Molecular Toxicology Protocols

by Keohavong, Phouthone; Grant, S. G.

• ISBN13: 9781588290847
• ISBN10: 1588290840
• Format: Hardcover
• Copyright: 2004-10-22
• Publisher: Humana Pr Inc

Summary

A collection of cutting-edge techniques for analyzing genotoxic exposure and detecting the resulting biological effects-including endogenous metabolites-up to and including the development of cancer. The authors emphasize analytical methods that can be specifically applied to human populations and patients. Among the applications detailed are the analysis of interactions between such cellular macromolecules as DNA and proteins and chemical and physical agents, the assessment of medically relevant toxicity, and the characterization of genetic alterations induced in transgenic animals by in vivo systems. There are also methods for the analysis of genotoxic exposure during gene expression, of cytotoxicity caused by the induction of apoptosis, of genetic alterations in reporter genes and oncogenes, early (premalignant) detection of altered oncogenes, and of individual variation in biotransformation and DNA repair capacity.

Author Biography

Volker M. Arlt: Section of Molecular Carcinogenesis, Institute of Cancer Research, Sutton, Surrey, UK Reetakshi Arora: National Centre of Applied Human Genetics, Jawaharlal Nehru University, Delhi, India Narendra K. Bairwa: National Centre of Applied Human Genetics, Jawaharlal Nehru University, Delhi, India Ramesh Bamezai: National Centre of Applied Human Genetics, Jawaharlal Nehru University, Delhi, India Christopher J. Betti: Program in Molecular Biology, Loyola University Chicago Medical Center, Maywood, IL William F. Blakely: Armed Forces Radiobiology Research Institute, Bethesda, MD Grigory G. Borisenko: Department of Environmental and Occupational Health, University of Pittsburgh, PA Anne-Lise Borresen-Dale: Department of Genetics, The Norwegian Radium Hospital, Oslo, Norway Shama C. Buch: Center for Clinical Pharmacology, University of Pittsburgh, PA R. C. Chaubey: Genetic Toxicology and Chromosome Studies Section, Radiation Biology and Health Sciences Division, Bhabha Atomic Research Centre, Mumbai, India Walter A. Deutsch: Pennington Biomedical Research Center, Louisiana State University, Baton Rouge, LA Karen H. Dingley: Biology and Biotechnology Research Program, Lawrence Livermore National Laboratory, CA Vasily N. Dobrovolsky: Division of Genetic and Reproductive Toxicology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR James P. Fabisiak: Department of Environmental and Occupational Health, University of Pittsburgh, PA Elke Feldmann: Institute of Genetics, University of Essen, Essen, Germany James C. Fuscoe: Center for Functional Genomics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR Weimin Gao: Department of Environmental and Occupational Health, University of Pittsburgh, PA Michael E. Gehring: Department of Pediatrics, Wake Forest University School of Medicine, Winston-Salem, NC Tony E. Godfrey: Department of Medicine, Mount Sinai School of Medicine, New York Wolfgang Goedecke: Institute of Genetics, University of Essen, Germany Stephen G. Grant: Department of Environmental and Occupational Health, University of Pittsburgh, PA Jan Grawe: Cell Analysis Core Facility, Uppsala University, Rudbeck Laboratory, Uppsala, Sweden Karl Otto Greulich: Department for Single Cell and Single Molecule Techniques, Institute for Molecular Biotechnology Jena, Germany Vibhuti Gupta: National Centre of Applied Human Genetics, Jawaharlal Nehru University, Delhi, India Kurt W. Haack: Center for Accelerator Mass Spectrometry, Lawrence Livermore National Laboratory, CA Andreas Hartmann: Novartis Pharma AG, Basel, Switzerland Michael Hausmann: Kirchhoff-Institute for Physics, University of Heidelberg, Germany Tomonori Hayashi: Laboratory of Immunology, Department of Radiobiology/Molecular Epidemiology, Radiation Effects Research Foundation, Hiroshima, Japan John B. Hays: Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis Robert H. Heflich: Division of Genetic and Reproductive Toxicology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR Vijay Hegde: Pennington Biomedical Research Center, Louisiana State University, Baton Rouge Alan Hewer: Section of Molecular Carcinogenesis, Institute of Cancer Research, Sutton, Surrey, UK Stephen R. Hewitt: Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis Sai-Mei Hou: Department of Biosciences, Karolinska Institute, Huddinge, Sweden T. C. Hsu: Department of Cancer Biology, M. D. Anderson Cancer Center, Houston, TX Maria Jasin: Cell Biology Program, Memorial Sloan-Kettering Cancer Center and Cornell University Graduate School of Medical Sciences, New York Hilde Johnsen: Department