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Managing and Maintaining Windows 8: Exam 70-688,9781118591932
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Managing and Maintaining Windows 8: Exam 70-688

by ;
ISBN13:

9781118591932

ISBN10:
1118591933
Format:
Paperback
Pub. Date:
7/10/2013
Publisher(s):
John Wiley & Sons Inc
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Table of Contents

PART I THE MICROBES 1

The Microbial World 2

1.1 The Microbes 4

Toolbox 1.1 POLYMERASE CHAIN REACTION AMPLIFICATION OF rRNA GENES 12

Mini-Paper: A Focus on the Research THE THREE DOMAINS OF LIFE 14

1.2 Microbial Genetics 16

Perspective 1.1 CREATING LIFE IN THE LABORATORY: THE MILLER–UREY EXPERIMENT 18

Perspective 1.2 RIBOZYMES: EVIDENCE FOR AN RNA-BASED WORLD 19

1.3 Microbial Metabolism and Ecology 24

1.4 Microbes and Disease 27

2 Bacteria 36

2.1 Morphology of Bacterial Cells 38

2.2 The Cytoplasm 41

2.3 The Bacterial Cytoskeleton 44

2.4 The Cell Envelope 45

Perspective 2.1 MARVELOUS MAGNETOSOMES! 46

Toolbox 2.1 THE GRAM STAIN 55

Perspective 2.2 THE PROTECTIVE SHELLS OF ENDOSPORES 57

Mini-Paper: A Focus on the Research NEW MICROSCOPY METHODS REVEAL A PERIPLASM IN GRAM-POSITIVE BACTERIAL CELLS 60

2.5 The Bacterial Cell Surface 62

2.6 Bacterial Taxonomy 68

3 Eukaryal Microbes 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

3.2 Diversity of Eukaryal Microbes 87

3.3 Replication of Eukaryal Microbes 92

3.4 The Origin of Eukaryal Cells 95

Perspective 3.2 EXPLOITING A SHARED EVOLUTIONARY HISTORY WITH PLANTS IN THE TREATMENT OF MALARIA 99

3.5 Interactions Between Eukaryal Microbes and Animals, Plants, and the Environment 100

4 Archaea 106

4.1 Distinctive Properites of Archaea 108

4.2 Archaeal Cell Structure 110

Toolbox 4.1 VACCINE DELIVERY STRATEGIES 115

4.3 Diversity of Archaea 119

Perspective 4.1 EXTREMOPHILES AND BIOTECHNOLOGY 121

Mini-Paper: A Focus on the Research THE ROLE OF ARCHAEONS IN OUR DIGESTIVE SYSTEM 126

5 Viruses 130

5.1 A Basic Overview of Viruses 132

5.2 Origins of Viruses 140

5.3 Cultivation, Purification, and Quantification of Viruses 142

Toolbox 5.1 CELL CULTURE TECHNIQUES 143

Perspective 5.1 MEASUREMENT OF HIV VIRAL LOAD 147

5.4 Diversity of Viruses 149

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

5.5 Virus-Like Particles 155

5.6 Virology Today 157

Mini-Paper: A Focus on the Research NEW FINDINGS IN THE PACKAGING OF DNA BY THE MODEL BACTERIOPHAGE T4 158

6 Cultivating Microorganisms 164

6.1 Nutritional Requirements of Microorganisms 166

6.2 Factors Affecting Microbial Growth 168

Toolbox 6.1 PHENOTYPE MICROARRAYS FOR EXAMINING MICROBIAL GROWTH 169

6.3 Growing Microorganisms in the Laboratory 173

Perspective 6.1 THE DISCOVERY OF HELICOBACTER PYLORI 178

Toolbox 6.2 FISHING FOR UNCULTIVATED MICROBES 180

Mini-Paper: A Focus on the Research BRINGING TO LIFE THE PREVIOUSLY UNCULTURABLE USING THE SOIL SUBSTRATE MEMBRANE SYSTEM (SSMS) 182

