Cellular and Molecular Bioengineering

  1. Core Methodologies and Tools
    1. Cell Culture Engineering
      1. Aseptic Technique and Sterilization
        1. Sterilization Methods
          1. Autoclaving Principles and Applications
            1. Filtration Sterilization
              1. UV Irradiation
                1. Chemical Sterilization
                2. Contamination Prevention
                  1. Sterile Work Environment
                    1. Personal Protective Equipment
                      1. Contamination Detection
                    2. Cell Culture Media and Environments
                      1. Media Components
                        1. Essential Nutrients
                          1. Buffering Systems
                            1. Growth Factors and Hormones
                              1. Antibiotics and Antimycotics
                              2. Serum vs. Serum-Free Media
                                1. Serum Components and Functions
                                  1. Defined Media Formulations
                                    1. Advantages and Limitations
                                    2. pH and Gas Control
                                      1. CO2 Incubation Systems
                                        1. pH Buffering Strategies
                                          1. Oxygen Tension Control
                                        2. Primary Cell Culture vs. Cell Lines
                                          1. Isolation of Primary Cells
                                            1. Tissue Dissociation Methods
                                              1. Cell Separation Techniques
                                                1. Characterization and Validation
                                                2. Immortalization and Transformation
                                                  1. Spontaneous Immortalization
                                                    1. Viral Transformation
                                                      1. Genetic Modifications
                                                      2. Advantages and Limitations
                                                        1. Primary Cell Characteristics
                                                          1. Cell Line Properties
                                                            1. Model System Selection
                                                          2. 3D Cell Culture Techniques
                                                            1. Spheroids and Organoids
                                                              1. Formation Methods
                                                                1. Hanging Drop Method
                                                                  1. Ultra-Low Attachment Plates
                                                                    1. Microwell Arrays
                                                                    2. Applications in Disease Modeling
                                                                      1. Cancer Spheroids
                                                                        1. Organoid Models
                                                                          1. Drug Screening Applications
                                                                        2. Hydrogel Scaffolds
                                                                          1. Natural vs. Synthetic Hydrogels
                                                                            1. Collagen and Matrigel
                                                                              1. Alginate and Chitosan
                                                                                1. PEG and Synthetic Polymers
                                                                                2. Crosslinking Methods
                                                                                  1. Physical Crosslinking
                                                                                    1. Chemical Crosslinking
                                                                                      1. Photo-Crosslinking
                                                                                    2. Bioprinting
                                                                                      1. Bioink Formulation
                                                                                        1. Cell-Laden Hydrogels
                                                                                          1. Rheological Properties
                                                                                            1. Biocompatibility Requirements
                                                                                            2. Printing Technologies
                                                                                              1. Inkjet Bioprinting
                                                                                                1. Extrusion-Based Printing
                                                                                                  1. Laser-Assisted Bioprinting
                                                                                                    1. Stereolithography
                                                                                              2. Molecular Engineering Techniques
                                                                                                1. Recombinant DNA Technology
                                                                                                  1. DNA Cloning and Vectors
                                                                                                    1. Plasmid Vectors
                                                                                                      1. Vector Design and Features
                                                                                                        1. Selection Markers
                                                                                                          1. Multiple Cloning Sites
                                                                                                          2. Viral Vectors
                                                                                                            1. Retroviral Vectors
                                                                                                              1. Adenoviral Vectors
                                                                                                                1. Lentiviral Vectors
                                                                                                                2. Restriction Enzymes and Ligation
                                                                                                                  1. Restriction Enzyme Types
                                                                                                                    1. DNA Ligase Mechanisms
                                                                                                                      1. Cloning Strategies
                                                                                                                    2. Polymerase Chain Reaction
                                                                                                                      1. PCR Components and Setup
                                                                                                                        1. DNA Polymerases
                                                                                                                          1. Primer Design
                                                                                                                            1. Thermal Cycling
                                                                                                                            2. PCR Variants
                                                                                                                              1. Reverse Transcription PCR
                                                                                                                                1. Quantitative PCR
                                                                                                                                  1. Multiplex PCR
                                                                                                                                    1. Digital PCR
                                                                                                                                  2. DNA Sequencing Methods
                                                                                                                                    1. Sanger Sequencing
                                                                                                                                      1. Chain Termination Method
                                                                                                                                        1. Capillary Electrophoresis
                                                                                                                                          1. Data Analysis
                                                                                                                                          2. Next-Generation Sequencing
                                                                                                                                            1. Illumina Sequencing
                                                                                                                                              1. Ion Torrent Sequencing
                                                                                                                                                1. Oxford Nanopore Sequencing
                                                                                                                                                  1. PacBio Sequencing
                                                                                                                                              2. Gene Expression Analysis
                                                                                                                                                1. Quantitative PCR
                                                                                                                                                  1. Primer Design
                                                                                                                                                    1. Specificity and Efficiency
                                                                                                                                                      1. Primer-Dimer Avoidance
                                                                                                                                                        1. Reference Gene Selection
                                                                                                                                                        2. Data Analysis and Normalization
                                                                                                                                                          1. Ct Value Interpretation
                                                                                                                                                            1. Relative Quantification
                                                                                                                                                              1. Statistical Analysis
                                                                                                                                                            2. Microarrays
                                                                                                                                                              1. Probe Design and Hybridization
                                                                                                                                                                1. Oligonucleotide Probes
                                                                                                                                                                  1. Hybridization Conditions
                                                                                                                                                                    1. Signal Detection
                                                                                                                                                                    2. Data Interpretation
                                                                                                                                                                      1. Normalization Methods
                                                                                                                                                                        1. Differential Expression Analysis
                                                                                                                                                                          1. Pathway Analysis
