Note: Cover -- The Coronavirus Pandemic and the Future Volume 2: Virology, Epidemiology, Translational Toxicology and Therapeutics -- Dedication -- Foreword -- Preface -- Contents -- Contents -- Chapter 1 - In Silico Approaches for Drug Repurposing for SARS-CoV- 2 Infection -- 1.1 Introduction -- 1.1.1 What is Drug Repurposing -- 1.1.2 Why Drug Repurposing -- 1.1.2.1 Regulatory Considerations -- 1.1.3 Why Drug Repurposing for COVID-19? -- 1.1.4 Why In Silico Approaches for Drug Repurposing -- 1.1.4.1 Gene Profiling -- 1.1.4.2 In Vitro Screening -- 1.1.4.3 Phenotypic Screening -- 1.1.4.4 Binding Assays for Target Interactions -- 1.1.4.5 Cellular Thermal Shift Assay -- 1.1.4.6 The In Silico Effort -- 1.2 Understanding SARS-CoV- 2 from an In Silico Perspective -- 1.2.1 Structural Proteins of SARS-CoV- 2 -- 1.2.1.1 Surface Spike Protein (S-protein) -- 1.2.1.2 Nucleocapsid Protein (N-protein) -- 1.2.1.3 Envelope Protein (E-protein) -- 1.2.1.4 Membrane Protein (M-protein) -- 1.2.2 Non-structural and Accessory Proteins of SARS-CoV- 2 -- 1.2.3 Structure of SARS-CoV- 2 Proteins -- 1.3 Structure-based Approaches for Drug Repurposing -- 1.3.1 Docking Studies in the Main Protease (Mpro/3CLpro) -- 1.3.1.1 Crystal Structures Used in Docking -- 1.3.1.2 Methods or Programs Used in Docking -- 1.3.1.3 Ligands and Databases Used for Screening -- 1.3.1.4 Molecular Dynamics Programs Used -- 1.3.1.5 Duration of MD Simulation -- 1.3.1.6 Free-energy Estimation Method Used -- 1.3.1.7 Analysis of Hit Drugs from Docking -- 1.3.1.8 Some Noteworthy Studies on Mpro -- 1.3.1.8.1 Study Reporting Good Correlation of Predicted Binding Affinity with Experiments.Huynh et al. performed MD simulation of apo and ... -- 1.3.1.8.2 Studies Using Pharmacophore or Shape-based Methods for Screening of Drugs. Arun. , 1.3.1.8.3 Novel Methods of Screening. Sencanski et al. reported a novel two-step approach to identify -- 1.3.1.8.4 Studies in which Important Observations are Reported.Jin et al. reported identification of lead compounds by combining structure... -- 1.3.2 Docking Studies in RNA-dependent RNA Polymerase -- 1.3.3 Docking Studies in Papain-like Protease -- 1.3.4 Docking Studies in the Nucleocapsid Protein (N-protein) -- 1.3.5 Docking Studies in the Spike Glycoprotein (S-protein) -- 1.3.6 Docking Studies in NSP1 -- 1.3.7 Docking Studies in NSP13/Helicase -- 1.3.8 Docking Studies in NSP15/Endonucleases -- 1.3.9 Docking Studies in NSP16 -- 1.3.10 Docking in Main Protease and Spike Glycoprotein -- 1.3.11 Docking in Multiple Structural Proteins -- 1.3.12 Docking in Proteases -- 1.3.13 Docking in Multiple Targets -- 1.3.13.1 Studies Involving Large Numbers of Targets -- 1.3.13.2 Studies Involving Main Protease and Other Targets -- 1.3.13.3 Studies on Mixed Targets -- 1.3.14 Discussion and Consensus Screening Protocol from the Reviewed Literature -- 1.4 Ligand-based Approaches for Drug Repurposing -- 1.4.1 QSAR-based Approaches -- 1.4.2 Pharmacophore-based Approaches -- 1.5 Other Approaches for Drug Repurposing -- 1.5.1 Machine Learning-based Methods -- 1.5.1.1 Machine Learning Using Molecular Descriptors -- 1.5.1.2 Machine Learning Using Docking Interactions -- 1.5.2 Pharmacology-based Network Analysis Methods -- 1.5.2.1 Protein-Protein Interactions -- 1.5.2.2 Expression Profiling -- 1.6 Understanding Human Targets in COVID-19 From an In Silico Perspective -- 1.6.1 Host Proteins Involved in the SARS-CoV- 2 Life Cycle -- 1.6.2 Host Response to SARS-CoV- 2 Infection -- 1.6.2.1 SARS-CoV- 2 Induced Immune Response -- 1.6.3 Structural Information of Human Proteins in COVID-19 -- 1.7 Structure-based Approaches for Drug Repurposing Using Human Proteins. , 1.7.1 Docking Studies in Angiotensin Converting Enzyme-2 -- 1.7.1.1 Targeting the ACE-2 Receptor -- 1.7.1.2 Targeting ACE-2 and Spike Receptor -- 1.7.1.3 Targeting ACE-2 and Spike Receptor in Addition to Network-based Associations -- 1.7.2 Docking Studies in Transmembrane Protease, Serine 2 (TMPRSS2) -- 1.7.3 Docking Studies in Glucose-Regulated Protein 78 (GRP78) -- 1.7.4 Docking Studies in Furin -- 1.7.5 Docking Studies in ARDS Targets -- 1.7.5.1 TNF-­α -- 1.8 Summary of Hits from Reviewed Literature -- 1.9 Concluding Remarks -- 1.10 Executive Summary -- Author Contributions -- Acknowledgements -- References -- Chapter 2 - Vaccination and Vaccines for COVID-19 -- 2.1 Introduction -- 2.2 Vaccination in the Context of a Pandemic Outbreak -- 2.3 COVID-19 -- 2.3.1 Specific Strategies for COVID-19 -- 2.3.1.1 DNA Vaccines -- 2.3.1.2 mRNA Vaccines -- 2.3.1.3 Attenuated Vaccines -- 2.4 Mental Health Aspects of Immunization and Vaccination -- 2.5 Vaccines for COVID-19 -- 2.5.1 SARS-CoV-2 -- 2.5.2 Immune Response to SARS-CoV- 2 and Previous Coronavirus Infections -- 2.5.3 Platforms for COVID-19 Vaccine Development -- 2.5.3.1 DNA-based Vaccines -- 2.5.3.1.1 Inovio.Inovio Pharmaceuticals is an American company based in Plymouth Meeting, Pennsylvania, USA, that specializes in manufactu... -- 2.5.3.2 RNA-based Vaccines -- 2.5.3.2.1 Moderna/NIAID. Moderna is an American company based in Cambridge, Massachusetts, that has developed an mRNA -based vaccine, mRNA -1273. The mRNA vaccine -- 2.5.3.2.2 BioNTech/Fosun/Pfizer.BioNTech, a German company, together with Pfizer, an American company, have developed another mRNA- based ... -- 2.5.3.3 Non-replicating Viral Vector Vaccines -- 2.5.3.3.1 AstraZeneca/University of Oxford. The University of Oxford has formed a partnership with the -- 2.5.3.4 Inactivated Vaccines. , 2.5.3.4.1 Wuhan Institute of Biological Products/Beijing Institute of Biological Products.The above institutions and the pharmaceutical co... -- 2.5.3.4.2 Indian Vaccine Development.There are several institutions including academic/research and vaccine manufacturing companies in Ind... -- 2.5.3.5 Challenges in COVID-19 Vaccine Development -- 2.6 Executive Summary -- References -- Chapter 3 - Understanding the Emergence of SARS-CoV- 2 Viral Variants From a Genomic Perspective -- 3.1 Introduction -- 3.2 A History of Pandemics -- 3.3 Origin and Classification of SARS-CoV-2 -- 3.4 Genomic Architecture of SARS-CoV- 2 -- 3.4.1 Overview -- 3.4.2 Structural Proteins -- 3.4.3 Non-structural Proteins -- 3.5 The Emergence