Handbook of Molecular Microbial Ecology, Edition: 1st, Two Volumes Set, June 2011, Frans J. de Bruijn, ISBN: 9780470924181, Hardcover, Language: English, Hardcover, Wiley-Blackwell

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Handbook of Molecular Microbial Ecology, Edition: 1st, Two Volumes Set, June 2011, Frans J. de Bruijn, ISBN: 9780470924181, Hardcover, Language: English, Hardcover, Wiley-Blackwell

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Product Details

 
Hardcover: 1424 pages

Publisher: Wiley-Blackwell; 1 edition (June 7, 2011)

Language: English

ISBN-10: 0470924187

ISBN-13: 978-0470924181

Product Dimensions: 11.2 x 8.9 x 2.8 inches

Shipping Weight: 9.6 pound

 

Description


Metagenomics has revolutionized microbiology and many associated health and environmental fields. This is the first comprehensive treatise covering the various -omics in a large variety of habitats, which could not previously have been analysed without metagenomic methodology. This is a reference work both for people in the field and those who would like to enter it.Two volume set covers topics including:


Volume One


Species designations in microbiology

Metagenomics

Consortia and databases

Bioinformatics

Microarrays

Other -omics applications


Volume Two


Viral genomes

Metagenomics studies in a variety of habitats, including marine, soil, and the digestive tract

Biodegradation

Biocatalysts and natural products

 

See More

 

Handbook of Molecular Microbial Ecology I: Metagenomics and Complementary Approaches

 
Frans J. de BruijnISBN: 978-0-470-64479-9800 pagesJuly 2011, Wiley-Blackwell

Description


The premiere two-volume reference on revelations from studying complex microbial communities in many distinct habitats

 

Metagenomics is an emerging field that has changed the way microbiologists study microorganisms. It involves the genomic analysis of microorganisms by extraction and cloning of DNA from a group of microorganisms, or the direct use of the purified DNA or RNA for sequencing, which allows scientists to bypass the usual protocol of isolating and culturing individual microbial species. This method is now used in laboratories across the globe to study microorganism diversity and for isolating novel medical and industrial compounds.

 

Handbook of Molecular Microbial Ecology is the first comprehensive two-volume reference to cover unculturable microorganisms in a large variety of habitats, which could not previously have been analyzed without metagenomic methodology. It features review articles as well as a large number of case studies, based largely on original publications and written by international experts. This first volume, Metagenomics and Complementary

 

Approaches, covers such topics as:

 

- Background information on DNA reassociation and use of 16 rRNA and other DNA fingerprinting approaches
- Species designation in microbiology
- Metagenomics: Introduction to the basic tools with examples
- Consortia and databases
- Bioinformatics
- Computer-assisted analysis
- Complementary approaches—microarrays, metatranscriptomics, metaproteomics, metabolomics, and single cell analysis

 

A special feature of this volume is the highlighting of the databases and computer programs used in each study; they are listed along with their sites in order to facilitate the computer-assisted analysis of the vast amount of data generated by metagenomic studies.

 

Handbook of Molecular Microbial Ecology I is an invaluable reference for researchers in metagenomics, microbiology, and environmental microbiology; those working on the Human Microbiome Project; microbial geneticists; molecular microbial ecologists; and professionals in molecular microbiology and bioinformatics.

 

Table of Contents

 

Preface.

Contributors.