of Genetics, The Norwegian Radium Hospital, Oslo, Norway Jennifer M. Johnson: Department of Molecular Genetics and Biochemistry, University of Pittsburgh School of Medicine, PA Nina Joshi: Department of Environmental and Occupational Health, University of Pittsburgh, PA Valerian E. Kagan: Department of Environmental and Occupational Health, University of Pittsburgh, PA Crystal M. Kelly: Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, PA Lori A. Kelly: Department of Surgery, University of Pittsburgh School of Medicine, PA Phouthone Keohavong: Department of Environmental and Occupational Health, University of Pittsburgh, PA Patrick P. Koty: Department of Pediatrics, Wake Forest University School of Medicine, Winston-Salem, NC Steffi Kuhfittig-Kulle: Institute of Genetics, University of Essen, Germany Yoichiro Kusunoki: Laboratory of Immunology, Department of Radiobiology/Molecular Epidemiology, Radiation Effects Research Foundation, Hiroshima, Japan Seishi Kyoizumi: Laboratory of Immunology, Department of Radiobiology/Molecular Epidemiology, Radiation Effects Research Foundation, Hiroshima, Japan Jean J. Latimer: Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, PA Guro Elisabeth Lind: Department of Genetics, The Norwegian Radium Hospital, Oslo, Norway Ragnhild Lothe: Department of Genetics, The Norwegian Radium Hospital, Oslo, Norway Hitoshi Maeda: Department of Legal Medicine, Osaka City University Medical School, Osaka, Japan Dheeraj K. Malhotra: National Centre of Applied Human Genetics, Jawaharlal Nehru University, Delhi, India Toshinari Minamoto: Divisions of Diagnostic Molecular Oncology and Surgical Oncology, Cancer Research Institute, Kanazawa University, Japan Shirley McCready: School of Biological and Molecular Sciences, Oxford Brookes University, UK Page B. McKinzie: Division of Genetic and Reproductive Toxicology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR Minako Nagao: Biochemistry Division, National Cancer Center Research Institute, Tokyo, Japan Masako Ochiai: Biochemistry Division, National Cancer Center Research Institute, Tokyo, Japan Andrea Odersky: Institute of Genetics, University of Essen, Germany Iovanna Pandelova: Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis Barbara L. Parsons: Division of Genetic and Reproductive Toxicology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR Petra Pfeiffer: Institute of Genetics, University of Essen, Germany David H. Phillips: Section of Molecular Carcinogenesis, Institute of Cancer Research, Sutton, Surrey, UK Andrew J. Pierce: Markey Cancer Center, University of Kentucky, Lexington Pataje G. S. Prasanna: Armed Forces Radiobiology Research Institute, Bethesda, MD Anand Ranjan: National Centre of Applied Human Genetics, Jawaharlal Nehru University, Delhi, India Alexander Rapp: Department for Single Cell and Single Molecule Techniques, Institute for Molecular Biotechnology Jena, Germany Marjorie Romkes: Center for Clinical Pharmacology, University of Pittsburgh, PA Anjana Saha: National Centre of Applied Human Genetics, Jawaharlal Nehru University, Delhi, India Joseph G. Shaddock: Division of Genetic and Reproductive Toxicology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR Kaori Shintani-Ishida: Department of Forensic Medicine, Graduate School of Medicine, University of Tokyo, Japan Therese Sorlie: Department of Genetics, The Norwegian Radium Hospital, Oslo, Norway Gunter Speit: Abteilung Humangenetik, Universitatsklinkum Ulm, Germany Takashi Sugimura: National Cancer Center, Tokyo, Japan Roy R. Swiger: Midwest Research Institute, Palm Bay, FL Vladimir A. Tyurin: Department of Environmental and Occupational Health, University of Pittsburgh, PA Yulia Y. Tyurina: Department of Environmental and Occupational Health, University of Pittsburgh, PA Esther A. Ubick: Biology and Biotechnology Research Program, Lawrence Livermore National Laboratory, CA P. T. Udhayasuriyan: National Centre of Applied Human Genetics, Jawaharlal Nehru University, Delhi, India Andrew T. M. Vaughan: Department of Radiation Oncology, Loyola University Chicago Medical Center, Maywood, IL Michael J. Villalobos: Program in Molecular Biology, Loyola University Chicago Medical Center, Maywood, IL John S. Vogel: Center for Accelerator Mass Spectrometry, Lawrence Livermore National Laboratory, CA Phuong Vu: Department of Genetics, The Norwegian Radium Hospital, Oslo, Norway Xifeng Wu: Department of Epidemiology, M. D. Anderson Cancer Center, Houston, TX Liqiang Xi: Hillman Cancer Center, University of Pittsburgh, PA Yun-Ling Zheng: Laboratory of Human Carcinogenesis, National Cancer Institute, Bethesda, MD Bao-Li Zhu: Department of Legal Medicine, Osaka City University Medical School, Japan

