Note: Front Cover -- Pericyclic Reactions -- Copyright -- To Our Families -- Contents -- Preface -- Chapter 1 - Pericyclic Reactions and Molecular Orbital Symmetry -- 1.1 CLASSIFICATION OF PERICYCLIC REACTIONS -- 1.2 MOLECULAR ORBITALS OF ALKENES AND CONJUGATED POLYENE SYSTEMS -- 1.3 MOLECULAR ORBITALS OF CONJUGATED IONS OR RADICALS -- 1.4 SYMMETRY PROPERTIES OF π OR σ-MOLECULAR ORBITALS -- 1.5 ANALYSIS OF PERICYCLIC REACTIONS -- FURTHER READING -- Chapter 2 - Electrocyclic Reactions -- 2.1 CONROTATORY AND DISROTATORY MODES -- 2.2 STEREOCHEMISTRY OF ELECTROCYCLIC REACTIONS -- 2.3 SELECTION RULES FOR ELECTROCYCLIC REACTIONS -- 2.4 ANALYSIS OF ELECTROCYCLIC REACTIONS -- 2.5 ELECTROCYCLIC REACTIONS OF IONIC SPECIES -- Chapter 3 - Sigmatropic Rearrangements -- 3.1 SUPRAFACIAL AND ANTARAFACIAL PROCESSES -- 3.2 ANALYSIS OF SIGMATROPIC REARRANGEMENTS OF HYDROGEN -- 3.3 ANALYSIS OF SIGMATROPIC REARRANGEMENTS OF ALKYL GROUP -- 3.4 [3,3] SIGMATROPIC REARRANGEMENTS -- 3.5 [5,5] SIGMATROPIC SHIFT -- 3.6 [2,3] SIGMATROPIC REARRANGEMENTS -- 3.7 PERIPATETIC CYCLOPROPANE BRIDGE: WALK REARRANGEMENTS -- 3.8 SIGMATROPIC REARRANGEMENTS INVOLVING IONIC TRANSITION STATES -- Chapter 4 - Cycloaddition Reactions -- 4.1 STEREOCHEMICAL MODES OF CYCLOADDITION -- 4.2 FEASIBILITY OF CYCLOADDITION REACTIONS -- 4.3 [2+2] CYCLOADDITIONS -- 4.4 [4+2] CYCLOADDITIONS -- 4.5 HIGHER CYCLOADDITIONS -- 4.6 CYCLOADDITION OF MULTIPLE COMPONENTS -- Chapter 5 - Cheletropic Reactions and 1,3-Dipolar Cycloadditions -- 5.1 CHELETROPIC REACTIONS -- 5.2 1,3-DIPOLAR CYCLOADDITIONS -- Chapter 6 - Group Transfer, Elimination, and Related Reactions -- 6.1 GROUP TRANSFER REACTIONS -- 6.2 ELIMINATION REACTIONS -- 6.3 DYOTROPIC REARRANGEMENTS -- 6.4 ENE REACTIONS -- 6.5 β-ELIMINATIONS INVOLVING CYCLIC TRANSITION STRUCTURES -- Chapter 7 - Unsolved Problems -- Appendix - Solution Manual -- Index.

Note: Intro -- Preface -- Contents -- Contributors -- Chapter 1: Expression Analysis and Genome Annotations with RNA Sequencing -- Introduction -- Sequencing Strategy -- Genome Sequencing -- mRNA Sequencing -- Read Mapping on Reference Sequences -- Pre-processing -- Read Mapping -- SNP Detecting from Genome Sequencing -- Digital Gene Expression Profiling by mRNA-Seq -- Mapping -- Assembly -- Expression Level Estimation and Correction -- Statistical Methods for Gene Expression Data -- Hierarchical Clustering -- Multivariate Analysis Methods -- Principal Component Analysis (PCA) and Correspondence Analysis (CA) -- Self-Organizing Maps and k-Means Clustering -- References -- Chapter 2: The Application of Next Generation Sequencing Techniques to Plant Epigenomics -- Introduction -- Major Findings in Plants -- Development of Genome-Wide Approaches -- Bisulfite-Seq Experiments -- Methods -- General Considerations -- Techniques for Assaying DNA Methylation in Plants Using NGS -- DNA Methylation -- ChIP-Seq -- Nucleosome Positioning -- Small RNA-Seq -- PART3: Analysis of Next Generation Sequencing Data for Epigenomics -- Computing Requirements for Data Analysis -- Quality Control -- Pre-alignment Filtering -- Alignment -- BS-Seq Alignment -- Methylation Calling -- Estimation of Conversion Efficiency -- Downstream Analysis -- Differential Methylation Analysis -- ChIP-Seq Analysis -- Web Services -- Post-Processing -- Peak Calling -- Higher-Level Analysis -- Nucleosome Positioning Analysis -- Small RNA-Seq Analyses -- Data Visualization -- References -- Chapter 3: Whole Genome Sequencing