Molecular Genetics of Bacteria 5th Edition (PDF)

Author:	Jeremy W. Dale, Simon F. Park
Release at:	2010
Pages:	403
Edition:	5th Edition
File Size:	8 MB
File Type:	Pdf
Language:	English

Description of Molecular Genetics of Bacteria 5th Edition (PDF)

Molecular Genetics of Bacteria 5th edition by Jeremy W. Dale, Simon F. Park is a great bacterial Genetics book available in (PDF) download. In the preface to the fourth edition (published in 2004) we referred to the revolution in bacterial genetics that was started by gene cloning and sequencing, coupled with related techniques such as the polymerase chain reaction (PCR) and microarrays, and culminated in the knowledge of genome sequences of a rapidly expanding range of bacteria. This posed a dilemma. How could we accommodate these new techniques, and the wealth of exciting new information they provided, while not losing sight of classical bacterial genetics? This dilemma has become even more acute.

True, many of the older methods are now no longer used and could be relegated to the pages of history. But there is a danger of throwing out the baby with the bathwater. Not only is there a need to maintain some sense of how the subject has got to the stage we are now at, but also a discussion of some of these methods is useful in establishing an understanding of how bacterial genetics operates in natural environments. Genetics is not just about how we find out about bacteria: it is about how bacteria have evolved, and continue to evolve and continue to adapt to changing environments. Molecular genetics, in isolation, is essentially reductionist. Even genome sequencing, and global analysis of gene expression, by themselves merely provide catalogs of genes. Ultimately, those lists have to be related to the behavior of the whole organism, and from there to how organisms interact with one another and with their environment.

Content of Molecular Genetics of Bacteria 5th Edition (PDF)

Chapter 1: Nucleic Acid Structure and Function

Structure of nucleic acids

DNA

RNA

Hydrophobic interactions

Different forms of the double helix

Supercoiling

Denaturation and hybridization

Orientation of nucleic acid strands

Replication of DNA

Unwinding and rewinding

Fidelity of replication; proofreading

Chromosome replication and cell division

DNA repair

Mismatch repair

Excision repair

Recombination (post-replication) repair

SOS repair

Gene expression

Transcription

Translation

Post-translational events

Gene organization

Chapter 2: Mutation and Variation

Variation and evolution

Fluctuation test

Replica plating

Directed mutation in bacteria?

Types of mutation

Point mutations

Conditional mutants

Variation due to larger-scale DNA alterations

Extrachromosomal agents and horizontal gene transfer

Recombination

A model of the general (homologous) recombination process

Enzymes involved in recombination

Phenotypes

Restoration of phenotype

chanisms of mutation

Spontaneous mutation

Chemical mutagens

Ultraviolet irradiation

Isolation and identification of mutants

Mutation and selection

Replica plating

Isolation of other mutants

Molecular methods

Chapter 3: Regulation of Gene Expression

Gene copy number

Transcriptional control

Promoters

Terminators, attenuators and anti-terminators

Induction and repression: regulatory proteins

Two-component regulatory systems

Global regulatory systems

Quorum sensing

Translational control

Ribosome binding

Codon usage

Stringent response

Regulatory RNA

Phase variation of

Chapter 4: Genetics of Bacteriophages

Bacteriophage structure

Single-strand DNA bacteriophages

φX174

M13

RNA-containing phages: MS2

Double-stranded DNA phages

Bacteriophage T4

Bacteriophage λ

Lytic and lysogenic regulation of bacteriophage λ

Restriction and modification

Bacterial resistance to phage attack

Complementation and recombination

Why are bacteriophages important?

Phage typing

Phage therapy

Phage display

Phages in the natural environment

Bacterial virulence and phage conversion

Chapter 5: Plasmids

Some bacterial characteristics are determined by plasmids

Antibiotic resistance

Colicins and bacteriocins

Virulence determinants

Plasmids in plant-associated bacteria

Metabolic activities

Molecular properties of plasmids

Plasmid replication and control

Partitioning

Host range

Plasmid incompatibility

Plasmid stability

Plasmid integrity

Partitioning

Differential growth rate of

Associating a plasmid with a phenotype

Chapter 6: Gene Transfer

Transformation

Conjugation

Mechanism of conjugation

The F plasmid

Conjugation in other bacteria

Transduction

Specialized transduction

Recombination

Consequences of recombination

Site-specific and non-homologous (illegitimate) recombination

Mosaic genes and chromosome plasticity

Chapter 7: Genomic Plasticity: Movable Genes and Phase Variation

Insertion sequences

Structure of insertion sequences

Occurrence of insertion sequences

Transposons

Structure of transposons

Integrons

ISCR elements

Mechanisms of transposition

Replicative transposition

Non-replicative (conservative) transposition

Regulation of transposition

Activation of genes by transposable elements

Mu: A transposable bacteriophage

Conjugative transposons

Phase variation of

Variation mediated by simple DNA inversion

Variation mediated by nested DNA inversion

Antigenic variation in the gonococcus

Phase variation by slipped-strand mispairing

Phase variation mediated by differential DNA methylation

Clustered regularly interspersed short palindromic repeats

Chapter 8: Genetic Modification: Exploiting the Potential of Bacteria

Strain development

Generation of variation

Selection of desired variants

Overproduction of primary metabolites

Simple pathways

Branched pathways

Overproduction of secondary metabolites

Gene cloning

Cutting and joining DNA

Plasmid vectors

Bacteriophage λ vectors

Cloning larger fragments

Bacteriophage M13 vectors

Gene libraries

Construction of genomic libraries

Screening a gene library

Cloning PCR products

Construction of a cDNA library

Products from cloned genes

Expression vectors

Making new genes

Other bacterial hosts

Novel vaccines

Other uses of gene technology

Chapter 9: Genetic Methods for Investigating Bacteria

Metabolic pathways

Complementation

Cross-feeding

Microbial physiology

Reporter genes

Chromatin immunoprecipitation

Cell division

Motility and chemotaxis

Cell differentiation

Bacterial virulence

Wide-range mechanisms of bacterial pathogenesis

Detection of virulence genes

Specific mutagenesis

Gene replacement

Antisense RNA

Taxonomy, evolution and epidemiology

Molecular taxonomy

GC content

16 S rRNA

Denaturing-gradient gel electrophoresis and temperature-gradient gel electrophoresis

Diagnostic use of PCR

Molecular epidemiology

Chapter 10: Gene Mapping to Genomics and Beyond

Gene mapping

Conjugational analysis

Gene libraries

Restriction mapping and pulsed-field gel electrophoresis

DNA sequence determination

Sanger sequencing

Dye terminator sequencing

Pyrosequencing

Massively parallel sequencing

Genome sequencing

Genome-sequencing strategies

Relating sequence to function

Metagenomics

Comparative genomics

Microarrays

Analysis of gene expression

Transcriptional analysis

Translational analysis

Metabolomics

Systems biology and synthetic genomics

Systems biology

Synthetic genomics

Conclusion

Appendix A Further Reading

Appendix B Abbreviations Used

Appendix C Glossary

Appendix D Enzymes and other Proteins

Appendix E Genes

Appendix F Standard Genetic Code

Appendix G Bacterial Species

Index

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