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  • © 2018

Viral Metagenomics

Methods and Protocols

  • Includes cutting-edge methods and protocols

  • Provides step-by-step detail essential for reproducible results

  • Contains key notes and implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 1746)

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eBook USD 109.00
Price excludes VAT (USA)
  • ISBN: 978-1-4939-7683-6
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  • Tax calculation will be finalised during checkout
Softcover Book USD 139.99
Price excludes VAT (USA)
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Table of contents (17 protocols)

  1. Front Matter

    Pages i-xi
  2. Small RNA Isolation from Tissues of Grapevine and Woody Plants

    • Annalisa Giampetruzzi, Michela Chiumenti, Angelantonio Minafra, Pasquale Saldarelli
    Pages 27-36
  3. Viral Double-Stranded RNAs (dsRNAs) from Plants: Alternative Nucleic Acid Substrates for High-Throughput Sequencing

    • Armelle Marais, Chantal Faure, Bernard Bergey, Thierry Candresse
    Pages 45-53
  4. Workup of Human Blood Samples for Deep Sequencing of HIV-1 Genomes

    • Marion Cornelissen, Astrid Gall, Antoinette van der Kuyl, Chris Wymant, François Blanquart, Christophe Fraser et al.
    Pages 55-61
  5. Monolith Chromatography as Sample Preparation Step in Virome Studies of Water Samples

    • Ion Gutiérrez-Aguirre, Denis Kutnjak, Nejc Rački, Matevž Rupar, Maja Ravnikar
    Pages 63-75
  6. Viral Metagenomics Approaches for High-Resolution Screening of Multiplexed Arthropod and Plant Viral Communities

    • Sarah François, Denis Filloux, Emmanuel Fernandez, Mylène Ogliastro, Philippe Roumagnac
    Pages 77-95
  7. Different Approaches to Discover Mycovirus Associated to Marine Organisms

    • Luca Nerva, Giovanna C. Varese, Massimo Turina
    Pages 97-114
  8. Use of siRNAs for Diagnosis of Viruses Associated to Woody Plants in Nurseries and Stock Collections

    • Nikoletta Czotter, János Molnár, Réka Pesti, Emese Demián, Dániel Baráth, Tünde Varga et al.
    Pages 115-130
  9. The Use of High-Throughput Sequencing for the Study and Diagnosis of Plant Viruses and Viroids in Pollen

    • Kris De Jonghe, Annelies Haegeman, Yoika Foucart, Martine Maes
    Pages 131-149
  10. High-Resolution Screening of Viral Communities and Identification of New Pathogens in Fish Using Next-Generation Sequencing

    • Arnfinn Lodden Økland, Are Nylund, Ali May, Adalberto Costessi, Walter Pirovano
    Pages 151-159
  11. Metagenomic Analyses of the Viruses Detected in Mycorrhizal Fungi and Their Host Orchid

    • Hanako Shimura, Chikara Masuta, Yasunori Koda
    Pages 161-172
  12. DNA Multiple Sequence Alignment Guided by Protein Domains: The MSA-PAD 2.0 Method

    • Bachir Balech, Alfonso Monaco, Michele Perniola, Monica Santamaria, Giacinto Donvito, Saverio Vicario et al.
    Pages 173-180
  13. Shannon Entropy to Evaluate Substitution Rate Variation Among Viral Nucleotide Positions in Datasets of Viral siRNAs

    • Aysan Ghasemzadeh, Marta Małgorzata ter Haar, Masoud Shams-bakhsh, Walter Pirovano, Vitantonio Pantaleo
    Pages 187-195
  14. Insect Virus Discovery by Metagenomic and Cell Culture-Based Approaches

    • Finny S. Varghese, Ronald P. van Rij
    Pages 197-213
  15. Erratum to: Shannon Entropy to Evaluate Substitution Rate Variation Among Viral Nucleotide Positions in Datasets of Viral siRNAs

    • Aysan Ghasemzadeh, Marta Małgorzata ter Haar, Masoud Shams-bakhsh, Walter Pirovano, Vitantonio Pantaleo
    Pages E1-E1
  16. Back Matter

    Pages 215-217

About this book

This volume explores the use of viral metagenomics to diagnose known viruses for plant and food production, human and animal health, and identifying viral vectors like insects. The chapters in this book cover topics, such as sRNAs isolation from tissues of grapevines and woody plants, high-resolution screening of arthropod and plant viral communities, identifying new pathogens in fish, detecting viruses in mycorrhizal fungi and their orchid host, and insect virus discovery through metagenomic and cell culture-based approaches. Written in the highly successful Methods in Molecular Biology series format, chapters include 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 comprehensive, Viral Metagenomics: Methods and Protocols is a valuable resource for researchers and specialists who are interested in learning more about this evolving field.

Keywords

  • deep sequencing
  • Next Generation Sequencing
  • cDNA library preparation
  • bioinformatics
  • siRNAs

Editors and Affiliations

  • Institute Sustainable Plant Protection of the CNR, Research Unit of Bari, Italy

    Vitantonio Pantaleo, Michela Chiumenti

Bibliographic Information

  • Book Title: Viral Metagenomics

  • Book Subtitle: Methods and Protocols

  • Editors: Vitantonio Pantaleo, Michela Chiumenti

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-7683-6

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC 2018

  • Hardcover ISBN: 978-1-4939-7682-9

  • Softcover ISBN: 978-1-4939-9257-7

  • eBook ISBN: 978-1-4939-7683-6

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XI, 217

  • Number of Illustrations: 9 b/w illustrations, 23 illustrations in colour

  • Topics: Plant Science

Buying options

eBook USD 109.00
Price excludes VAT (USA)
  • ISBN: 978-1-4939-7683-6
  • Instant PDF download
  • Readable on all devices
  • Own it forever
  • Exclusive offer for individuals only
  • Tax calculation will be finalised during checkout
Softcover Book USD 139.99
Price excludes VAT (USA)
Hardcover Book USD 139.99
Price excludes VAT (USA)