Bacterial And Bacteriophage Genetics,9780387239194

Bacterial And Bacteriophage Genetics

by
Edition: 5th
ISBN13: 9780387239194
ISBN10: 0387239197
Format: Hardcover
Pub. Date: 2006-01-01
Publisher(s): Springer Verlag
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Summary

Genetic investigations of prokaryotic cells and their viruses have made enormous contributions to our knowledge of classical genetics, molecular biology, and biotechnology. Bacterial and Bacteriophage Genetics surveys the genetics of bacteria, including the rapidly expanding study of the Archaea, and the viruses that infect them. It provides a thorough overview of these rapidly changing subjects. The book is written for upper-class undergraduate and beginning graduate students, particularly those who have already had an introductory genetics course. A beginning course in microbiology would be helpful but is not essential.

Table of Contents

Preface vii
Fundamentals of Bacterial and Viral Genetics
1(30)
Nomenclature
2(3)
Prokaryotic Cells and Eukaryotic Cells
5(5)
Structure
5(3)
Ploidy
8(2)
DNA Structure
10(3)
Chromosome Structure
13(9)
Eukaryotes
13(2)
Prokaryotes
15(7)
Selection: An Essential Element of Microbial Genetics
22(1)
Major Genetic Transfer Processes Observed in Microorganisms and Their Viruses
23(4)
Genetic Transformation
23(1)
Transduction
24(1)
Conjugation
25(1)
Protoplast Fusion
25(1)
Electroporation
26(1)
Bacteriophage Genetic Exchange
26(1)
Summary
27(1)
Questions for Review and Discussion
27(1)
References
27(4)
General
27(1)
Specialized
28(1)
Reference Books for Specific Organisms
29(2)
Replication and Analysis of DNA
31(38)
DNA Replication
32(10)
Linking DNA in Arbitrary Ways
42(7)
Enzymology of DNA Restriction and Modification
43(4)
Use of Restriction Fragments to Make New DNA Molecules
47(2)
Analytical Techniques for DNA Molecules
49(16)
Electrophoresis
49(1)
Atomic Force Microscopy
50(1)
Detection of Specific DNA Sequences
50(4)
Polymerase Chain Reaction
54(2)
DNA Sequence Analysis
56(5)
Custom Synthesis of DNA
61(1)
Footprinting
62(2)
Gel Mobility Shift Analysis
64(1)
Yeast Two-Hybrid Systems
65(1)
Summary
65(1)
Questions for Review and Discussion
66(1)
References
67(2)
General
67(1)
Specialized
68(1)
Mutations and Mutagenesis
69(38)
Bacterial Variation
70(1)
Plate Spreading
70(1)
Replica Plating
71(1)
Fluctuation Test
72(4)
Measurement of Mutation Rate
76(5)
Expression and Selection of Mutant Cell Phenotypes
81(6)
Expression
81(4)
Selection
85(2)
Genetic Code
87(1)
Kinds of Mutation
88(9)
Base Substitutions
89(3)
Insertion and Deletion Mutations
92(1)
Frameshift Mutations
93(1)
Suppressors of Mutations
94(3)
Mutagens
97(6)
Radiation
98(1)
Chemical Modifiers
98(1)
Base Analogs
99(1)
Cross-Linking Agents
100(1)
Transposons
100(1)
Mutator Mutations
101(1)
Site-Directed Mutagenesis
101(2)
Summary
103(1)
Questions for Review and Discussion
104(1)
References
104(3)
General
104(1)
Specialized
105(2)
Transcription and Translation: Processes and Basic Regulation
107(42)
RNA Structure
108(1)
Transcription
109(4)
RNA Processing
113(3)
Translation of the Genetic Message
116(7)
Ribosome Function
116(5)
Protein Folding
121(2)
Regulation
123(1)
Examples of Regulation in Simple Functional Units
124(20)
Operon: The Basic Regulatory Unit
124(1)
Lactose Operon
125(7)
Galactose Operon
132(3)
Tryptophan Operon
135(9)
Summary
144(1)
Questions for Review and Discussion
145(1)
Suggestions for Further Reading
145(4)
General
145(1)
Specialized
146(3)
DNA Repair and Simple Recombination
149(28)
DNA Repair
150(10)
Mismatch Repair: An Example of Intrareplicational Repair
153(1)
Ultraviolet-Irradiated DNA as a Model Repair System
154(3)
The SOS Global Regulatory Network
157(3)
A Conceptual Model for Generalized Recombination
160(4)
Genetic and Functional Analysis of Recombination
164(9)
RecA and Similar Proteins
164(4)
Other Genes Affecting Recombination
168(2)
