1. Maternal-Fetal Toxicology : A Cinician‘s Guide. Third Edition / by by Gideon KorenMarcel Dekker, Inc. 2001
Content
1. Pharmacokinetic Changes During Pregnancy and Their Clinical Relevance 1
2. Developmental Risk Assessments 23
3. Drugs in Pregnancy 37
4. Teratogenic Drugs and Chemicals in Humans 57
5. Treatment for Epilepsy in Pregnancy 73
6. The Safety of Commonly Used Antidepressants in Pregnancy 85
7. Benzodiazipine Use in Pregnancy and Major Malformations or Oral Cleft: Meta-Analysis of Cohort and Case-Control Studies 105
8. Drugs and Chemicals Most Commonly Used by Pregnant Women 115
9. Periconceptional Folate and Neural Tube Defects: Time for Rethinking 137
10. The Effectiveness of Preectiveness of Preconceptional Counseling on Women‘s Compliance with Folic Acid Supplementation 141
11. Pregnancy Outcome Following Maternal Exposure to Corticosteroids: A Prospective Controlled Cohort Study and Meta-Analysis of Epidemiological Studies 151
2. Toxicology of Skin / by by Howard I. MaibachTaylor & Francis 2001
Content
1. Irritant Dermatitis 3
2. Percutaneous Absorption 129
3. Allergic Contact Dermatitis 207
4. Contact Urticaria 383
5. Miscellaneous 403
3. Genetically Engineered Organisms : Assessing Environmental and Human Health Effects / by by Deborah K. Letourneau and Beth Elpern BurrowsCRC Press 2002
Content
1. Variability and uncertainty in crop-to-wild hybridization 1
2. Factors affecting the spread of resistant Arabidopsis thaliana populations 17
3. Bt-Crops: Evaluating benefits under cultivation and risks from escaped transgenes in the wild 33
4. Resisting resistance to Bt-corn 99
5. Ecological risks of transgenic virus-resistant crops 125
6. Impacts of genetically engineered crops on non-target herbivores: Bt-corn and monarch butterflies as a case study 143
7. Transgenic host plant resistance and non-target effects 167
8. Release, persistence, and biological activity in soil of insecticidal proteins from Bacillus thuringiensis 187
9. Survival, persistence, transfer: The fate of genetically modified microorganisms and recombinant DNA in different environments 223
10. The spread of genetic constructs in natural insect populations 251
11. Ecological and community considerations in engineering arthropods to suppress vector-borne disease 315
12. Environmental risks of genetically engineered vaccines 331
13. Methods to assess ecological risks of transgenic fish releases 355
14. Controversies in designing useful ecological assessments of genetically engineered organisms 385
5. Food Toxicology / by William Helferich and Carl K. WinterCRC Press 2001
Content
1. Food Allergies and Sensitivities 1
2. Dietary Estrogens and Antiestrogens 37
3. Nonnutrient Antitoxicants in Food 57
4. Safety of Genetically Engineered Foods 77
5. Microbial Toxins in Foods: Algal, fungal, and Bacterial 93
6. Natural Toxins and Chemopreventives in Plants 137
7. Pesticide Residues in the Food Supply 163
8. Food Additives 187
9. Analysis of Chemical Toxicants and Contaminants in Foods 203
6. Toxicology Secrets / by by Louis J. Ling and Richard F. Clark et alHanley & Belfus, Inc. 2001
Content
1. General Principles 1
2. Over-The-Counter Drugs 23
3. Prescription Medications 45
4. Antibiotics 63
5. Cardiac Drugs 73
6. Psychopharmacologic Medications 87
7. Drugs of Abuse 113
8. Metals 153
9. Chemicals 171
10. Pesticides 185
11. Gases 203
12. Food Poisoning 227
13. Botanicals 245
14. Envenomations 261
15. Toxic Terrorist Threats 285
7. Toxicological Carcinogenesis / by by David B. ClaysonCRC Press 2001
Content
1. Investigation of Cancer Causation 9
2. Possible in the Workplace 39
3. Reducing the Risk of Cancer 113
8. Functional Genomics: methods and protocols / edited by Michael J. Brownstein and Arkady B. KhodurskyHumana Press c2003
Content
