Plant Molecular Biology

  1. Techniques and Technologies in Plant Molecular Biology
    1. Nucleic Acid Techniques
      1. DNA and RNA Extraction
        1. Tissue Preparation
          1. Extraction Methods
            1. CTAB Method
              1. SDS Method
                1. Commercial Kits
                2. Quality Assessment
                  1. Spectrophotometry
                    1. Gel Electrophoresis
                      1. Fluorometry
                    2. Gel Electrophoresis
                      1. Agarose Gel Electrophoresis
                        1. Gel Preparation
                          1. Sample Loading
                            1. Visualization
                            2. Polyacrylamide Gel Electrophoresis
                              1. High Resolution Separation
                                1. Denaturing Conditions
                              2. Hybridization Techniques
                                1. Southern Blotting
                                  1. DNA Transfer
                                    1. Probe Hybridization
                                    2. Northern Blotting
                                      1. RNA Analysis
                                        1. Gene Expression
                                        2. In Situ Hybridization
                                          1. Tissue Localization
                                            1. Single-Cell Resolution
                                          2. DNA Sequencing
                                            1. Sanger Sequencing
                                              1. Chain Termination Method
                                                1. Capillary Electrophoresis
                                                2. Next-Generation Sequencing
                                                  1. Illumina Sequencing
                                                    1. Library Preparation
                                                      1. Data Analysis
                                                        1. Quality Control
                                                    2. Protein Analysis Techniques
                                                      1. Protein Extraction and Purification
                                                        1. Extraction Buffers
                                                          1. Protein Quantification
                                                            1. Bradford Assay
                                                              1. BCA Assay
                                                                1. Lowry Assay
                                                                2. Protein Purification
                                                                  1. Chromatography Methods
                                                                    1. Affinity Purification
                                                                  2. Protein Electrophoresis
                                                                    1. SDS-PAGE
                                                                      1. Gel Preparation
                                                                        1. Sample Preparation
                                                                          1. Molecular Weight Determination
                                                                          2. Native PAGE
                                                                            1. Isoelectric Focusing
                                                                            2. Western Blotting
                                                                              1. Protein Transfer
                                                                                1. Antibody Detection
                                                                                  1. Chemiluminescent Detection
                                                                                  2. Mass Spectrometry
                                                                                    1. Sample Preparation
                                                                                      1. Ionization Methods
                                                                                        1. Protein Identification
                                                                                          1. Quantitative Proteomics
                                                                                          2. Protein Interaction Analysis
                                                                                            1. Yeast Two-Hybrid System
                                                                                              1. Co-Immunoprecipitation
                                                                                                1. Pull-Down Assays
                                                                                                  1. Protein Crosslinking
                                                                                                2. Gene Cloning and Transformation
                                                                                                  1. Recombinant DNA Technology
                                                                                                    1. Restriction Enzymes
                                                                                                      1. Recognition Sequences
                                                                                                        1. Cleavage Patterns
                                                                                                        2. DNA Ligation
                                                                                                          1. T4 DNA Ligase
                                                                                                            1. Ligation Strategies
                                                                                                            2. Cloning Strategies
                                                                                                              1. Directional Cloning
                                                                                                                1. TA Cloning
                                                                                                                  1. Gateway Cloning
                                                                                                                2. Cloning Vectors
                                                                                                                  1. Plasmid Vectors
                                                                                                                    1. Selection Markers
                                                                                                                      1. Multiple Cloning Sites
                                                                                                                      2. Bacterial Artificial Chromosomes
                                                                                                                        1. Large Insert Cloning
                                                                                                                        2. Binary Vectors
                                                                                                                          1. T-DNA Borders
                                                                                                                            1. Agrobacterium Compatibility
                                                                                                                          2. Plant Transformation
                                                                                                                            1. Agrobacterium-Mediated Transformation
                                                                                                                              1. T-DNA Transfer
                                                                                                                                1. Virulence Genes
                                                                                                                                  1. Plant Regeneration
                                                                                                                                  2. Biolistics
                                                                                                                                    1. Particle Bombardment
                                                                                                                                      1. Transient Expression
                                                                                                                                      2. Protoplast Transformation
                                                                                                                                        1. Protoplast Isolation
                                                                                                                                          1. DNA Uptake Methods
                                                                                                                                          2. Electroporation
                                                                                                                                            1. Microinjection
                                                                                                                                          3. Functional Genomics Approaches
                                                                                                                                            1. Forward Genetics
                                                                                                                                              1. Mutagenesis
                                                                                                                                                1. Chemical Mutagenesis
                                                                                                                                                  1. Radiation Mutagenesis
                                                                                                                                                    1. Insertional Mutagenesis
                                                                                                                                                    2. Mutant Screening
                                                                                                                                                      1. Phenotypic Screening
                                                                                                                                                        1. Molecular Screening
                                                                                                                                                        2. Map-Based Cloning
                                                                                                                                                          1. Genetic Mapping
                                                                                                                                                            1. Physical Mapping
                                                                                                                                                              1. Chromosome Walking
                                                                                                                                                            2. Reverse Genetics
                                                                                                                                                              1. T-DNA Insertion Lines
                                                                                                                                                                1. T-DNA Libraries
                                                                                                                                                                  1. Insertion Site Analysis
                                                                                                                                                                  2. Transposon Tagging
                                                                                                                                                                    1. Ac/Ds System
                                                                                                                                                                      1. Mu Elements
                                                                                                                                                                      2. Targeted Mutagenesis
                                                                                                                                                                        1. Site-Directed Mutagenesis
                                                                                                                                                                      3. Gene Silencing
                                                                                                                                                                        1. RNA Interference
                                                                                                                                                                          1. dsRNA Design
                                                                                                                                                                            1. Silencing Efficiency
                                                                                                                                                                            2. Virus-Induced Gene Silencing
                                                                                                                                                                              1. VIGS Vectors
                                                                                                                                                                                1. Transient Silencing
                                                                                                                                                                                2. Antisense Technology
                                                                                                                                                                                3. Genome Editing
                                                                                                                                                                                  1. CRISPR-Cas9
                                                                                                                                                                                    1. Guide RNA Design
                                                                                                                                                                                      1. Cas9 Variants
                                                                                                                                                                                        1. Off-Target Analysis
