Managing and maintaining Windows 8 : exam 70-688

 Content: 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