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 -- 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.