarded the Nobel Prize in Chemistry in 1993 for this discovery. The technique basically mirrors the process of DNA replication utilized by all cells. However, rather than replicating an entire DNA molecule, PCR results in the repeated replication, or amplification, of a small, defined segment of a larger DNA molecule. The reaction requires only a few basic reagents: W

    @

    Extract total DNA from environmental sample.

    Amplify 16S rRNA genes using PCR.

    • • • •

    DNA containing the sequence to be amplified Deoxyribonucleotides (dATP, dCTP, dTTP, and dGTP) DNA polymerase Oligonucleotide primers

    The process begins with the denaturation of double‐stranded DNA, making it single‐stranded. This step is achieved by heating the DNA to around 95°C for a short period of time. The primers, 15–30 nucleotide‐long pieces download mathtype 7.0 full crack - Activators Patch single‐stranded DNA synthesized in the Media Player Classic 1.8Key Genrator - Crack Key For U, then bind to complementary regions on this newly denatured DNA. The primers are designed such that one primer binds to one strand of the denatured DNA, while the other primer binds to the other strand of the DNA. Additionally, the two primers bind to regions of the DNA flanking the sequence to be amplified (Figure B1.1). After the primers bind, the DNA polymerase begins generating new DNA, using the denatured DNA as a template. We will see in Section 7.2 that DNA polymerases generate new DNA by

    Separate the amplified DNA molecules.

    Analyze DNA sequences to determine species in sample.

    Figure B1.2. Use of PCR to identify microorganisms With PCR, microbial species can be identified simply by isolating a little of their DNA. As shown in this schematic, DNA can be isolated from an environmental source without isolating and growing pure cultures of specific bacterial species. By doing PCR with primers specific for the 16S rRNA gene, this region of the genome can be amplified and subsequently sequenced, thereby providing the investigator with enough information to determine which species are present.

    12 Chapter 1 The Microbial World

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    CONNECTIONS Viruses infect all cellular forms of life. They replicate in various ways, but all depend on using host cell machinery for their replication. This makes them obligate intracellular parasites. We will examine viral replication in Section 8.3.

    attaching deoxyribonucleotides to primers bound to a template strand. Because PCR usually employs only two primers that bind on either side of a specific region of DNA, these primers delineate which segment of the original DNA molecule will be replicated. The whole process, then, involves three steps: • • •

    Denaturation, or melting, of the DNA Attachment, or annealing, of the primers Generation of new DNA by DNA polymerase

    These steps are repeated multiple times, resulting in the exponential amplification of the region bounded by the two primers. After 10 cycles, the number of these amplified DNA molecules increases over 1000‐fold. After 20 cycles, the increase is over one million‐fold, and 30 cycles will generate over one billion new copies! The crucial development that made PCR widely usable was the discovery of thermostable DNA polymerases that could withstand the high temperature (> 90°C) used to separate DNA strands. The first thermostable polymerase used for PCR was Taq DNA polymerase, which came originally from the bacterium Thermus aquaticus, isolated from hot springs in Yellowstone National Park in the United States. Today, a variety of thermostable DNA polymerases are commercially available, several of which have been isolated from heat‐loving archaea. We will discuss these fascinating microorganisms more throughout Chapter 4. PCR has revolutionized SSU rRNA gene sequence analysis and species identification. Today, just a bit of chromosomal DNA, extracted from an environmental sample, can be used as a template for PCR (Figure B1.2). The PCR‐amplified DNA products then can be separated and sequenced. By analyzing the sequences, researchers can accurately identify the species present in the original sample without isolating and growing pure cultures. The techniques available today certainly represent big improvements over Woese’s method of sequencing fragments of rRNA molecules. The uses of PCR in microbiology extend much further. PCR‐based tests have been developed to detect the human pathogen Chlamydophila pneumoniae, a bacterium that typically is difficult to identify. As we will see in Perspective 5.1, a form of PCR routinely is used to monitor the viral load, or amount of virus present, in people with HIV disease. PCR also allows us to learn more about microbes that currently cannot be grown in the laboratory, a topic we will explore in Section 6.3. Virtually all areas of microbiology have been affected by the conceptually simple polymerase chain reaction.

