Differential Display Methods and Protocols

About this book

Based on a new mathematical model of differential display (DD), this updated second edition takes advantage of automation, as well as digital data acquisition and analysis. The authors explain and highlight all the recent methodological refinements, including automated liquid handling of hundreds of DD PCR reaction setups combined with capillary electrophoresis, a prototype computer program to automatically allow positive band identification from a fluorescence differential display (FD) image, and restriction fragment-based DD screenings. Other improvements discussed are the combining of DD and DNA microarrays by reducing the complexity of cDNA probes while increasing the sensitivity of detection, and a DD approach to detect prokaryotic mRNA expression. The authors also demonstrate the power of DD technology with a collection of outstanding examples of DD applications and detailed experimental procedures. The elegant studies described here have led to the discovery of many important genes involved in viral infection, Prion disease, cancer, ovulation, circadian clock, floral color, transcription repression gene silencing, mRNA polymorphism, and protein-RNA interaction.

Contents

Part I. Methodologies Global Analysis of Gene Expression by Differential Display: A Mathematical Model Shitao Yang and Peng Liang Automation of Fluorescent Differential Display With Digital Readout Jonathan D. Meade, Yong-jig Cho, Jeffrey S. Fisher, Jamie C. Walden, Zhen Guo, and Peng Liang Ordered Differential Display Mikhail V. Matz and Ella A. Meleshkevitch GeneCalling(R): Transcript Profiling Coupled to a Gene Database Query Richard A. Shimkets High-Density Sampling Differential Display of Prokaryotic mRNAs With RAP-PCR Dana M. Walters and Pierre E. Rouviere Vertical Arrays: Microarrays of Complex Mixtures of Nucleic Acids Rosana Risques, Gaelle Rondeau, Martin Judex, Michael McClelland, and John Welsh Automated Pattern Ranking in Differential Display Data Analysis Tero Aittokallio, Pekka Ojala, Timo J. Nevalainen, and Olli S. Nevalainen Linking cDNA-AFLP-Based Gene Expression Patterns and ESTs Ling Qin, Pjotr Prins, and Johannes Helder Part II. Applications Differentially Expressed Genes Associated With Hepatitis B Virus HBx and MHBs Protein Function in Hepatocellular Carcinoma Dae-Ghon Kim Identification of Disease Markers by Differential Display: Prion Disease Michael Clinton, Gino Miele, Sunil Nandi, and Derek McBride Saturation Screening for p53 Target Genes by Digital Fluorescent Differential Display Yong-Jig Cho, Susanne Stein, Roger S. Jackson II, and Peng Liang Identification of p53-Regulated Genes by the Method of Differential Display Yunping Lin, Roger P. Leng, and Samuel Benchimol Identification by Differential Display of IL-24 Autocrine Loop Activated by Ras Oncogenes Zhongjia Tan, Mai Wang, and Peng Liang Comprehensive Analysis of Ovarian Gene Expression During Ovulation Using Differential Display Lawrence L. Espey Functional Analysis of Nocturnin: A Circadian Clock-Regulated Gene Identified by Differential Display Julie E. Baggs and Carla B. Green Isolation and Characterization of Anthocyanin 5-O-Glucosyltransferase in Perilla frutescens var. crispa by Differential Display Mami Yamazaki and Kazuki Saito Identification of Target Genes of a Yeast Transcriptional Repressor Bernard Mai and Linda L. Breeden Detection of an mRNA Polymorphism by Differential Display Shan Liang, S. Paul Rossby, Peng Liang, Richard C. Shelton, D. Hal Manier, Amitabha Chakrabarti, and Fridolin Sulser Silencing in Yeast: Identification of Clr4 Targets Sergey V. Ivanov and Alla V. Ivanova Identification of mRNA Bound to RNA Binding Proteins by Differential Display Anne Carr-Schmid, Xinfu Jiao, and Megerditch Kiledjian Index

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