1. Introduction (Frans J. de Bruijn).
Background Chapters.
2. DNA reassociation yields broad-scale information on metagenome complexity and microbial diversity (V. Torsvik).
3. Diversity of 23S rRNA genes within individual prokaryotic genomes (Zhiheng Pei).
4. Use of the rRNA operon and genomic repetitive sequences for the identification of bacteria (A. Nascimento).
5. Use of different PCR primer-based strategies for characterization of natural microbial communities (James Prosser).
6. Horizontal gene transfer and recombination shape mesorhizobial populations in the gene center of the host plants Astragalus luteolus and Astragalus ernestii in Sichuan, China (Xiaoping Zhang).
7. Amplified rDNA restriction analysis (ARDRA)for identification and phylogenetic placement of 16S-rDNA clones (Menachim Sklarz).
8. Clustering-based peak alignment algorithm for objective and quantitative analysis of DNA fingerprinting data (Satoshi Ishii).
The Species Concept.
9. Population genomics informs our understanding of the bacterial species concept (Margaret Riley).
10. Genome analysis of Streptococcus agalactiae: Implication for the microbial “pan-genome” (R. Rappuoli).
11. Metagenomic insights into bacterial species (Kostas Konstantinidis).
12. Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology (E. Stackebrandt).
13. Metagenomic Approaches for the Identification of Microbial Species (David Ward).
Metagenomics.
14. Microbial Ecology in the age of metagenomics (Jianping Xu).
15. The enduring legacy of small rRNA in microbiology (Susan Tringe).
16. Pitfalls of PCR-based rRNA gene sequence analysis:  an update on some parameters (Stackebrandt).
17. Empirical testing of 16S rRNA gene PCR primer pairs reveals variance in target specificity and efficacy not suggested by in silico analysis (Sergio Morales and Bill Holben).
18. The impact of next-generation sequencing technologies on (meta)genomics (George Weinstock).
19. Accuracy and quality of massively parallel DNA pyrosequencing (Susan Huse and David Mark Welch).
20. Environmental shotgun sequencing: Its potential and challenges for studying the hidden world of microbes (Jonathan Eisen).
21. Comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library (C. Manischan).
22. Metagenomic libraries for functional screeing (Svein Valla).
23. GC Fractionation Allows Comparative Total Microbial Community  Analysis, Enhances Diversity Assessment, and Facilitates of Minority Populations of Bacteria (Bill Holben).
24. Enriching plant microbiota for a metagenomic library construction (Ying Zeng).
25. Towards Automated Phylogenomic Inference (Wu and Eisen).
26. Integron first gene cassettes: a target to find adaptive genes in metagenomes (Christine Cagnon).
27. High-resolution metagenomics: assessing specific functional types in complex microbial communities (Christoserdova).
28. Gene-targeted –metagenomics (GT-metagenomics) to explore the extensive diversity of genes of interest in microbial communities (J. Tiedje).
29. Phylogenetic screening of metagenomic libraries using homing endonuclease restriction and marker insertion (Torsten Thomas).
30. ArrayOme- & tRNAcc-facilitated mobilome discovery: comparative genomics approaches for identifying rich veins of novel bacterial DNA sequences (Hong-Yu OU).
31. Sequence-Based Characterization of Microbiomes by Serial Analysis of Ribosomal Sequence Tags (SARST) (Zhongtang Yu).
Consortia and Databases.
32. The metagenomics of plant pathogen-suppressive soils (J.D. Van Elsas).
33. Soil Metagenomic Exploration of the Rare Biosphere (Pascal Simonet and Timothy Vogel).
34. The BIOSPAS consortium: Soil Biology and agricultural production (Luis Wall).
35. The Human Microbiome Project (George Weinstock).
36. The Ribosomal Database Project: sequences and Software for high-throughput rRNA analysis (J. R. Cole, G. M. Garrity and Jim Tiedje).
37. The metagenomics RAST server- a public resource for the automatic phylogenetic and functional analysis of metagenomes (Folker Meyer).
38. The EBI Metagenomics Archive, Integration and Analysis resource (Apweiler).
Computer Assisted Analysis.
39. Comparative metagenome analysis using MEGAN (Suparna Mitra and Daniel Huson).
40. Phylogenetic binning of metagenome sequence samples (Alice C. McHardy).
