{"product_id":"snyder-and-champness-molecular-genetics-of-bacteria-hardback-9781555819750","title":"Snyder and Champness Molecular Genetics of Bacteria (Hardback) 9781555819750","description":"\u003cfont face=\"Georgia\"\u003e\r\n\u003cp\u003e\u003cfont size=\"6\"\u003eSnyder and Champness Molecular Genetics of Bacteria\u003c\/font\u003e\u003cbr\u003e\r\n\r\n\r\n\r\n\r\n\r\n\u003c\/p\u003e\n\u003cp\u003e\u003cfont size=\"4\"\u003eTina M. Henkin (Author), Joseph E. Peters (Author)\u003c\/font\u003e\u003c\/p\u003e\r\n\r\n\u003cp\u003e\u003cfont size=\"3\"\u003e9781555819750, Wiley\u003c\/font\u003e\u003c\/p\u003e\r\n\r\n\u003cp\u003e\u003cfont size=\"3\"\u003eHardback, published 15 October 2020\u003c\/font\u003e\u003c\/p\u003e\r\n\r\n\u003cp\u003e\u003cfont size=\"3\"\u003e640 pages\u003cbr\u003e28.2 x 22.4 x 4.1 cm, 1.95 kg\u003c\/font\u003e\u003c\/p\u003e\r\n\r\n\r\n\r\n\u003cp align=\"justify\"\u003e\u003cem\u003e\u003cfont size=\"3\"\u003e\"... A thorough and digestible text ... skillfully updated to address the latest advances in scientific knowledge and technology\" (\u003ci\u003eEmerging Infectious Diseases\u003c\/i\u003e, January 2022)\u003c\/font\u003e\u003c\/em\u003e\u003c\/p\u003e\r\n\r\n\u003cp align=\"justify\"\u003e\u003cstrong\u003e\u003cfont size=\"3\"\u003e\u003cp\u003e\u003cb\u003eThe single most comprehensive and authoritative textbook on bacterial molecular genetics\u003c\/b\u003e\u003c\/p\u003e \u003cp\u003e\u003ci\u003eSnyder \u0026amp; Champness Molecular Genetics of Bacteria\u003c\/i\u003e is a new edition of a classic text, updated to address the massive advances in the field of bacterial molecular genetics and retitled as homage to the founding authors.\u003c\/p\u003e \u003cp\u003eIn an era experiencing an avalanche of new genetic sequence information, this updated edition presents important experiments and advanced material relevant to current applications of molecular genetics, including conclusions from and applications of genomics; the relationships among recombination, replication, and repair and the importance of organizing sequences in DNA; the mechanisms of regulation of gene expression; the newest advances in bacterial cell biology; and the coordination of cellular processes during the bacterial cell cycle. The topics are integrated throughout with biochemical, genomic, and structural information, allowing readers to gain a deeper understanding of modern bacterial molecular genetics and its relationship to other fields of modern biology.\u003c\/p\u003e \u003cp\u003eAlthough the text is centered on the most-studied bacteria, \u003ci\u003eEscherichia coli\u003c\/i\u003e and \u003ci\u003eBacillus subtilis\u003c\/i\u003e, many examples are drawn from other bacteria of experimental, medical, ecological, and biotechnological importance. The book's many useful features include\u003c\/p\u003e \u003cul\u003e \u003cli\u003eText boxes to help students make connections to relevant topics related to other organisms, including humans\u003c\/li\u003e \u003cli\u003eA summary of main points at the end of each chapter\u003c\/li\u003e \u003cli\u003eQuestions for discussion and independent thought\u003c\/li\u003e \u003cli\u003eA list of suggested readings for background and further investigation in each chapter\u003c\/li\u003e \u003cli\u003eFully illustrated with detailed diagrams and photos in full color\u003c\/li\u003e \u003cli\u003eA glossary of terms highlighted in the text\u003c\/li\u003e \u003c\/ul\u003e \u003cp\u003eWhile intended as an undergraduate or beginning graduate textbook, Molecular Genetics of Bacteria is an invaluable reference for anyone working in the fields of microbiology, genetics, biochemistry, bioengineering, medicine, molecular biology, and biotechnology.