                                                                                                                                                                                        2. TALENs
                                                                                                                                                                                          1. TALE Repeats
                                                                                                                                                                                            1. Nuclease Design
                                                                                                                                                                                            2. Zinc Finger Nucleases
                                                                                                                                                                                              1. Zinc Finger Domains
                                                                                                                                                                                                1. Nuclease Engineering
                                                                                                                                                                                            3. Omics Technologies
                                                                                                                                                                                              1. Genomics
                                                                                                                                                                                                1. Genome Sequencing
                                                                                                                                                                                                  1. Whole Genome Sequencing
                                                                                                                                                                                                    1. Targeted Sequencing
                                                                                                                                                                                                    2. Genome Assembly
                                                                                                                                                                                                      1. De Novo Assembly
                                                                                                                                                                                                        1. Reference-Based Assembly
                                                                                                                                                                                                        2. Genome Annotation
                                                                                                                                                                                                          1. Gene Prediction
                                                                                                                                                                                                            1. Functional Annotation
                                                                                                                                                                                                            2. Comparative Genomics
                                                                                                                                                                                                              1. Synteny Analysis
                                                                                                                                                                                                                1. Phylogenomics
                                                                                                                                                                                                              2. Transcriptomics
                                                                                                                                                                                                                1. Microarray Analysis
                                                                                                                                                                                                                  1. Array Design
                                                                                                                                                                                                                    1. Data Normalization
                                                                                                                                                                                                                    2. RNA Sequencing
                                                                                                                                                                                                                      1. Library Preparation
                                                                                                                                                                                                                        1. Differential Expression Analysis
                                                                                                                                                                                                                          1. Alternative Splicing Analysis
                                                                                                                                                                                                                          2. Single-Cell RNA-Seq
                                                                                                                                                                                                                            1. Cell Isolation
                                                                                                                                                                                                                              1. Data Analysis Challenges
                                                                                                                                                                                                                            2. Proteomics
                                                                                                                                                                                                                              1. Protein Identification
                                                                                                                                                                                                                                1. Mass Spectrometry
                                                                                                                                                                                                                                  1. Database Searching
                                                                                                                                                                                                                                  2. Quantitative Proteomics
                                                                                                                                                                                                                                    1. Label-Free Quantification
                                                                                                                                                                                                                                      1. Isotope Labeling
                                                                                                                                                                                                                                      2. Post-Translational Modifications
                                                                                                                                                                                                                                        1. Phosphoproteomics
                                                                                                                                                                                                                                          1. Glycoproteomics
                                                                                                                                                                                                                                        2. Metabolomics
                                                                                                                                                                                                                                          1. Metabolite Extraction
                                                                                                                                                                                                                                            1. Analytical Platforms
                                                                                                                                                                                                                                              1. GC-MS
                                                                                                                                                                                                                                                1. LC-MS
                                                                                                                                                                                                                                                  1. NMR
                                                                                                                                                                                                                                                  2. Data Processing
                                                                                                                                                                                                                                                    1. Peak Detection
                                                                                                                                                                                                                                                      1. Metabolite Identification
                                                                                                                                                                                                                                                      2. Pathway Analysis
                                                                                                                                                                                                                                                      3. Epigenomics
                                                                                                                                                                                                                                                        1. DNA Methylation Analysis
                                                                                                                                                                                                                                                          1. Bisulfite Sequencing
                                                                                                                                                                                                                                                            1. Methylation Arrays
                                                                                                                                                                                                                                                            2. Chromatin Immunoprecipitation
                                                                                                                                                                                                                                                              1. ChIP-Seq
                                                                                                                                                                                                                                                                1. Histone Modifications
                                                                                                                                                                                                                                                                2. Chromatin Accessibility
                                                                                                                                                                                                                                                                  1. ATAC-Seq
                                                                                                                                                                                                                                                                    1. DNase-Seq
                                                                                                                                                                                                                                                                3. Bioinformatics and Data Analysis
                                                                                                                                                                                                                                                                  1. Sequence Analysis
                                                                                                                                                                                                                                                                    1. Sequence Alignment
                                                                                                                                                                                                                                                                      1. Pairwise Alignment
                                                                                                                                                                                                                                                                        1. Multiple Sequence Alignment