of SARS-CoV- 2 Variants -- 3.6 Antigenic Variations and Immune Escape Mutations -- 3.7 Leading Vaccines Across the Globe -- 3.8 Conclusion -- References -- Chapter 4 - Susceptibility and Spread of SARS-CoV- 2 in Animals -- 4.1 Introduction -- 4.2 Wild Animals -- 4.3 Laboratory Animals -- 4.4 Companion Animals -- 4.5 Farmed Animals -- 4.6 Conclusions -- References -- Chapter 5 - Profiling Some Plant-based Immunomodulatory Bioactive Compounds for COVID-19 Prophylaxis and Treatment Based on Indian Traditional Medicine -- 5.1 Introduction -- 5.2 Prevention of SARS-CoV- 19 Infection: Stage 1 -- 5.3 Incubation to Non-severe Symptomatic Phase - Stage 2 -- 5.4 Severe Respiratory Symptomatic Phase with Hyperinflammation - Stage 3 -- 5.5 Multi-organ Response to COVID-19 Infection - Stage 4 -- 5.6 Summary and Outlook -- 5.7 Executive Summary -- List of Abbreviations -- Authors' Contributions -- Declaration of Competing Interest -- Acknowledgements -- References -- Chapter 6 - The Potential Therapeutic Effects of Natural Products, Herbs, and Mushrooms Against COVID-19 -- 6.1 Origins and Pathogenesis of COVID-19. , 6.2 The Immune Profile in COVID-19Infection -- 6.3 Natural Marine Compounds as Potent Inhibitors Against SARS-CoV- 2 -- 6.4 Potential Use of Mushrooms and Herbs Against COVID-19 Infection -- 6.5 Conclusion -- References -- Chapter 7 - Application of Chinese Herbal Medicine in COVID-19 -- 7.1 Introduction -- 7.2 Representative Prescriptions -- 7.2.1 Qingfei Paidu Decoction (QFPDD, 清 排毒汤) -- 7.2.2 Huashi Baidu Formula (HSBDF, 化湿 毒方) -- 7.2.3 XuanFei Baidu Formula (XFBDF, 宣 毒方) -- 7.3 Finished Patent Medicines -- 7.3.1 Lianhua Qingwen Capsules (LH-­C, 清瘟 囊) -- 7.3.2 Jinhua Qingan Granules (JH-­G, 清感 粒) -- 7.3.3 Xuebijing Injection (XBJ, 必净注射液) -- 7.4 Other Chinese Herbs -- 7.4.1 Ephedra Herba (Ma Huang, ) -- 7.4.2 Honeysuckle (Jin Yin Hua, ) -- 7.4.3 Scutellariae (Huang Qin, ) -- 7.4.4 Glycyrrhizae Radix (Gan Cao, 甘 ) -- 7.4.5 Armeniacae Semen (Ku Xing Ren, 杏仁) -- 7.4.6 Sophorae flavescentis Radix (Ku Shen, 参) -- 7.4.7 Curcuma longa (Jiang Huang, 姜 ) -- 7.5 Conclusion -- List of Abbreviations -- References -- Chapter 8 - COVID-19 Interventional and Therapeutic Clinical Trials: Small Molecules, Interactions, Outcomes and Opportunities -- 8.1 Introduction -- 8.2 Removal-of- treatment Preventative Clinical Trials -- 8.2.1 Trial Aims -- 8.2.2 Trial Populations -- 8.2.3 Potential Therapeutics -- 8.2.4 Trial Designs -- 8.2.5 Primary Outcomes -- 8.2.6 Secondary Outcomes -- 8.2.7 Toxicities -- 8.2.8 Opportunities -- 8.3 Addition-of- treatment Preventative and/or Curative Trials -- 8.3.1 Trial Aims -- 8.3.2 Trial Populations -- 8.3.3 Potential Therapeutics -- 8.3.4 Trial Designs -- 8.3.5 Primary Outcomes -- 8.3.6 Secondary Outcomes -- 8.3.7 Toxicity -- 8.3.7.1 Population-specific Toxicity -- 8.3.7.2 Interactions -- 8.3.8 Opportunities -- 8.4 Supportive Clinical Trials -- 8.4.1 Trial Aims -- 8.4.2 Trial Populations -- 8.4.3 Potential Therapeutics. , 8.4.4 Trial Designs.

Note: Cover -- The Coronavirus Pandemic and the Future Volume 1: Virology, Epidemiology, Translational Toxicology and Therapeutics -- Dedication -- Foreword -- Preface -- Contents -- Contents -- Chapter 1 - What We Know About the Life- threatening Novel Human Coronavirus -- 1.1 Introduction -- 1.2 The Chronology of the Outbreak -- 1.3 Initial Transmission -- 1.3.1 Worldwide Spread of the Virus -- 1.4 SARS-CoV- 2 and Its Etiology -- 1.5 Classification and Grouping -- 1.5.1 Alpha- CoVs -- 1.5.2 Beta- CoVs -- 1.5.3 Gamma- CoVs -- 1.5.4 Delta- CoVs -- 1.6 Epidemiological History of Human Coronaviruses -- 1.6.1 Severe Acute Respiratory Syndrome -- 1.6.2 Middle East Respiratory Syndrome -- 1.6.3 Detailed Documentation of SARS- CoV- 2 and COVID- 19 -- 1.7 Introductory Virology and Pathophysiology of SARS- CoV- 2 -- 1.7.1 Viral Genome -- 1.7.2 Interaction of the Spike and Receptor for Entry -- 1.7.3 Genomic Differences -- 1.7.4 Pathophysiology -- 1.8 Executive Summary and Conclusions -- List of Abbreviations -- Acknowledgements -- References -- Chapter 2 - Severe Acute Respiratory Syndrome Coronavirus- 2 (SARS-CoV- 2): Structure, Lifecycle, and Replication Machinery -- 2.1 Introduction -- 2.2 Classification of Coronaviruses -- 2.3 Genomic Structure of SARS- CoV-Ł2 -- 2.4 Life Cycle of SARS- CoV- 2 -- 2.4.1 Attachment and Entry -- 2.4.2 Replicase Protein Expression -- 2.4.3 Replication and Transcription -- 2.4.4 Assembly and Release -- 2.5 SARS- CoV- 2 RNA Replication Machinery -- References -- Chapter 3 - Accumulated Epidemiological Lessons and China's COVID- 19 Response -- 3.1 Introduction -- 3.2 Accumulated Lessons from China's Response to SARS in 2003 -- 3.3 Epidemiologicial Perspective on China's COVID- 19 Response -- 3.4 China's Control and Prevention Measures in COVID- 19 -- 3.4.1 Mask- wearing and its Comforting Effect. , 3.4.2 Epidemiological Source- tracking and Slow- down of Community Transmission -- 3.5 Comparing China's Response Against SARS and COVID- 19 -- 3.6 Concluding Remarks -- 3.7 Executive Summary -- References -- Chapter 4 - Clinical Presentation, Pathophysiology and Histopathology -- 4.1 Introduction -- 4.1 Introduction -- 4.2 The Distinct Clinical Trajectory and Disease Spectrum of COVID- 19 -- 4.3 A Novel Application of Smartphone Technology -- 4.4 COVID- 19 and Comorbidities in Severe Cases -- 4.5 ARDS and its Sequelae in COVID- 19 -- 4.5.1 ARDS in COVID- 19 -- 4.5.2 Sepsis -- 4.5.3 Septic Shock -- 4.6 Pathophysiology -- 4.6.1 Mechanism of SARS-Cov- 2 Invasion into Host Cells -- 4.7 Histopathology and Disease Manifestations: Introduction -- 4.7.1 Histopathology -- 4.7.2 Pulmonary Manifestations -- 4.7.3 Cardiovascular Manifestations -- 4.7.4 Gastrointestinal Manifestations -- 4.7.5 Renal Manifestations -- 4.7.6 Neurological Manifestations -- 4.7.7 Musculocutaneous Manifestations -- 4.7.8 Hematological Manifestations -- 4.8 Executive Summary -- Acknowledgements -- References -- Chapter 5 - Evaluation of the Disease, Sample Collection and Diagnostics -- 5.1 Introduction -- 5.1.1 Symptoms of COVID- 19 -- 5.1.2 Detection of Disease Based on Symptoms -- 5.1.3 Evaluation Criteria for COVID- 19 Based on ICMR and WHO Guidelines -- 5.2 Sample