A Model for General Recombination
170(2)
Interrelation of Repair and Recombination Pathways
172(1)
Summary
173(1)
Questions for Review and Discussion
174(1)
References
175(2)
General
175(1)
Specialized
175(2)
T4 Bacteriophage as a Model Genetic System
177(44)
Morphology and Composition
178(3)
Experimental Methods Used to Study Phage Infection
181(5)
Genetic Organization of T4
186(16)
Types of Mutations Observed in the T4 Genome
186(2)
Genetic Crosses
188(8)
Visconti--Delbruck Analysis
196(3)
Phage Heterozygotes
199(3)
DNA Replication
202(2)
Molecular Biology of T4 Phage Infection
204(10)
Initial Stages of Infection
204(2)
Regulatory Issues
206(8)
Morphogenesis and Maturation
214(2)
Summary
216(1)
Questions for Review and Discussion
217(1)
References
218(3)
General
218(1)
Specialized
218(3)
Genetics of Other Intemperate Bacteriophages
221(40)
Other Members of the T Series
224(11)
Bacteriophages T2 and T6
224(3)
Bacteriophage T1
227(1)
Bacteriophage T5
228(2)
Bacteriophages T7 and T3
230(5)
Bacteriophages Containing Single-Strand DNA
235(9)
Bacteriophages Belonging to the Ff Group
235(7)
Bacteriophage φX174
242(2)
RNA-Containing Bacteriophages
244(7)
Single-Stranded RNA Viruses
244(6)
Double-Stranded RNA Viruses
250(1)
Bacteriophages Infecting Bacillus subtilis
251(4)
Bacteriophage SP01
251(2)
Bacteriophage φ29
253(2)
Bacteriophages Infecting the Archaea
255(1)
Summary
255(1)
Questions for Review and Discussion
256(1)
References
257(4)
General
257(1)
Specialized
257(4)
Genetics of Temperate Bacteriophages
261(44)
General Nature of the Temperate Response
264(1)
Bacteriophage Lambda as the Archetypal Temperate Phage
265(21)
Lytic Life Cycle
266(11)
Temperate Life Cycle
277(8)
Genetic Map of Lambda
285(1)
Other Lambdoid Phages
286(2)
Bacteriophage P22
288(2)
Bacteriophages P2 and P4
290(3)
Bacteriophage P1
293(2)
Bacteriophage Mu
295(4)
SSV1 and SSV2
299(1)
Summary
299(1)
Questions for Review and Discussion
300(1)
References
301(4)
General
301(1)
Specialized
301(4)
Transduction
305(22)
Bacteriophage Lambda: A Specialized Transducing Phage
306(4)
Production of Transducing Particles
306(3)
Physiology and Genetic Consequences of Transduction
309(1)
Lambda Phages That Transduce Additional Genetic Markers
310(1)
Specialized Transducing Phages Other than Lambda
310(4)
Bacteriophage φ80
310(2)
Bacteriophage P1
312(1)
Bacteriophage P22
312(2)
Generalized Transduction
314(5)
Bacteriophage P22
314(3)
Bacteriophage P1
317(1)
Other Phages
318(1)
Analysis of Transductional Data
319(4)
Generalized Transduction
319(3)
Specialized Transduction
322(1)
Summary
323(1)
Questions for Review and Discussion
323(1)
References
324(3)
General
324(1)
Specialized
324(3)
Genetic Transformation
327(24)
Standard Genetic Transformation Systems
328(11)
Discovery of Genetic Transformation
328(2)
Competent Cells
330(3)
DNA Uptake and Entry
333(2)
Establishment of Donor DNA in the Recipient Cell
335(4)
Other Transformation Systems
339(2)
Escherichia coli
339(1)
Electroporation
340(1)
Transfection
341(4)
E. coli as a Recipient
342(1)
B. subtilis as a Recipient
343(2)
Genetic Mapping Using Transformation
345(1)
Analysis of Transformational Data
345(1)
Genetic Map for B. subtilis
345(1)
Summary
346(3)
Questions for Review and Discussion
349(1)
References
349(2)
General
349(1)
Specialized
350(1)
Conjugation and the Escherichia coli Paradigm
351(32)
Basic Properties of the E. coli Conjugation System
352(10)
Discovery of Conjugation
352(1)
Discovery of Efficient Donor Strains and Partial Transfer
353(2)
Nature of the Transfer Process
355(3)
Recombination Following Conjugation
358(1)
Construction of the First Genetic Map
359(3)
Interactions of the F Plasmid with the Bacterial Chromosome
362(5)
Integration of the F Plasmid
362(3)
Excision of the F Plasmid
365(2)
Physiology of Conjugation
367(6)
Formation of Mating Aggregates
367(3)
Transfer DNA Synthesis
370(3)
