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The goal of Environmental Genomics is to serve as a manual for an environmental scientist who wishes to embrace genomics to answer environmental questions. The volume is divided into the sections: gene expression profiling, whole genome and chromosome mutation detection, and methods to assay genome diversity and polymorphisms within a particular environment. The studies presented will reduce the uncertainties associated with environmental risk assessment and provide a systematic framework for determining environmental impact and ensuring human health and the sustainability of natural populations.
TABLE OF CONTENTS Methods in Molecular Biology - Environmental Genomics Preface - C. Cristofre Martin Section 1: Gene expression profiling Chapters: 1. High-throughput Whole Mount in situ Hybridization of Zebrafish Embryos for Analysis Tissue Specific Gene Expression Changes Following Environmental Perturbation. Louise E. Coverdale, Lindsay E. Burton, and C. Cristofre Martin 2. Fluorescent RNA Arbitrarily Primed (FRAP) PCR - A New Differential Display Approach To Detect Contaminant-Induced Alterations Of Gene Expression In Wildlife Species. Doug Crump, Suzanne Chiu, Vance Trudeau & Sean Kennedy 3. Isolation of O3-response Genes from Arabidopsis thaliana using cDNA Macroarray. Masanori Tamaoki 4. Use Of cDNA Macroarrays And Gene Profiling For Detection Of Effects By Environmental Toxicants. Jason L. Blum, Melinda S. Prucha, Vishal J. Patel, and Nancy D. Denslow 5. Constructing and Screening a cDNA library: Methods for Identification and Characterization of Novel Genes Expressed Under Conditions of Environmental Stress. Kevin Larade and Kenneth B. Storey 6. Comparative Molecular Physiological Genomics: Heterologous probing of cDNA arrays. Sean F. Eddy and Kenneth B. Storey 7. Proteomic Analysis of Neuroendocrine Peptidergic System Disruption Using the AtT20 Pituitary Cell Line as a Model. Fumin Dong, Liming Ma, Michel Chretien and Majambu Mbikay 8 Proteomics Based Method For Risk Assessment Of Peroxisome Proliferating Pollutants In The Marine Environment. Susana Cristobal 9. Environmental Metabolomics using 1H NMR Spectroscopy. Mark R. Viant Section 2: Detection of whole genome mutation 10. Restriction Landmark Genome Scanning for the Detection of Mutations. Jun-ichi Asakawa, 11. Use of the Comet Assay in Environmental Toxicology. Loren Knopper and James P. McNamee 12. The Micronucleus Assay Determination of Chromosomal Level DNA Damage. Michael Fenech 13. Fluorescence In Situ Hybridization (FISH) For The Detection Of Chromosome Aberrations And Aneuploidy Induced By Environmental Toxicants. Francesca Pacchierotti and Antonella Sgura 14. Laboratory Methods For The Detection Of Chromosomal Structural Aberrations In Human And Mouse Sperm By Fluorescence In Situ Hybridization (FISH). Francesco Marchetti, Debby Cabreros and Andrew J Wyrobek Section 3: Determination of Species Diversity 15. Assembling DNA Barcodes: Analytical Protocols. Jeremy R. deWaard, Natalia V. Ivanova, Mehrdad Hajibabaei and Paul D.N. Hebert 16. Application of Suppressive Subtractive Hybridization to Uncover the Metagenomic Diversity of Environmental Samples. Elizabeth A. Galbraith, Dionysios A. Antonopoulos and Bryan A. White 17. 16S rRNA Targeted DGGE Fingerprinting Of Microbial Communicities. Vesela A. Tzeneva, Hans G. H. J. Heilig, Wilma Akkermans van Vliet, Antoon D. L. Akkermans, Willem M. de Vos, Hauke Smidt 18. An Emulsion PCR-Based Method for Molecular Haplotyping. James G. Wetmur and Jia Chen
From the reviews: "This book provides a thought-provoking selection of well-described and diverse techniques to apply to further our understanding of how organisms respond to the environment. ... The techniques are all accessible to a laboratory equipped for molecular biology and this book would provide an excellent addition to any environmental molecular biology laboratory book shelf, institutional library or individual researcher's collection." (Elizabeth Wellington and Emma Travis, Microbiology Today, November, 2008)