This volume provides a comprehensive collection of classical and cutting edge protocols and techniques to examine the normal development and physiological functions of the gastrointestinal system and to model the most common digestive diseases. The chapters focus on diverse research topics including ex vivo systems to study gastrointestinal development and functions, in vivo imaging of the gastrointestinal tract, isolation and characterization of intestinal immune cells, and animal models of gastrointestinal inflammation and cancer. The Gastrointestinal Physiology and Diseases: Methods and Protocols book targets wide audience of physiologists, cell and developmental biologists, immunologists, and physician-scientists working in the field of gastroenterology and beyond. 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.

Highly practical and clearly written, Gastrointestinal Physiology and Diseases: Methods and Protocols will serve both seasoned researchers as well as newcomers to the field and will provide a unique resource and expert guidance to modern laboratory techniques developed for examining normal functions and diseases of the gastrointestinal tract.

Contents:
Part I In Vitro and Ex Vivo Systems to Study Gastrointestinal Functions and Diseases
1. CRISPR/Cas9-Mediated Genome Editing of Mouse Small Intestinal Organoids
2. Lentivirus-Based Stable Gene Delivery into Intestinal Organoids
3. Co-culture of Gastric Organoids and Immortalized Stomach Mesenchymal Cells
4. An Air–Liquid Interface Culture System for 3D Organoid Culture of Diverse Primary Gastrointestinal Tissues
5. Organotypical Tissue Cultures from Fetal and Neonatal Murine Colon
6. Using Chamber Technique to Measure Intestinal Epithelial Permeability
7. HPLC-Based Metabolomic Analysis of Normal and Inflamed Gut
8. NMR-Based Metabolomic Analysis of Normal and Inflamed Gut
9. Analysis of microRNA Levels in Intestinal Epithelial Cells

Part II Imaging Analysis of the Gastrointestinal System in Vivo
10. Detecting Reactive Oxygen Species Generation and Stem Cell Proliferation in the Drosophila Intestine
11. Imaging Inflammatory Hypoxia in the Murine Gut
12. Label-Free Imaging of Eosinophilic Esophagitis Mouse Models Using Optical Coherence Tomography
13. Near-Infrared Fluorescence Endoscopy to Detect Dysplastic Lesions in the Mouse Colon
14. Visualization of Signaling Molecules During Neutrophil Recruitment in Transgenic Mice Expressing FRET Biosensors
15. In Vivo Myeloperoxidase Imaging and Flow Cytometry Analysis of Intestinal Myeloid Cells

Part III Isolation and Characterization of Intestinal Immune Cells
16. Macrophage Isolation from the Mouse Small and Large Intestine
17. Isolation and Functional Analysis of Lamina Propria Dendritic Cells from the Mouse Small Intestine
18. Purification and Adoptive Transfer of Group 3 Gut Innate Lymphoid Cells
19. Immunotherapy with iTreg and nTreg Cells in a Murine Model of Inflammatory Bowel Disease
20. Isolation of Eosinophils from the Lamina Propria of the Murine Small Intestine

Part IV Animal Models of Gastrointestinal Inflammation and Injury
21. Investigation of Host and Pathogen Contributions to Infectious Colitis Using the Citrobacter rodentium Mouse Model of Infection
22. Murine Trinitrobenzoic Acid-Induced Colitis as a Model of Crohn’s Disease
23. Oxazolone-Induced Colitis as a Model of Th2 Immune Responses in the Intestinal Mucosa
24. The Mongolian Gerbil: A Robust Model of Helicobacter pylori-Induced Gastric Inflammation and Cancer
25. A Rapid Screenable Assay for Compounds That Protect Against Intestinal Injury in Zebrafish Larva

Part V Animal Models of Gastrointestinal Cancer
26. AOM/DSS Model of Colitis-Associated Cancer
27. Characterization of Colorectal Cancer Development in Apc min/+ Mice
28. Modeling Murine Gastric Metaplasia Through Tamoxifen-Induced Acute Parietal Cell Loss
29. The Hamster Buccal Pouch Model of Oral Carcinogenesis