6.4 Measuring Microbial Population Growth 184

Perspective 6.2 MYCOBACTERIUM LEPRAE, AN EXTRAORDINARILY SLOW-GROWING PATHOGEN 190

Perspective 6.3 THE HUMAN INTESTINE—A CONTINUOUS CULTURE 192

6.5 Eliminating Microbes and Preventing Their Growth 192

PART II MICROBIAL GENETICS

7 DNA Replication and Gene Expression 202

7.1 The Role of DNA 204

7.2 DNA Replication 210

7.3 Transcription 216

Toolbox 7.1 USING A GEL SHIFT ASSAY TO IDENTIFY DNA-BINDING PROTEINS 219

7.4 Translation 233

7.5 The Effects of Mutations 229

Mini-Paper: A Focus on the Research TELOMERES WITH PROMOTER ACTIVITY 232

Perspective 7.1 USING MUTATIONS TO CONTROL VIRAL INFECTIONS 234

8 Viral Replication Strategies 238

8.1 Recognition of Host Cells 240

Toolbox 8.1 THE WESTERN BLOT 242

8.2 Viral Entry and Uncoating 244

8.3 Viral Replication 248

8.4 Viral Assembly and Egress 256

8.5 Antiviral Drugs 258

Perspective 8.1 DNA MICROARRAYS AND THE SARS VIRUS 258

Mini-Paper: A Focus on the Research THE DISCOVERY OF REVERSE TRANSCRIPTASE 262

9 Bacterial Genetic Analysis 266

9.1 Bacteria as Subjects of Genetic Research 268

9.2 Mutations, Mutants, and Strains 271

Toolbox 9.1 ISOLATING NUTRITIONAL MUTANTS 274

9.3 Restriction Enzymes, Vectors, and Cloning 278

9.4 Recombination and DNA Transfer 285

Perspective 9.1 PLASMIDS THAT PRODUCE PATHOGENS 290

Mini-Paper: A Focus on the Research THE DISCOVERY OF TRANSDUCTION 299

10 Microbial Genomics 302

10.1 Genome Sequencing 304

Perspective 10.1 RATE OF DNA SEQUENCING 307

Toolbox 10.1 GENOME DATABASES 310

10.2 Genomic Analysis of Gene Expression 312

10.3 Comparative Genomics 318

Perspective 10.2 THE MINIMAL GENOME 319

Mini-Paper: A Focus on the Research GENOME SEQUENCE OF A KILLER BUG 320

10.4 Metagenomics 323

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 EXPRESSION STUDIES 342

11.4 Post-initiation Control of Gene Expression 346

Toolbox 11.1 USING RNA MOLECULES TO DECREASE GENE EXPRESSION 347

11.5 Quorum Sensing 350

11.6 Two-Component Regulatory Systems 352

11.7 Chemotaxis 355

12 Microbial Biotechnology 362

12.1 Microbes for Biotechnology 365

Perspective 12.1 BIOPROSPECTING: WHO OWNS THE MICROBES? 366

12.2 Molecular Genetic Modification 368

Toolbox 12.1 SITE-DIRECTED MUTAGENESIS 370

Toolbox 12.2 FUSION PROTEIN PURIFICATION 375

Mini-Paper: A Focus on the Research MAKING A SYNTHETIC GENOME 378

Perspective 12.2 THE INTERNATIONAL GENETICALLY ENGINEERED MACHINE (IGEM) COMPETITION, STANDARD BIOLOGICAL PARTS, AND SYNTHETIC BIOLOGY 380

12.3 Red Biotechnology 381

12.4 White Biotechnology 382

Perspective 12.3 BIOFUELS: BIODIESEL AND ALGAE 386

12.5 Green Biotechnology 391

Toolbox 12.3 PLANT TRANSFORMATION USING BACTERIA 394

PART III MICROBIAL PHYSIOLOGY AND ECOLOGY

13 Metabolism 400

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 422

Perspective 13.2 ELECTRICIGENIC BACTERIA AND MICROBIAL FUEL CELLS 426

13.5 Metabolism of Non-glucose Carbon Sources 429

Toolbox 13.1 METABOLISM AND RAPID BACTERIAL IDENTIFICATION SYSTEMS 432

13.6 Phototrophy and Photosynthesis 433

13.7 Nitrogen and Sulfur Metabolism 443

13.8 Biosynthesis of Cellular Components 447

Mini-Paper: A Focus on the Research GENOME SEQUENCE OF A DEEP SEA SYMBIONT 450

14 Biogeochemical Cycles 456

14.1 Nutrient Cycling 459

Toolbox 14.1 USING MICROARRAYS TO EXAMINE MICROBIAL COMMUNITIES: THE GeoCHIP 461

14.2 Cycling Driven by Carbon Metabolism 463

Perspective 14.1 CO2 AS A GREENHOUSE GAS AND ITS INFLUENCE ON CLIMATE CHANGE 464

14.3 Cycling Driven by Nitrogen Metabolism 472

Mini-Paper: A Focus on the Research THE FIRST ISOLATION AND CULTIVATION OF A MARINE ARCHAEON 476