                                                                                                                                                                        2. RNA-Sequencing
                                                                                                                                                                          1. Library Preparation
                                                                                                                                                                            1. RNA Extraction and Quality Control
                                                                                                                                                                              1. cDNA Synthesis
                                                                                                                                                                                1. Adapter Ligation
                                                                                                                                                                                2. Bioinformatic Analysis
                                                                                                                                                                                  1. Read Alignment
                                                                                                                                                                                    1. Transcript Assembly
                                                                                                                                                                                      1. Differential Expression Analysis
                                                                                                                                                                                  2. Protein Engineering and Analysis
                                                                                                                                                                                    1. Protein Expression and Purification
                                                                                                                                                                                      1. Expression Systems
                                                                                                                                                                                        1. Bacterial Expression Systems
                                                                                                                                                                                          1. Yeast Expression Systems
                                                                                                                                                                                            1. Mammalian Expression Systems
                                                                                                                                                                                              1. Insect Cell Systems
                                                                                                                                                                                              2. Purification Techniques
                                                                                                                                                                                                1. Affinity Chromatography
                                                                                                                                                                                                  1. Ion Exchange Chromatography
                                                                                                                                                                                                    1. Size Exclusion Chromatography
                                                                                                                                                                                                      1. Hydrophobic Interaction Chromatography
                                                                                                                                                                                                    2. Western Blotting
                                                                                                                                                                                                      1. Gel Electrophoresis
                                                                                                                                                                                                        1. SDS-PAGE Principles
                                                                                                                                                                                                          1. Native PAGE
                                                                                                                                                                                                            1. Gradient Gels
                                                                                                                                                                                                            2. Transfer and Detection
                                                                                                                                                                                                              1. Protein Transfer Methods
                                                                                                                                                                                                                1. Antibody Selection and Validation
                                                                                                                                                                                                                  1. Detection Systems
                                                                                                                                                                                                                2. Mass Spectrometry
                                                                                                                                                                                                                  1. Sample Preparation
                                                                                                                                                                                                                    1. Protein Digestion
                                                                                                                                                                                                                      1. Peptide Separation
                                                                                                                                                                                                                        1. Ionization Methods
                                                                                                                                                                                                                        2. Peptide Mass Fingerprinting
                                                                                                                                                                                                                          1. Database Searching
                                                                                                                                                                                                                            1. Protein Identification
                                                                                                                                                                                                                              1. Quantitative Proteomics
                                                                                                                                                                                                                            2. Protein Structure Determination
                                                                                                                                                                                                                              1. X-ray Crystallography
                                                                                                                                                                                                                                1. Protein Crystallization
                                                                                                                                                                                                                                  1. Data Collection and Processing
                                                                                                                                                                                                                                    1. Structure Refinement
                                                                                                                                                                                                                                    2. Cryo-Electron Microscopy
                                                                                                                                                                                                                                      1. Sample Preparation
                                                                                                                                                                                                                                        1. Image Processing
                                                                                                                                                                                                                                          1. 3D Reconstruction
                                                                                                                                                                                                                                          2. Nuclear Magnetic Resonance Spectroscopy
                                                                                                                                                                                                                                            1. NMR Principles
                                                                                                                                                                                                                                              1. Structure Calculation
                                                                                                                                                                                                                                                1. Dynamics Studies
                                                                                                                                                                                                                                            2. Gene Editing Technologies
                                                                                                                                                                                                                                              1. CRISPR-Cas Systems
                                                                                                                                                                                                                                                1. Guide RNA Design
                                                                                                                                                                                                                                                  1. Target Site Selection
                                                                                                                                                                                                                                                    1. Off-Target Prediction
                                                                                                                                                                                                                                                      1. gRNA Optimization
                                                                                                                                                                                                                                                      2. Cas9 and Other Nucleases