to Identify Genes and QTL in Rice -- Overview of Genetic Analysis for Identifying Genes -- Genetic Markers to Become Obsolete? -- Rice Genetic Resources at IBRC -- MutMap -- MutMap+ -- MutMap-Gap -- QTL-Seq -- SNP-Index -- Summary -- References. , Chapter 4: Variant Calling Using NGS Data in European Aspen (Populus tremula) -- Introduction -- Raw Reads Pre-processing (Step I) -- The Short-Read Alignment (Step II) -- Alignment Algorithms -- Mismatches Between Sample and Reference Genome -- Multiple Mapping -- Post-processing Alignment (Step III) -- Local Realignment Around Indels -- Mark Duplicates -- Base Quality Score Recalibration -- Variant and Genotype Calling (Step IV) -- Methods for Genotype Calling -- Software Tools for Variant Discovery and Genotyping -- SAMtools mpileup and BCFtools -- GATK UnifiedGenotyper -- SNVer -- GATK HaplotypeCaller -- Variant Filtration (Step V) -- Conclusion -- References -- Chapter 5: Leafy Spurge Genomics: A Model Perennial Weed to Investigate Development, Stress Responses, and Invasiveness -- Introduction -- Initial Forays into the Molecular Biology of Leafy Spurge -- Leafy Spurge Enters the Genomic Era -- Experimenting with Transcriptomics -- Outcomes Obtained Using the 23,000 Element Leafy Spurge/Cassava Microarrays -- BAC Library Construction: An Important Tool for Promoter Analysis and the First Step in Full Genome Sequencing -- Shotgun Sequencing of the Leafy Spurge Genome -- Mining Old Data and New -- References -- Chapter 6: Utilization of NGS and Proteomic-Based Approaches to Gain Insights on Cellular Responses to Singlet Oxygen and Improve Energy Yields for Bacterial Stress Adaptation -- Introduction -- Reactive Oxygen Species and Singlet Oxygen -- Sources of 1O2 -- 1O2 Production in Photosynthetic Organisms -- Energy Generation in R. sphaeroides -- Quenching of 1O2 by Carotenoids -- Transcriptional Response to 1O2 by R. sphaeroides -- Alternative Responses to 1O2 by Other Organisms -- Utilization of Next-Generation Sequencing (NGS) Technologies, Proteomic, and Metabolomic Approaches to Characterize Cellular Responses. , Investigations into the Cellular Response to 1O2 and Identification of the σE Regulon -- Coupling Insights to Improved Energy Generation -- References -- Chapter 7: Experimental Evolution and Next Generation Sequencing Illuminate the Evolutionary Trajectories of Microbes -- Introduction -- What Makes Microbes Attractive to Test Evolutionary Processes? -- Experimental Evolution and Mutation Accumulation Dynamics -- The Evolutionary Trajectories of Adaptive Mutations -- Convergent Evolution in Bacterial Experimental Populations -- Experimental Evolution Under Inefficient Natural Selection -- Concluding Remarks -- References -- Chapter 8: Plant Carbohydrate Active Enzyme (CAZyme) Repertoires: A Comparative Study -- Why Do We Study Plant Cell Walls? -- How CAZymes Are Related to Cell Wall Studies? -- What Are CAZymes and the CAZyDB? -- Existing Studies on Plant CAZyomes -- dbCAN: A HMM Database for Large-Scale Analysis of CAZymes -- CAZyome of Fully Sequenced Plants -- Phylogenetic Analysis Is Useful to the Study of the Function and Evolution of CAZymes -- Future Development -- References -- Chapter 9: Metagenomics of Plant-Microbe Interactions -- References -- Chapter 10: Genes and Trans-Factors Underlying Embryogenic Transition in Plant Soma-Cells -- In Vitro Regeneration of Plant Species -- Somatic Embryogenesis -- Initiation of Somatic Embryogenesis -- Somatic Embryogenesis Is Genotype/Explant Source Dependent -- Stress-Mediated Up-regulation of Phytohormone in SE -- Auxin -- Cytokinin -- Abscisic Acid (ABA) -- Gibberellins -- Ethylene -- Induced Cell-Fate For SE -- Cellular Morphology, Physiology and Histological Pattern -- Changes in Gene Expression -- Somatic Embryo Receptor Kinase (SERK) -- WUSCHEL (WUS) -- Baby Boom (BBM) Gene -- WRKY, AOX and Ca2+ -- Altered Cellular Homeostasis Is Essential for Soma Cell-to-­Embryo Transition. , Genomics of Somatic Embryogenesis -- References -- Chapter 11: Bioinformatics Tools to Analyze Proteome and Genome Data -- Introduction -- Bioinformatics Tool to Analyze Proteomics Data -- Bioinformatics Tool to Analyze Genomics Data -- Genomic Repositories -- Similarity Search and Sequence Alignment Tools -- Variation Related Databases -- Gene Prediction Tools -- Expression Profiling Tools -- Tools for Promoter Prediction -- Genome Annotation Tools -- References -- Chapter 12: High-Throughput Transcriptome Analysis of Plant Stress Responses -- Plant Stresses and Its Genetic Regulation -- Transcriptome Analysis Upon Stress Conditions -- Transcriptome De Novo Assembly -- Functional Annotation of Unigenes by BLASTx Against Protein Databases -- Functional Classification of Unigenes by Clusters of Orthologous Groups (COG), Gene Ontology (GO), and KEGG Pathway Enrichment -- Protein Coding Region Prediction (CDS) -- Digital Gene Expression Profiling -- Unigene Expression Difference Analysis -- References -- Chapter 13: CNV and Structural Variation in Plants: Prospects of NGS Approaches -- Copy Number Variation Is Part of Genome Structural Variation -- Diffusion of CNVs Within Genomes -- Mechanisms Leading to Variation in Number of Copies -- Do CNVs Have a Biological Meaning? -- Association to Phenotypes -- Evolutionary and Adaptive Value of CNVs -- NGS Approaches and Bioinformatic Tools for CNV Detection -- The Computational Problem -- NGS and the Main Techniques of CNV Discovery -- A Classification of NGS Technologies -- NGS Technologies vs. Computational Techniques -- Future Perspectives -- References -- Index.

Note: Intro -- Preface -- Contents -- Editors and Contributors -- 1 Molecular Approaches in Plant Biology and Environmental Challenges -- References -- 2 Promising Transcription Factors for Salt and Drought Tolerance in Plants -- 2.1 Introduction -- 2.2 Plant Growth During Drought and/or Salinity Stress -- 2.3 Plant Response Towards Stress -- 2.3.1 Stress Perception and Signal Transduction -- 2.3.2 Physiological, Biochemical and Molecular Responses to Drought and Salinity Stress -- 2.4 Transcription Factors: Potential Candidates for Enhancing Multiple Stress Tolerance -- 2.4.1 Transcriptional Regulatory Network Under Drought and Salinity Stress -- 2.4.2 Downstream Targets of Stress-Responsive Transcription Factors -- 2.4.3 Major Transcription Factor Families that Participate in Drought and Salinity Tolerance -- 2.5 Stress-Inducible Promoters: A Potential Tool to Develop Plants with Sustainable Stress Tolerance -- 2.6 Conclusions -- References -- 3 Role of Superoxide Dismutases (SODs) in Stress Tolerance in Plants -- 3.1 Introduction -- 3.2 Different Classes of SODs -- 3.2.1 Cu-ZnSODs -- 3.2.2 FeSODs -- 3.2.3 MnSODs -- 3.3 Evolution of SOD Isoforms -- 3.4 Role of SODs Under Abiotic Stress Conditions -- 3.4.1 Heat Stress -- 3.4.2 Drought Stress -- 3.4.3 Cold Stress -- 3.4.4 Salinity Stress -- 3.4.5 Heavy Metal Stress -- 3.5 Biotic Stress -- 3.6 Industrial Uses of SODs -- 3.6.1 Agriculture and Horticulture Uses -- 3.6.2 Human Health Benefits -- 3.6.3 Uses in Cosmetics -- 3.7 Conclusions -- References -- 4 Receptor-Like Kinases and Environmental Stress in Plants -- 4.1 Introduction -- 4.2 Origin of RLKs -- 4.3 Types of RLKs -- 4.4 Evolutionary Study of RLKs in Plant Lineages -- 4.5 Role of RLKs in Signal Transduction Pathways -- 4.5.1 Brassinosteroid Complexes Mediated Signaling -- 4.5.2 CLAVATA Complexes Mediated Signaling. , 4.6 Role of RLKs in Biotic Stress -- 4.7 Role of RLKs in Abiotic Stress -- 4.7.1 RLKs Against Drought Stress -- 4.7.2 RLKs Against Heat Stress -- 4.7.3 RLKs Against Salt Stress -- 4.7.4 RLKs Against Cold Stress -- 4.7.5 RLKs Against Metal Stress -- 4.7.6 RLKs Against Other Abiotic Stresses -- 4.8 Conclusion -- References -- 5 Role of Histone Acetyltransferases in Plant Abiotic Stress -- 5.1 Introduction -- 5.1.1 Types of HATs -- 5.2 Abiotic Stress and Epigenetics -- 5.2.1 Cold Stress -- 5.2.2 Heat Stress -- 5.2.3 Water Stress -- 5.2.4 Salt Stress -- 5.2.5 Nutritional Stress -- 5.2.6 Light Stress -- 5.3 Conclusion -- References -- 6 Function of Plant Heat Shock Transcription Factors in Abiotic Stress -- 6.1 Introduction -- 6.2 Structure of Plant Heat Shock Transcription Factors -- 6.3 Hsfs in Abiotic Stress Response -- 6.3.1 Heat Stress -- 6.3.2 Salt Stress -- 6.3.3 Drought Stress -- 6.3.4 Heavy Metal Stress -- 6.3.5 Cold/Chilling Stress -- 6.3.6 Anoxia Stress -- 6.4 Conclusion -- References -- 7 Mode of Communication Between Plants During Environmental Stress -- 7.1 Introduction -- 7.2 The Need of Communication in Plant -- 7.3 Different Mode of Communication -- 7.3.1 Communication via Mediator -- 7.3.2 Communication Without Mediator -- 7.4 Molecular Mechanism Underlying Plant Communications -- 7.5 Conclusion and Future Prospects -- References -- 8 Molecular Approaches for Combating Multiple Abiotic Stresses in Crops of Arid and Semi-arid Region -- 8.1 Introduction -- 8.2 Effect of Various Abiotic Stresses on Crop Plants -- 8.2.1 Drought -- 8.2.2 Salt Stress -- 8.2.3 High Temperature Stress -- 8.3 Common Effector Molecules and Signal Transduction Mechanism Under Multiple Abiotic Stresses -- 8.3.1 Plants Response to Individual and Interactive Abiotic Stress Condition -- 8.3.2 Physio-Biochemical Response of Plants to Various Abiotic Stress. , 8.3.3 Molecular Response of Plants to Various Abiotic Stresses -- 8.3.4 Plant Signal Transduction Mechanism Under the Influence of Abiotic Stresses -- 8.3.5 Gene Expression Regulation and Transcription Factors -- 8.4 Combating Abiotic Stresses Using Physiological and Biochemical Approaches -- 8.4.1 Role of Proline and Glycine Betaine -- 8.4.2 Role of Plant Antioxidants in Improving Plant Tolerance to Stress -- 8.4.3 Role of Mineral Nutrition and Management of Nutrient Supply -- 8.4.4 Role of Plant Growth Hormones -- 8.5 Combating Abiotic Stresses Using Molecular Approaches -- 8.5.1 Sequencing Based Approaches -- 8.5.2 Hybridization Based Approaches -- 8.5.3 Gene Inactivation-Based Approaches -- 8.5.4 Genome Editing Based Approaches -- 8.6 Conclusion -- References -- 9 Applications of Landscape Genetics to Study the Effect of Varying Landscapes and Environmental Challenges in Plant Populations -- 9.1 Introduction -- 9.1.1 Definition -- 9.2 Landscape Ecology: The Basics -- 9.2.1 Landscape -- 9.2.2 Effect of Landscapes on Genetic Processes -- 9.2.3 Population Dynamics and