Horizontal gene transfer: genomes in flux / ed. by M.B.Gogarten, J.P.Gogarten, L.Olendzenski. - New York: Humana Press, 2009. - xix, 551 p.: ill. (some col.). - (Springer protocols) (Methods in molecular biology; 532). - ISBN 978-1-60327-852-2; ISSN 1064-3745  Место хранения:   03 | Центральная библиотека Иркутского научного центра СО РАН | Иркутск

Оглавление / Contents

Preface ....................................................... vii Acknowledgments ................................................ IX Contributors ................................................... XV Color Plates .................................................. XIX Part I. Introduction 1 Gene Transfer: Who Benefits? Lorraine Olendzenski and Johann Peter Gogarten ............... 3 Part II. Definitions, Philosophy, and Implications of HGT 2 Defining the Mobilome Janet L. Siefert ............................................ 13 3 The Interplay of Homologous Recombination and Horizontal Gene Transfer in Bacterial Speciation Jeffrey G. Lawrence and Adam C. Retchless ................... 29 4 Epistemological Impacts of Horizontal Gene Transfer on Classification in Microbiology Eric Bapteste and Yan Boucher ............................... 55 5 Persistence Mechanisms of Conjugative Plasmids Martin Iain Bahl, Lars Hestbjerg Hansen, and Søren J. Sørensen .................................................... 73 6 The Integron/Gene Cassette System: An Active Player in Bacterial Adaptation Maurizio Labbate, Rebecca Josephine Case, and Hatch W. Stokes .................................................. 103 7 Ancient Gene Transfer as a Tool in Phylogenetic Reconstruction Jinling Huang and Johann Peter Gogarten .................... 127 8 The Tree of Life Viewed Through the Contents of Genomes Christopher H. House ....................................... 141 9 Horizontal Gene Transfer and the Evolution of Methanogenic Pathways Greg Fournier .............................................. 163 10 Genome Acquisition in Horizontal Gene Transfer: Symbiogenesis and Macromolecular Sequence Analysis Lynn Margulis .............................................. 181 Part III. Methods 11 Detection and Quantitative Assessment of Horizontal Gene Transfer Olga Zhaxybayeva ........................................... 195 12 Composition-Based Methods to Identify Horizontal Gene Transfer Diego Cortez, Luis Delaye, Antonio Lazcano, and Arturo Becerra .................................................... 215 13 Testing Phylogenetic Methods to Identify Horizontal Gene Transfer Maria Poptsova ............................................. 227 14 Untangling Hybrid Phylogenetic Signals: Horizontal Gene Transfer and Artifacts of Phylogenetic Reconstruction Robert G. Beiko and Mark A. Ragan .......................... 241 15 Construction and Use of Flow Cytometry Optimized Plasmid- Sensor Strains Martin Iain Bahl, Gunnar Oregaard, Søren J. Sørensen, and Lars Hestbjerg Hansen ...................................... 257 16 Experimental Evolution of an Essential Bacillus Gene in an E. coli Host Maia Larios-Sanz and Michael Travisano ..................... 269 17 Mass Action Models Describing Extant Horizontal Transfer of Plasmids: Inferences and Parameter Sensitivities Barth F. Smets and Laurent Lardon .......................... 289 Part IV. Case Studies 18 Interdomain Transfers of Sugar Transporters Overcome Barriers to Gene Expression Kenneth M. Noll and Kamolwan Thirangoon .................... 309 19 The Role of Horizontal Gene Transfer in Photosynthesis, Oxygen Production, and Oxygen Tolerance Jason Raymond .............................................. 323 20 Horizontal Gene Transfer in Cyanobacterial Signature Genes Shailaja Yerrapragada, Janet L. Siefert, and George E. Fox ..................................................... 339 21 Population Genomics and the Bacterial Species Concept Margaret A. Riley and Michelle Lizotte-Waniewski ........... 367 22 A Critique of Prokaryotic Species Concepts R. Thane Papke ............................................. 379 23 What Antimicrobial Resistance Has Taught Us About Horizontal Gene Transfer Miriam Barlow .............................................. 397 24 Potential for Horizontal Gene Transfer in Microbial Communities of the Terrestrial Subsurface Jonna M. Coombs ............................................ 413 25 Horizontal Gene Transfer and Mobile Genetic Elements in Marine Systems Patricia A. Sobecky and Tracy H. Hazen ..................... 435 26 Horizontal Gene Transfer in Metal and Radionuclide Contaminated Soils Patricia A. Sobecky and Jonna M. Coombs .................... 455 27 Horizontal Gene Transfer Between Microbial Eukaryotes Jan O. Andersson ........................................... 473 28 Horizontal Gene Transfer in Eukaryotic Parasites: A Case Study of Entamoeba histolytica and Trichomonas vaginalis U. Cecilia Alsmark, Thomas Sicheritz-Ponten, Peter G. Foster, Robert P. Hirt, and T. Martin Embley ............... 489 29 Role of Horizontal Gene Transfer in the Evolution of Photosynthetic Eukaryotes and Their Plastids Patrick J. Keeling ......................................... 501 30 Role of Horizontal Gene Transfer in the Evolution of Plant Parasitism Among Nematodes Makedonka Mitreva, Geert Smant, and Johannes Helder ........ 517 Index ......................................................... 537