41. Gene prediction in metagenomic fragments with Orphelia: A large scale machine learning approach (Katharina Hoff).
42. Binning metagenomic sequences using seeded GSOm (Sen-Lin Tang).
43. Iterative read mapping and assembly allows the use of a more distant reference in metagenomic assembly (Bas E. Dutilh).
44. Ribosomal RNA identification in metagenomic and metatranscriptomic datasets (Li).
45. SILVA: comprehensive databases for quality checked and aligned ribosomal RNA sequence data compatible with ARB (Frank Gloeckner).
46. ARB; a software environment for sequence data (Wolfgang Ludwig).
47. The Phyloware Project: A software framework for phylogenomic virtue (Daniel Frank).
48. Metasim- A sequencing simulator for genomics and metagenomics (Daniel Richter).
49. ClustScan: an integrated program package for the detection and semi-automatic annotation of secondary metabolite clusters in genomic and metagenomic DNA datasets (Daslav Hranueli).
50. MetaGene; Prediction of prokaryotic and phage genes in metagenomic sequences (Noguchi).
51. primers4clades, a web server to design lineage-specific PCR primers for gene-targeted metagenomics (Pablo Vinuesa).
52. A parsimony approach to biological pathway reconstruction/inference for genomes and metagenomes (Y. Ye).
53. ESPRIT: estimating species richness using large collections of 16S rRNA data (Yijun Sun).
Complementary Approaches.
54. (Meta) genomics approaches in systems biology (Manuel Ferrer).
55. Towards “focused metagenomics”: a case study combining DNA stable-isotope probing, multiple displacement amplification and metagenomics (J. Colin Murrell).
56. Galbraith, E. A., D. A. Antonopoulos, K. E. Nelson, and B. A. White . Suppressive subtractive hybridization reveals extensive horizontal transfer in the rumen metagenome (Bryan White).
Microarrays.
57. GeoChip: A high throughout metagenomics technology for dissecting microbial community functional structure (J. Zhou).
58. Phylogenetic microarrays (PhyloChips) for analysis of complex microbial communities (Eoin Brodie).
59. Phenomics and Phenotype MicroArrays: Applications Complementing Metagenomics (Barry Bochner).
60. Microbial persistence in low biomass, extreme environments: The great unknown (Kasthuri Venkateswaran).
61. Application of phylogenetic oligonucleotide microarrays in microbial analysis (Nian Wang).
Metatranscriptomics.
62. Isolation of mRNA from environmental microbial communities for metatranscriptomic analyses (P. Schenk).
63. Comparative day/night metatrancriptomic analysis of microbial communities in the North Pacific subtropical gyre (Rachel Poretski).
64. The “double RNA” approach to simultaneously assess the structure and function of environmental microbial communities by meta-transcriptomics (Tim Urich and Christa Schleper).
65. Soil eukaryotic diversity, a metatranscriptomic approach (Marmeisse).
Metaproteomics.
66. Proteomics for the analysis of environmental stress responses in prokaryotes (Mark Suter).
67. Microbial community proteomics (Paul Wilmes).
68. Synchronicity between population structure and proteome profiles: A metaproteomic  analysis of Chesapeake Bay bacterial communities (Feng Chen).
69. High-Throughput Cyanobacterial Proteomics: Systems-level Proteome Identification and Quantitation   (Phillip Wright).
70. Protein Expression Profile of an Environmentally Important Bacterial Strain: the Chromate Response of Arthrobacter sp. strain FB24 (K. Henne).
Metabolomics.
71. The small molecule dimension: Mass spectrometry based metabolomics, enzyme assays, and imaging (Trent R. Northen).
72. Metabolomics: high resolution tools offer to follow bacterial growth on a molecular level (Lucio Marianna and Philipp Schmitt-Kopplin).
73. Metabolic profiling of plant tissues by electrospray mass spectrometry (Heather Walker).
74. Metabolite identification, pathways and omic integration using online databases and tools (Matthew Davey).
Single cell analysis.
75. Application of cytomics to separate natural microbial communities by their physiological properties (Susann Müller).
76. Capturing microbial populations for environmental genomics (A. Pernthaler/Wendeberg).
77. Microscopic single-cell isolation and multiple displacement amplification of genomes from uncultured prokaryotes (Peter Westermann).