Dispersal -- 9.2.4 Influence of Landscapes on Genetic Variation -- 9.2.5 Gene Flow -- 9.3 Overview of Dna Types and Molecular Methods -- 9.3.1 Types of DNA -- 9.3.2 Molecular Methods -- 9.3.3 Measures of Genetic Diversity -- 9.3.4 Bayesian Clustering Methods -- 9.3.5 Barrier Detection Methods -- 9.4 Genomic Approaches in Landscape Genetics -- 9.5 Effect of Climate Change and Spatial Data Collection -- 9.6 Conclusion and Future Perspectives -- References -- 10 Arsenic in Rice Grain: Role of Transporters in Arsenic Accumulation -- 10.1 Introduction -- 10.2 Arsenic in Soil -- 10.3 Arsenic Toxicity -- 10.3.1 Human -- 10.3.2 Plant -- 10.4 Arsenic in Rice Grain -- 10.5 Arsenic Transport in Plant -- 10.5.1 Arsenite Transport -- 10.5.2 Arsenate Acquisition -- 10.5.3 Organo-Arsenic Transport. , 10.6 Arsenic Metabolism in Plant -- 10.7 Root to Shoot Translocation of as in Plant -- 10.8 Role of Transporters in Arsenic Uptake and Movement -- 10.8.1 Lsi -- 10.8.2 ABCC -- 10.8.3 NRAMP -- 10.8.4 MATE -- 10.9 Conclusions -- References -- 11 Metabolic Engineering of Stress Protectant Secondary Metabolites to Confer Abiotic Stress Tolerance in Plants -- 11.1 Introduction -- 11.2 Abiotic Stress Protectant Secondary Metabolites -- 11.2.1 Isoprenoids -- 11.2.2 Phenolics and Flavonoids -- 11.2.3 Carotenoids -- 11.3 Changes in Metabolic Pathways During Abiotic Stress -- 11.4 Metabolic Engineering of Secondary Metabolites -- 11.4.1 Manipulation of Isoprenoids -- 11.4.2 Manipulation of Flavonoids -- 11.4.3 Manipulation of Carotenoids -- 11.5 Conclusion -- References -- 12 An Update on Molecular Strategies of Transgenic Rice Tolerance to Abiotic Stresses -- 12.1 Introduction -- 12.2 Development of Transgenic Rice Tolerant to Various Abiotic Stresses -- 12.2.1 Development of Transgenic Rice for Salt Tolerance -- 12.2.2 Development of Transgenic Rice Tolerant to Drought Stress -- 12.2.3 Transgenic Rice Developed for Tolerance to Cold Stress -- 12.2.4 Transgenic Rice Developed for Tolerance to Heat Stress -- 12.3 Pleiotropic Effects of Transgenes for Multiple Stress Tolerance -- 12.4 Conclusion -- References -- 13 An Update on the Applications of CRISPR/Cas9 Technology in Tomato -- 13.1 Introduction -- 13.1.1 An Array of Cas9 Activities -- 13.2 Uses of CRISPR/Cas9 in Crop Improvement -- 13.2.1 Experimental -- 13.2.2 Applications -- 13.3 Conclusion -- References -- 14 Transgenic Approaches for Enhancement of Salinity Stress Tolerance in Plants -- 14.1 Introduction -- 14.2 Mechanisms of Salt Stress Response in Plants -- 14.2.1 Biphasic Response -- 14.2.2 Strategies to Combat Salt Stress in Plants. , 14.3 Genetic Engineering Approaches to Improve Salinity Stress Tolerance in Plants -- 14.3.1 Genes Involved in Direct Protection (Functional Proteins/Stress-Adaptive Compounds) -- 14.3.2 Genes for Regulatory Proteins and Signaling Intermediates -- 14.3.3 Genes for Ion Homeostasis -- 14.4 Conclusions and Future Perspective -- References -- 15 Genome Engineering in Rice: Applications, Advancements and Future Perspectives -- 15.1 Introduction -- 15.2 Gene Editing Tools: ZFN, TALEN & -- CRISPR-Cas System -- 15.3 Applications of Genome Editing in Rice Crop Improvement -- 15.4 Innovations in Genome Editing -- 15.5 The Need for Genome Editing and Its Social Acceptance -- 15.6 Conclusion and Future Perspective -- References -- 16 Secondary Metabolite Pathways in Medicinal Plants: Approaches in Reconstruction and Analysis -- 16.1 Introduction -- 16.2 