\u003c\/p\u003e \u003cp\u003e\"This is a marvelous textbook that is completely up-to-date and comprehensive, but not overwhelming. The clear prose and excellent figures make it ideal for use in teaching bacterial molecular genetics.\"\u003cbr\u003e—\u003cb\u003eCaroline Harwood\u003c\/b\u003e, University of Washington\u003cbr\u003e\u003cbr\u003eWatch an interview with the authors as they discuss their book further: https:\/\/www.youtube.com\/watch?v=NEl-dfatWUU\u003c\/p\u003e\u003c\/font\u003e\u003c\/strong\u003e\u003c\/p\u003e\r\n\r\n\u003cp\u003e\u003cfont size=\"3\"\u003e\u003cp\u003ePreface xv\u003c\/p\u003e \u003cp\u003eAcknowledgments xix\u003c\/p\u003e \u003cp\u003eAbout the Authors 1\u003c\/p\u003e \u003cp\u003e\u003cb\u003eIntroduction 3\u003c\/b\u003e\u003c\/p\u003e \u003cp\u003eThe Biological Universe 5\u003c\/p\u003e \u003cp\u003eThe Bacteria 5\u003c\/p\u003e \u003cp\u003eThe Archaea 7\u003c\/p\u003e \u003cp\u003eThe Eukaryotes 7\u003c\/p\u003e \u003cp\u003eWhat is Genetics? 8\u003c\/p\u003e \u003cp\u003eBacterial Genetics 8\u003c\/p\u003e \u003cp\u003eBacteria Are Haploid 9\u003c\/p\u003e \u003cp\u003eShort Generation Times 9\u003c\/p\u003e \u003cp\u003eAsexual Reproduction 9\u003c\/p\u003e \u003cp\u003eColony Growth on Agar Plates 9\u003c\/p\u003e \u003cp\u003eColony Purification 9\u003c\/p\u003e \u003cp\u003eSerial Dilutions 9\u003c\/p\u003e \u003cp\u003eSelections 10\u003c\/p\u003e \u003cp\u003eStoring Stocks of Bacterial Strains 10\u003c\/p\u003e \u003cp\u003eGenetic Exchange 10\u003c\/p\u003e \u003cp\u003ePhage Genetics 10\u003c\/p\u003e \u003cp\u003ePhages Are Haploid 11\u003c\/p\u003e \u003cp\u003eSelections\u003c\/p\u003e \u003cp\u003ewith Phages 11\u003c\/p\u003e \u003cp\u003eCrosses with Phages 11\u003c\/p\u003e \u003cp\u003eA Brief History of Bacterial Molecular Genetics 11\u003c\/p\u003e \u003cp\u003eInheritance in Bacteria 11\u003c\/p\u003e \u003cp\u003eTransformation 11\u003c\/p\u003e \u003cp\u003eConjugation 12\u003c\/p\u003e \u003cp\u003eTransduction 12\u003c\/p\u003e \u003cp\u003eRecombination within Genes 12\u003c\/p\u003e \u003cp\u003eSemiconservative DNA Replication 12\u003c\/p\u003e \u003cp\u003emRNA 12\u003c\/p\u003e \u003cp\u003eThe Genetic Code 12\u003c\/p\u003e \u003cp\u003eThe Operon Model 12\u003c\/p\u003e \u003cp\u003eEnzymes for Molecular Biology 12\u003c\/p\u003e \u003cp\u003eSynthetic Genomics 13\u003c\/p\u003e \u003cp\u003eWhat is Ahead 13\u003c\/p\u003e \u003cp\u003e\u003cb\u003e1 The Bacterial Chromosome: DNA Structure, Replication, and Segregation 17\u003c\/b\u003e\u003c\/p\u003e \u003cp\u003eDNA Structure 17\u003c\/p\u003e \u003cp\u003eThe Deoxyribonucleotides 17\u003c\/p\u003e \u003cp\u003eThe DNA Chain 18\u003c\/p\u003e \u003cp\u003eThe 5’ and 3’ Ends 18\u003c\/p\u003e \u003cp\u003eBase Pairing 20\u003c\/p\u003e \u003cp\u003eAntiparallel Construction 20\u003c\/p\u003e \u003cp\u003eThe Major and Minor Grooves 21\u003c\/p\u003e \u003cp\u003eThe Mechanism of DNA Replication 21\u003c\/p\u003e \u003cp\u003eDeoxyribonucleotide Precursor Synthesis 21\u003c\/p\u003e \u003cp\u003eReplication of the Bacterial Chromosome 21\u003c\/p\u003e \u003cp\u003eReplication of Double- Stranded DNA 26\u003c\/p\u003e \u003cp\u003eReplication Errors 30\u003c\/p\u003e \u003cp\u003eEditing 30\u003c\/p\u003e \u003cp\u003eRNA Primers and Editing 31\u003c\/p\u003e \u003cp\u003eImpediments to DNA Replication 31\u003c\/p\u003e \u003cp\u003eDamaged DNA and DNA Polymerase III 31\u003c\/p\u003e \u003cp\u003eMechanisms To Deal with Impediments on Template DNA Strands 32\u003c\/p\u003e \u003cp\u003ePhysical Blocks to Replication Forks 32\u003c\/p\u003e \u003cp\u003eReplication of the Bacterial Chromosome and Cell Division 32\u003c\/p\u003e \u003cp\u003eStructure of Bacterial Chromosomes 34\u003c\/p\u003e \u003cp\u003eReplication of the Bacterial Chromosome 34\u003c\/p\u003e \u003cp\u003eInitiation of Chromosome Replication 34\u003c\/p\u003e \u003cp\u003eRNA