de Bruijn / Lupski / Weinstock Bacterial Genomes

Physical Structure and Analysis
Erscheinungsjahr 2012
ISBN: 978-1-4615-6369-3
Verlag: Springer US
Format: PDF
Kopierschutz: 1 - PDF Watermark

E-Book, Englisch, 793 Seiten, eBook

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.

Zielgruppe

Research

Autoren/Hrsg.

de Bruijn, F.J.

Lupski, James R.

Weinstock, G.M.

Inhaltsverzeichnis

1. Genome Structure, Stability, and Evolution.- 1. Structure and Sizes of the Genomes of the Archaea and Bacteria.- 2. Chromosomal Organization: Nucleoids, Chromosomal Folding, and DNA Topology.- 3. Prophages and Cryptic Prophages.- 4. Insertion Sequences and Transposons.- 5. Interspersed Repetitive Sequences in Bacterial Genomes.- 6. Chi Sites and Their Consequences.- 7. Origins of Chromosome Replication.- 8. Restriction Modification Systems: Where They Are and What They Do.- 9. Genome Ploidy.- 10. Segregation of the Bacterial Chromosome.- 11. Chromosomal Rearrangements.- 12. Mechanism of Avoidance of 5-methylcytosine to Thymine Mutations in Bacteria.- 13. Conjugative Transposons.- 14. Phase Variation.- 15. The Dynamic Genome of Rhizobium.- 16. Programmed DNA Rearrangements in Cyanobacteria.- 17. Evolution of the E. coli Genome.- 18. E. coli Genes: Ancestries and Map Locations.- 19. Prokaryotic Genome-Wide Comparisons and Evolutionary Implications.- 20. Insertion Sequences and their Evolutionary Role.- 21. Multiplicity of Ribosomal RNA Operons in Prokaryotic Genomes.- 22. Genome Evolution in the Salmonellae.- 23. Structure and Evolution of Escherichia coli Rhs Elements.- 2. Strategies for Genome Analysis.- 24. Physical Mapping and Fingerprinting of Bacterial Genomes using Rare Cutting Restriction Enzymes.- 25. One-dimensional Pulsed-field Gel Electrophoresis.- 26. Two-dimensional Pulsed-field Gel Electrophoresis.- 27. Use of Bacteriophage Mu-P22 Hybrids for Genome Mapping.- 28. Encyclopedias of Bacterial Genomes.- 29. Localizing Genes by the Introduction of Rare Restriction Sites.- 30. Towards a Cosmid-derived Physical Map of Synechococcus PCC Genome.- 31. Fingerprinting Bacterial Genomes Using Restriction Fragment Length Polymorphisms.- 32. Use of Endogenous RepeatedSequences to Fingerprint Bacterial Genomic DNA.- 33. Applications of DNA and RNA Fingerprinting by the Arbitrarily Primed Polymerase Chain Reaction.- 34. Repetitive Sequence-based PCR (rep-PCR) DNA Fingerprinting of Bacterial Genomes.- 35. Organization of the European Bacillus subtilis Genome Sequencing Project.- 36. Sequence Features of the Genome of a Unicellular Cyanobacterium Synechocystis sp. strain PCC6803.- 37. A Minimal Gene Complement for Cellular Life and Reconstruction of Primitive Life Forms by Analysis of Complete Bacterial Genomes.- 38. Resources for the Escherichia coli Genome Project.- 39. The Mycobacterial Database MycDB and the Mycobacterial Genome Sequencing Project.- 40. Mycoplasma genitalium.- 41. Other Mycoplasma sp..- 42. Mycoplasma capricolum Genome Project.- 43. Sequence Skimming of Chromosome II of Rhodobacter sphaeroides 2.4.1T.- 44. Sequencing the Genome of Sulfolobus solfataricus P2.- 45. MAGPIE: A Multipurpose Automated Genome Project Investigation Environment for Ongoing Sequencing Projects.- 46. Integrated Genome Informatics.- 3. Physical Maps of Bacteria and Their Methods for Construction.- 47. Anabaena sp. Strain PCC 7120.- 48. Aquifex pyrophilus.- 49. Bacillus cereus/Bacillus thuringiensis.- 50. Bacillus subtilis 168.- 51. Bordetella pertussis Strain Tohama I.- 52. Borrelia burgdorferi and the Other Lyme Disease Spirochetes.- 53. Bradyrhizobium japonicum Strain 3I1b110.- 54. Brucella melitensis 16M (ATCC 23456).- 55. Campylobacter jejuni TGH9011 (ATCC 43431).- 56. Caulobacter crescentus CB15.- 57. Clostridium beijerinckii NCIMB.- 58. Clostridium perfringens CPN50.- 59. Enterococcus faecalis.- 60. Escherichia coli.- 61. Haemophilus influenzae Rd.- 62. Haloferax volcanii DS2 and Halobacterium salinarium GRB.- 63. Helicobacter pylori CH19.- 64. Lactococcus lactis subsp.lactis ILI403 and Lactococcus lactis subsp. cremoris MG1363.- 65. Leptospira interrogans.- 66. Listeria monocyto genes.- 67. Methanobacterium thermoautotrophicum Marburg.- 68. Mycobacterium leprae.- 69. Mycoplasma genitalium G-37 (ATCC 33530).- 70. Myxococcus xanthus DK1622.- 71. Neisseria gonorrhoeae MS11-N198 (ATCC 49759).- 72. Planctomyces limnophilus DSM 3776T.- 73. Burkholderia (Pseudomonas) cepacia Strain ATCC and 25416; Pseudomonas aeruginosa Strain C and PAO (DSM 1707).- 74. Rhizobium meliloti.- 75. Rhodobacter capsulatus SB1003.- 76. Rhodobacter sphaeroides 2.4.1T.- 77. Salmonella typhi.- 78. Salmonella typhimurium.- 79. Serpulina hyodysenteriae B78T.- 80. Staphylococcus aureus.- 81. Streptococcus pneumoniae R6.- 82. Sulfolobus tokodaii 7.- 83. Synechococcus PCC.- 84. Thermus thermophilus HB8.- 85. Treponema pallidum subsp. pallidum (Nichols).