About this book
A wide range of microbiologists, molecular biologists, and molecular evolutionary biologists will find this new volume of singular interest. It summarizes the present knowledge about the structure and stability of microbial genomes, and reviews the techniques used to analyze and fingerprint them. Maps of approximately thirty important microbes, along with articles on the construction and relevant features of the maps are included. The volume is not intended as a complete compendium of all information on microbial genomes, but rather focuses on approaches, methods and good examples of the analysis of small genomes.
Contents
Section I: Genome structure, stability, and evolution. A: Genome Structure - Structure and sizes of Archaeal and Bacterial genomes, Chromosomal organization: nucleoids, chromosomal folding, and DNA topology, Prophages and cryptic prophages, Insertion sequences and transposons, Interspersed repetitive sequences in bacterial genomes, Chi sites and their consequences, Origins of chromosome replication, Termini of replication, Restrictions modification systems: Where they are and what they do; B: Genome stability - Genome ploidy, Partitioning and segregation of the bacterial chromosome, Chromosome duplication/deletion, Transposon mediated rearrangements, Very short patch repairs, Mismatch repair and genomic stability, Conjugative transposons, Phase variation, The dynamic genome of Rhizobium, Programmed DNA rearrangements in Cyanobacteria; C: Genome evolution - The evolution of the Escherichia coli genome, E. coli: ancestries and map locations, Genomic sequences and bacterial phylogeny, Insertion sequences and their evolutionary role, rRNA operons and genome evolution, Genome evolution in the salmonellae, Structure and evolution of escherichia coli Rhs elements. Section II: Strategies for genome analysis. A: Physical mapping strategies - Physical mapping of bacteria genomes with rare cutting enzymes, One-dimensional pulsed-field gel electrophoresis, Two-dimensional pulsed-field gel electrophoresis, Use of Mu-P22 hybrids for genome mapping, Encyclopedias of bacterial genomes, Locating genes by the insertion of rare restriction sites, Ordered cosmic map from Synechococcus, Achilles heel approach to locating single sites in total genomes; B: Genomic Fingerprinting Methods - Fingerprinting bacterial genomes using restriction fragment length polymorphisms, Use of endogeneous repeated sequences to fingerprint bacterial genomic DNA, Arbitrary primed PCR, rep-PCR fingerprinting; C: Genomic sequencing projects - Organization of the European bacillus subtilis genome sequencing project, Sequence features of the genome of a unicellular cyanobacterium synechocystis sp. strain PCC6803, Haemophilus influenzae, Escherichia coli, Methanococcus jannaschii, The mycobacterial database MycDB and the mycobacterial genome sequencing project, Mycoplasma, Mycoplasma genitalium, Mycoplasma capricolum, Rhodobacter sphaeroides, Sequencing the genome of Sulfolobus solfataricus P2, Chloroplasts, Mitochondria, Magpie: A Multipurpose automated genome project investigation environment for ongoing sequencing projects, Construction and use of databases: the E. coli example, Integrated genome informatics, The bacteriophage genome project Section III: Physical maps of bacteria and their methods for construction.
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