1.Fabrication of cDNA Microarrays 1
2.Nylon cDNA Expression Arrays 9
3.Plastic Microarrays:A Novel Array Support Combining the Benefits of Macro- and Microarrays 31
4.Preparing Fluorescent Probes for Microarray Studies 55
5.Escherichia coli Spotted Double-Strand DNA Microarrays: RNA Extraction, Labeling, Hybridization, Quality Control, and Data Management 61
6.Isolation of Polysomal RNA for Microarray Analysis 79
7.Parallel Analysis of Gene Copy Number and Expression Using cDNA Microarrays 89
8.Genome-wide Mapping of Protein-DNA Internations by Chromatin immunoprecipitation and DNA Microarray Hybridization 99
9.Statisical Issues in CDNA Microarray Data Analysis 111
10.Experimental Design to Make the Most of Microarray Studies 137
11.Statistical Methods for Identifying Differentially Expressed 149
12.Detecting Stable Clusters Using Principal Component Analysis 159
13.Clustering in Life Sciences 183
14.A Primer on the Visualization of Microarray Data 219
15.Microarray Databases:Storage and Retrieval of Microarray Data 235
9. Tumor Suppressor Genes. V.2:Regulation, Function, and Medicinal Applications / edited by Wafik S. El-DeiryHumana Press c2003
Content
1.Pt.1:Understanding the Function and Regulation of Tumor Suppressor Genes 3
2.Pt.2:Medicinal Applications of Tumor Suppressors 415
10. Guide to Cytochromes P450 / by David F.V.LewisTaylor & Francis 2001
Content
1.Introduction 1
2.Evolution of the P450 Superfamily 20
3.The P450 Catalytic Cycle 51
4.Substrate Selectivity and Metabolism 76
5.Regulation of P450 Enzymes 118
6.The Structures of Cytochromes P450 140
11. Bioinformatics / by David R. Westhead et. AlBIOS Scientific Publishers Limited 2002
Content
1. Overview of bioinformatics 1
2. Data acquisition 9
3. Databases - contents, structure and annotation 29
4. Retrieval of biological data 51
5. Searching sequence databases by sequence 59
6. Multiple sequence alignment: gene and protein families 83
7. Phylogenetics 97
8. Sequence annotation 113
9. Structural bioinformatics 123
10. Microarray data analysis 165
11. Proteomic data analysis 179
12. Higher-order systems 189
13. Cheminformatics in biology 203
14. Bioinformatics in the pharmaceutical industry 215
15. Basic principles of computing in bioinformatics 227
12. RT-PCR Protocols / by Joe O‘ConnellHumana Press 2002
Content
Preface v
Contritutors xi
1.Introduction 3
2.Highly Sensitive Detection and Analysis of mRNA 29
3.Quantitative RT-PCR 83
4.Detection and Analysis of RNA Viruses 151
5.In Situ Localization of mRNA Expression 191
6.Differenital mRNA Expression 227
7.Genetic Analysis 253
8.RT-PCR in Immunology 267
9.RT-PCR in Anti-Sense Technology 341
10.RT-PCR in cDNA Cloning 349
Index 375
13. DNA Microarrays and Gene Expression : From experiments to data analysis and modeling / by Pierre Baldi and G. Wesley HatfieldCambridge University Press 2002
Content
1.A brief history of genomics 1
2.DNA array formats 7
3.DNA array readout methods 17
4.Gene expression profiling experiments: Problems,pitfalls, and solutions 29
5.Statistical analysis of array data: Inferring changes 53
6.Statistical analysis of array data: Dimensionality reduction, clustering, and regulatory regions 73
7.The design, analysis, and interpretation of gene expression profiling experiments 97
8.Systems biology 135
14. Proteomics in Practice : A Laboratory Manual of Proteome Analysis / by Reiner WestermeierWiley-VCH 2002
Content
Preface ix
Foreword xi
Abbreviations, symbols, units xiii
Glossary of terms xvii
1.Proteomics Technology 1
2.Course Manual 161
References 295
Index 311
15. In Situ Detection of DNA Damage : Methods and Protocols / by Vladimir V. DidenkoHumana Press 2002
Content
Preface v
Contributors xiii
Color Plates xvii
1.Labeling DNA Breaks Using Terminal Transferase (TUNEL Assay) 3