Collection -- 5.2.1 Overview of Sample Collection Guidelines from the WHO -- 5.2.1.1 Nasopharyngeal or Oropharyngeal Swabs -- 5.2.1.2 Nasal Mid- turbinate Swab -- 5.2.1.3 Anterior Nares Specimen -- 5.2.1.4 Nasopharyngeal Wash/Aspirate or Nasal Wash/Aspirate -- 5.2.1.5 Bronchoalveolar Lavage, Tracheal Aspirate, Pleural Fluid, Lung Biopsy -- 5.2.1.6 Sputum (Phlegm) -- 5.2.1.7 Saliva -- 5.2.1.8 Other -- 5.3 Recent Diagnostics -- 5.3.1 Molecular Diagnostics -- 5.3.2 Laboratory Examinations (Modified from Cascella et al.17). , 5.3.3 Imaging -- 5.3.3.1 Chest X- ray -- 5.3.3.2 Chest CT -- 5.3.3.3 Lung Ultrasound -- 5.3.3.4 Scanning Techniques -- 5.3.4 Blood Parameter Levels (Laboratory Diagnostics) -- 5.3.5 Genetic Susceptibility to COVID- 19 -- 5.3.6 Importance of Real-time RT-PCR in the Detection of COVID- 19 -- 5.3.6.1 Viral Nucleic Acid Detection -- 5.3.7 Serological Assays -- 5.3.8 Enzyme- linked Immunosorbent Assay -- 5.3.9 Magnetic Chemiluminescence Enzyme Immunoassay -- 5.3.10 Colloidal Gold Immunochromatographic Assay -- 5.3.11 Lateral Flow Immunoassay -- 5.3.12 Rapid Antigen Test -- 5.3.13 Neutralization Antibody Assay -- 5.3.14 Other Useful Diagnostics for COVID- 19 -- 5.3.15 False Negatives and Positives -- 5.4 Advantages and Disadvantages of Different Diagnostic Approaches -- 5.4.1 Detection Based on Patient History -- 5.4.2 Detection of Disease Based on Symptoms -- 5.4.3 Scanning Techniques -- 5.4.3.1 CT Scan -- 5.4.3.2 Chest X- ray -- 5.4.3.3 18F- FDG PET/CT -- 5.4.4 Laboratory Serum Diagnostics (e.g. WBC, Inflammatory Markers) -- 5.4.5 Molecular Diagnosis -- 5.4.5.1 RT- PCR -- 5.4.5.2 RT- LAMP -- 5.4.5.3 Transcription- mediated Amplification -- 5.4.6 CRISPR- based Diagnosis -- 5.4.7 Serological Assays -- 5.4.7.1 ELISA -- 5.4.7.2 GICA -- 5.4.7.3 MCLIA -- 5.4.7.4 Lateral Flow Immunoassay -- 5.4.7.5 Neutralization Bioassay -- 5.4.7.6 Rapid Antigen Test -- 5.5 Executive Summary -- Acknowledgements -- References -- Chapter 6 - Therapeutic Options Initially Available for COVID- 19 Patients and Initial Clinical Trials -- 6.1 Introduction to Therapeutic Options Initially Available for COVID- 19 Patients -- 6.1.1 General Guidelines for the Treatments Provided to COVID- 19 Patients -- 6.1.2 Common Treatment Regimens Provided to COVID- 19 Patients -- 6.1.3 Medicinal Plants as Therapy for COVID- 19 -- 6.1.4 Convalescent Plasma Therapy. , 6.1.5 Mesenchymal Stem Cell-Derived Exosomes as Therapy for COVID- 19 -- 6.1.6 Other Treatment Options -- 6.1.6.1 Corticosteroids -- 6.2 Introduction to Ongoing Clinical Trials -- 6.2.1 Ongoing Trials on Various Antiviral Agents -- 6.2.2 Immunosuppressants/Immunomodulators -- 6.2.3 Current Trials on MSCs for COVID- 19 -- 6.3 Executive Summary -- Acknowledgements -- References -- Chapter 7 - Clinical Epidemiology of Coronavirus Disease 2019: Infectivity, Clinical Spectrum and Presentation, and Population Distribution -- 7.1 Introduction -- 7.2 Infection and Tests -- 7.2.1 Viral Tests -- 7.2.2 Population- based Infection Rate -- 7.2.3 Antibody Tests -- 7.3 Clinical Spectrum of COVID- 19 -- 7.3.1 Classification by Clinical Type -- 7.3.2 Asymptomatic Cases -- 7.3.3 Severe Cases and Comorbidity -- 7.3.4 Clinical and Immunological Response -- 7.4 Regional Variation in Clinical Presentation -- 7.4.1 Clinical Manifestation -- 7.4.2 Chemosensory Dysfunction -- 7.4.3 Common Symptoms -- 7.4.3.1 Asia -- 7.4.3.2 USA -- 7.4.3.3 Europe -- 7.5 Population Distribution -- 7.5.1 Pregnancy and Pregnant Women -- 7.5.2 Infants and Pediatric Patients -- 7.5.3 Asymptomatic Cases and Clinical Severity in Children -- 7.5.4 Older Adults -- 7.5.5 Sex Differences -- 7.5.6 Occupation -- 7.6 Case- fatality Rate -- 7.7 Executive Summary and Conclusions -- References -- Chapter 8 - SARS-CoV-2 Genomics and Host Cellular Susceptibility Factors of COVID- 19 -- 8.1 Introduction -- 8.2 Coronavirus and Human Diseases -- 8.2.1 Classification of Coronaviruses -- 8.2.2 Human Coronaviruses and Diseases -- 8.2.3 The Natural Origin of HCoVs -- 8.3 Genomic Structure and Genetics -- 8.3.1 Viral Genomic Structure -- 8.3.2 The Replicase Locus and Proteins -- 8.3.2.1 Nonstructural Proteins -- 8.3.2.2 Structural Proteins -- 8.3.2.3 Accessory Proteins -- 8.3.3 Genomic Mutations. , 8.4 Viral Replication -- 8.4.1 Attachment and Cell Entry -- 8.4.2 Translation and RNA Replication -- 8.4.3 Assembly and Release of Virion -- 8.5 Host Cellular Factors -- 8.5.1 ACE2 -- 8.5.2 TMPRSS2 -- 8.5.3 Furin -- 8.5.4 DPP4 -- 8.5.5 CD147 -- 8.5.6 GRP78 -- 8.5.7 Cathepsins -- 8.5.8 Ly6E -- 8.5.9 L- SIGN and DC- SIGN -- 8.5.10 Sialic Acid -- 8.5.11 Plasmin and Other Proteases -- 8.6Executive Summary -- References -- Chapter 9 - Infection and Pathogenesis of SARS-CoV- 2: an Immunological Perspective -- 9.1 Introduction -- 9.2 SARS-CoV- 2 Virology -- 9.2.1 Structure -- 9.2.2 Genome -- 9.2.3 Proteome -- 9.2.4 Mutation -- 9.2.5 Transmission -- 9.3 Pathogenesis -- 9.3.1 Attachment to the Host Cell -- 9.3.2 Penetration of SARS-CoV- 2 Inside the Host Cell -- 9.3.3 Assembly of the RTC -- 9.3.4 Genome Replication, Transcription, and Translation -- 9.3.5 Virion Assembly and Release -- 9.3.6 Incubation Period -- 9.4 Disease Progression -- 9.5 Immunology -- 9.5.1 Innate Immune Response -- 9.5.1.1 Evasion of Innate Sensing by SARS-CoV- 2 -- 9.5.1.1.1 Evasion of PRR Sensing.Coronavirus- mediated antagonism starts with the evasion of PRR recognition. The ssRNA of coronaviruses c... -- Inhibition of Signalling Cascades. As described, TLR and RLR activation induces signalling cascades, which leads to the release ... -- Inhibition of IFN-1396983920I. Based on previous studies, various mechanisms have been adopted by coronaviruses to inhibit IFN-1... -- 9.5.1.2 Imbalanced Antiviral Defense and Pro- inflammatory Cytokine Production -- 9.5.1.3 Macrophages -- Macrophage Responses to SARS-CoV- 2 Infection.Macrophages and monocytes accumulate and trigger cytokine secretion, leading to c... -- 9.5.1.4 Alveolar type II ATII Cells in the Innate Immune Response -- 9.5.1.5 Neutrophils -- 9.5.1.6 Dendritic Cells -- 9.5.1.7 Natural Killer Cells. , 9.5.1.7.1 Modification of NK Cells Upon SARS-CoV- 2 Infection.Studies on peripheral blood samples of COVID- 19 patients have shown that i.