Analysis of the F Plasmid
373(6)
General Structure
373(2)
Genetic Analysis of the F Plasmid
375(4)
Something Completely Different---Possible Diploidy
379(1)
Summary
379(1)
Questions for Review and Discussion
380(1)
References
381(2)
General
381(1)
Specialized
381(2)
Plasmids and Conjugation Systems Other than F
383(34)
Major Chromosome-Mobilizing Plasmids
384(12)
Salmonella
384(2)
Pseudomonas
386(2)
Enterococcus
388(2)
Streptomyces
390(2)
Agrobacterium
392(3)
Sulfolobus
395(1)
Bacteriocins
396(6)
General Properties
396(2)
Colicins: The Best-Studied Bacteriocins
398(2)
Conjugative Colicin Plasmids
400(1)
Nonconjugative Colicin Plasmids
401(1)
Resistance Plasmids
402(9)
General Properties
402(1)
Plasmid R100
403(3)
Genetic Analysis of Plasmid R100
406(3)
Conjugal Plasmid Interactions
409(2)
Summary
411(1)
Questions for Review and Discussion
412(1)
References
413(4)
General
413(1)
Specialized
414(3)
Plasmid Molecular Biology
417(26)
Plasmid DNA Replication
418(12)
Interactions Between Plasmid and Host
418(2)
DNA Replication Processes
420(2)
Control of Copy Number
422(4)
Partitioning
426(4)
Incompatibility
430(1)
Conjugal Functions
431(7)
Pilus Production
431(3)
Transfer DNA Replication
434(2)
Broad Host Range Plasmids
436(2)
Summary
438(1)
Questions for Review and Discussion
439(1)
References
439(4)
General
439(1)
Specialized
440(3)
Advanced Regulatory Topics
443(20)
Regulons
444(6)
Maltose
444(4)
Heat Shock Proteins
448(2)
Global Regulatory Networks
450(7)
Nitrogen Regulation
450(3)
Endospore Formation in Bacillus
453(4)
Inteins
457(1)
Small RNA Molecules
458(1)
Summary
458(1)
Questions for Review and Discussion
459(1)
References
459(4)
Generalized
459(1)
Specialized
460(3)
Site-Specific Recombination
463(16)
General Principles
464(1)
Double Site-Specific Recombination
464(6)
Phage Lambda Integration
464(2)
Circular Chromosome Segregation
466(1)
Inversion Systems
467(1)
Integrons
468(2)
Transposons: Single Site-Specific Recombination
470(6)
Transposon Tn10
470(4)
Phage Mu Transposition
474(2)
Summary
476(1)
Questions for Review and Discussion
477(1)
References
477(2)
General
477(1)
Specialized
477(2)
Applied Bacterial Genetics
479(26)
More Information About Recombinant DNA Technology
480(8)
Restriction Mapping
480(1)
Sources of DNA for Linking
481(3)
Safety Considerations
484(3)
Difficulties with the Expression of Cloned DNA
487(1)
Cloning Vectors
488(8)
Phage λ Vectors
489(1)
Phage M13 Vectors
490(1)
Expression Vectors
491(3)
Broad Host Range Vectors
494(1)
Runaway Replication Vectors
494(1)
Artificial Chromosomes
495(1)
Applications of DNA Cloning
496(2)
Peptide Display Systems
496(1)
Laboratory Reagents
497(1)
Phage as Therapeutic Agents
498(1)
Other Applications of Bacterial Genetics
498(4)
Mutagenicity Testing
498(2)
Recombineering
500(1)
Genetic Transfer in Nature
501(1)
Ecogenomics
501(1)
Summary
502(1)
Questions for Review and Discussion
502(1)
References
503(2)
General
503(1)
Specialized
503(2)
Bacterial and Bacteriophage Evolution
505(26)
What Is Evolution?
506(4)
Implications of Strain Differences
506(1)
Cryptic Genes
507(3)
Expression of Evolutionary Relationships
510(9)
Genomics and Proteomics
519(1)
Bacteria
519(1)
Bacteriophage
520(1)
Specific Examples of Evolution
520(5)
Evolution of Genomes
521(1)
Evolution of the Genetic Code
522(1)
Evolution of Proteins
522(1)
Evolution of Regulatory Sequences
523(1)
Evolution of Mitochondria and Other Endosymbionts
523(2)
Genetic Structure of the Chromosome
525(1)
Bacteria
525(1)
Bacteriophage
526(1)
Summary
526(1)
Questions for Review and Discussion
527(1)
References
528(3)
General
528(1)
Specialized
529(2)
Appendix 1 Laws of Probability and Their Application to Prokaryote Cultures 531(18)
Appendix 2 Useful World Wide Web Sites for Bacterial Genetics 549(2)
Appendix 3 Answers to Application Questions 551(2)
Glossary 553(14)
Index 567

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