Priming of Initiation 35\u003c\/p\u003e \u003cp\u003eTermination of Chromosome Replication 35\u003c\/p\u003e \u003cp\u003eChromosome Segregation 37\u003c\/p\u003e \u003cp\u003eCoordination of Cell Division with Replication of the Chromosome 47\u003c\/p\u003e \u003cp\u003eTiming of Initiation of Replication 49\u003c\/p\u003e \u003cp\u003eThe Bacterial Nucleoid 51\u003c\/p\u003e \u003cp\u003eSupercoiling in the Nucleoid 51\u003c\/p\u003e \u003cp\u003eTopoisomerases 52\u003c\/p\u003e \u003cp\u003eThe Bacterial Genome 55\u003c\/p\u003e \u003cp\u003eBox 1.1 Structural Features of Bacterial Genomes 37\u003c\/p\u003e \u003cp\u003eBox 1.2 Antibiotics That Affect Replication and DNA Structure 54\u003c\/p\u003e \u003cp\u003e\u003cb\u003e2 Bacterial Gene Expression: Transcription, Translation, Protein Folding, and Localization 61\u003c\/b\u003e\u003c\/p\u003e \u003cp\u003eOverview 61\u003c\/p\u003e \u003cp\u003eThe Structure and Function of RNA 62\u003c\/p\u003e \u003cp\u003eTypes of RNA 62\u003c\/p\u003e \u003cp\u003eRNA Precursors 62\u003c\/p\u003e \u003cp\u003eRNA Structure 62\u003c\/p\u003e \u003cp\u003eRNA Processing and Modification 64\u003c\/p\u003e \u003cp\u003eTranscription 64\u003c\/p\u003e \u003cp\u003eStructure of Bacterial RNA Polymerase 64\u003c\/p\u003e \u003cp\u003eOverview of Transcription 65\u003c\/p\u003e \u003cp\u003eDetails of Transcription 67\u003c\/p\u003e \u003cp\u003erRNAs and tRNAs 74\u003c\/p\u003e \u003cp\u003eRNA Degradation 77\u003c\/p\u003e \u003cp\u003eRNases 77\u003c\/p\u003e \u003cp\u003eThe Structure and Function of Proteins 78\u003c\/p\u003e \u003cp\u003eProtein Structure 78\u003c\/p\u003e \u003cp\u003eTranslation 80\u003c\/p\u003e \u003cp\u003eStructure of the Bacterial Ribosome 80\u003c\/p\u003e \u003cp\u003eOverview of Translation 83\u003c\/p\u003e \u003cp\u003eDetails of Protein Synthesis 84\u003c\/p\u003e \u003cp\u003eThe Genetic Code 92\u003c\/p\u003e \u003cp\u003ePolycistronic mRNA 96\u003c\/p\u003e \u003cp\u003eProtein Folding and Degradation 98\u003c\/p\u003e \u003cp\u003eProtein Chaperones 98\u003c\/p\u003e \u003cp\u003eProtein Degradation 101\u003c\/p\u003e \u003cp\u003eProtein Localization 101\u003c\/p\u003e \u003cp\u003eThe Translocase System 101\u003c\/p\u003e \u003cp\u003eThe Signal Sequence 103\u003c\/p\u003e \u003cp\u003eThe Targeting Factors 103\u003c\/p\u003e \u003cp\u003eThe Tat Secretion Pathway 104\u003c\/p\u003e \u003cp\u003eDisulfide Bonds 105\u003c\/p\u003e \u003cp\u003eProtein Secretion and Export 105\u003c\/p\u003e \u003cp\u003eProtein Secretion Systems in Bacteria with an Outer Membrane 106\u003c\/p\u003e \u003cp\u003eProtein Secretion in Bacteria That Lack an Outer Membrane 110\u003c\/p\u003e \u003cp\u003eSortases 110\u003c\/p\u003e \u003cp\u003eRegulation of Gene Expression 111\u003c\/p\u003e \u003cp\u003eTranscriptional Regulation 112\u003c\/p\u003e \u003cp\u003ePosttranscriptional Regulation 113\u003c\/p\u003e \u003cp\u003eWhat You Need To Know 114\u003c\/p\u003e \u003cp\u003eOpen Reading Frames 115\u003c\/p\u003e \u003cp\u003eTranscriptional and Translational Fusions 115\u003c\/p\u003e \u003cp\u003eBox 2.1 Antibiotic Inhibitors of Transcription 72\u003c\/p\u003e \u003cp\u003eBox 2.2 Molecular Phylogeny 75\u003c\/p\u003e \u003cp\u003eBox 2.3 Antibiotic Inhibitors of Translation 81\u003c\/p\u003e \u003cp\u003eBox 2.4 Mimicry in Translation 91\u003c\/p\u003e \u003cp\u003eBox 2.5 Exceptions to the Code 94\u003c\/p\u003e \u003cp\u003e\u003cb\u003e3 Bacterial Genetic Analysis: Fundamentals and Current Approaches 123\u003c\/b\u003e\u003c\/p\u003e \u003cp\u003eDefinitions 123\u003c\/p\u003e \u003cp\u003eTerms Used in Genetics 123\u003c\/p\u003e \u003cp\u003eGenetic Names 124\u003c\/p\u003e \u003cp\u003eAuxotrophic and Catabolic Mutants 125\u003c\/p\u003e \u003cp\u003eConditional- Lethal Mutants 126\u003c\/p\u003e \u003cp\u003eResistant Mutants 128\u003c\/p\u003e \u003cp\u003eInheritance in Bacteria 128\u003c\/p\u003e \u003cp\u003eThe Luria and Delbrück Experiment 129\u003c\/p\u003e \u003cp\u003eMutants Are Clonal 130\u003c\/p\u003e \u003cp\u003eEsther and Joshua Lederberg’s Experiment 130\u003c\/p\u003e \u003cp\u003eMutation Rates 132\u003c\/p\u003e \u003cp\u003eCalculating Mutation Rates 133\u003c\/p\u003e \u003cp\u003eCalculating the Mutation Rate from the Rate of Increase in the Proportion of Mutants 135\u003c\/p\u003e \u003cp\u003eTypes of Mutations 136\u003c\/p\u003e \u003cp\u003eProperties of Mutations 136\u003c\/p\u003e \u003cp\u003eBase Pair Changes 136\u003c\/p\u003e \u003cp\u003eFrameshift Mutations 140\u003c\/p\u003e \u003cp\u003eDeletion Mutations 141\u003c\/p\u003e \u003cp\u003eTandem- Duplication Mutations 143\u003c\/p\u003e \u003cp\u003eInversion Mutations 144\u003c\/p\u003e \u003cp\u003eInsertion Mutations 145\u003c\/p\u003e \u003cp\u003eReversion versus Suppression 147\u003c\/p\u003e \u003cp\u003eIntragenic Suppressors 147\u003c\/p\u003e \u003cp\u003eIntergenic Suppressors 147\u003c\/p\u003e \u003cp\u003eGenetic Analysis in Bacteria 151\u003c\/p\u003e \u003cp\u003eIsolating Mutants 151\u003c\/p\u003e \u003cp\u003eGenetic Characterization of Mutants 155\u003c\/p\u003e \u003cp\u003eComplementation Tests 160\u003c\/p\u003e \u003cp\u003eGenetic Crosses in Bacteria 166\u003c\/p\u003e \u003cp\u003eMapping of Bacterial Markers by Transduction and Transformation 168\u003c\/p\u003e \u003cp\u003eOther Uses of Transformation and Transduction 171\u003c\/p\u003e \u003cp\u003eGenetic Mapping by Hfr Crosses 172\u003c\/p\u003e \u003cp\u003ePerspective 176\u003c\/p\u003e \u003cp\u003eBox 3.1 Inversions and the Genetic Map 146\u003c\/p\u003e \u003cp\u003e\u003cb\u003e4 Plasmids 181\u003c\/b\u003e\u003c\/p\u003e \u003cp\u003eWhat is a Plasmid? 181\u003c\/p\u003e \u003cp\u003eNaming Plasmids 182\u003c\/p\u003e \u003cp\u003eFunctions Encoded by Plasmids 182\u003c\/p\u003e \u003cp\u003ePlasmid Structure 183\u003c\/p\u003e \u003cp\u003eProperties of Plasmids 184\u003c\/p\u003e \u003cp\u003eReplication 184\u003c\/p\u003e \u003cp\u003eFunctions of the \u003ci\u003eori \u003c\/i\u003eRegion 187\u003c\/p\u003e \u003cp\u003ePlasmid Replication Control Mechanisms 193\u003c\/p\u003e \u003cp\u003eMechanisms To Prevent Curing of Plasmids 200\u003c\/p\u003e \u003cp\u003eThe Par Systems of Plasmids 203\u003c\/p\u003e \u003cp\u003ePlasmid Cloning Vectors 206\u003c\/p\u003e \u003cp\u003eExamples of Plasmid Cloning Vectors 208\u003c\/p\u003e \u003cp\u003eBroad- Host- Range Cloning Vectors 210\u003c\/p\u003e \u003cp\u003eBox 4.1 Linear Chromosomes and Plasmids in Bacteria 188\u003c\/p\u003e \u003cp\u003eBox 4.2 Determining the Inc Group 191\u003c\/p\u003e \u003cp\u003eBox 4.3 Toxin- Antitoxin Systems and Plasmid Maintenance 201\u003c\/p\u003e \u003cp\u003e\u003cb\u003e5 Conjugation 215\u003c\/b\u003e\u003c\/p\u003e \u003cp\u003eOverview 215\u003c\/p\u003e \u003cp\u003eClassification of Self- Transmissible Plasmids and Integrating Elements 217\u003c\/p\u003e \u003cp\u003eThe Fertility Plasmid 217\u003c\/p\u003e \u003cp\u003eMechanism of DNA Transfer during Conjugation in \u003ci\u003eProteobacteria \u003c\/i\u003e218\u003c\/p\u003e \u003cp\u003eTransfer (\u003ci\u003etra\u003c\/i\u003e) Genes 218\u003c\/p\u003e \u003cp\u003eThe \u003ci\u003eoriT \u003c\/i\u003eSequence 221\u003c\/p\u003e \u003cp\u003eEfficiency of Transfer 222\u003c\/p\u003e \u003cp\u003eInterspecies Transfer of Plasmids 225\u003c\/p\u003e \u003cp\u003eConjugation and Type IV Secretion Systems Capable of Translocating Proteins 225\u003c\/p\u003e \u003cp\u003eMobilizable Plasmids 229\u003c\/p\u003e \u003cp\u003eChromosome Transfer by Plasmids 230\u003c\/p\u003e \u003cp\u003eFormation of Hfr Strains of \u003ci\u003eE. coli \u003c\/i\u003e230\u003c\/p\u003e \u003cp\u003eTransfer of Chromosomal DNA by Integrated Plasmids 230\u003c\/p\u003e \u003cp\u003eChromosome Mobilization 231\u003c\/p\u003e \u003cp\u003ePrime Factors 231\u003c\/p\u003e \u003cp\u003eDiversity in Transfer Systems 233\u003c\/p\u003e \u003cp\u003eIntegrating Conjugative Elements 234\u003c\/p\u003e \u003cp\u003eSXT\/R391 ICE 234\u003c\/p\u003e \u003cp\u003eICE\u003ci\u003eBs\u003c\/i\u003e1 236\u003c\/p\u003e \u003cp\u003eTn\u003ci\u003e916 \u003c\/i\u003e237\u003c\/p\u003e \u003cp\u003eTn\u003ci\u003eGBS\u003c\/i\u003e1 and Tn\u003ci\u003eGBS\u003c\/i\u003e2 240\u003c\/p\u003e \u003cp\u003eBox 5.1 Pilus- Specific Phages 220\u003c\/p\u003e \u003cp\u003eBox 5.2 Delivery of Conditional Plasmids by Conjugation 223\u003c\/p\u003e \u003cp\u003eBox 5.3 Gene Exchange between Domains 226\u003c\/p\u003e \u003cp\u003eBox 5.4 Conjugation and Synthetic Genomics 232\u003c\/p\u003e \u003cp\u003e\u003cb\u003e6 Transformation 245\u003c\/b\u003e\u003c\/p\u003e \u003cp\u003eNatural Transformation 246\u003c\/p\u003e \u003cp\u003eDiscovery of Transformation 246\u003c\/p\u003e \u003cp\u003eOverview of Natural Transformation 247\u003c\/p\u003e \u003cp\u003eDNA Uptake Mechanisms 247\u003c\/p\u003e \u003cp\u003eSpecificity of DNA Uptake 251\u003c\/p\u003e \u003cp\u003eDNA Pro cessing after Uptake 253\u003c\/p\u003e \u003cp\u003eNatural Transformation as a Tool 253\u003c\/p\u003e \u003cp\u003eRegulation of Natural Competence 254\u003c\/p\u003e \u003cp\u003eIdentification of Competence in Other Organisms 258\u003c\/p\u003e \u003cp\u003eRole of Natural Transformation 258\u003c\/p\u003e \u003cp\u003eArtificially Induced Competence 260\u003c\/p\u003e \u003cp\u003eChemical Induction 260\u003c\/p\u003e \u003cp\u003eElectroporation 261\u003c\/p\u003e \u003cp\u003eProtoplast Transformation 261\u003c\/p\u003e \u003cp\u003eBox 6.1 Experimental Measurements of DNA Uptake 248\u003c\/p\u003e \u003cp\u003eBox 6.2 Genetic Evidence for Single- Stranded DNA Uptake 252\u003c\/p\u003e \u003cp\u003eBox 6.3 Role of Natural Transformation in Pathogens 260\u003c\/p\u003e \u003cp\u003e\u003cb\u003e7 Bacteriophages and Transduction 265\u003c\/b\u003e\u003c\/p\u003e \u003cp\u003eLytic Development 268\u003c\/p\u003e \u003cp\u003eThe Lytic Cycle 268\u003c\/p\u003e \u003cp\u003eTranscriptional Regulation of Phage Gene Expression 268\u003c\/p\u003e \u003cp\u003ePhage Genome Replication and Packaging 279\u003c\/p\u003e \u003cp\u003eHost Cell Lysis 289\u003c\/p\u003e \u003cp\u003eLysogenic Development 292\u003c\/p\u003e \u003cp\u003eThe λ System 292\u003c\/p\u003e \u003cp\u003eOther Lysogenic Systems 299\u003c\/p\u003e \u003cp\u003eGenetic Analysis of Phages 302\u003c\/p\u003e \u003cp\u003eInfection of Cells 302\u003c\/p\u003e \u003cp\u003ePhage Crosses 303\u003c\/p\u003e \u003cp\u003eRecombination and Complementation Tests with Phages 303\u003c\/p\u003e \u003cp\u003eThe Genetic- Linkage Map of a Phage 305\u003c\/p\u003e \u003cp\u003ePhage- Mediated Genetic Transfer 306\u003c\/p\u003e \u003cp\u003eGeneralized Transduction 306\u003c\/p\u003e \u003cp\u003eSpecialized Transduction 308\u003c\/p\u003e \u003cp\u003eLysogenic Conversion and Bacterial Pathogenesis 310\u003c\/p\u003e \u003cp\u003eHost Defenses Against Phage Infection 313\u003c\/p\u003e \u003cp\u003eRestriction- Modification Systems 313\u003c\/p\u003e \u003cp\u003eAbi Systems 313\u003c\/p\u003e \u003cp\u003eCRISPR\/Cas Systems 314\u003c\/p\u003e \u003cp\u003eSmall Molecules and Phage Defense 314\u003c\/p\u003e \u003cp\u003ePhage versus Phage 314\u003c\/p\u003e \u003cp\u003ePhages as Tools 315\u003c\/p\u003e \u003cp\u003eCloning Vectors 315\u003c\/p\u003e \u003cp\u003ePhage Display 315\u003c\/p\u003e \u003cp\u003ePhage Therapy 317\u003c\/p\u003e \u003cp\u003eBox 7.1 Phage Genomics 266\u003c\/p\u003e \u003cp\u003eBox 7.2 Phage T7- Based Tools 271\u003c\/p\u003e \u003cp\u003eBox 7.3 Protein Priming 285\u003c\/p\u003e \u003cp\u003e\u003cb\u003e8 Transposition, Site- Specific Recombination, and Families of Recombinases 321\u003c\/b\u003e\u003c\/p\u003e \u003cp\u003eTransposition 321\u003c\/p\u003e \u003cp\u003eOverview of Transposition 322\u003c\/p\u003e \u003cp\u003eStructure of Bacterial DNA Transposons 322\u003c\/p\u003e \u003cp\u003eTypes of Bacterial DNA Transposons 323\u003c\/p\u003e \u003cp\u003eAssays of Transposition 326\u003c\/p\u003e \u003cp\u003eMechanisms of Transposition 328\u003c\/p\u003e \u003cp\u003eDDE Transposons 328\u003c\/p\u003e \u003cp\u003eHUH Transposons 332\u003c\/p\u003e \u003cp\u003eGeneral Properties of Transposons 334\u003c\/p\u003e \u003cp\u003eTransposition Regulation 334\u003c\/p\u003e \u003cp\u003eTarget Site Specificity 335\u003c\/p\u003e \u003cp\u003eEffects on Genes Adjacent to the Insertion Site 337\u003c\/p\u003e \u003cp\u003eTarget Immunity 337\u003c\/p\u003e \u003cp\u003eTransposon Mutagenesis 337\u003c\/p\u003e \u003cp\u003eTransposon Mutagenesis \u003ci\u003eIn Vivo \u003c\/i\u003e339\u003c\/p\u003e \u003cp\u003eTransposon Mutagenesis \u003ci\u003eIn Vitro \u003c\/i\u003e340\u003c\/p\u003e \u003cp\u003eTransposon Mutagenesis of Plasmids 341\u003c\/p\u003e \u003cp\u003eTransposon Mutagenesis of the Bacterial Chromosome 341\u003c\/p\u003e \u003cp\u003eTransposon Mutagenesis of All Bacteria 342\u003c\/p\u003e \u003cp\u003eUsing Transposon Mutagenesis To Make Random Gene Fusions 342\u003c\/p\u003e \u003cp\u003eSite- Specific Recombination 343\u003c\/p\u003e \u003cp\u003eIntegrases 343\u003c\/p\u003e \u003cp\u003eResolvases 345\u003c\/p\u003e \u003cp\u003eDNA Invertases 345\u003c\/p\u003e \u003cp\u003eY and S Recombinases 347\u003c\/p\u003e \u003cp\u003eY Recombinases: Mechanism 347\u003c\/p\u003e \u003cp\u003eS Recombinases: Mechanism 351\u003c\/p\u003e \u003cp\u003eGroup II Mobile Introns: Elements That Move Using an RNA Intermediate 352\u003c\/p\u003e \u003cp\u003eImportance of Transposition and Site- Specific Recombination in Bacterial Adaptation 354\u003c\/p\u003e \u003cp\u003eBox 8.1 Mobile Elements and DNA Replication 333\u003c\/p\u003e \u003cp\u003eBox 8.2 Transposons and Genomics 338\u003c\/p\u003e \u003cp\u003e\u003cb\u003e9 Molecular Mechanisms of Homologous Recombination 359\u003c\/b\u003e\u003c\/p\u003e \u003cp\u003eHomologous Recombination and DNA Replication in Bacteria 360\u003c\/p\u003e \u003cp\u003eEarly Evidence for the Interdependence of Homologous Recombination and DNA Replication 361\u003c\/p\u003e \u003cp\u003eThe Molecular Basis for Recombination in \u003ci\u003eE. coli \u003c\/i\u003e361\u003c\/p\u003e \u003cp\u003e\u003ci\u003echi \u003c\/i\u003e(χ) Sites and the RecBCD Complex 361\u003c\/p\u003e \u003cp\u003eThe RecF Pathway 367\u003c\/p\u003e \u003cp\u003eSynapse Formation and the RecA Protein 368\u003c\/p\u003e \u003cp\u003eThe Ruv and RecG Proteins and the Migration and Cutting of Holliday Junctions 371\u003c\/p\u003e \u003cp\u003eRecombination between Different DNAs in Bacteria 373\u003c\/p\u003e \u003cp\u003eHow Are Linear DNA Fragments Recombined into the \u003ci\u003eE. coli \u003c\/i\u003eChromosome? 373\u003c\/p\u003e \u003cp\u003eRecombination during Natural Transformation 375\u003c\/p\u003e \u003cp\u003ePhage Recombination Pathways 375\u003c\/p\u003e \u003cp\u003eRec Proteins of Phages T4 and T7 375\u003c\/p\u003e \u003cp\u003eThe RecE Pathway of the \u003ci\u003erac \u003c\/i\u003eProphage 375\u003c\/p\u003e \u003cp\u003eThe Phage λ Red System 375\u003c\/p\u003e \u003cp\u003eRecombineering: Gene Replacements in \u003ci\u003eE. coli \u003c\/i\u003ewith Phage λ Recombination Functions 376\u003c\/p\u003e \u003cp\u003eGene Conversion and Other Manifestations of Heteroduplex Formation during Recombination 379\u003c\/p\u003e \u003cp\u003eBox 9.1 Discovery of χ sites 