    Test Your Understanding

    .

    Explain how PCR amplification would differ if a standard DNA polymerase, Enfocus PitStop Pro Free Download of a thermostable DNA polymerase such as Taq, were used. What would be the result and why?

    Although viruses are not cellular, they are still very important biological entities to study (Figure 1.9). Viruses are molecular parasites that probably have been around since shortly after the first cells evolved. Microbiologists are interested in viruses not only because they cause many important infectious diseases in humans, crop plants, and livestock, but also because they are fascinating biological systems in their own right. Viruses have taught us a great deal about how cellular organisms function. As parasites, viruses must adapt to their host organism. To be taken up by host cells, most viruses have evolved to bind to host cell surface molecules and often enter cells by hijacking host systems ordinarily used for taking up non‐viral molecules. Many viruses rely on host enzymes for the production of mRNA, and all viruses use host cell ribosomes for the production of proteins. By studying how viruses use the machinery of their host cells, scientists have gained insight into many critical processes in eukaryal, bacterial, and archaeal cells.

    Microbes as research models Basic research on the structure and function of microbes has laid a solid foundation for understanding the biology of all cells, including our own. Unicellular microorganisms generally possess the same genetic code and many of the same biochemical pathways as multicellular organisms. Additionally, microbes have many advantages for use artlantis 2019 download - Free Activators research: • Many are easily cultivated in the lab using inexpensive equipment; they grow rapidly to high cell density on cheap nutrient sources. • They facilitate the production of enzymes, other proteins, and various biomolecules for industrial and medical uses. • Most have relatively small numbers of genes to analyze. Even the largest bacterial and archaeal genomes are smaller than the smallest eukaryal genomes, and eukaryal microorganisms have substantially fewer genes than complex multicellular eukarya. • Many can be genetically manipulated much more easily than complex eukarya. Popular microbial model systems for research include the intestinal bacterium Escherichia coli and the eukaryal yeast Saccharomyces cerevisiae, which is also known as baker’s yeast or brewer’s yeast, because of its long historical use in food and beverage production (Figure 1.10). These model microorganisms have been subjected to the vast experimental armaments of the fields of biochemistry, genetics, molecular biology, and cell biology. Our current understanding of the complexities of biochemical pathways, DNA replication and cell division, the nature of genes, control of gene expression, and protein synthesis, folding, and function has arisen largely from studies of model microbes. 1.1 The Microbes

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    S el ec ted c h arac ter i s ti c s of t h e t hre e d om a i ns Bacteria Archaea

    Eukarya

    Nuclear membrane

    No

    No

    Yes

    Membrane‐bound organelles

    Rare, a few types found in a few species

    Rare, a few types found in a few species

    Multiple distinct types, found in all species

    Plasma membrane

    Similar to Eukarya

    Different from Bacteria and Eukarya

    Similar to Bacteria

    Cell wall

    Found in nearly all species, constructed of peptidoglycan

    Found in nearly all species, constructed of various materials

    Found in some species, constructed of various materials

    RNA polymerases

    Single polymerase

    Single polymerase, eukaryal‐like RNA pol II

    Three main polymerases (RNA pol I, II, and III)

    Histones

    Histone‐like proteins

    Yes

    Yes

    TEM D. Tobacco mosaic virus

    Figure 1.9. Viruses Different viruses have different shapes, and some can cause horrific infectious diseases. All images are artificially colored to enhance their appearance. A. Poliovirus, the cause of paralytic polio. B. Ebola virus, the cause of hemorrhagic fever, a rapidly progressing, highly fatal disease. C. T4 bacteriophage, a virus that infects bacteria and has been extensively used in research. D. Tobacco mosaic virus, a virus that infects plants, was the first virus to be discovered.