Table of Contents

Preface	v
Contributors	xi
PART I: ANALYSIS OF DNA ADDUCTS
32P-Postlabeling Analysis of DNA Adducts	3	(10)
David H. Phillips
Alan Hewer
Volker M. Arlt
Modification of the 32P-Postlabeling Method to Detect a Single Adduct Species as a Single Spot	13	(8)
Masako Ochiai
Takashi Sugimura
Minako Nagao
DNA Isolation and Sample Preparation for Quantification of Adduct Levels by Accelerator Mass Spectrometry	21	(8)
Karen H. Dingley
Esther A. Ubick
John S. Vogel
Kurt W. Haack
Fluoroimaging-Based Immunoassay of DNA Photoproducts in Ultraviolet-B-Irradiated Tadpoles	29	(10)
Iovanna Pandelova
Stephen R. Hewitt
John B. Hays
Analysis of DNA Strand Cleavage at Abasic Sites	39	(10)
Walter A. Deutsch
Vijay Hegde
Part II: Detection of Chromosomal and Genome-Wide Damage
Premature Chromosome Condensation in Human Resting Peripheral Blood Lymphocytes for Chromosome Aberration Analysis Using Specific Whole-Chromosome DNA Hybridization Probes	49	(10)
Pataje G. S. Prasanna
William F. Blakely
Mutagen-Induced Chromatid Breakage as a Marker of Cancer Risk	59	(10)
Xifeng Wu
Yun-Ling Zheng
T. C. Hsu
Flow Cytometric Analysis of Micronuclei in Erythrocytes	69	(16)
Jan Grawe
The Comet Assay: A Sensitive Genotoxicity Test for the Detection of DNA Damage	85	(12)
Gunter Speit
Andreas Hartmann
Computerized Image Analysis Software for the Comet Assay	97	(10)
R. C. Chaubey
The Comet-FISH Technique: A Tool for Detection of Specific DNA Damage and Repair	107	(14)
Alexander Rapp
Michael Hausmann
Karl Otto Greulich
DNA Double-Strand Break Damage and Repair Assessed by Pulsed-Field Gel Electrophoresis	121	(12)
Nina Joshi
Stephen G. Grant
Part III: Detection and Characterization of Surrogate Gene Mutation
Analysis of In Vivo Mutation in the Hprt and Tk Genes of Mouse Lymphocytes	133	(12)
Vasily N. Dobrovolsky
Joseph G. Shaddock
Robert H. Heflich
Quantifying In Vivo Somatic Mutations Using Transgenic Mouse Model Systems	145	(10)
Roy R. Swiger
Methods for Detecting Somatic Mutations In Vitro: The Human T-Cell Cloning Assay Selecting for HPRT Mutants	155	(6)
Sai-Mei Hou
Molecular Analysis of Mutations in the Human HPRT Gene	161	(10)
Phouthone Keohavong
Liqiang Xi
Stephen G. Grant
Simultaneous Quantification of t(14;18) and HPRT Exon 2/3 Deletions in Human Lymphocytes	171	(8)
James C. Fuscoe
The GPA In Vivo Somatic Mutation Assay	179	(18)
Stephen G. Grant
Flow Cytometric Measurement of Mutant T Cells With Altered Expression of TCR: Detecting Somatic Mutations in Humans and Mice	197	(10)
Seishi Kyoizumi
Yoichiro Kusunoki
Tomonori Hayashi
Part IV: Detection and Characterization of Cancer Gene Mutation
Mutation Screening of the TP53 Gene by Temporal Temperature Gradient Gel Electrophoresis	207	(10)
Therese Sorlie
Hilde Johnsen
Phuong Vu
Guro Elisabeth Lind
Ragnhild Lothe
