Biofilms

  1. Methods for Studying Biofilms
    1. Culturing and Growth Models
      1. Static Models
        1. Microtiter Plates
          1. Petri Dish Assays
            1. Calgary Biofilm Device
            2. Flow Cell Systems
              1. Continuous Flow Reactors
                1. Visualization of Biofilm Development
                  1. Real-time Monitoring
                  2. Drip-Flow Reactors
                    1. Simulation of Shear Forces
                      1. Applications in Industrial Studies
                      2. Rotating Disk Reactors
                        1. Center for Disease Control (CDC) Biofilm Reactor
                        2. Imaging and Microscopy Techniques
                          1. Confocal Laser Scanning Microscopy (CLSM)
                            1. 3D Visualization
                              1. Live/Dead Staining
                                1. Fluorescent Labeling
                                2. Scanning Electron Microscopy (SEM)
                                  1. Surface Morphology
                                    1. High-resolution Imaging
                                    2. Transmission Electron Microscopy (TEM)
                                      1. Internal Structure
                                        1. Ultrastructural Details
                                        2. Atomic Force Microscopy (AFM)
                                          1. Surface Topography
                                            1. Mechanical Properties
                                            2. Light Microscopy Techniques
                                              1. Phase Contrast
                                                1. Differential Interference Contrast
                                                2. Two-Photon Microscopy
                                                3. Molecular and "-Omics" Approaches
                                                  1. Genomics
                                                    1. Whole Genome Sequencing
                                                      1. Identification of Biofilm Genes
                                                        1. Comparative Genomics
                                                        2. Metagenomics
                                                          1. Community Composition Analysis
                                                            1. Functional Gene Analysis
                                                            2. Transcriptomics
                                                              1. Gene Expression Profiling
                                                                1. RNA Sequencing
                                                                2. Proteomics
                                                                  1. Protein Identification and Quantification
                                                                    1. Post-translational Modifications
                                                                    2. Metabolomics
                                                                      1. Metabolic Profiling
                                                                        1. Metabolic Pathway Analysis
                                                                        2. Single-Cell Analysis Techniques
                                                                        3. Quantification of Biofilm Mass
                                                                          1. Crystal Violet Staining
                                                                            1. Biomass Measurement
                                                                              1. Standardization Issues
                                                                              2. Viable Cell Counting
                                                                                1. Colony Forming Units (CFU)
                                                                                  1. Most Probable Number (MPN)
                                                                                  2. Dry Weight Measurement
                                                                                    1. ATP Assays
                                                                                      1. Protein Quantification
                                                                                        1. DNA Quantification
                                                                                        2. Chemical Analysis Methods
                                                                                          1. EPS Composition Analysis
                                                                                            1. Metabolite Detection
                                                                                              1. pH Microelectrodes
                                                                                                1. Oxygen Microelectrodes

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                                                                                              7. Biofilms in Industrial and Environmental Systems

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                                                                                              9. Strategies for Biofilm Control and Eradication