Main description:

This fully revised book includes new and improved protocols to analyze toxicity at the DNA, RNA, and protein levels using genomic, epigenomic, transcriptomic, and proteomic approaches. Sections of the book address key subjects such as bioinformatics and biostatistics, toxicant-induced lung inflammation and tumors, analysis of protein and gene expression and silencing, gene promoter methylation, detection of chromosomal and genome-wide damage, analysis of DNA-adducts and surrogate gene mutations, detection and characterization of cancer gene mutation, and many other areas of study. Written for the highly successful 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.
Comprehensive and up-to-date, Molecular Toxicology Protocols, Third Edition will prove to play an important role in generating a better understanding of the field of toxicology and its sub-disciplines.

Contents:

Part I: Bioinformatics and Biostatistics

1. Bioenergetic Analyses of In Vitro and In Vivo Samples to Guide Toxicological Endpoints

Jonathan W. Boyd, Julia A. Penatzer, Nicole Prince, Julie V. Miller, Alice A. Han, and Holly N. Currie

2. Next Generation Sequencing (NGS) Application in Multi-Parameter Gene Expression Analysis

Degeng Wang and Andrey L. Karamychev

3. Integrated Chip-Seq and RNA-Seq Data Analysis Coupled with Bioinformatics Approaches to Investigate Regulatory Landscape of Transcription Modulators in Breast Cancer Cells

Jairo Ramos, Quentin Felty, and Deodutta Roy

4. Analysis of RNA Sequencing Data using CLC Genomics Workbench

Chia-Hsin Liu and Y. Peter Di

Part II: Toxicant-Induced Lung Inflammation and Lung Tumors

5. Using Bronchoalveolar Lavage to Evaluate Changes in Pulmonary Diseases

Marissa E. Di, Dandan Yang, and Y. Peter Di

6. Fast and Efficient Measurement of Clinical and Biological Samples Using Immunoassay-Based Multiplexing Systems

Yingze Zhang, Xiaoyun Li, and Y. Peter Di

7. Induction of Lung Tumors and Mutational Analysis in FVB/N Mice Treated with the Tobacco Carcinogen 4-(Methylnitrosamino)-1-(3-pyridyl)-1-Butanone

Natalie J. Rothenberger and Laura P. Stabile

Part III: Analysis of Protein and Gene Expression and Silencing

8. Two-Dimensional Difference Gel Electrophoresis: A Gel-Based Proteomic Approach for Protein Analysis

Weimin Gao

9. Determination and Quantification of Bacterial Virulent Gene Expression Using Quantitative Real Time PCR

Qiao Lin and Y. Peter Di

10. Using a Lentivirus-Based Inducible RNAi Vector to Silence a Gene

Si Chen, Dongying Li, Zhen Ren, Dianke Yu, Baitang Ning, Nan Mei, and Lei Guo

Part IV: Gene Promoter Methylation

11. Analysis of Toxicants-Induced Alterations in DNA Methylation by Methylation-Sensitive Random Amplified Polymorphic DNA-Polymerase Chain Reaction (MS-RAPD-PCR)

Kamaleshwar P. Singh

12. Detection of DNA Methylation by MeDIP and MBDCap Assays: An Overview of Techniques

Hang-Kai Hsu, Yu-I Weng, Pei-Yin Hsu, Tim H.-M. Huang, and Yi-Wen Huang

Part V: Detection of Chromosomal and Genome-Wide Damage

13. Analysis of Telomere Length and Aberrations by Quantitative FISH

Elise Fouquerel and Patricia Opresko

14. Detection of Loss of Heterozygosity in Tk-Deficient Mutants from L5178Y Tk+/--3.7.2C Mouse Lymphoma Cells

Xiaoqing Guo, Ying Chen, Martha M. Moore, and Nan Mei

15. Detection of DNA Double-Strand Breaks and Chromosome Translocations Using Ligation-Mediated PCR and Inverse PCR

Sheetal Singh, Shyh-Jen Shih, and Andrew T. M. Vaughan

Part VI: Analysis of DNA-Adducts and Surrogate Gene Mutations

16. 32P-Postlabeling Analysis of DNA Adducts

David H. Phillips and Volker M. Arlt

17. Determination of Mutational Spectra Induced by Environmental Toxicants in Complex Human Cell Populations

Robert Gealy and Phouthone Keohavong

18. Detection of Pig-a Mutant Erythrocytes in the Peripheral Blood of Rats and Mice

Vasily N. Dobrovolsky, Xuefei Cao, Javed A. Bhalli, and Robert H. Heflich

19. Analysis of In Vivo Mutation in the Hprt and Tk Genes of Mouse Lymphocytes

Vasily N. Dobrovolsky, Joseph G. Shaddock, and Robert H. Heflich

20. Molecular Analysis of Mutations in the Human HPRT Gene

Phouthone Keohavong, Liqiang Xi, and Stephen G. Grant

21. Simultaneous Quantification of t(14;18) and HPRT Exon 2/3 Deletions In Human Lymphocytes

James C. Fuscoe

Part VII: Detection and Characterization of Cancer Gene Mutation

22. Analysis of Mutations in K-ras and p53 Genes in Sputum and Plasma Samples

Lifang Zhang, Wei-Min Gao, and Phouthone Keohavong

23. ACB-PCR Quantification of Low-Frequency Hotspot Cancer-Driver Mutations

Meagan B. Myers, Karen L. McKim, Yiying Wang, Malathi Banda, and Barbara L. Parsons

24. Detection and Characterization of Oncogene Mutations in Preneoplastic and Early Neoplastic Lesions

Toshinari Minamoto

Part VIII: Analysis of DNA Damage and Repair Mechanisms

25. The Sister Chromatid Exchange (SCE) Assay

Dawn M. Stults, Michael W. Killen, Paola Marco-Casanova, and Andrew J. Pierce

26. The Gene Cluster Instability (GCI) Assay for Recombination

Michael W. Killen, Dawn M. Stults, Paola Marco-Casanova, and Andrew J. Pierce

27. New Perspectives on Unscheduled DNA Synthesis: Functional Assay for Global Genomic DNA Nucleotide Excision Repair

Manasi R. Pimpley, Megan L. Foley, and Jean J. Latimer

28. Host Cell Reactivation: Assay for Actively Transcribed DNA Nucleotide Excision Repair Using Luciferase Family Expression Vectors

Jowaher S. Alanazi and Jean J. Latimer

Part IX: Analysis of Endoplasmic Reticulum Stress and miRNA/RNA Interaction

29. Methods for Establishing and Using a Stable Cell Line Expressing Both Gaussia Luciferase and Firefly Luciferase to Screen for Endoplasmic Reticulum Stress

Zhen Ren, Si Chen, and Lei Guo

30. FREMSA: A Method That Provides Direct Evidence of the Interaction Between MicroRNA and mRNA

Dianke Yu, Si Chen, Dongying Li, Bridgett Knox, Lei Guo, and Baitang Ning