Secondary Metabolites: Concept and Classification -- 16.2.1 Phenylpropanoids -- 16.2.2 Alkaloids -- 16.2.3 Terpenoids -- 16.3 Biosynthesis of Secondary Metabolite Is Under Tight Regulation -- 16.3.1 Abiotic and Biotic Effects -- 16.3.2 Other Regulatory Aspects -- 16.4 Gene Mining and Pathway Elucidation -- 16.4.1 Transcriptomics -- 16.4.2 Proteomics -- 16.4.3 Metabolomics -- 16.4.4 Bioinformatics Approaches -- 16.4.5 Systems Biology -- 16.5 Approaches for Functional Genomics -- 16.5.1 RNAi -- 16.5.2 VIGS -- 16.5.3 CRISPR-Cas9 System -- 16.6 Tools for Enhancement of Secondary Metabolites -- 16.6.1 Bioprocessing -- 16.6.2 Heterologous Production -- 16.6.3 Particle Bombardment Mediated Transformation -- 16.7 Conclusion -- References -- 17 Molecular Biology of Glandular Trichomes and Their Functions in Environmental Stresses -- 17.1 Introduction -- 17.2 Morphology and Classification of Glandular Trichomes -- 17.3 Glandular Trichomes as Source of Economically Important Natural Products. , 17.4 Role of Glandular Trichomes in Plant Biology.

Note: Intro -- Foreword -- Preface -- Contents -- Contributors -- Abbreviations -- 1 An Introduction to Microbial Biofilm -- 1.1 Introduction -- 1.1.1 Biofilm Growth and Development -- 1.1.2 Beneficial and Naturally Occurring Biofilms -- 1.1.3 The Harmful Effects of Biofilm Formation -- 1.1.4 Naturally Occurring Biofilms -- 1.1.5 Biofilms in Health and Medicine -- 1.1.6 Control of Biofilms -- 1.1.7 Biofilm and Antibiotic Resistance -- 1.1.8 The Future of Studying Biofilms -- References -- 2 Biofilms: The Good and the Bad -- 2.1 Introduction -- 2.2 Mechanism of Bacterial Biofilm Formation -- 2.2.1 The Conditioning Layer -- 2.2.2 Reversible Adhesion -- 2.2.3 Irreversible Adhesion -- 2.2.4 Micro-colony Formation and Three-Dimensional Growth -- 2.2.5 Biofilm Formation -- 2.2.6 Maturation and Dispersal -- 2.3 Applications of Biofilms -- 2.3.1 Biofilm Uses -- 2.3.2 Bioremediation -- 2.4 Oil Spills and Contaminated Groundwater -- 2.5 Microbial Leaching -- 2.6 Biofilm Reactors -- 2.7 Biofilms in Biosensors -- 2.8 Biofilm Integrated Nanofiber Display -- 2.9 The Harmful Effects of Biofilms -- 2.9.1 The Food and Dairy Industry -- 2.9.2 Aquaculture and the Sea Food Industry -- 2.9.3 The Brewing Industry -- 2.9.4 Bio-corrosion -- 2.9.5 The Medical Industry -- References -- 3 Biofilms in Human Health -- 3.1 Introduction -- 3.2 Biofilm Structure -- 3.3 Biofilm Development -- 3.3.1 Growth of Conditioning Film on Surface -- 3.3.2 Movement of Microorganisms Towards Surface -- 3.3.3 Adherence -- 3.3.4 Colonization for Development and Division of Microbe, Formation of Microcolony and Biofilms, Change in Genotype and Phenotype -- 3.3.5 Interaction of Microorganisms inside Biofilm -- 3.4 Antibiotics and Biofilms -- 3.5 Pathogenic Mechanisms -- 3.6 Biofilm and Human Diseases -- 3.6.1 Oral Cavity -- 3.6.2 Upper Airways -- 3.6.3 Lower Airways. , 3.6.4 Gastrointestinal and Urinary Tracts -- 3.6.5 Wounds -- 3.7 Main Characteristics of Biofilm Mediated Diseases -- References -- 4 The Role of Biofilm in Originating, Mediating, and Proliferating Infectious Diseases -- 4.1 Introduction -- 4.1.1 Biofilm Origination and Mediation -- 4.2 Indwelling Devices Where Microbes Frequently Cause Biofilms -- 4.3 Biofilm-Mediated Infectious Diseases -- 4.3.1 Barrett's Esophagus and Gastric Cancer -- 4.3.2 Endotracheal Tube Colonization and Ventilator-Associated Pneumonia -- 4.3.3 Cystic Fibrosis -- 4.3.4 Chronic Otitis Media -- 