 

Handbook of Molecular Microbial Ecology II: Metagenomics in Different Habitats

Frans J. de BruijnISBN: 978-0-470-64719-6640 pagesSeptember 2011, Wiley-Blackwell

Description


The premiere two-volume reference on revelations from studying complex microbial communities in many distinct habitats

 

Metagenomics is an emerging field that has changed the way microbiologists study microorganisms. It involves the genomic analysis of microorganisms by extraction and cloning of DNA from a group of microorganisms, or the direct use of the purified DNA or RNA for sequencing, which allows scientists to bypass the usual protocol of isolating and culturing individual microbial species. This method is now used in laboratories across the globe to study microorganism diversity and for isolating novel medical and industrial compounds.

 

Handbook of Molecular Microbial Ecology is the first comprehensive two-volume reference to cover unculturable microorganisms in a large variety of habitats, which could not previously have been analyzed without metagenomic methodology. It features review articles as well as a large number of case studies, based largely on original publications and written by international experts. This second volume, Metagenomics in Different Habitats, covers such topics as:

 

- Viral genomes
- Metagenomics studies in a variety of habitats, including marine environments and lakes, soil, and human and animal digestive tracts
- Other habitats, including those involving microbiome diversity in human saliva and functional intestinal metagenomics; diversity of archaea in terrestrial hot springs; and microbial communities living at the surface of building stones
- Biodegradation
- Biocatalysts and natural products

 

A special feature of this book is the highlighting of the databases and computer programs used in each study; they are listed along with their sites in order to facilitate the computer-assisted analysis of the vast amount of data generated by metagenomic studies. Such studies in a variety of habitats are described here, which present a large number of different system-dependent approaches in greatly differing habitats.

 

Handbook of Molecular Microbial Ecology II is an invaluable reference for researchers in metagenomics, microbial ecology, microbiology, and environmental microbiology; those working on the Human Microbiome Project; microbial geneticists; and professionals in molecular microbiology and bioinformatics.

 

Table of Contents

 

Preface xiii

Contributors xv
1. Introduction 1
Frans J. de Bruijn

 

Part 1 Viral Genomes


2. Viral Metagenomics 5

Shannon J. Williamson
3. Methods in Viral Metagenomics 15

Rebecca Vega Thurber
4. Metagenomic Contrasts of Viruses in Soil and Aquatic Environments 25

K. Eric Wommack, Sharath Srinivasiah, Mark R. Liles, Jaysheel Bhavsar, Shellie Bench, Kurt E. Williamson, and Shawn W. Polson
5. Biodiversity and Biogeography of Phages in Modern Stromatolites and Thrombolites 37

Christelle Desnues, Beltran Rodriguez-Brito, Steve Rayhawk, Scott Kelley, Tuong Tran, Matthew Haynes, Hong Liu, Mike Furlan, Linda Wegley, Betty Chau, Yijun Ruan, Dana Hall, Florent E. Angly, Robert A. Edwards, Linlin Li, Rebecca Vega Thurber, R. Pamela Reid, Janet Siefert, Valeria Souza, David L. Valentine, Brandon K. Swan, Mya Breitbart, and Forest Rohwer
6. Assembly of Viral Metagenomes from Yellowstone Hot Springs Reveals Phylogenetic Relationships and Host Co-Evolution 45

Thomas W. Schoenfeld and David Mead
7. Next-Generation Sequencing and Metagenomic Analysis: A Universal Diagnostic Tool in Plant Pathology 63

Ian P. Adams, Rachel H. Glover, Wendy A. Monger, Richard Thwaites, Rick Mumford, Elena Jackeviciene, Meletele Navalinskiene, Marija Samuitiene, and Neil Boonham
8. Direct Metagenomic Detection of Viral Pathogens in Human Specimens Using an Unbiased High-Throughput Sequencing Approach 73

Takaaki Nakaya, Shota Nakamura, Yoshiko Okamoto, Yoshiyuki Nagai, Jun Kawai, Yoshihide Hayashizaki, Tetsuya Iida, and Toshihiro Horii

 

Part 2 The Soil Habitat


9. Soil-Based Metagenomics 83

Rolf Daniel

10. Methods in Metagenomic DNA, RNA, and Protein Isolation from Soil 93

T. Rajesh, J. Rajendhran, P. Lavanya Pushpam, and P. Gunasekaran
11. Soil Microbial DNA Purification Strategies for Multiple Metagenomic Applications 109

Larissa C. Parsley, Chengcang Wu, David Mead, Robert M. Goodman, and Mark R. Liles
12. Application of PCR-DGGE and MetagenomeWalking to Retrieve Full-Length Functional Genes from Soil 117

Sho Morimoto and Takeshi Fujii
13. Actinobacterial Diversity Associated with Antarctic Dry Valley Mineral Soils 125

Bronwyn M. Kirby, Marilize Le Roes-Hill, S. Craig Cary, Stephanie G. Burton, I. Marla Tuffin, and Don A. Cowan
14. Targeting Major Soil-Borne Bacterial Lineages Using Large-Insert MetagenomicApproaches 135