Note: The Comet Assay in Toxicology -- Contents -- Section I: Genesis of Comet Assay -- Chapter 1 The Comet Assay: A Versatile Tool for Assessing DNA Damage -- 1.1 Introduction -- 1.2 Bacteria -- 1.3 Plant Models -- 1.3.1 The Comet Assay in Lower Plants -- 1.3.2 The Comet Assay in Higher Plants -- 1.4 Animal Models -- 1.4.1 Lower Animals -- 1.5 Higher Animals -- 1.5.1 Vertebrates -- 1.6 The Specificity, Sensitivity and Limitations of the Comet Assay -- 1.7 Conclusions -- Acknowledgements -- References -- Section II: Various Procedures for the Comet Assay -- Chapter 2 Detection of Oxidised DNA Using DNA Repair Enzymes -- 2.1 Introduction -- 2.2 Methods for Measuring DNA Oxidation Damage -- 2.3 Enzyme Specificity -- 2.4 Applications -- 2.5 Protocol -- 2.5.1 Equipment -- 2.5.2 Supplies -- 2.5.3 Reagents, Buffers and Enzymes -- 2.5.4 Procedure -- Acknowledgment -- References -- Chapter 3 Microplate-Based Comet Assay -- 3.1 Introduction -- 3.2 Microplate Comet Assay -- 3.3 Drinking-Water Disinfection Byproducts -- 3.4 Chinese Hamster Ovary Cells -- 3.5 CHO Cell Microplate Comet Assay Protocol -- 3.5.1 CHO Cell Treatment -- 3.5.2 Preparation of Comet Microgels -- 3.5.3 Comet Microscopic Examination -- 3.5.4 Normalisation of CHO Cell Comet Data and Statistical Analysis -- 3.6 Utility of the Microplate Comet Assay in Comparing Classes of DBPs -- 3.6.1 Microplate Comet Analysis of the Haloacetonitriles -- 3.6.2 Microplate Comet Analysis of the Haloacetamides -- 3.6.3 Comparison of SCGE Genotoxic Potency Values of the Haloacetonitriles and Haloacetamides -- 3.7 Advantages of the Mammalian CellMicroplate Comet Assay -- Acknowledgements -- References -- Chapter 4 The Use of Higher Plants in the Comet Assay -- 4.1 Introduction -- 4.2 Differences between the Animal and Plant Comet Assay -- 4.3 Cultivation and Treatment of Plants for the Comet Assay. , 4.3.1 Onion (Allium cepa) -- 4.3.2 Tobacco (Nicotiana tabacum) -- 4.3.3 Broad Bean (Vicia faba) -- 4.3.4 Plants used for In-Situ Studies -- 4.4 Isolation of Nuclei from Plant Tissues -- 4.4.1 Isolation of Nuclei via Protoplast Formation -- 4.4.2 Isolation of Nuclei by Mechanical Destruction of the Cell Wall -- 4.5 Preparation of Comet Assay Slides -- 4.6 DNA Unwinding and Electrophoresis -- 4.7 DNA Staining -- 4.8 Reading the Slides, Expressing DNA Damage, Statistics -- 4.9 Comet Assay Procedure -- 4.10 Reagents, Media, Buffers -- 4.11 Equipment and Software -- 4.12 Determination of Toxicity -- 4.13 Correlation between the DNA Damage Evaluated by the Comet Assay and Other Genetic Endpoints in Plants -- 4.14 The Utility of the Comet Assay for Genotoxic Studies in the Laboratory -- 4.15 The Utility of the Comet Assay as an In Situ Marker -- 4.16 Comet Assay with Irradiated Food of Plant Origin -- 4.17 Recommendations for Plant Comet Assay Users -- Abbreviations -- References -- Chapter 5 Methods for Freezing Blood Samples at -80°C for DNA Damage Analysis in Human Leukocytes -- 5.1 Introduction -- 5.2 Materials and Methods -- 5.2.1 Protocol I -- 5.2.2 Protocol II -- 5.2.3 Fresh Blood -- 5.2.4 Fresh Blood Stored on Ice Prior to Freezing -- 5.2.5 Image and Data Analysis -- 5.3 Results and Discussion -- References -- Chapter 6 Development and Applications of the Comet-FISH Assay for the Study of DNA Damage and Repair -- 6.1 Introduction -- 6.2 The Comet-FISH Assay Procedure -- 6.3 Applications of the Comet-FISH Assay -- 6.3.1 Discovery of the Comet-FISH Assay -- 6.3.2 Using Comet-FISH to Measure DNA Damage -- 6.3.3 Using Comet-FISH to Quantify DNA Repair -- 6.3.4 Summary of Studies -- 6.4 Limitations of Comet-FISH Assay -- 6.4.1 Practical Difficulties -- 6.4.2 Imaging Difficulties -- 6.4.3 Interpretation of Results -- 6.5 Conclusion -- References. , Chapter 7 Detection of DNA Damage in Drosophila and Mouse -- 7.1 General Protocol for the Assessment of DNA Damage Using the Alkaline Comet Assay -- 7.1.1 Chemicals and Materials -- 7.1.2 Preparation of Reagents -- 7.1.3 Preparation of Agarose-Coated (Base) Slides for the Comet Assay -- 7.1.4 Preparation of Microgel Slides for the Comet Assay -- 7.1.5 Electrophoresis of Microgel Slides -- 7.1.6 Evaluation of DNA Damage -- 7.2 The Alkaline Comet Assay in Multiple Organs of Mouse -- 7.2.1 Chemicals and Materials -- 7.2.2 Methodology -- 7.3 The Alkaline Comet Assay in Drosophila melanogaster -- 7.3.1 Chemicals and Materials -- 7.3.2 Methodology -- 7.4 Conclusions -- Acknowledgements -- References -- Section III: Applications of Comet Assay -- Chapter 8 Clinical Applications of the Comet Assay -- 8.1 Introduction -- 8.2 The Comet Assay Methodology -- 8.3 Clinical Studies -- 8.4 Discussion and Conclusions -- References -- Chapter 9 Applications of the Comet Assay in Human Biomonitoring -- 9.1 Biomonitoring and Biomarkers - An Introduction -- 9.2 The (Modified) Comet Assay -- 9.3 Guidelines for Biomonitoring Studies -- 9.4 Biomonitoring with the Comet Assay: Special Considerations -- 9.4.1 Surrogate and Target Cells -- The Use of White Blood Cells -- 9.4.2 Sampling Time and Transport -- 9.4.3 Reference Standards -- 9.4.4 What Affects the Background Level of DNA Damage? -- 9.5 DNA Damage as a Marker of Environmental Exposure and Risk -- 9.6 DNA Repair as a Biomarker of Individual Susceptibility -- 9.7 Protocols -- 9.7.1 Protocol for Blood Sample Collection and Long-Term Storage of Lymphocytes for the Measurement of DNA Damage and Repair -- 9.7.2 Comet Assay - Determination of DNA Damage (Strand Breaks and Oxidised Bases) -- 9.7.3 In Vitro Assays for DNA Repair -- 9.8 Solutions, etc. -- 9.8.1. Lysis Solution. , 9.8.2. Buffer F (Enzyme Reaction Buffer for FPG, Endonuclease III, and In Vitro BER Assay) -- 9.8.3 Buffer F+Mg (Used for In Vitro NER Assay) -- 9.8.4 Buffer A (Used in In Vitro Repair Assays) -- 9.8.5 Triton Solution -- 9.8.6 Ro 19-8022 (Photosensitiser) -- 9.8.7 Electrophoresis Solution -- 9.8.8 Neutralising Buffer -- 9.8.9 Agarose -- 9.8.10 Enzymes -- 9.9 Analysis and Interpretation of Results -- 9.9.1 Quantitation -- 9.9.2 Calculation of Net Enzyme-Sensitive Sites -- 9.9.3 Calibration -- 9.9.4 How to Deal with Comet Assay Data Statistically -- 9.10 Conclusions -- Acknowledgements -- References -- Chapter 10 The Comet Assay in Human Biomonitoring -- 10.1 Introduction -- 10.2 Human Monitoring -- 10.3 Environmental Exposure -- 10.4 Lifestyle Exposure -- 10.5 Occupational Exposure -- 10.6 Reviews -- 10.7 Usefulness of the Comet Assay in Human Monitoring -- 10.8 Conclusions -- References -- Chapter 11 Comet Assays in Dietary Intervention Trials -- 11.1 Introduction -- 11.2 Experimental Design of Human Studies -- 11.3 Indicator Cells and Media -- 11.4 Conventional SCGE Trials with Complex Foods and Individual Components - The Current State of Knowledge -- 11.5 Use of SCGE Trials to Detect Protection Against DNA-Reactive Carcinogens -- 11.6 Use of SCGE Experiments to Monitor Alterations of the DNA-Repair Capacity -- 11.7 What Have We Learned from Intervention Studies so Far? -- 11.8 Future Perspectives -- References -- Chapter 12 The Comet Assay for the Evaluation of Genotoxic Exposure in Aquatic Species -- 12.1 Introduction -- 12.2 Protocols, Cell Types and Target Organs -- 12.3 Application of the Comet Assay to Invertebrate Species -- 12.3.1 Freshwater Invertebrates -- 12.3.2 Marine Invertebrates -- 12.4 Application of the Comet Assay to Vertebrate Species -- 12.4.1 Freshwater Vertebrates -- 12.4.2 Marine Vertebrates -- 12.5 Conclusions -- References. , Chapter 13 The Alkaline Comet Assay in Prognostic Tests for Male Infertility and Assisted Reproductive Technology Outcomes -- 13.1 Introduction -- 13.2 Sites of DNA Damage in Sperm -- 13.2.1 Oxidative Stress, a Major Cause of DNA Damage -- 13.2.2 Oxidative Stress, Antioxidant Therapies -- 13.2.3 Sperm DNA Damage Tests -- 13.2.4 Modifications to the Alkaline Comet Assay for Use with Sperm -- 13.2.5 Sperm DNA Adducts and their Relationship with DNA Fragmentation -- 13.3 Can Sperm DNA Integrity Predict Success? Relationships with Assisted Conception Outcomes -- 13.4 Clinically Induced DNA Damage -- 13.4.1 Cryopreservation -- 13.4.2 Vasectomy -- 13.5 A Major Barrier to Progress -- 13.6 Opportunities and Challenges - The Establishment of Clinical Thresholds and the Integration of DNA Testing into Clinical Practice -- Acknowledgements -- References -- Chapter 14 The Comet Assay in Sperm - Assessing Genotoxins in Male Germ Cells -- 14.1 Introduction -- 14.2 Single-Cell Gel Electrophoresis -- 14.3 The Use of Sperm with the Comet Assay -- 14.3.1 Human Sperm -- 14.3.2 Modifying Existing Comet Protocols for the Use of Sperm -- 14.3.3 Sperm DNA and the Comet Assay -- 14.3.4 The Sperm Comet Assay and the Use of Repair Enzymes -- 14.3.5 Assessing the Sperm Comet -- 14.3.6 Comet-FISH on Sperm -- 14.3.7 Cryopreserved versus Fresh Sperm -- 14.3.8 Viability Considerations -- 14.3.9 Statistical Analysis -- 14.4 Utilising Male Germ Cells with the Comet Assay -- 14.4.1 In Vivo Comet Assay -- 14.4.2 In Vitro Comet Assay -- 14.5 The Sperm Comet Assay versus Other Assays Used in Reproductive Toxicology -- 14.6 Conclusions -- Acknowledgements -- References -- Section IV: Regulatory, Imaging and Statistical Considerations -- Chapter 15 Comet Assay - Protocols and Testing Strategies -- 15.1 Introduction -- 15.2 Applications of the In Vivo Comet Assay for Regulatory Purposes. , 15.3 Recommendations for Test Performance.

Note: Cover -- Preface -- Contents -- Section I: Genesis of Comet Assay -- Chapter 1 The Comet Assay: A Versatile Tool for Assessing DNA Damage -- 1.1 Introduction -- 1.1.1 Bacteria -- 1.2 Plant Models -- 1.2.1 The Comet Assay in Lower Plants and Fungi -- 1.2.2 The Comet Assay in Higher Plants -- 1.3 Animal Models -- 1.3.1 Lower Animals -- 1.4 Higher Animals -- 1.4.1 Vertebrates -- 1.5 The Specificity, Sensitivity and Limitations of the Comet Assay -- 1.6 Conclusions -- References -- Section II: Various Procedures for the Comet Assay -- Chapter 2 High-throughput Measurement of DNA Breaks and Oxidised Bases with the Comet Assay -- 2.1 Introduction -- 2.2 Methods for Measuring DNA Oxidation Damage -- 2.3 Enzyme Specificity -- 2.4 Applications -- 2.5 Protocol -- 2.5.1 Equipment -- 2.5.2 Supplies -- 2.5.3 Reagents, Buffers and Enzymes -- 2.5.4 Procedure -- Acknowledgments -- References -- Chapter 3 Microplate-based Comet Assay -- 3.1 Introduction -- 3.2 Microplate Comet Assay -- 3.3 Drinking-water Disinfection Byproducts -- 3.4 Chinese Hamster Ovary Cells -- 3.5 CHO Cell Microplate Comet Assay Protocol -- 3.5.1 CHO Cell Treatment -- 3.5.2 Preparation of Comet Microgels -- 3.5.3 Comet Microscopic Examination -- 3.5.4 Normalisation of CHO Cell Comet Data and Statistical Analysis -- 3.6 Utility of the Microplate Comet Assay in Comparing Classes of DBPs -- 3.6.1 Microplate Comet Analysis of the Haloacetonitriles -- 3.6.2 Microplate Comet Analysis of the Haloacetamides -- 3.6.3 Comparison of SCGE Genotoxic Potency Values of the Haloacetonitriles and Haloacetamides -- 3.7 Advantages of the Mammalian Cell Microplate Comet Assay -- Acknowledgments -- References -- Chapter 4 The Use of Higher Plants in the Comet Assay -- 4.1 Introduction -- 4.2 Differences between the Animal and Plant Comet Assay -- 4.3 Cultivation and Treatment of Plants for the Comet Assay. , 4.3.1 Onion (Allium cepa) -- 4.3.2 Tobacco (Nicotiana tabacum) -- 4.3.3 Broad Bean (Vicia faba) -- 4.3.4 Plants Used for In situ Studies -- 4.4 Isolation of Nuclei from Plant Tissues -- 4.4.1 Isolation of Nuclei via Protoplast Formation -- 4.4.2 Isolation of Nuclei by Mechanical Destruction of the Cell Wall -- 4.5 Preparation of Comet Assay Slides -- 4.6 DNA Unwinding and Electrophoresis -- 4.7 DNA Staining -- 4.8 Reading the Slides, Expressing DNA Damage, Statistics -- 4.9 Comet Assay Procedure -- 4.10 Reagents, Media, Buffers -- 4.11 Equipment and Software -- 4.12 Determination of Toxicity -- 4.13 Correlation between the DNA Damage Evaluated by the Comet Assay and Other Genetic Endpoints in Plants -- 4.14 The Utility of the Comet Assay for Genotoxic Studies in the Laboratory -- 4.15 The Utility of the Comet Assay as an In situ Marker -- 4.16 Comet Assay with Irradiated Food of Plant Origin -- 4.17 Recommendations for Plant Comet Assay Users -- Abbreviations -- References -- Chapter 5 Methods for Freezing Blood Samples at -80°C for DNA Damage Analysis in Human Leukocytes -- 5.1 Introduction -- 5.2 Materials and Methods -- 5.2.1 Protocol I -- 5.2.2 Protocol II -- 5.2.3 Fresh Blood -- 5.2.4 Fresh Blood Stored on Ice Prior to Freezing -- 5.2.5 Image and Data Analysis -- 5.3 Results and Discussion -- References -- Chapter 6 Development and Applications of the Comet-FISH Assay for the Study of DNA Damage and Repair -- 6.1 Introduction -- 6.2 The Comet-FISH Assay Procedure -- 6.3 Applications of the Comet-FISH Assay -- 6.3.1 Discovery of the Comet-FISH Assay -- 6.3.2 Using Comet-FISH to Measure DNA Damage -- 6.3.3 Using Comet-FISH to Quantify DNA Repair -- 6.3.4 Summary of Studies -- 6.4 Limitations of Comet-FISH Assay -- 6.4.1 Practical Difficulties -- 6.4.2 Imaging Difficulties -- 6.4.3 Interpretation of Results -- 6.5 Conclusion -- References. , Chapter 7 Detection of DNA Damage in Different Organs of the Mouse -- 7.1 Introduction -- 7.2 The Alkaline Comet Assay in Multiple Organs of Mice -- 7.2.1 Chemicals and Materials -- 7.2.2 Methodology -- 7.3 Conclusions -- Acknowledgments -- References -- Chapter 8 Detection of DNA Damage in Drosophila -- 8.1 Introduction -- 8.2 General Protocol for the Assessment of DNA Damage Using the Alkaline Comet Assay -- 8.2.1 Chemicals and Materials -- 8.2.2 Preparation of Reagents -- 8.2.3 Preparation of Agarose Coated (Base) Slides for the Comet Assay -- 8.2.4 Preparation of Microgel Slides for the Comet Assay -- 8.2.5 Electrophoresis of Microgel Slides -- 8.2.6 Evaluation of DNA Damage -- 8.3 The Alkaline Comet Assay in Drosophila melanogaster -- 8.3.1 Chemicals and Materials -- 8.3.2 Methodology -- 8.4 Conclusion -- Acknowledgments -- References -- Section III: Applications of Comet Assay -- Chapter 9 The Comet Assay: Clinical Applications -- 9.1 Introduction -- 9.2 The Comet Assay Methodology -- 9.3 Clinical Studies -- 9.4 Discussion and Conclusions -- References -- Chapter 10 Applications of the Comet Assay in Human Biomonitoring -- 10.1 Biomonitoring and Biomarkers - An Introduction -- 10.2 The (Modified) Comet Assay -- 10.3 Guidelines for Biomonitoring Studies -- 10.4 Biomonitoring with the Comet Assay: Special Considerations -- 10.4.1 Surrogate and Target Cells -- The Use of White Blood Cells -- 10.4.2 Sampling Time and Transport -- 10.4.3 Reference Standards -- 10.4.4 What Affects the Background Level of DNA Damage? -- 10.5 DNA Damage as a Marker of Environmental Exposure and Risk -- 10.6 DNA Repair as a Biomarker of Individual Susceptibility -- 10.7 Protocols -- 10.7.1 Protocol for Blood Sample Collection and Long-term Storage of Lymphocytes for the Measurement of DNA Damage and Repair. , 10.7.2 Comet Assay - Determination of DNA Damage (Strand Breaks and Oxidised Bases) -- 10.7.3 In vitro Assays for DNA Repair -- 10.8 Solutions, etc. -- 10.8.1 Lysis Solution -- 10.8.2 Buffer F (Enzyme Reaction Buffer for FPG, End on uclease III, and In vitro BER Assay) -- 10.8.3 Buffer F+Mg (Used for In vitro NER Assay) -- 10.8.4 Buffer A (Used in In vitro Repair Assays) -- 10.8.5 Triton Solution -- 10.8.6 Ro 19-8022 (Photosensitiser) -- 10.8.7 Electrophoresis Solution -- 10.8.8 Neutralising Buffer -- 10.8.9 Agarose -- 10.8.10 Enzymes -- 10.9 Analysis and Interpretation of Results -- 10.9.1 Quantitation -- 10.9.2 Calculation of Net Enzyme-sensitive Sites -- 10.9.3 Calibration -- 10.9.4 How to Deal with Comet Assay Data Statistically -- 10.10 Conclusions -- Acknowledgments -- References -- Chapter 11 Comet Assay in Human Biomonitoring -- 11.1 Introduction -- 11.2 Human Monitoring -- 11.3 Environmental Exposure -- 11.4 Lifestyle Exposure -- 11.5 Occupational Exposure -- 11.6 Reviews -- 11.7 Usefulness of the Comet Assay in Human Monitoring -- 11.8 Conclusions -- References -- Chapter 12 Use of Single-cell Gel Electrophoresis Assays in Dietary Intervention Trials -- 12.1 Introduction -- 12.2 Different Endpoints -- 12.3 Experimental Design of Human Studies -- 12.4 Indicator Cells and Media -- 12.5 Conventional SCGE Trials With Complex Foods and Individual Components-The Current State of Knowledge -- 12.5.1 Definition of the Quality Score (QS) -- 12.6 Use of SCGE Trials to Detect Protection Against DNA-reactive Carcinogens -- 12.7 Use of SCGE-experiments to Monitor Alterations of the DNA-repair Capacity (Base- and Nucleotide-excision Repair) -- 12.8 What Have We Learned From Intervention Studies So Far? -- 12.9 Future Perspectives -- 12.9.1 Hot Topics -- 12.9.2 Detection of Antioxidants -- 12.9.3 Standardization. , 12.9.4 Search for Mechanistic Explanations -- 12.9.5 Interpretation Problems -- References -- Chapter 13 The Application of the Comet Assay in Aquatic Environments -- 13.1 Introduction -- 13.2 Protocols, Cell Types and Target Organs -- 13.3 Application of the Comet Assay to Invertebrate Species -- 13.3.1 Freshwater Invertebrates -- 13.3.2 Marine Invertebrates -- 13.4 Application of the Comet Assay to Vertebrate Species -- 13.4.1 Freshwater Vertebrates -- 13.4.2 Marine Vertebrates -- 13.5 Conclusions -- References -- Chapter 14 The Alkaline Comet Assay in Prognostic Tests for Male Infertility and Assisted Reproductive Technology Outcomes -- 14.1 Introduction -- 14.2 Sites of DNA Damage in Sperm -- 14.2.1 Oxidative Stress, a Major Cause of DNA Damage -- 14.2.2 Oxidative Stress, Antioxidant Therapies -- 14.2.3 Sperm DNA Damage Tests -- 14.2.4 Modifications to the Alkaline Comet Assay for Use with Sperm -- 14.2.5 Sperm DNA Adducts and their Relationship with DNA Fragmentation -- 14.3 Can Sperm DNA Integrity Predict Success? Relationships with Assisted Conception Outcomes -- 14.4 Clinically Induced DNA Damage -- 14.4.1 Cryopreservation -- 14.4.2 Vasectomy -- 14.5 A Major Barrier to Progress -- 14.6 Opportunities and Challenges - The Establishment of Clinical Thresholds and the Integration of DNA Testing into Clinical Practice -- Acknowledgments -- References -- Chapter 15 The Comet Assay in Sperm-Assessing Genotoxins in Male Germ Cells -- 15.1 Introduction -- 15.2 The Comet Assay (Single-cell Gel Electrophoresis) -- 15.3 The Use of Sperm with the Comet Assay -- 15.3.1 Human Sperm -- 15.3.2 Sperm DNA and the Comet Assay -- 15.3.3 Modifying Existing Comet Protocols for Somatic Cells for Use with Sperm -- 15.3.4 The Two-tailed Sperm Comet Assay -- 15.3.5 The Sperm Comet Assay and the Use of Repair Enzymes -- 15.3.6 Assessing the Sperm Comet. , 15.3.7 Comet-FISH on Sperm.