    target microbial invaders were feasible. He had little knowledge of the actual structures present on or in cells of any kind, but this concept that certain drugs may adversely affect specific types of cells, while sparing other types of cells, remains at the heart of our drug development initiatives today. Members of Ehrlich’s research group discovered an organic arsenic‐containing compound, arsphenamine, which in 1910 became the first effective commercial drug for the treatment of Treponema pallidum, the bacterium that causes the sexually transmitted disease syphilis (Figure 1.11). Because it also exhibited toxicity to host cells, arsphenamine, known by its trade name Salvarsan, was abandoned in the 1940s in favor of penicillin, the first widely used antibiotic capable of killing many different kinds of bacteria. Salvarsan’s historical importance was in establishing that lethal agents specifically targeted at microbial cells are indeed possible. In the century since Salvarsan came on the market, an enormous amount has been learned about the molecular differences between bacterial and eukaryal cells. Hundreds of new antimicrobial and antiviral drugs have been discovered, and hopefully there will be many more to come.

    © NIAID /CDC/Science Source Images

    TEM C. T4 bacteriophage

    © CAMR/A. Barry Dowsett/Science Source Images

    TEM B. Ebola virus

    TEM A. Poliovirus

    © Omikron/Science Source Images

    © Department of Microbiology, Biozentrum, University ScreenHunter Pro 7.0.1145 Crack With Serial Key Basel/Science Source Images

    © Science Source Images

    Research on the biology of microbial cells has virtually unlimited practical applications. For example, to understand how some antimicrobial drugs work against their microbial targets while sparing host cells, we need to understand differences in structure between bacterial and eukaryal cells, or perhaps between fungal and human cells. Paul Ehrlich, a towering figure in the history of medicine and immunology, was among the first to recognize that such differences had medical implications. From his experience in the field of histology, Ehrlich was familiar with dyes that differentially stained bacterial and human cells. Based on this observation, he speculated that molecular “magic bullets” that specifically

    SEM

    SEM

    A. Escherichia coli

    © Science Photo Library/Science Source Images

    TA B L E 1. 3

    B. Saccharomyces cerevisiae

    Figure 1.10. Microbes as model organisms Microbes have been used extensively in research. Because they replicate quickly, are cheap to grow, and have relatively simple structures, they have been used extensively to study basic cellular processes like DNA replication, transcription, and translation. Two of the most-studied microbial model organisms are A. the bacterium Escherichia coli and B. the eukarya Saccharomyces cerevisiae, a yeast.

    14 Chapter 1 The Microbial World

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    Figure 1.11. The development of antimicrobial drugs The bacterium Treponema pallidum causes syphilis, a sexually transmitted disease. Salvarsan, the first commercially available drug to combat syphilis, was developed in 1910. Although Salvarsan prevented the replication of this bacterium, it also was toxic to human cells, and its use was curtailed after the development of penicillin.

    © Science Source/Science Source Images

    SEM

    CONNECTIONS Basic research into the structure and replication of microbes has led to the development of numerous antimicrobial and antiviral drugs. Many of the currently approved drugs for the treatment of HIV, for instance, interfere with specific viral enzymes needed for the production of new virus particles. We will discuss how a particular class of these drugs—nucleoside analogs—works in Section 24.2.

    1.1 Fact Check 1. 2. 3. 4.

    What are the key features of living organisms? Describe the macromolecules found in cells. What are the three domains of living organisms? Explain why microbes are useful model systems in research and provide examples of microbial model systems.

    1.2 Microbial genetics What do we know about the evolution of life and the genetics of microbes? Although groups of microbes may be different from each other, they all share common information processes. Indeed, one of the most remarkable aspects of life as we know it is the constancy of these information processes. In all cells, the main informational molecule is double‐stranded DNA. In all cells, a specific type of RNA, messenger RNA, or mRNA, serves as the conduit between the information in DNA and the actual production of proteins. In all cells, the code used to convert the information present in DNA to RNA to protein is the same. This conserved genetic code probably represents the most compelling evidence for evolution. All living organisms share a common informational pathway, suggesting that all living organisms share a common ancestor. Because all living organisms, and the genetic processes of these organisms, are evolutionarily related, we will begin our exploration of microbial genetics by examining the origins of life. We then will look at how genetic processes occur in microbes and how microbiologists study these processes. We will end this section with a brief overview of how researchers today use these processes to learn more about living organisms.