Anna M. Kielak and George A. Kowalchuk
15. Novelty and Uniqueness Patterns of Rare Members of the Soil Biosphere 143

Mostafa S. Elshahed and Noha H. Youssef
16. Extensive Phylogenetic Analysis of a Soil Bacterial Community Illustrates Extreme Taxon Evenness and the Effects of Amplicon Length, Degree of Coverage, and DNA Fractionation on Classification and Ecological Parameters 151

Sergio E. Morales, Theodore F. Cosart, Jesse V. Johnson, and William E. Holben
17. The Antibiotic Resistome: Origins, Diversity, and Future Prospects 165

Erin L.Westman and Gerard D.Wright


Part 3 The Digestive Tract


18. Functional Intestinal Metagenomics 177

Bartholomeus van den Bogert, Milkha M. Leimena, Willem M. de Vos, Erwin G. Zoetendal, and Michiel Kleerebezem
19. Assessment and Improvement of Methods for Microbial DNA Preparation from Fecal Samples 191

Mariko Ueno, Mami Kikuchi, Kenshiro Oshima, Seok-won Kim, Hidetoshi Morita, and Masahira Hattori
20. The Role of Dysbiosis in Inflammatory Bowel Diseases 199

Johan Dicksved and Ben Willing
21. Culture-Independent Analysis of the Human Gut Microbiota and their Activities 207

Jonathan Swann, Selena E. Richards, Qing Shen, Elaine Holmes, Julian R. Marchesi, and Kieran Tuohy
22. Complete Genome of an Uncultured Endosymbiont Coupling Nitrogen Fixation to Cellulolysis within Protist Cells in Termite Gut 221

Yuichi Hongoh
23. Cloning and Identification of Genes Encoding Acidic Cellulases from the Metagenomes of Buffalo Rumen 229

Cheng-Jie Duan, Jun-Liang Liu, and Jia-Xun Feng


Part 4 Marines and Lakes


24. Microbial Diversity in the Deep Sea and the Underexplored “Rare Biosphere” 245

David B. Mark Welch and Susan M. Huse
25. Bacterial Community Structure and Dynamics in a Seasonally Anoxic Fjord: Saanich Inlet, British Columbia 253

David A. Walsh and Steven J. Hallam
26. Adaptation to Nutrient Availability in Marine Microorganisms by Gene Gain and Loss 269

Adam C. Martiny, Ying Huang, and Weizhong Li
27. Detection of Large Numbers of Novel Sequences in the Metatranscriptomes of Complex Marine Microbial Communities 277

Jack A. Gilbert, Dawn Field, Ying Huang, Robert A. Edwards, Weizhong Li, Paul Gilna, and Ian Joint
28. Metagenomic Approach Studying the Taxonomic and Functional Diversity of the Bacterial Community in a Lacustrine Ecosystem 287

Didier Debroas, Fran¸cois Enault, Isabelle Jouan-Dufournel, Gis`ele Bronner, and Jean-Fran¸cois Humbert
29. Metagenomics of the Marine Subsurface: The First Glimpse from the Peru Margin, ODP Site 1229 295

Jennifer F. Biddle
30. A Targeted Metagenomic Approach to Determine the “Population Genome” of Marine Synechococcus 301

Sophie Mazard, Martin Ostrowski, Laurence Garczarek, and David J. Scanlan
31. Diversity and Role of Bacterial Integron/Gene Cassette Metagenome in Extreme Marine Environments 309

Hosam Elsaied and Akihiko Maruyama


Part 5 Other Habitats


32. The Olavius algarvensis Metagenome Revisited: Lessons Learned from the Analysis of the Low-Diversity Microbial Consortium of a Gutless Marine Worm 321

Manuel Kleiner, Tanja Woyke, Caroline Ruehland, and Nicole Dubilier
33. Microbiome Diversity in Human Saliva 335

Ivan Nasidze and Mark Stoneking
34. Approaches to Understanding Population Level Functional Diversity in a Microbial Community 341

Devaki Bhaya
35. A Functional Metagenomic Approach for Discovering Nickel Resistance Genes from the Rhizosphere of an Acid Mine Drainage Environment 355