Anne-Lise Børresen-Dale
Analysis of K-RAS and P53 Mutations in Sputum Samples	217	(18)
Weimin Gao
Phouthone Keohavong
Allele-Specific Competitive Blocker-PCR Detection of Rare Base Substitution	235	(12)
Barbara L. Parsons
Page B. McKinzie
Robert H. Heflich
Gel-Based Nonradioactive Single-Strand Conformational Polymorphism and Mutation Detection: Limitations and Solutions	247	(16)
Vibhuti Gupta
Reetakshi Arora
Anand Ranjan
Narendra K. Bairwa
Dheeraj K. Malhotra
P. T. Udhayasuriyan
Anjana Saha
Ramesh Bamezai
Detection and Characterization of Oncogene Mutations in Preneoplastic and Early Neoplastic Lesions	263	(16)
Toshinari Minamoto
Detection of DNA Double-Strand Breaks and Chromosome Translocations Using Ligation-Mediated PCR and Inverse PCR	279	(14)
Michael J. Villalobos
Christopher J. Betti
Andrew T. M. Vaughan
Part V: Analysis of DNA Repair Mechanisms
Microsatellite Instability: An Indirect Assay to Detect Defects in the Cellular Mismatch Repair Machinery	293	(10)
Anjana Saha
Narendra K. Bairwa
Ramesh Bamezai
Unscheduled DNA Synthesis: A Functional Assay for Global Genomic Nucleotide Excision Repair	303	(18)
Crystal M. Kelly
Jean J. Latimer
Analysis of DNA Repair Using Transfection-Based Host Cell Reactivation	321	(16)
Jennifer M. Johnson
Jean J. Latimer
An Immunoassay for Measuring Repair of Ultraviolet Photoproducts	337	(14)
Shirley McCready
Analysis of DNA Double-Strand Break Repair by Nonhomologous End Joining in Cell-Free Extracts From Mammalian Cells	351	(22)
Petra Pfeiffer
Elke Feldmann
Andrea Odersky
Steffi Kuhfitting-Kulle
Wolfgang Goedecke
Measuring Recombination Proficiency in Mouse Embryonic Stem Cells	373	(14)
Andrew J. Pierce
Maria Jasin
Part VI: Array Technologies
Strategies for Measurement of Biotransformation Enzyme Gene Expression	387	(12)
Marjorie Romkes
Shama C. Buch
Genotyping Technologies: Application to Biotransformation Enzyme Genetic Polymorphism Screening	399	(16)
Marjorie Romkes
Shama C. Buch
TaqMan® Fluorogenic Detection System to Analyze Gene Transcription in Autopsy Material	415	(8)
Kaori Shintani-Ishida
Bao-Li Zhu
Hitoshi Maeda
Development of Quantitative Reverse Transcriptase PCR Assays for Measuring Gene Expression	423	(26)
Tony E. Godfrey
Lori A. Kelly
Part VII: Apoptosis
Quantification of Selective Phosphatidylserine Oxidation During Apoptosis	449	(8)
James P. Fabisiak
Yulia Y. Tyurina
Vladimir A. Tyurin
Valerian E. Kagan
Quantitative Method of Measuring Phosphatidylserine Externalization During Apoptosis Using Electron Paramagnetic Resonance Spectroscopy and Annexin-Conjugated Iron	457	(8)
James P. Fabisiak
Grigory G. Borisenko
Valerian E. Kagan
Detection of Programmed Cell Death in Cells Exposed to Genotoxic Agents Using a Caspase Activation Assay	465	(8)
Michael E. Gehring
Patrick P. Koty
Index	473