                                                                                                                                                                                                                                                        1. Cas9 Variants and Engineering
                                                                                                                                                                                                                                                          1. Cas12 and Cas13 Systems
                                                                                                                                                                                                                                                            1. Base Editors and Prime Editors
                                                                                                                                                                                                                                                            2. Off-Target Effects and Validation
                                                                                                                                                                                                                                                              1. Detection Methods
                                                                                                                                                                                                                                                                1. Minimization Strategies
                                                                                                                                                                                                                                                                  1. Validation Approaches
                                                                                                                                                                                                                                                                2. Zinc-Finger Nucleases
                                                                                                                                                                                                                                                                  1. DNA Recognition and Engineering
                                                                                                                                                                                                                                                                    1. Zinc-Finger Domains
                                                                                                                                                                                                                                                                      1. Modular Assembly
                                                                                                                                                                                                                                                                        1. Specificity Determination
                                                                                                                                                                                                                                                                      2. Transcription Activator-Like Effector Nucleases
                                                                                                                                                                                                                                                                        1. Modular Design and Targeting
                                                                                                                                                                                                                                                                          1. TALE Repeat Structure
                                                                                                                                                                                                                                                                            1. Target Site Recognition
                                                                                                                                                                                                                                                                              1. Assembly Methods
                                                                                                                                                                                                                                                                        2. Bioimaging and Microscopy
                                                                                                                                                                                                                                                                          1. Light Microscopy
                                                                                                                                                                                                                                                                            1. Bright-field and Phase Contrast
                                                                                                                                                                                                                                                                              1. Principles and Applications
                                                                                                                                                                                                                                                                                1. Light Path and Image Formation
                                                                                                                                                                                                                                                                                  1. Contrast Enhancement Methods
                                                                                                                                                                                                                                                                                    1. Resolution Limitations
                                                                                                                                                                                                                                                                                  2. Fluorescence Microscopy
                                                                                                                                                                                                                                                                                    1. Fluorophores and Labeling
                                                                                                                                                                                                                                                                                      1. Fluorescent Proteins
                                                                                                                                                                                                                                                                                        1. Organic Dyes
                                                                                                                                                                                                                                                                                          1. Quantum Dots
                                                                                                                                                                                                                                                                                          2. Filter Sets and Detection
                                                                                                                                                                                                                                                                                            1. Excitation and Emission Filters
                                                                                                                                                                                                                                                                                              1. Dichroic Mirrors
                                                                                                                                                                                                                                                                                                1. Detection Systems
                                                                                                                                                                                                                                                                                              2. Confocal Microscopy
                                                                                                                                                                                                                                                                                                1. Optical Sectioning
                                                                                                                                                                                                                                                                                                  1. Pinhole Aperture Function
                                                                                                                                                                                                                                                                                                    1. Z-Stack Acquisition
                                                                                                                                                                                                                                                                                                      1. Deconvolution
                                                                                                                                                                                                                                                                                                      2. 3D Imaging
                                                                                                                                                                                                                                                                                                        1. Volume Rendering
                                                                                                                                                                                                                                                                                                          1. Maximum Intensity Projections
                                                                                                                                                                                                                                                                                                            1. Orthogonal Views
                                                                                                                                                                                                                                                                                                          2. Super-Resolution Microscopy
                                                                                                                                                                                                                                                                                                            1. STED Microscopy
                                                                                                                                                                                                                                                                                                              1. Stimulated Emission Depletion
                                                                                                                                                                                                                                                                                                                1. Resolution Enhancement