Salvador Mirete, Carolina G. de Figueras, and Jose E. Gonz´alez-Pastor
36. The Microbiome of Leaf-Cutter Ant Fungus Gardens 367

Garret Suen, Jarrod J. Scott, Frank O. Aylward, and Cameron R. Currie
37. Diversity of Archaea in Terrestrial Hot Springs and Role in Ammonia Oxidation 381

Chuanlun L. Zhang, Brian P. Hedlund, and Jun Meng
38. Colonization of Nascent, Deep-Sea Hydrothermal Vents by a Novel Archaeal and Nanoarchaeal Assemblage 395

Thomas D. Niederberger, Elizabeth A. McCliment, and S. Craig Cary
39. Analysis of the Metagenome from a Biogas-Producing Microbial Community by Means of Bioinformatics Methods 403

Sebastian Jaenicke, Martha Zakrzewski, Sebastian J¨unemann, Alfred P¨uhler, Alexander Goesmann, and Andreas Schl¨uter
40. Amplicon Pyrosequencing Analysis of Endosymbiont Population Structure 415

Frank J. Stewart and Colleen M. Cavanaugh
41. Investigating Bacterial Diversity Along Alkaline Hot-Spring Thermal Gradients by Barcoded Pyrosequencing 423

Scott R. Miller and Michael Weltzer
42. Genetic Characterization of Microbial Communities Living at the Surface of Building Stones 429

Ma¨ıt´e Berdoulay and Jean-Claude Salvado


Part 6 Biodegradation


43. Novel Aromatic Degradation Pathway Genes and their Organization as Revealed byMetagenomic Analysis 439

Kentaro Miyazaki
44. Functional Screening a Wide Host-Range Metagenomic Library from a WastewaterTreatment Plant Yields a Novel Alcohol/Aldehyde Dehydrogenase 451

Margaret Wexler, Philip L. Bond, David J. Richardson, and Andrew W. B. Johnston
45. Aromatic Hydrocarbon Degradation Genes from Chronically Polluted SubantarcticMarine Sediments 461

Hebe M. Dionisi, Mariana Lozada, Magal´ı S. Marcos, Walter D. Di Marzio, and Claudia L. Loviso
46. Isolation and Characterization of Alkane Hydroxylases from a Metagenomic Library of Pacific Deep-Sea Sediment 475

Fengping Wang, Meixiang Xu, and Xiang Xiao


Part 7 Biocatalysts and Natural Products

 

47. Emerging Fields in Functional Metagenomics and Its Industrial Relevance: Overcoming Limitations and Redirecting the Search for Novel Biocatalysts 483

Mirjam Perner, Nele Ilmberger, Hans Ulrich K¨ohler, Jennifer Chow, and Wolfgang R. Streit
48. Carboxylesterases and Lipases from Metagenomes 499

Jennifer Chow, Ulrich Krauss, Karl-Erich Jaeger, and Wolfgang R. Streit
49. Expanding Small-Molecule Functional Metagenomics through Parallel Screening of Broad Host-Range Cosmid Environmental DNA Libraries in Diverse Proteobacteria 507

Jeffrey W. Craig and Sean F. Brady
50. Biomedicinals from the Microbial Metagenomes of Marine Invertebrates 517

Walter C. Dunlap, Paul F. Long, and Marcel Jaspars
51. Molecular Characterization of TEM-Type Beta-Lactamases Identified in Cold-Seep Sediments of Edison Seamount (South of Lihir Island, Papua New Guinea) 545

Sang Hee Lee and Jung-Hyun Lee
52. Identification of Novel Bioactive Compounds from the Metagenome of the Marine  Sponge Haliclona simulans 553

David P. H. Lejon, Jonathan Kennedy, and Alan D. W. Dobson
53. Functional Viral Metagenomics and the Development of New Enzymes for DNAand RNA Amplification and Sequencing 563

Thomas W. Schoenfeld, Nick Hermersmann, Mike Moser, Darby Renneckar, Vinay Dhodda, and David Mead

 

Part 8 Summary

 

54. Metagenomics: The Paths Forward 581

C. Titus Brown and James M. Tiedje
55. Darwin in the Twenty-First Century: Natural Selection, Molecular Biology, and Species Concepts 589

Francisco J. Ayala

 

Index 597

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