14.4 The Interconnectedness of Cycles 478

Perspective 14.2 THE MICROBIOLOGY OF ENVIRONMENTALLY TOXIC ACID MINE DRAINAGE 479

15 Microbial Ecosystems 484

15.1 Microbes in the Environment 486

15.2 Microbial Community Structure 490

Toolbox 15.1 FLOW CYTOMETRY 494

Mini-Paper: A Focus on the Research A METHOD FOR THE IDENTIFICATION OF CATABOLIC GENES FROM METAGENOMIC LIBRARIES BASED ON THEIR GENE EXPRESSION CHARACTERISTICS 496

Perspective 15.1 NAMING THE UNCULTURABLE AND UNCHARACTERIZED 498

15.3 Aquatic Ecosystems 498

Perspective 15.2 DEAD ZONES 499

15.4 Terrestrial Ecosystems 506

15.5 Deep Subsurface and Geothermal Ecosystems 512

16 The Microbiology of Food and Water 522

16.1 Food Spoilage 524

16.2 Food Preservation 528

16.3 Food Fermentation 534

PART IV MICROBES AND DISEASE

18 Introduction to Infectious Diseases 600

18.1 Pathogenic Microbes 603

Toolbox 18.1 MEASURING THE VIRULENCE OF PATHOGENS 606

18.2 Microbial Virulence Strategies 608

Perspective 18.1 HOST DEFENSES IN BACTERIA 612

18.3 The Transmission of Infectious Diseases 613

18.4 Proving Cause and Effect in Microbial Infections 621

Perspective 18.2 THE ARMADILLO—AN IDEAL ANIMAL MODEL? 624

18.5 The Evolution of Pathogens 625

Mini-Paper: A Focus on the Research EPIDEMIOLOGY OF AN INFECTIOUS DISEASE 626

19 Innate Host Defenses Against Microbial Invasion 636

19.1 Immunity 638

19.2 Barriers to Infection 639

Perspective 19.1 MESSY MUCUS 642

19.3 The Inflammatory Response 643

19.4 The Molecules of the Innate System 644

Toolbox 19.1 THE COMPLEMENT FIXATION TEST 650

19.5 The Cells of Innate Immunity 653

Perspective 19.2 NATURAL BORN KILLERS 659

19.6 Invertebrate Defenses 663

Mini-Paper: A Focus on the Research MAMMALIAN CELLS CAN RECOGNIZE BACTERIAL DNA 664

Toolbox 19.2 THE LIMULUS AMOEBOCYTE ASSAY FOR LPS 667

16.4 Foodborne and Waterborne Illness 541

16.5 Microbiological Aspects of Water Quality 543

Perspective 16.1 IMPLICATIONS OF SLUDGE BULKING 549

Toolbox 16.1 MEASURING BIOCHEMICAL OXYGEN DEMAND (BOD) 550

Mini-Paper: A Focus on the Research ENHANCED BIOLOGICAL REMOVAL OF PHOSPHORUS 552

17 Microbial Symbionts 560

17.1 Types of Microbe–Host Interactions 563

17.2 Symbionts of Plants 564

17.3 Lichens 569

17.4 Symbionts of Vertebrates 571

Toolbox 17.1 GERMFREE AND GNOTOBIOTIC ANIMALS 571

Perspective 17.1 PROBIOTICS—DO THEY WORK? 577

Mini-Paper: A Focus on the Research DO MICROBES CAUSE OBESITY? 579

Perspective 17.2 COWS CONTRIBUTE TO CLIMATE CHANGE 586

17.5 Symbionts of Invertebrates 587

Perspective 17.3 MIDICHLORIANS—NOT JUST FOR JEDI 592

Perspective 17.4 DEATH OF CORAL REEFS 595

21.2 Survival in the Host: Strategies and Consequences 743

Toolbox 21.2 THE TUBERCULIN TEST FOR TUBERCULOSIS 750

21.3 Evolution of Bacterial Pathogens 751

Perspective 21.4 ANTIBIOTICS TRIGGER TOXINS? 754

22 Viral Pathogenesis 760

22.1 Recurring Themes in Viral Pathogenesis 762

Perspective 22.1 VERTICAL TRANSMISSION OF HIV 767

22.2 Interactions with the Host: Strategies and Consequences 770

Perspective 22.2 VIRAL INDUCTION OF APOPTOSIS 772

22.3 Viral Infections and Cancer 775

Toolbox 22.1 IMMUNOPRECIPITATION 778

Perspective 22.3 SV40 AND HUMAN CANCERS 779

Mini-Paper: A Focus on the Research VIRUSES THAT CAUSE CANCER BY AFFECTING CELLULAR PROLIFERATION 782