Note: Front Cover -- MUTAGENICITY: ASSAYS AND APPLICATIONS -- MUTAGENICITY: ASSAYS AND APPLICATIONS -- Copyright -- CONTENTS -- LIST OF CONTRIBUTORS -- FOREWORD -- PREFACE -- ACKNOWLEDGMENTS -- 1 - Mutagenesis, Genetic Disorders and Diseases -- 1. INTRODUCTION -- 2. MUTAGENS -- 2.1 Physical Mutagens -- 2.2 Chemical Mutagens -- 2.3 Biological Mutagens -- 3. MUTATIONS -- 3.1 Break in Homologous Chromosome -- 3.2 Breaks in Nonhomologous Chromosomes -- 4. DNA DAMAGE RESPONSE AND REPAIR -- 5. DNA REPAIR PATHWAYS -- 5.1 Direct Repair -- 5.2 Single-Strand Break Repair -- 5.2.1 Base Excision Repair -- 5.2.2 Nucleotide Excision Repair -- 5.2.3 Mismatch Repair -- 5.2.4 Interstrand Cross-Linking Repair -- 5.3 Double-Strand DNA Breaks Repair -- 6. GENETIC DISORDERS AND DISEASES -- 6.1 Noonan Syndrome (OMIM 163950) -- 6.2 Costello Syndrome (OMIM 218040) -- 6.3 Cardio-Facio-Cutaneous Syndrome (OMIM 115150) -- 6.4 Hirschsprung Disease (OMIM 142623) -- 6.5 Hutchinsons-Gilford Progeria Syndrome (OMIM 176670) -- 6.6 Cancer -- 6.7 Parkinson Disease (OMIM 168600) -- 6.8 Alzheimer Disease (OMIM 104300) -- 6.9 Ataxia-Telangiectasia (OMIM 208900) -- 6.10 Seckel Syndrome (OMIM 210600) -- 6.11 Cockayne Syndrome (OMIM 216400) -- 6.12 Fanconi Anemia (OMIM 227650) -- 6.13 Bloom Syndrome (OMIM 210900) -- 6.14 Werner Syndrome (OMIM 277700) -- 6.15 Xeroderma Pigmentosum (OMIM 278700) -- 7. SUMMARY -- ACKNOWLEDGMENT -- REFERENCES -- 2 - Detection of Mutation in Prokaryotic Cells -- 1. INTRODUCTION -- 2. MATERIALS AND METHODOLOGIES -- 2.1 Preparation of Mammalian Liver S9 Fraction -- 2.1.1 Induction of Rat Liver Enzymes -- 2.1.2 Removal of Liver From Rats -- 2.1.3 Preparation of Liver S9 Fraction -- 2.2 Preparation of Reagents -- 2.2.1 Vogel-Bonner (VB Salt) Solution (50×) -- 2.2.2 Glucose Solution (10% W/V) -- 2.2.3 Minimal Glucose Agar Plates. , 2.2.4 Histidine-Biotin Solution (0.5mM) -- 2.2.5 Top Agar Supplemented With Histidine-Biotin Solution -- 2.2.6 Buffers for Metabolic Activation -- 2.2.6.1 Sodium Phosphate Buffer (0.1mM, pH 7.4) -- 2.2.6.2 To Activate the NADP Regenerating System in Presence of Liver S9 Fraction -- 2.3 Methodology -- 2.3.1 Culture Preparation -- 2.3.2 Genetic Analysis of the Tester Strains -- 2.3.3 Histidine and Biotin (his, bio) or Tryptophan (trp) Dependence -- 2.3.4 rfa (Deep Rough) Mutation -- 2.3.5 Treatment of Culture -- 2.3.6 Plating of Treated Culture -- 3. RESULT EVALUATION -- 4. RESULT INTERPRETATION -- 5. EXPERIMENTAL DESIGN -- 6. PRECAUTION -- REFERENCES -- FURTHER READING -- 3 - Detection of Gene Mutation in Cultured Mammalian Cells -- 1. INTRODUCTION -- 2. PCR-BASED MUTATION DETECTION -- 3. DETECTION OF MUTATIONS BY DENATURING GRADIENT GEL ELECTROPHORESIS -- 4. SINGLE-STRAND CONFORMATION POLYMORPHISM -- 5. HETERODUPLEX ANALYSIS -- 6. MICROARRAY -- 7. ARRAYED PRIMER EXTENSION TECHNOLOGY -- 8. SINGLE-BASE EXTENSION-TAGS TECHNOLOGY -- 9. ATOMIC FORCE MICROSCOPY -- 10. FLUORESCENCE IN SITU HYBRIDIZATION -- 11. DNA SEQUENCING -- 12. KARYOTYPING -- 13. HYPOXANTHINE PHOSPHORIBOSYL TRANSFERASE, THYMIDINE KINASE, AND XANTHINE-GUANINE PHOSPHORIBOSYL TRANSFERASE GENE MUTATION DET... -- 14. CONCLUSION -- ACKNOWLEDGMENT -- REFERENCES -- 4 - Chromosomal Aberrations -- 1. INTRODUCTION -- 2. CHARACTERISTICS OF HUMAN CHROMOSOMES -- 3. SOURCES OF SPECIMEN FOR CYTOGENETIC ANALYSIS -- 4. CYTOGENETIC ANALYSIS -- 5. TYPES OF CHROMOSOME ABERRATION -- 5.1 Numeric Chromosomal Aberration -- 5.1.1 Euploidy -- 5.1.2 Aneuploidy -- 5.2 Structural Chromosomal Aberration -- 5.2.1 Inversion -- 5.2.2 Translocation -- 5.2.3 Deletion -- 5.2.4 Duplication -- 5.2.5 Isochromosome -- 5.2.6 Ring Chromosome -- 6. MECHANISM OF THE FORMATION OF CHROMOSOME ABERRATION. , 7. CAUSES OF CHROMOSOME ABERRATION -- 7.1 Ionizing Radiation -- 7.2 Spontaneous dsDNA Break -- 7.2.1 Endogenous Reactive Oxygen Species -- 7.2.2 Topoisomerases -- 7.2.3 Replication Error -- 7.3 Chemicals -- 8. FREQUENCY OF CHROMOSOME ABERRATION -- 9. METHODS FOR DETECTION OF CHROMOSOMAL ABERRATION -- 9.1 Cytogenetic Testing -- 9.1.1 Chromosomal Aberration Test -- 9.1.2 Micronucleus Assay -- 9.1.2.1 Cytokinesis-Blocked Micronucleus Assay -- 9.1.2.2 Micronucleus Assay Using Flow Cytometry -- 9.1.3 Karyotyping -- 9.2 Molecular Cytogenetic Testing -- 9.2.1 Fluorescence In Situ Hybridization -- 9.3 Microarray Comparative Genomic Hybridization Testing -- 9.4 Prenatal Screening to Detect Fetal Abnormalities -- 10. CLINICAL MANIFESTATION OF CHROMOSOMAL ABNORMALITIES -- 10.1 Chromosomal Aberration and Spontaneous Abortions -- 10.2 Chromosomal Aberration and Cancer -- 10.3 Behavior Peculiarities Associated With Chromosomal Aberration -- 10.4 Changes in Course of Adolescence and Fertility -- 10.5 Pattern of Dysmorphic Signs in Chromosomal Aberration -- 10.6 Congenital Malformations and Chromosomal Aberration -- 11. APPLICATIONS OF CHROMOSOMAL ABERRATION ANALYSES -- 11.1 Radiation- and Chemical-Induced Cancer Risk Assessment -- 11.2 Genotoxicity Assessment of Environmental Chemicals -- 11.3 Testing of New Pharmaceuticals and Chemical Substances -- 12. FUTURE PERSPECTIVE -- 13. CONCLUSION -- REFERENCES -- 5 - In Vivo Cytogenetic Assays -- 1. INTRODUCTION -- 2. CYTOGENETIC END POINTS -- 3. TREATMENT PROTOCOLS -- 3.1 Selection of Animal Species, Number, and Sex of Animals -- 3.2 Dose Selection -- 3.3 Route of Administration -- 3.4 Proof of Exposure -- 3.5 Duration of Treatment and Sampling Time -- 3.5.1 Micronucleus Test -- 3.5.2 Chromosome Aberration Assay -- 4. ANALYSIS -- 4.1 Target Tissues Processing Staining and Scoring -- 4.1.1 Micronucleus Test. , 4.1.2 Chromosomal Aberration Test -- 4.2 Size of Samples and Statistical Power -- 4.2.1 Micronucleus Test -- 4.2.2 Chromosome Aberration Assay -- 4.3 Cytotoxicity Evaluations -- 4.4 Relevance of Historical Control Data -- 4.5 Data Interpretation and Criteria for a Positive/Negative Result -- 4.6 False-Positive Outcome -- REFERENCES -- 6 - Mutagenicity and Genotoxicity Testing in Environmental Pollution Control -- 1. INTRODUCTION -- 2. TYPES AND SOURCES OF POLLUTION -- 2.1 Air Pollution -- 2.2 Water Pollution -- 2.3 Soil Pollution -- 3. IMPACT OF ENVIRONMENTAL POLLUTION -- 3.1 Effect of Pollution on Ecosystem -- 3.2 Effect of Pollution on Humans -- 3.3 Mutagenic Effects of Environmental Pollution -- 4. NEED OF MUTAGENICITY ASSAYS TO ASSESS ENVIRONMENTAL POLLUTION -- 5. APPLICATION OF MUTAGENICITY ASSAYS TO CONTROL ENVIRONMENTAL POLLUTION -- REFERENCES -- 7 - Mutagens in Food -- 1. INTRODUCTION -- 2. ADDITIVES -- 2.1 Preservatives -- 2.2 Food Colors -- 2.3 Sweeteners -- 3. CONTAMINANTS -- 3.1 Mycotoxins -- 3.2 Pesticides -- 3.3 Metals -- 3.4 Intrinsic Dietary Components -- 4. ADULTERANTS IN FOOD -- 4.1 Edible Oils -- 4.2 Nonpermitted Food Colors -- 5. MUTAGENS PRODUCED AS AN OUTCOME OF FOOD PROCESSING -- 5.1 Acrylamide -- 5.2 Benzene -- 5.3 Heterocyclic Amines/Polycyclic Aromatic Hydrocarbons -- 5.4 Chloropropanols -- 5.5 Nitrosamines -- 5.6 Furan -- 6. SUMMARY -- ACKNOWLEDGMENTS -- REFERENCES -- 8 - Emerging Computational Methods for Predicting Chemically Induced Mutagenicity -- 1. INTRODUCTION -- 2. RELATIONSHIP BETWEEN MUTAGENS AND THEIR ABILITY TO CAUSE CANCER -- 3. CRUCIAL ASPECTS OF COMPUTATIONAL PREDICTIVE MODELING -- 4. IN SILICO TOOLS AND TECHNIQUES FOR CHEMICAL MUTAGENIC PREDICTION -- 4.1 Virtual Screening -- 4.2 Quantitative Structure-Activity Relationship -- 4.3 Molecular Docking -- 4.4 Molecular Dynamics Simulation. , 5. FRAMEWORK OF COMPUTATIONAL APPROACH FOR UNDERSTANDING MUTAGENICITY -- 5.1 Evaluation and Screening of Chemicals -- 5.2 Identification and Prediction of Mutagenicity -- 5.2.1 Expert System -- 5.2.2 Statistical Learning Methods -- 5.3 Analysis of Mutagens -- 5.3.1 Molecular Descriptors and Fingerprints -- 5.3.2 Substructures or Structural Alerts -- 5.3.3 Scaffold Analysis -- 5.4 Understanding Mechanism and Interaction of Mutagens -- 6. SUMMARY -- ACKNOWLEDGMENTS -- REFERENCES -- 9 - Overview of Nonclinical Aspects for Investigational New Drugs Submission: Regulatory Perspectives -- 1. INTRODUCTION -- 2. TARGET IDENTIFICATION -- 3. TARGET VALIDATION -- 4. HIT SERIES IDENTIFICATION -- 5. ASSAY DEVELOPMENT -- 6. HIT TO LEAD IDENTIFICATION -- 7. LEAD OPTIMIZATION -- 8. INVESTIGATIONAL NEW DRUG SUBMISSION -- 8.1 M4S(R2) Guidelines -- 8.2 Metabolites in Safety Testing for Investigational New Drug -- 8.3 Nonclinical Data Required for Exploratory Investigational New Drug Studies -- 8.4 Specific Concerns With Investigational New Drug Submission -- 9. CONCLUSIONS -- REFERENCES -- 10 - Mutagenicity Testing: Regulatory Guidelines and Current Needs -- 1. BACKGROUND -- 2. MUTAGENICITY ENDPOINTS -- 3. REGULATORY FRAMEWORK -- 4. REGULATORY STUDIES FOR MUTAGENICITY TESTING -- 4.1 In Vitro Studies -- 4.2 In Vivo Studies -- 5. REGULATORY REQUIREMENTS FOR REGISTRATION -- 5.1 Pesticides -- 5.2 Pharmaceuticals -- 5.2.1 Option 1 -- 5.2.2 Option 2 -- 5.2.3 Quantitative Structure-Activity Relationships Modeling of Pharmaceuticals -- 5.2.4 DNA Reactive Drug Impurities -- 5.2.5 Biotechnology-Derived Products -- 5.2.6 Concerns of Anticancer, Photogenotoxic, and Liposomal Drugs -- 5.3 Medical Devices -- 5.4 Food Additives Ingredients -- 5.5 Industrial Chemicals -- 5.6 Cosmetics -- 5.7 Nanomaterials -- 6. PREDICTIVE MUTAGENICITY TESTING. , 7. LIMITATIONS AND CHALLENGES OF MUTAGENICITY ASSESSMENT.

Note: Ebook , Preface-- Part I: Genesis of Comet assay-- Part II: Various procedures for the Comet assay-- Oxidative damage-- Water disinfection by-products-- Comet assay in Plants-- Double Strand-- Breaks in bacteria-- Comet - FISH-- Double strand breaks (DSBs) - radiation/challenge assay - Radiation-- Apoptosis-- Multiple mouse organs-- Part III: Applications of Comet assay-- Dietary intervention studies-- Comet assay in Mussels-- Exercise-- Arsenic-- DSBs - radiation/challenge assay - Radiation-- In vivo Comet assay-- In vitro parallelogram approaches-- Photobiology-- Comet assay in sperm-- Comet assay in Human monitoring-- Part IV: Guidelines for comet assay-- In Vitro And In Vivo Guidelines for the Comet Assay-- In vivo Guidelines for Comet-- Part V: Image analysis and Statistics-- Models for image analysis-- Statistics in comet assay.