4.3.5 Dental Plaque -- 4.3.6 Urinary Tract and Catheter-Associated Infections -- 4.3.7 Skin Infections by Staphylococcus -- 4.3.8 Chronic Ulcers -- 4.3.9 Prosthetic Graft Infection -- 4.3.10 Healthcare-Associated Infections -- 4.4 Other Biofilm-Mediated Infections -- 4.5 Conclusion -- References -- 5 Modern Methods in Microscopy for the Assessment of Biofilms -- 5.1 Introduction -- 5.2 Diagnosis of Biofilm Infections -- 5.2.1 Routine Microbiological Examination -- 5.2.2 Different Microscopic Methods -- 5.3 Conclusion -- References -- 6 Molecular Methods for the Assessment of Microbial Biofilms -- 6.1 Introduction -- 6.2 Why Molecular Methods? -- 6.3 Different Methods Used to Assess Biofilm: Ergin (2017) -- 6.4 Next-Generation Sequencing Technology -- 6.4.1 Advantages of NGS -- 6.4.2 Utility of NGS in Clinical Microbiology: Deurenberg et al. (2016) -- 6.4.3 Workflow of NGS -- 6.4.4 Clinical Sample/Specimen -- 6.4.5 Nucleic Acids Sequencing -- 6.4.6 Sequence Data Analysis -- 6.4.7 Application of NGS -- 6.5 Polymerase Chain Reaction (PCR) -- 6.5.1 Advantage of PCR -- 6.5.2 Workflow of PCR -- 6.5.3 Procedure and General Protocol -- 6.5.4 1-1.8% Agarose Gel Electrophoresis -- 6.5.5 Application of PCR -- 6.6 DNA-DNA Hybridization -- 6.6.1 Principle of DNA-DNA Hybridization. , 6.6.2 Major Disadvantages -- 6.6.3 DDH Protocol and Procedure -- 6.6.4 Application of DNA-DNA Hybridization -- 6.7 Microarray Technology -- 6.7.1 Application of Microarray -- References -- 7 Biofilm-Mediated Dental Diseases -- 7.1 Introduction -- 7.2 Oral Flora -- 7.3 Development -- 7.4 Oral Microbiota: Beneficial Functions -- 7.5 Oral Niches -- 7.5.1 Tongue and Buccal Mucosa -- 7.5.2 Tooth Surface -- 7.5.3 Gingival Crevice and Its Epithelium -- 7.5.4 Dental Appliances and Prosthetics -- 7.6 Factors Modulating Microbial Growth -- 7.6.1 Anatomic Factors -- 7.6.2 Saliva -- 7.6.3 Gingival Crevicular Fluid -- 7.6.4 Microbial Factors -- 7.6.5 Environmental Factors -- 7.6.6 Miscellaneous -- 7.7 Nutrition -- 7.7.1 Host Resources -- 7.7.2 Microbial Resources -- 7.8 Dental Plaque -- 7.9 Dental Plaque and Caries -- 7.9.1 Caries Origin Hypothesis -- 7.10 Dental Plaque, Dental Calculus, and Periodontitis -- 7.10.1 Calculus -- 7.10.2 Classification of Periodontal Disease -- 7.10.3 Etiology of Periodontal Disease -- 7.11 The Systemic Connection of Oral Biofilms -- 7.12 Approaches for Control of Dental Biofilm -- 7.12.1 Conventional Treatment -- 7.12.2 Mechanical Plaque Control -- 7.12.3 Oral Irrigators (Mandal et al. 2017) -- 7.12.4 Chemical Plaque Control -- 7.12.5 Local Delivery of Drugs -- References -- 8 Biofilm-Mediated Diseases of the Eye -- 8.1 Introduction -- 8.2 Endophthalmitis -- 8.3 Contact Lens Associated Keratitis -- 8.4 Crystalline Keratopathy -- 8.5 Dry Eye -- 8.6 Ocular Implants and Biofilms -- 8.6.1 Conjunctival Plug -- 8.6.2 Scleral Buckles -- 8.6.3 Lacrimal Intubation Devices -- 8.6.4 Orbital Implants -- 8.6.5 Other Biomaterials Used in Ophthalmology -- 8.7 Prevention and Treatment of Biofilms -- References -- 9 Biofilm-Mediated Diseases of the Ear, Nose, and Throat (ENT) -- 9.1 Introduction -- 9.2 Chronic Rhino-sinusitis. , 9.3 Otitis Media with Effusion -- 9.4 Cholesteatoma -- 9.5 Adenotonsillitis -- 9.6 Biofilms in Ear, Nose, and Throat Implants and Prostheses -- 9.7 Treatment -- 9.8 Prevention -- 9.9 Conclusion -- References -- 10 Biofilm-Mediated Diseases of the Heart and Lungs -- 10.1 Introduction -- 10.2 Biofilms Related to Endotracheal