22.4 Evolution of Viral Pathogens 785

Perspective 22.4 ETHICAL CONCERNS ABOUT AVIAN FLU RESEARCH 789

23 Eukaryal Microbe Pathogenesis 792

23.1 Mechanisms of Eukaryal Microbe Pathogenesis 794

Mini-Paper: A Focus on the Research AN EXPERIMENTAL SYSTEM FOR THE GENOMIC STUDY OF DUTCH ELM DISEASE 798

Perspective 23.1 PNEUMOCYSTIS JIROVECII OR CARINII: THE EVOLVING FIELD OF TAXONOMY 801

Perspective 23.2 MAGIC MUSHROOMS 807

20 Adaptive Immunity 672

20.1 Features of Adaptive Immunity 674

20.2 T Cells 677

20.3 Antigen Processing 681

20.4 Antigen-Presenting Cells 686

20.5 Humoral and Cell-Mediated Immune Responses 690

Perspective 20.1 TOO MUCH OF A GOOD THING 693

Mini-Paper: A Focus on the Research ATTEMPTING TO ENGINEER A VIRUS TO IMPROVE IMMUNOCONTRACEPTION 694

20.6 B Cells and the Production of Antibody 694

Perspective 20.2 VACCINES AGAINST T-INDEPENDENT ANTIGENS 699

Toolbox 20.1 MONOCLONAL ANTIBODY (mAb) PRODUCTION 702

Toolbox 20.2 ENZYME-LINKED IMMUNOSORBENT ASSAY (ELISA) 706

Perspective 20.3 TURNING ANTIBODY UPSIDE DOWN 708

21 Bacterial Pathogenesis 714

21.1 Bacterial Virulence Factors 716

Mini-Paper: A Focus on the Research E. COLI INJECTS ITS OWN RECEPTOR 722

Toolbox 21.1 SEROTYPING 724

Perspective 21.1 THE GOOD, THE BAD, AND THE UGLY SIDE OF BOTULINUM TOXIN 730

Perspective 21.2 SUPERABSORBENT TAMPONS AND SUPERANTIGENS 736

Perspective 21.3 IRON, VAMPIRES, FASHION, AND THE WHITE PLAGUE 742

Perspective 24.1 THE PURSUIT OF NEW ANTIBIOTICS: WHY BOTHER? 847

Perspective 24.2 HEALTH CARE-ASSOCIATED INFECTIONS: A RECIPE FOR RESISTANCE 848

Perspective 24.3 PHAGE THERAPY: BIOCONTROL FOR INFECTIONS 849

24.4 Predicting and Controlling Epidemics 850

Perspective 24.4 VARIOLATION: DELIBERATE INFECTION WITH SMALLPOX VIRUS 853

24.5 Immunization and Vaccines 853

Appendix A Reading and Understanding the Primary Literature A-1

Appendix B Microscopy A-9

Appendix C Classification of Bacteria A-13

Appendix D Classification of Eukarya A-14

Appendix E Classification of Archaea A-15

Appendix F Classification of Viruses A-16

Appendix G Origin of Blood Cells A-17

GLOSSARY G-1

INDEX I-1

23.2 Pathogen Study: Plasmodium falciparum 808

Toolbox 23.1 TESTING FOR MALARIA 812

23.3 Macroscopic Eukaryal Pathogens 814

23.4 Evolution of Eukaryal Pathogens 816

Perspective 23.3 CHYTRID FUNGUS: AN EMERGING FUNGAL PATHOGEN 817

24 Control of Infectious Diseases 822

24.1 Historical Aspects of Infectious Disease Treatment and Control 824

24.2 Antimicrobial Drugs 825

24.3 Antimicrobial Drug Resistance 836

Toolbox 24.1 DRUG SUSCEPTIBILITY TESTING AND MIC 842

Mini-Paper: A Focus on the Research SOIL MICROBES POSSESS EXTENSIVE RESISTANCE TO ANTIBIOTICS 844



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