    The evolution of life on Earth Earth is home to a huge variety of microbes. To understand how this incredible diversity evolved, we need to consider the history of Earth and the origins of life itself. The geochemical changes that have occurred on Earth in the past four billion

    years—in the oceans, on land, and in the atmosphere—have been dramatic. These changes have profoundly affected, and were profoundly affected by, microorganisms. The vast majority of the living organisms we see today, at least without microscopes, are large multicellular eukarya that arose within the last few hundred million years, the last 10 percent of Earth’s history. But most of the major evolutionary events that moved life toward today’s world occurred in the distant past, when microbes alone ruled the planet. To get some perspective on this point, let’s take a brief walk through the history of life.

    Prebiotic Evolution When Earth formed approximately 4.5 billion years ago (abbreviated ybp, for years before present), it was a hot and sterile place. Oceans of liquid water formed around 4 billion ybp, once the crust and atmosphere had cooled sufficiently for liquid water to condense (Figure 1.12). These oceans may have been partially or completely converted to steam on multiple occasions by the energy of asteroid impacts, which were far more common in the early solar system. Depending on when the first life‐forms evolved, such impacts could have resulted in mass extinctions, coupled with selection for life‐forms that could live in this extreme environment. By 3.8 billion ybp, life clearly had gained a permanent foothold. The first microorganisms appeared as life transformed from a semiorganized set of chemicals and reactions to a true cellular form. By 3.5 billion ybp, microbial cells were abundant on Earth, as is 1.2 Microbial Genetics 15

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    “Higher” organisms

    0

    Origin of flowering plants Origin of mammals

    Origin of land plants

    1

    20%

    Origin of simple animals Origin of multicellular organisms

    Origin of complex eukarya

    10%

    O2 atmosphere established

    1% 0.1%

    O2 (percent in atmosphere)

    2

    Euro truck simulator 2 download cracked games org - Free Activators of microbial life

    Years before present (billions of years)

    Endosymbiosis

    Oxic First O2-producing bacteria 3

    evident from fossilized stromatolites containing cyanobacteria‐ like structures (Figure 1.13). Cyanobacteria, we should note, are photosynthetic bacteria. The evolution of these organisms, and their oxygen‐ releasing photosynthetic capabilities, led to the eventual oxygenating of Earth’s atmosphere. Given that multicellular algae and marine invertebrates are not evident in the fossil record until 0.5 billion ybp, it appears that microbial life ruled Earth for over 3 billion years. Only during the last 500 million years has Earth seen the rise of plants and animals! Our planet has changed drastically since its violent birth, but, with the exception of dramatic events like asteroid impacts and volcanic eruptions, changes have occurred gradually. Microbes had plenty of time to evolve an incredible array of talents, allowing them to exploit every possible habitat. Given the eons that have gone by, we can only imagine the diversity of microbial life that has existed since Earth’s origins; we still do not fully comprehend the richness of microbial life on present‐day Earth. When life first appeared, Earth was a harsh place. The average temperature was quite hot, probably over 50°C. The composition of the atmosphere is not known for sure, but researchers hypothesize that it had a high concentration of CO2, perhaps up to 30 percent. Other atmospheric gases may have included nitrogen (N2) and hydrogen (H2). Whether gases such as ammonia (NH3), methane (CH4), cyanide (HCN), and hydrogen sulfide (H2S) were present in substantial concentrations is not known with certainty. It is clear, though, that there was little or no molecular oxygen (O2). The oceans probably were fairly acidic due to the high concentration of dissolved CO2. By comparison, today’s atmosphere consists of about 0.03 percent CO2 and 21 percent O2, with a moderate average temperature of 13°C. What changed the O2 and CO2 concentrations so dramatically since life began? Microbial activities over the past four billion years are part of the answer.

    The First Microbial Life

    Origin of life 4

    ~4.5

    Chemical evolution and synthesis of biomolecules

    Anoxic

    Formation of Earth

    Источник: https://dokumen.pub/microbiology-second-edition-binder-ready-version-1119279410-9781119279419.html

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