364\u003c\/p\u003e \u003cp\u003eBox 9.2 Other Types of Double- Strand Break Repair in Bacteria 365\u003c\/p\u003e \u003cp\u003e\u003cb\u003e10 DNA Repair and Mutagenesis 385\u003c\/b\u003e\u003c\/p\u003e \u003cp\u003eEvidence for DNA Repair 386\u003c\/p\u003e \u003cp\u003eSpecific Repair Pathways 387\u003c\/p\u003e \u003cp\u003eDeamination of Bases 387\u003c\/p\u003e \u003cp\u003eDamage Due to Reactive Oxygen 389\u003c\/p\u003e \u003cp\u003eDamage Due to Alkylating Agents 393\u003c\/p\u003e \u003cp\u003eDamage Due to UV Irradiation 395\u003c\/p\u003e \u003cp\u003eGeneral Repair Mechanisms 396\u003c\/p\u003e \u003cp\u003eBase Analogs 396\u003c\/p\u003e \u003cp\u003eFrameshift Mutagens 397\u003c\/p\u003e \u003cp\u003eMismatch Repair 398\u003c\/p\u003e \u003cp\u003eNucleotide Excision Repair 403\u003c\/p\u003e \u003cp\u003eDNA Damage Tolerance Mechanisms 405\u003c\/p\u003e \u003cp\u003eHomologous Recombination and DNA Replication 405\u003c\/p\u003e \u003cp\u003eSOS- Inducible Repair 409\u003c\/p\u003e \u003cp\u003eMechanism of TLS by the Pol V Mutasome 416\u003c\/p\u003e \u003cp\u003eOther Specialized Polymerases and Their Regulation 417\u003c\/p\u003e \u003cp\u003eSummary of Repair Pathways in \u003ci\u003eE. coli \u003c\/i\u003e418\u003c\/p\u003e \u003cp\u003eBacteriophage Repair Pathways 418\u003c\/p\u003e \u003cp\u003eBox 10.1 The Role of Reactive Oxygen Species in Cancer and Degenerative Diseases 391\u003c\/p\u003e \u003cp\u003eBox 10.2 DNA Repair and Cancer 401\u003c\/p\u003e \u003cp\u003eBox 10.3 The Ames Test 417\u003c\/p\u003e \u003cp\u003e\u003cb\u003e11 Regulation of Gene Expression: Genes and Operons 425\u003c\/b\u003e\u003c\/p\u003e \u003cp\u003eTranscriptional Regulation in Bacteria 426\u003c\/p\u003e \u003cp\u003eGenetic Evidence for Negative and Positive Regulation 427\u003c\/p\u003e \u003cp\u003eNegative Regulation of Transcription Initiation 428\u003c\/p\u003e \u003cp\u003eNegative Inducible Systems 428\u003c\/p\u003e \u003cp\u003eNegative Repressible Systems 437\u003c\/p\u003e \u003cp\u003eMolecular Mechanisms of Transcriptional Repression 439\u003c\/p\u003e \u003cp\u003ePositive Regulation of Transcription Initiation 439\u003c\/p\u003e \u003cp\u003ePositive Inducible Systems 440\u003c\/p\u003e \u003cp\u003ePositive Repressible Systems 447\u003c\/p\u003e \u003cp\u003eMolecular Mechanisms of Transcriptional Activation 447\u003c\/p\u003e \u003cp\u003eRegulation by Transcription Attenuation 449\u003c\/p\u003e \u003cp\u003eModulation of RNA Structure 449\u003c\/p\u003e \u003cp\u003eChanges in Processivity of RNA Polymerase 459\u003c\/p\u003e \u003cp\u003eRegulation of mRNA Degradation 460\u003c\/p\u003e \u003cp\u003eProtein- Dependent Effects on RNA Stability 460\u003c\/p\u003e \u003cp\u003eRNA- Dependent Effects on RNA Stability 461\u003c\/p\u003e \u003cp\u003eRegulation of Translation 461\u003c\/p\u003e \u003cp\u003eRegulation of Translation Initiation 462\u003c\/p\u003e \u003cp\u003eTranslational Regulation in the Exit Channel of the Ribosome 464\u003c\/p\u003e \u003cp\u003eRegulation of Translation Termination 465\u003c\/p\u003e \u003cp\u003ePosttranslational Regulation 467\u003c\/p\u003e \u003cp\u003ePosttranslational Protein Modification 467\u003c\/p\u003e \u003cp\u003eRegulation of Protein Turnover 467\u003c\/p\u003e \u003cp\u003eFeedback Inhibition of Enzyme Activity 468\u003c\/p\u003e \u003cp\u003eWhy Are There So Many Mechanisms of Gene Regulation? 