2.Labeling DNA Breaks Using DNA Polymerase I or Its Klenow Fragment 81
3.Labeling DNA Breaks Using Ligase 133
4.Detection of DNA Breaks in Agarose Trapped Cells: Comet Assay and Related Techniques 163
5.Detection of Modified Bases and AP Sites in DNA 219
16. High Throughput Screening : Methods and Protocols / by William P. JanzenHumana Press 2002
Content
1. Design and Implementation of High Throughput Screening Assays 1
2. Configuring Radioligand Receptor Binding Assays for HTS Using Scintillation Proximity Assay Technology 31
3. Homogeneous Techniques for Monitoring Receptor-Ligand Interactions 51
4. Comparison of SPA, FRET, and FP for kinase Assays 65
5. Electrochemiluminescence 87
6. Cellular Assays in HTS 107
7. Compound Library Management 117
8. Compound Library Management: An Overview of an Automated System 129
9. Natural Products or Not? 153
10. Introduction to Screening Automation 169
11. Unit Automation in High Throughput Screening 195
12. Fully Automated Screening Systems 213
13. Management and Maintenance of High Throughput Screening Systems 229
17. In Vitro Mutagenesis Protocols--- Second Edition / by Jeff Braman : Humana Press Inc. 2002
Contents
Dedication v
Preface vii
Contributors xiii
1. Rapid and Reliable Site-Directed Mutagenesis Using Kunkel‘s Approach 1
2. Site-Directed Mutagenesis Using Altered β-Lactamase Specificity 7
3. Site-Directed Mutagenesis Facilitated by DpnI Selection on Hemimethylated DNA 19
4. Multiple Site-Directed Mutagenesis In Vitro 29
5. Two-Stage Polymerase Chain Reaction Protocol Allowing Introduction of Multiple Mutations, Deletions, and Insertions, Using QuikChangeTM Site-Directed Mutagenesis 37
6. Efficient and Accurate Site-Directed Mutagenesis of Large Plasmids 45
7. Combining Site-Specific Chemical Modification with Site-Directed Mutagenesis : Versatile Strategy to Move Beyong Structural Limitations of 20 Natural Amino Acids Side Chains in Protein Engineering 55
8. Site-Directed Mutagenesis Mediated by a Single Polymerase Chain Reaction Product 67
9. Megaprimer Method for Polymerase Chain Reaction-Mediated Generation of Specific Mutations in DNA 71
10. Generation of Epitope-Tagged Proteins by Inverse Polymerase Chain Reaction Mutagenesis 77
11. Site-Directed Mutagenesis by Polymerase Chain Reaction 85
12. Generation of Multiple Site-Specific Mutations by Polymerase Chain Reaction 95
13. Phenotypic Expression of Polymerase Chain Reaction-Generated Random Mutations in a Foreign Gene After its Introduction into an Acinetobacter Chromosome by Natural Transformation 103
14. Polymerase Chain Reaction-Mediated Mutagenesis in Sequences Resistant to Homogeneous Amplification 117
15. Polymerase Chain Reaction-Based Signature-Tagged Mutagenesis 127
16. High-Throughput Scanning Mutagenesis by Recombination Polymerase Chain Reaction 139
17. In Vitro Scanning-Saturation Mutagenesis 149
18. Random Transposon Mutagenesis of Large DNA Molecules in Escherichia coli 165
19. Random Chromosomal Gene disruption Using Cassette Mutagenesis 173
20. Transplacement Mutagenesis : A Recombination-Based In Situ Mutagenesis Protocol 189
21. Preparation of Transposon Insertion Lines and Determination of Insertion Sites in Arabidopsis Genome 209
22. Evolutionary Molecular Engineering by Random Elongation Mutagenesis 221
23. Random Mutagenesis for Protein Breeding 231
24. DNA Shuffling and Family Shuffling for In Vitro Gene Evolution 243
25. Mutagenic Polymerase Chain Reaction of Protein-Coding Genes for In Vitro Evolution 259
Index 269
18. Comprehensive Toxicology : Volume 14 - Cellular and Molecular Toxicology / Edited by John P. Vanden Heuvel and Gary H. Perdew et al : Elsevier 2002
Contents
Preface vii
Contributors to Volume 14 ix
Introduction xiii
14.1 Basic Concepts 1
14.1.1 Introduction to Molecular Toxicology 1
