Main description:

This book explores methods to study the complex and evolving interplay between a virus and its host that range from model systems to the detection of chemical molecules. The collection starts with the application of humanized mice and zebrafish as model organisms to study virus-host interactions and induction of innate immune responses. Subsequent chapters outline diverse methods to detect small interfering RNAs, microRNAs, and virus-derived dsRNA from a variety of cells, tissues, and organisms, as well as to interrogating the cytosolic RNA and DNA sensing pathways, including using RNA PAMPs as molecular tools, purification of cGAMP from virus particles and infected cells, and mechanisms to visualize the subcellular localization and activation of the adaptor proteins MAVS and STING. Cutting-edge methods, including high-throughput and genome-wide CRISPR/Cas9 screens, chromosome conformation capture, and whole-exome sequencing, are described to identify novel mediators, pathways, and variants underlying host susceptibility. Given the importance of studying these pathways and players under physiologic conditions, methods describing the isolation of primary mouse sensory neurons and group 2 innate lymphoid cells are also provided. Finally, this collection comes full circle back to the whole organism level and concludes with epidemiological methods to investigate virus-host interactions and the induction of innate immunity. Written for the Methods in Molecular Biology series, 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 practical, Innate Antiviral Immunity: Methods and Protocols spans a diverse array of approaches to study and elucidate the intricacies of this vital area of study.
The chapter 'Morphological Separation of Clustered Nuclei in Histological Images' is published open access under a CC BY 4.0 license at link.springer.com.

Contents:

1. The Application of Humanized Mouse Models for the Study of Human Exclusive Viruses

Fatemeh Vahedi, Elizabeth C. Giles, and Ali A. Ashkar

2. Zebrafish as a Model for the Study of Host-Virus Interactions

Peng Fei Zou and Pin Nie

3. Northern Blot Detection of Virus-Derived Small Interfering RNAs in Caenorhabditis elegans Using Non-Radioactive Oligo Probes

Tianyun Long and Rui Lu

4. Extraction and qPCR-Based Detection of miRNAs from Cultured PBMCs of Bubaline Origin

Chandra S. Mukhopadhyay, Ramneek Verma, and Jasdeep Singh

5. Visualizing Virus-Derived dsRNA Using Antibody-Independent and -Dependent Methods

Sarah J. Poynter and Stephanie J. DeWitte-Orr

6. RNA PAMPs as Molecular Tools for Evaluating RIG-I Function in Innate Immunity

Renee C. Ireton, Courtney Wilkins, and Michael Gale, Jr.

7. Methods to Visualize MAVS Subcellular Localization

Christine Vazquez, Dia C. Beachboard, and Stacy M. Horner

8. Purification of Cyclic GMP-AMP from Viruses and Measurement of Its Activity in Cell Culture

Alice Mayer, Jonathan Maelfait, Anne Bridgeman, and Jan Rehwinkel

9. cGAMP Quantification in Virus-Infected Human Monocyte-Derived Cells by HPLC-Coupled Tandem Mass Spectrometry

Jennifer Paijo, Volkhard Kaever, and Ulrich Kalinke

10. Methods of Assessing STING Activation and Trafficking

Vladislav Pokatayev and Nan Yan

11. Genome-Wide CRISPR/Cas9 Screening for High-Throughput Functional Genomics in Human Cells

Shiyou Zhu, Yuexin Zhou, and Wensheng Wei

12. High Throughput Screening for Identification of Novel Innate Immune Activators

Bryan J. Gall and Victor R. DeFilippis

13. Chromosome Conformation Capture for Research on Innate Antiviral Immunity

Yoon Jung Kim and Tae Hoon Kim

14. Discovery of Variants Underlying Host Susceptibility to Virus Infection Using Whole-Exome Sequencing

Gabriel A. Leiva-Torres, Nestor Nebesio, and Silvia M. Vidal

15. Isolation, Purification, and Culture of Primary Murine Sensory Neurons

Sarah Katzenell, Jorge R. Cabrera, Brian J. North, and David A. Leib

16. Isolation of Group 2 Innate Lymphoid Cells from Mouse Lungs

Claudia U. Duerr and Joerg H. Fritz

17. Epidemiological Methods

Biao Wang and Mark Loeb