Tubes and Ventilator-Associated Pneumonia -- 10.3 Biofilms in Cystic Fibrosis -- 10.4 Biofilms in Pulmonary Infections -- 10.5 Biofilms in Indwelling Vascular Catheters -- 10.6 Mechanical Heart Valve Biofilms -- 10.7 Biofilms in Infective Endocarditis -- 10.8 Biofilms in Atherosclerosis -- 10.9 Cardiovascular Implantable Electronic Devices -- 10.10 Conclusion -- References -- 11 The Role of Biofilms in Medical Devices and Implants -- 11.1 Introduction -- 11.2 Mechanism of Biofilm Formation -- 11.3 Prevention and Control of Biofilms -- 11.3.1 Cell Repellent and Non-adhesive Coatings -- 11.3.2 The Active Release of Antimicrobial Compounds and Biofilm Inhibitors -- 11.3.3 Antimicrobial Coatings with Tethered Biocides -- 11.3.4 Competitive Adherence by Benign Organisms -- 11.4 Biofilms and Healthcare-Associated Infections -- 11.4.1 Central Venous Catheters -- 11.4.2 Urinary Catheters -- 11.4.3 Ventilator-Associated Pneumonia and Endotracheal Tubes -- 11.4.4 Surgical Site Infection -- 11.4.5 Mechanical Heart Valves -- 11.4.6 Contact Lenses -- 11.4.7 Orthopedic Implants -- 11.4.8 Dental Implants -- 11.4.9 Breast Implants -- 11.5 Detection and Diagnosis of Bacterial Biofilms on Medical Devices -- 11.6 Preventive Measures for Biofilm Control and Future Perspectives -- 11.7 Conclusion -- References -- 12 Biofilm-mediated Gastrointestinal Diseases -- 12.1 Introduction -- 12.2 Esophagus -- 12.2.1 Gastroesophageal Reflux Disease and Barret's Esophagus -- 12.2.2 Carcinoma of the Esophagus -- 12.3 Stomach -- 12.3.1 Helicobacter pylori Infection. , 12.4 Intestines -- 12.4.1 Foodborne Bacterial Disease and Biofilm -- 12.4.2 Clostridium Difficile -- 12.4.3 Inflammatory Bowel Disease -- 12.4.4 Irritable Bowel Syndrome -- 12.4.5 Colorectal Malignancy -- References -- 13 Biofilm-Mediated Urinary Tract Infections -- 13.1 Infections in Urinary Tract -- 13.2 Pathogenesis of Biofilm-Mediated UTIs -- 13.2.1 Role of Biofilms in Recurrent UTIs -- 13.2.2 Role of Biofilm in ABU -- 13.2.3 Role of Biofilms in Catheter-Associated Infections -- 13.3 Microbial Factors Contributing to Biofilm Formation in Urinary Tract -- 13.3.1 Escherichia coli and Urinary Tract Infections -- 13.3.2 Proteus mirabilis and Urinary Tract Infections -- 13.3.3 Klebsiella pneumoniae and Urinary Tract Infections -- 13.3.4 Pseudomonas aeruginosa and Urinary Tract Infections -- 13.3.5 Miscellaneous Microorganisms and Urinary Tract Infections -- 13.4 Treatment and Prevention of Biofilm-Mediated UTIs -- 13.4.1 Antimicrobial Treatment of Biofilms -- 13.4.2 Newer Strategies -- 13.5 Future Prospects -- 13.5.1 Bladder Model -- 13.5.2 Urinary Tract Model -- 13.5.3 CAUTI Model -- 13.5.4 Meatus Model -- References -- 14 Biofilm-Mediated Skin Infections -- 14.1 Introduction -- 14.2 Role of Biofilm in Skin Infection -- 14.3 Biofilm Formation and Cell-to-Cell Communication -- 14.4 Pathogenesis and Types of Skin Infection Caused by Biofilms -- 14.4.1 Rosacea -- 14.4.2 Acne Vulgaris -- 14.4.3 Atopic Dermatitis -- 14.4.4 Cellulitis, Erythema Nosodum, and Erysipelas -- 14.4.5 Onychomycosis -- 14.4.6 Furuncles and Impetigo -- 14.4.7 Staphylococcal Scalded Skin Syndrome -- 14.4.8 Miliaria -- 14.4.9 Necrotizing Fasciitis -- 14.4.10 Pseudomonas Infections of the Skin -- 14.4.11 Paronychia -- 14.4.12 Chronic Non-healing Ulcers -- 14.4.13 Other Biofilm-Related Skin Infections -- 14.5 Conclusion -- References. , 15 Approaches Towards Microbial Biofilm Disruption by Natural Bioactive Agents.