Molecular Toxicology Protocols

ISBN-13: 9781071602225 / Angielski / Twarda / 2020 / 576 str.

Phouthone Keohavong; Kamaleshwar Singh; Weimin Gao

Spis treści

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

Blurb

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.