469\u003c\/p\u003e \u003cp\u003eBox 11.1 The Helix- Turn- Helix Motif of DNA- Binding Proteins 427\u003c\/p\u003e \u003cp\u003eBox 11.2 Families of Regulators 442\u003c\/p\u003e \u003cp\u003e\u003cb\u003e12 Global Regulation: Regulons and Stimulons 473\u003c\/b\u003e\u003c\/p\u003e \u003cp\u003eCarbon Catabolite Regulation 474\u003c\/p\u003e \u003cp\u003eCarbon Catabolite Regulation in \u003ci\u003eE. coli\u003c\/i\u003e: Catabolite Activator Protein (CAP) and cAMP 474\u003c\/p\u003e \u003cp\u003eCarbon Catabolite Regulation in \u003ci\u003eB. subtilis\u003c\/i\u003e: CcpA and Hpr 481\u003c\/p\u003e \u003cp\u003eRegulation of Nitrogen Assimilation 482\u003c\/p\u003e \u003cp\u003ePathways for Nitrogen Assimilation 483\u003c\/p\u003e \u003cp\u003eRegulation of Nitrogen Assimilation Pathways in \u003ci\u003eE. coli \u003c\/i\u003eby the Ntr System 484\u003c\/p\u003e \u003cp\u003eRegulation of Nitrogen Assimilation in \u003ci\u003eB. subtilis \u003c\/i\u003e491\u003c\/p\u003e \u003cp\u003eRegulation of Ribosome Components and tRNA Synthesis 491\u003c\/p\u003e \u003cp\u003eRibosomal Protein Gene Regulation 492\u003c\/p\u003e \u003cp\u003eRegulation of rRNA and tRNA Synthesis 493\u003c\/p\u003e \u003cp\u003eStringent Response 494\u003c\/p\u003e \u003cp\u003eStress Responses in Bacteria 498\u003c\/p\u003e \u003cp\u003eHeat Shock Regulation 498\u003c\/p\u003e \u003cp\u003eGeneral Stress Response in Enteric Bacteria 501\u003c\/p\u003e \u003cp\u003eGeneral Stress Response in \u003ci\u003eFirmicutes \u003c\/i\u003e505\u003c\/p\u003e \u003cp\u003eExtracytoplasmic (Envelope) Stress Responses 506\u003c\/p\u003e \u003cp\u003eIron Regulation in \u003ci\u003eE. coli \u003c\/i\u003e510\u003c\/p\u003e \u003cp\u003eThe Fur Regulon 510\u003c\/p\u003e \u003cp\u003eThe RyhB sRNA 512\u003c\/p\u003e \u003cp\u003eThe Aconitase Translational Repressor 512\u003c\/p\u003e \u003cp\u003eRegulation of Virulence Genes in Pathogenic Bacteria 513\u003c\/p\u003e \u003cp\u003eDiphtheria 513\u003c\/p\u003e \u003cp\u003eCholera and Quorum Sensing 514\u003c\/p\u003e \u003cp\u003eWhooping Cough 519\u003c\/p\u003e \u003cp\u003eDevelopmental Regulation: Sporulation in \u003ci\u003eB. subtilis \u003c\/i\u003e520\u003c\/p\u003e \u003cp\u003eIdentification of Genes That Regulate Sporulation 522\u003c\/p\u003e \u003cp\u003eRegulation of Sporulation Initiation 522\u003c\/p\u003e \u003cp\u003eCompartmentalized Regulation of Sporulation Genes 524\u003c\/p\u003e \u003cp\u003eThe Role of Sigma Factors in Sporulation Regulation 524\u003c\/p\u003e \u003cp\u003eIntercompartmental Regulation during Development 525\u003c\/p\u003e \u003cp\u003eOther Sporulation Systems 529\u003c\/p\u003e \u003cp\u003eBox 12.1 cAMP-Independent Carbon Catabolite Regulation in \u003ci\u003eE. coli \u003c\/i\u003e477\u003c\/p\u003e \u003cp\u003eBox 12.2 Nitrogen Fixation 483\u003c\/p\u003e \u003cp\u003eBox 12.3 Signal Transduction Systems in Bacteria 486\u003c\/p\u003e \u003cp\u003eBox 12.4 Sigma Factors 488\u003c\/p\u003e \u003cp\u003eBox 12.5 Regulatory RNAs 503\u003c\/p\u003e \u003cp\u003e\u003cb\u003e13 Genomes and Genomic Analysis 535\u003c\/b\u003e\u003c\/p\u003e \u003cp\u003eThe Bacterial Genome 535\u003c\/p\u003e \u003cp\u003eDNA Sequencing 537\u003c\/p\u003e \u003cp\u003eAdvanced Genome-Sequencing Techniques 545\u003c\/p\u003e \u003cp\u003ePolymerase Chain Reaction 547\u003c\/p\u003e \u003cp\u003eBarriers to Horizontal Transfer: Genome Gatekeepers and Molecular Biologist’s Toolkit 549\u003c\/p\u003e \u003cp\u003eRestriction Endonucleases 549\u003c\/p\u003e \u003cp\u003eTechniques for Nontraditional Cloning and Assembly 553\u003c\/p\u003e \u003cp\u003eCRISPR\/Cas Systems 559\u003c\/p\u003e \u003cp\u003eFinal Thoughts 568\u003c\/p\u003e \u003cp\u003eBox 13.1 Annotation and Comparative Genomics 538\u003c\/p\u003e \u003cp\u003eBox 13.2 Special Problems in Genetic Analysis of Operons 542\u003c\/p\u003e \u003cp\u003eBox 13.3 Synthesizing and Cloning Complete Bacterial Genomes 560\u003c\/p\u003e \u003cp\u003eGlossary 573\u003c\/p\u003e \u003cp\u003eIndex 599\u003c\/p\u003e\u003c\/font\u003e\u003c\/p\u003e\r\n\r\n\u003cp\u003e\u003cfont size=\"3\"\u003eSubject Areas: Clinical \u0026amp; internal medicine [\u003ca 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