Celiac Disease: Methods and Protocols

ISBN-13: 9781493947751 / Angielski / Miękka / 2018 / 235 str.

Ryan, Anthony W.

Opis

This volume provides detailed molecular analysis of the associated pathways and cell types involved in Celiac Disease, and embraces new technologies such as next generation sequencing. The book is divided into three parts: Part I gives a background overview with a number of reviews to describe the history and nature of the disease, its diagnosis, the role of animal models, and study designs for investigating genetic susceptibility. Part II describes molecular techniques, including tissue culture, isolation and cloning of relevant cell types, high content analysis of biopsies, and HLA genotyping. The final part of the book begins with an outline of scripting for data management, focusing on tools that are freely available to researchers who wish to explore them. It also describes analysis pipelines for bioinformatics prediction of antigenicity, quality control and analysis of GWAS data, and transcriptome analysis by next generation sequencing. 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 thorough, Celiac Disease: Methods and Protocols brings together novel and more traditional methods in molecular biology and immunology, in order to provide a tool-kit for all stages for Celiac Disease research-from the practicalities of identifying, obtaining, stabilizing and maintaining high quality samples, to molecular analysis and bioinformatics.

Spis treści

Part I

1. Celiac Disease: Background and Historical Context
Graham D. Turner, Margaret R. Dunne, and Anthony W. Ryan

2. Celiac Disease: Diagnosis
Greg Byrne and Con Feighery

3. Generating Transgenic Mouse Models for Studying Celiac Disease
Josephine M. Ju, Eric V. Marietta, and Joseph A. Murray

4. Study Designs for Exploring the Non-HLA Genetics in Coeliac Disease
Åsa Torinson Naluai

Part II

5. 24 Hour Ex Vivo Culture of Celiac Duodenal Biopsies
Sarah E. J. Cooper and Con F. Feighery

6. Isolation and Cloning of Gluten-Specific T Cells in Celiac Disease
Yvonne Kooy-Winkelaar and Frits Koning

7. Flow Cytometric Analysis of Human Small Intestinal Lymphoid Cells
Margaret R. Dunne

8. Adaptation of a Cell-Based High Content Screening System for the In-depth Analysis of Celiac Biopsy Tissue
Sarah Cooper, Bashir M. Mohammed, L. Elliott, Anthony Davies, Con Feighery, J. Kelly, and Jean Dunne

9. HLA Genotyping: Methods for the Identification of the HLA-DQ2, -DQ8 Heterodimers Implicated in Celiac Disease (CD) Susceptibility
Maria Edvige Fasano, Ennia Dametto, and Sandra D'Alfonso

10. Detecting Allelic Expression Imbalance at Candidate Genes Using 5' Nuclease Genotyping Technology
J.M. Gahan, M.M. Byrne, M. Hill, E. Quinn, R.T. Murphy, R.J.L. Anney, and A.W. Ryan

11. Gene Expression Profiling of Celiac Biopsies and Peripheral Blood Monocytes Using Taqman Assays
Martina Galatola, Renata Auricchio, and Luigi Greco

12. Cloning Gene Variants and Reporter Assays
Ben Molloy and Ross McManus

13. Epigenetic Methodologies for the Study of Celiac Disease
Antoinette S. Perry, Anne-Marie Baird, and Steven G.

Gray

14. Candidate Gene Knockdown in Celiac Disease
Ben Molloy, Michael Freeley, and Ross McManus

Part III

15. Perl One-Liners: Bridging the Gap Between Large Data-Sets and Analysis Tools
Karsten Hokamp

16. Bioinformatic Analysis of Antigenic Proteins
Cathal P. O'Brien

17. Quality Control Procedures for Genome Wide Association Studies using the Immunochip Platform
Ciara Coleman, Emma Quinn, and Ross McManus

18. Quality Control and Analysis of NGS RNA Sequencing Data
Emma Quinn and Ross McManus

O autorze

Anthony W. Ryan PhD Room 1.17, Institute of Molecular Medicine Trinity Centre for Health Sciences Trinity College Dublin St James's Hospital, Dublin 8, Ireland. tel +353 1 896 3273 (lab 896 3292) fax +353 1 454 2043 e-mail aryan12@tcd.ie