14.1.2 Exposure-Dose-Response: A Molecular Perspective 13
14.1.3 Receptor Theory and that Ligand-Macromolecule Complex 29
14.1.4 Control of Gene Expression 57
14.2 Xenobiotic Receptor Systems 81
14.2.1 Introduction and Overview 81
14.2.2 The (PAS) Protein Superfamily 107
14.2.3 The Aryl Hydrocarbon Receptor: A Model of Gene-Environment Interactions 119
14.2.4 Peroxisomes, Peroxisome Proliferators and Peroxisome Proliferator-Activated Receptors (PPARs) 133
14.2.5 The Physiological Role of Pregnane-X-Receptor (PXB) in Xenobiotic and Bile Acid Homeostasis 159
14.2.6 Regulation of Phenobarbital Responsiveness via the Constitutive Androstane Receptor (CAR) 173
14.2.7 Mechanisms of Metal-Induction of Metallothionein Gene Expression 187
14.2.8 Modulation of Soluble Receptor Signaling by Coregulators 201
14.2.9 Convergence of Multiple Nuclear Receptor Signaling Pathways in the Mediation of Xenobiotic-Induced Nongenotoxic Carcinogenesis 221
14.3 Genetic Determinants of Susceptibility to Environmental Agents 239
14.3.1 Introduction and Overview 239
14.3.2 Molecular Biomarkers for Human Liver Cancer 249
14.3.3 Inherited Susceptibility and Prostate Cancer Risk 267
14.3.4 Modeling Genetic Susceptibility to Cancer in the Mouse 283
14.3.5 DNA Methylation and Gene Silencing 299
14.4 Alterations of Cell Signaling by Xenobiotics 311
14.4.1 Introduction and Overview 311
14.4.2 Mitogen-Activated Protein Kinase (MAPK) Signal Transduction Pathways Regulated by Stresses and Toxicants 333
14.4.3 Antioxidant Induction of Genes Encoding Detoxifying Enzymes 377
14.4.4 Hypoxia Regulation of Genes Expression through HIF1 Signaling 389
14.4.5 Epigenetic-Toxicant Induced Modulated Gap Junctional Intercellular Communication 409
14.4.6 Environmental Influences on Cell Cycle Regulation 421
14.4.7 Biochemical Signals that Initiate Apoptosis 443
14.5 Emerging Technologies and Predictive Assays 463
14.5.1 Introduction and Overview 463
14.5.2 Bioinformatics 493
14.5.3 Interpretation of Toxicogenomic Data using Genetically-Altered Mice 515
14.5.4 Proteomic Applications in Toxicology 539
14.5.6 Mechanistically-Based Assays for the Identification and Characterization of Endocrine Disruptors 559
14.5.7 Metabonomic Technology as a Tool for Rapid Throughput in vivo Toxicity Screening 583
14.5.8 Data Mining Toxicology 611
Appendix 629
19. Transgenesis Techniques : Principles and Protocols--- Second Edition / by Alan R. Clarke : Humana Press Inc. 2002
Contents
Preface v
Contributors ix
Part I. Topical Reviews in Transgenesis
1. Biomedical and Agricultural Applications of Animal Transgenesis 3
Part II. Transgenesis in Invertebrate and Lower Vertebrate Species
2. Gene Transfer in Drosophila 27
Part III. Transgenesis in the Mouse : Oocyte Injection
3. Oocyte Injection in the Mouse 39
Part IV. Alternative Routes To The Germline
4. Adenoviral Infection 73
5. Retroviral Infection 83
Part V. Transgenesis in the Mouse : The ES Cell Route
6. In Vitro Isolation of Murine Embryonic Stem Cells 93
7. Production of Chimeras Derived from Murine Embryonic Stem Cells 127
8. Gene Targeting Strategies 151
9. Cre/IoxP Recombination System and Gene Targeting 175
Part VI. Cryopreservation of Mouse Lines
10. Cryopreservation of Transgenic Mouse Lines 207
11. Ovarian Tissue Transplantation and Cryopreservation : Application to Maintenance and Recovery of Transgenic and Inbred Mouse Lines 229
Part VII. Transgenesis in the Rat
12. Transgenesis in the Rat 255
Part VIII. Transgenesis in Domestic Species
13. Generation of Transgenic Livestock by Pronuclear Injection 273
14. Transgenic Sheep from Cultured Cells 289
Part IX. Characterization and Analysis of Transgenic Strains
15. Analysis of Transgenic Mice 305
Index 343
20. DNA Methylation Protocols / Edited by Ken I. Mills : Humana Press Inc. 2002
Contents
Preface v.