                                                                                                                                                                                                                                                                                                                2. PALM and STORM Techniques
                                                                                                                                                                                                                                                                                                                  1. Single-Molecule Localization
                                                                                                                                                                                                                                                                                                                    1. Photoactivatable Fluorophores
                                                                                                                                                                                                                                                                                                                      1. Image Reconstruction
                                                                                                                                                                                                                                                                                                                  2. Electron Microscopy
                                                                                                                                                                                                                                                                                                                    1. Transmission Electron Microscopy
                                                                                                                                                                                                                                                                                                                      1. Sample Preparation
                                                                                                                                                                                                                                                                                                                        1. Fixation and Embedding
                                                                                                                                                                                                                                                                                                                          1. Ultrathin Sectioning
                                                                                                                                                                                                                                                                                                                            1. Staining Methods
                                                                                                                                                                                                                                                                                                                            2. Imaging Resolution
                                                                                                                                                                                                                                                                                                                              1. Electron Beam Interactions
                                                                                                                                                                                                                                                                                                                                1. Contrast Mechanisms
                                                                                                                                                                                                                                                                                                                                  1. Resolution Limits
                                                                                                                                                                                                                                                                                                                                2. Scanning Electron Microscopy
                                                                                                                                                                                                                                                                                                                                  1. Surface Imaging
                                                                                                                                                                                                                                                                                                                                    1. Sample Coating
                                                                                                                                                                                                                                                                                                                                      1. Secondary Electron Detection
                                                                                                                                                                                                                                                                                                                                        1. Topographical Information
                                                                                                                                                                                                                                                                                                                                        2. Elemental Analysis
                                                                                                                                                                                                                                                                                                                                          1. Energy-Dispersive X-ray Spectroscopy
                                                                                                                                                                                                                                                                                                                                            1. Compositional Mapping
                                                                                                                                                                                                                                                                                                                                              1. Quantitative Analysis
                                                                                                                                                                                                                                                                                                                                          2. Live-Cell Imaging Techniques
                                                                                                                                                                                                                                                                                                                                            1. Time-Lapse Microscopy
                                                                                                                                                                                                                                                                                                                                              1. Temporal Resolution Considerations
                                                                                                                                                                                                                                                                                                                                                1. Phototoxicity Minimization
                                                                                                                                                                                                                                                                                                                                                  1. Environmental Control
                                                                                                                                                                                                                                                                                                                                                  2. Fluorescent Reporters and Biosensors
                                                                                                                                                                                                                                                                                                                                                    1. Genetically Encoded Indicators
                                                                                                                                                                                                                                                                                                                                                      1. FRET-Based Sensors
                                                                                                                                                                                                                                                                                                                                                        1. Calcium and pH Indicators
                                                                                                                                                                                                                                                                                                                                                        2. Environmental Control for Live Imaging
                                                                                                                                                                                                                                                                                                                                                          1. Temperature Control
                                                                                                                                                                                                                                                                                                                                                            1. CO2 and Humidity Regulation
                                                                                                                                                                                                                                                                                                                                                              1. Perfusion Systems

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                                                                                                                                                                                                                                                                                                                                                        1. Foundations of Cellular and Molecular Bioengineering

                                                                                                                                                                                                                                                                                                                                                        Go to top

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                                                                                                                                                                                                                                                                                                                                                        3. Quantitative Modeling of Cellular Systems