Metagenomics: Methods and Protocols

ISBN-13: 9781607618225 / Angielski / Twarda / 2010 / 341 str.

Wolfgang R. Streit; Rolf Daniel

Opis

Metagenomics has proven to be a powerful tool for exploring the ecology, metabolic profiling, and comparison of complex microbial communities as well as its important applications in the mining of metagenomes for genes encoding novel biocatalysts and drug molecules for bioindustries. In Metagenomics: Methods and Protocols, expert researches provide an overview and introduction to basic methods commonly used in laboratories that have a strong background in microbial metagenomics. The book attempts to address all of the working steps involved in this crucial field, beginning with DNA isolation from soils and marine samples and continuing with the construction and screening of libraries, along with key advise involving bioinformatic tools available to analyze large metagenomic sequence data sets. Written in the highly successful Methods in Molecular Biology series format, chapters include brief introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Metagenomics: Methods and Protocols serves as a very complete guide to available screening protocols for all major biocatalysts in order to allow for the easy setup of these screens in any microbiology lab.

Spis treści

1. Molecular Methods to Study Complex Microbial Communities María-Eugenia Guazzaroni, Ana Beloqui, José M. Vieites, Peter N. Golyshin, and Manuel Ferrer 2. Construction of Small-Insert and Large-Insert Metagenomic Libraries Carola Simon and Rolf Daniel 3. Construction and Screening of Marine Metagenomic Libraries Nancy Weiland, Carolin Löscher, Rebekka Metzger, and Ruth Schmitz 4. Metagenomic Analysis of Isotopically Enriched DNA Yin Chen, Josh D. Neufeld, Marc G. Dumont, Michael W. Friedrich, and J. Colin Murrell 5. Wide Host-Range Cloning for Functional Metagenomics Margaret Wexler and Andrew W.B. Johnston 6. Cloning and Expression Vectors for a Gram-Positive Host, Streptomyces lividans Kristof Vrancken and Jozef Anné 7. Heterologous Gene Expression in the Hyperthermophilic Archaeon Sulfolobus solfataricus Angel Angelov and Wolfgang Liebl 8. Novel Tools for the Functional Expression of Metagenomic DNA Sonja Christina Troeschel, Thomas Drepper, Christian Leggewie, Wolfgang R. Streit, and Karl-Erich Jaeger 9. Screening of Functional Promoter from Metagenomic DNA for Practical Use in Expression Systems So-Youn Park and Geun-Joong Kim 10. Substrate-Induced Gene Expression (SIGEX) Screening: A Method for High-Throughput Screening of Metagenome Libraries Taku Uchiyama and Kentaro Miyazaki 11. Screens for Active and Stereoselective Hydrolytic Enzymes Dominique Böttcher, Marlen Schmidt, and Uwe T. Bornscheuer 12. Screening for Cellulase Encoding Clones in Metagenomic Libraries Nele Ilmberger and Wolfgang R. Streit 13. Screening Metagenomic Libraries for Laccase Activities Manuel Ferrer, Ana Beloqui, and Peter N. Golyshin 14. Screening for N-AHSL-Based-Signaling Interfering Enzymes Phil M. Oger and Stéphane Uroz 15. Identification of Molecular Markers to Follow Up the Bioremediation of Sites Contaminated with Chlorinated Compounds Massimo Marzorati, Annalisa Balloi, Francesca De Ferra, and Daniele Daffonchio 16. Methods for the Isolationof Genes Encoding Novel PHB Cycle Enzymes from Complex Microbial Communities Ricardo Nordeste, Maria A. Trainer, and Trevor C. Charles 17. Metagenomic Approaches to Identify and Isolate Bioactive Natural Products from Microbiota of Marine Sponges Cristian Gurgui and Jörn Piel 18. Screening for Novel Antibiotic Resistance Genes Mindy G. Brown, Elizabeth H. Mitchell, and David L. Balkwill 19. Novel Metal Resistance Genes from Microorganisms: A Functional Metagenomic Approach José E. González-Pastor and Salvador Mirete 20. Retrieval of Full Length Functional Genes Using Subtractive Hybridization Magnetic Bead Capture Tracy Meiring, Inonge Mulako, Marla I. Tuffin, Quinton Meyer, and Donald A. Cowan 21. Detection and Isolation of Selected Genes of Interest from Metagenomic Libraries by a DNA Microarray Approach Gopal P. Pathak and Wolfgang Gärtner 22. Application of DNA Microarray for Screening Metagenome Library Clones Soo-Je Park, Jong-Chan Chae, and Sung-Keun Rhee 23. MetaGenomeThreader: A Software Tool for Predicting Genes in DNA-Sequences of Metagenome Projects David J. Schmitz-Hübsch and Stefan Kurtz