                                                                                                                                                                                                                                                                        2. Database Searching
                                                                                                                                                                                                                                                                          1. BLAST
                                                                                                                                                                                                                                                                            1. Hidden Markov Models
                                                                                                                                                                                                                                                                            2. Phylogenetic Analysis
                                                                                                                                                                                                                                                                              1. Tree Construction Methods
                                                                                                                                                                                                                                                                                1. Bootstrap Analysis
                                                                                                                                                                                                                                                                              2. Genome Analysis
                                                                                                                                                                                                                                                                                1. Gene Prediction
                                                                                                                                                                                                                                                                                  1. Ab Initio Methods
                                                                                                                                                                                                                                                                                    1. Evidence-Based Methods
                                                                                                                                                                                                                                                                                    2. Functional Annotation
                                                                                                                                                                                                                                                                                      1. Gene Ontology
                                                                                                                                                                                                                                                                                        1. Pathway Databases
                                                                                                                                                                                                                                                                                        2. Comparative Genomics
                                                                                                                                                                                                                                                                                          1. Synteny Analysis
                                                                                                                                                                                                                                                                                            1. Ortholog Identification
                                                                                                                                                                                                                                                                                          2. Expression Data Analysis
                                                                                                                                                                                                                                                                                            1. Normalization Methods
                                                                                                                                                                                                                                                                                              1. Statistical Analysis
                                                                                                                                                                                                                                                                                                1. Differential Expression
                                                                                                                                                                                                                                                                                                  1. Multiple Testing Correction
                                                                                                                                                                                                                                                                                                  2. Clustering Analysis
                                                                                                                                                                                                                                                                                                    1. Pathway Enrichment Analysis
                                                                                                                                                                                                                                                                                                    2. Network Analysis
                                                                                                                                                                                                                                                                                                      1. Gene Regulatory Networks
                                                                                                                                                                                                                                                                                                        1. Protein Interaction Networks
                                                                                                                                                                                                                                                                                                          1. Metabolic Networks
                                                                                                                                                                                                                                                                                                            1. Network Visualization
                                                                                                                                                                                                                                                                                                          2. Microscopy and Imaging
                                                                                                                                                                                                                                                                                                            1. Light Microscopy
                                                                                                                                                                                                                                                                                                              1. Bright Field Microscopy
                                                                                                                                                                                                                                                                                                                1. Fluorescence Microscopy
                                                                                                                                                                                                                                                                                                                  1. Fluorescent Proteins
                                                                                                                                                                                                                                                                                                                    1. Immunofluorescence
                                                                                                                                                                                                                                                                                                                    2. Confocal Microscopy
                                                                                                                                                                                                                                                                                                                      1. Optical Sectioning
                                                                                                                                                                                                                                                                                                                        1. 3D Reconstruction
                                                                                                                                                                                                                                                                                                                        2. Live Cell Imaging
                                                                                                                                                                                                                                                                                                                          1. Time-Lapse Microscopy
                                                                                                                                                                                                                                                                                                                            1. Photobleaching Recovery
                                                                                                                                                                                                                                                                                                                          2. Electron Microscopy
                                                                                                                                                                                                                                                                                                                            1. Transmission Electron Microscopy
                                                                                                                                                                                                                                                                                                                              1. Sample Preparation
                                                                                                                                                                                                                                                                                                                                1. Ultrastructural Analysis
                                                                                                                                                                                                                                                                                                                                2. Scanning Electron Microscopy
                                                                                                                                                                                                                                                                                                                                  1. Surface Morphology
                                                                                                                                                                                                                                                                                                                                3. Specialized Techniques
                                                                                                                                                                                                                                                                                                                                  1. Two-Photon Microscopy
                                                                                                                                                                                                                                                                                                                                    1. Super-Resolution Microscopy
                                                                                                                                                                                                                                                                                                                                      1. Atomic Force Microscopy

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                                                                                                                                                                                                                                                                                                                                  8. Applications in Plant Biotechnology