Contributors ix
1. Overview 1
2. Nearest-neighbor Analysis 9
3. Measurement of Genome-Wide DNA Cytosine-5 Methylation by Reversed-Phase High-Pressure Liquid Chromatography 17
4. Methylation Analysis by Chemical DNA Sequencing 29
5. Methylation-Sensitive Restriction Fingerprinting 43
6. Restriction Landmark Genome Scanning 53
7. Combined Bisulfite Restriction Analysis (COBRA) 71
8. Differential Methylation Hybridization Using CpG Island Arrays 87
9. Methylated CpG Island Amplification for Methylation Analysis and Cloning Differentially Methylated Sequences 101
10. Isolation of CpG Islands Using a Methyl-CpG Binding Column 111
11. Purification of MeCP2-Containing Deacetylase from Xenopus laevis 131
12. DNA-Methylation Analysis by the Bisulfite-Assisted Genomic Sequencing Method 143
13. Measuring DNA Demethylase Activity In Vitro 155
14. Extracting DNA Demethylase Activity from Mammalian Cells 163
Index 177
21. Apoptosis Techniques and Protocols : Second Edition / Edited by Andrea C. LeBlanc : Humana Press 2002
Contents
Preface to the Series v
Preface vii
Contributors xiii
Molecular Characterization of the Proapoptotic Protein Bax 1
Assessing Cytochrome-c Release from Mitochondria 21
Monitoring Caspases in Neuronal Cell Death 35
HSV Amplicon Vectors in Neuronal Apoptosis Studies 61
Microinjections to Study the Specific Role of Proapoptotic Proteins in Neurons 83
Designing Microarray Experiments for Neurobiology 107
Analysis of Gene Expression by Nylon Membrane cDNA Arrays 133
Glyceraldehyde-3-phosphate Dehydrogenase as a Target for Antiapoptotic Drugs 149
Analytical Approaches for Investigating Apoptosis and Other Biochemical Events in Compartmented Cultures of Sympathetic Neurons 163
Detection and Analysis of Synaptosis 177
In Situ Detection of Apoptotic Neurons 205
Apoptotic and Oxidative Indicators in Alzheimer,s Disease 225
22. Biomarkers of Disease: An Evidence-Based Approach
Contents
1. Assessing and utilizing the diagnostic or prognostic power of biomarkers 3
2. Biomarkers of kidney disease and dysfunction 45
3. Biomarkers of bone disease and dysfunction 99
4. Biomarkers of liver disease and dysfunction 167
5. Biomarkers of gastrointestinal disease and dysfunction 265
6. Biomarkers in toxicology 291
7. Biomarkers of cardiovascular disease and dysfunction 325
8. Biomarkers of neurological disease and dysfunction 391
9. Biomarkers in transplantation 415
Index 483
23. Handbook of Neurotoxicology Volume 1
contents
1. Acute Toxicities of Organophosphates and Carbamates 3
2. Organophosphate-Induced Delayed Neuropathy 17
3. Nonesterase Actions of Anticholinesterase Insecticides 29
4. Agents Affecting Sodium Channels 47
5. Agents Affecting Chloride Channels 65
6. The Neonicotinoid Insecticides 79
7. Miscellaneous Pesticides with Action on the Nervous System 91
8. Molecular Mechanisms of Low-Level Pb2+ Neurotoxicity 107
9. Elucidation of the Zinc-Finger Motif as a Target for Heavy-Metal Perturbations 135
10. Blood-Brain Barrier and Blood-CSF Barrier in Metal-Induced Neurotoxicities 161
11. Manganese in Health and Disease: From Transport to Neurotoxicity 195
12. Aluminum Neurotoxicity 211
13. Ecology of Microbial Neurotoxins 239
14. Biosynthesis of Important Marine Toxins of Microorganism Origins 257
15. Biological Assay and Detection Methods for Marine "Shellfish" Toxins 269
16. An Overview of Clostridial Neurotoxins 293
17. Molecular Mechanism of Action of Botulinal Neurotoxins and the Synaptic Remodeling They Induce In Vivo at the Skeletal Neuromuscular Junction 305
18. Marine Mammals as Sentinels of Environmental Biotoxins 349
19. The Epidemiology of Human Illnesses Associated with Harmful Algal Blooms 363
20. Snake Neurotoxins that Interact with Nicotinic Acetylcholine Receptors 385
21. Presynaptic Phospholipase A2 Neurotoxins from Snake Venoms 427
22. Dendrotoxins from Mamba Snakes 455
23. Neurotoxins from Spider Venoms 475
24. Neurotoxins from Scorpion Venoms 503
25. Anthozoan Neurotoxins 529
26. Nemertine Neurotoxins 573
27. Secretagogue Activity of Trachynilysin, a Neurotoxic Protein Isolated from Stonefish (Synanceia trachynis) Venom 595
28. Neurotoxins of Cone Snail Venoms 617
Index 653
24. Handbook of Neurotoxicology Volume II
contents
1. Developmental Neurotoxicology: Testing and Interpretation 3
2. Manifestations of CNS Insult During Development 57
3. Developmental Neurotoxicity: What Have We Learned from Guideline Studies? 81
4. Risk Assessment of Developmental Neurotoxicants 111
5. Electrophysiologic Evidence of Neural Injury or Adaptation in Cocaine Dependence 131
6. Addictive Basis of Marijuana and Cannabinoids 155
7. Dopamine and Its Modulation of Drug-Induced Neuronal Damage 175
8. NMDA Antagonist-Induced Neurotoxicity and Psychosis: The Dissociative Stimulation Hypothesis 199
9. Emerging Drugs of Abuse: Use Patterns and Clinical Toxicity 223
10. Mechanisms of Methamphetamine-Induced Neurotoxicity 259
11. Neurotoxic Effects of Substituted Amphetamines in Rats and Mice: Challenges to the Current Dogma 269
12. Studies of Neural Degeneration Indicate that Fasciculus Retroflexus Is a Weak Link in Brain for Mnay Drugs of Abuse 303
13. Microsensors Detect Neuroadaptation by Cocaine: Serotonin Released in motor Basal Ganglia Is Not Rhythmic 323
14. Impact of Intoxication: Structural and Functional Modifications in the Brain Induced by Ethanol Exposure 371
15. Structural and Functional Neuroimaging of the Effects of Opioids 397
16. Structural and Functional Neuroimaging of the Effects of Cocaine in Human and Nonhuman Primates 413
17. Functional Neuroimaging of Cannabinoid Effects 437
18. Neuroimaging of MDMA-Induced Neurotoxicity 445
19. Tier 1 Neurological Assessment in Regulated Animal Safety Studies 461
20. Neurological Assessment: The role of the Clinician in Clinical Neurotoxicology 507
21. Human Neuropsychological Testing and Evaluation 551
Index 581
25. Human Frontiers, Environments and Disease
contents
1. Disease patterns in human biohistory 1
2. Human biology: the pleistocene inheritance 30
3. Adapting to diversity: climate, food and infection 58
4. Infectious disease: humans and microbes coevolving 88
5. The Third horseman: food, farming and famines 123
6. The industrial era: the Fifth horseman? 152
7. Longer lives and lower birth rates 185
8. Modern affluence: lands of milk and honey 220
9. Cites, social environments and synapses 250
10. Global environmental change: overstepping limits 283
11. Health and disease: an ecological perspective 318
12. Footprints to the future: treading less heavily 341
Notes 366
Index 403