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| <div class="header"> |
| <h1>🦠 E. coli Batch 01: DNA Replication & Repair</h1> |
| <p>Programming Framework Analysis - 8 DNA Processes</p> |
| </div> |
| <div class="content"> |
| <div class="intro"> |
| <h2>🦠 DNA Replication & Repair Systems</h2> |
| <p><strong>Batch Overview:</strong> This batch contains 8 fundamental E. coli processes responsible for DNA replication and repair. These processes represent the core computational systems that ensure genomic integrity and faithful inheritance of genetic information.</p> |
| <p>Each process demonstrates sophisticated biological programming with error correction and quality control.</p> |
| </div> |
| |
| <div class="toc"> |
| <h2>📋 Table of Contents - 8 DNA Processes</h2> |
| <ul> |
| <li><a href="#dna-replication-initiation">1. DNA Replication Initiation</a></li> |
| <li><a href="#dna-replication-elongation">2. DNA Replication Elongation</a></li> |
| <li><a href="#dna-replication-termination">3. DNA Replication Termination</a></li> |
| <li><a href="#dna-repair">4. DNA Repair</a></li> |
| <li><a href="#base-excision-repair">5. Base Excision Repair</a></li> |
| <li><a href="#nucleotide-excision-repair">6. Nucleotide Excision Repair</a></li> |
| <li><a href="#mismatch-repair">7. Mismatch Repair</a></li> |
| <li><a href="#sos-response">8. SOS Response</a></li> |
| </ul> |
| </div> |
| |
| |
| <div class="process-item" id="dna-replication-initiation"> |
| <h3 id="process-1">Process 1: DNA Replication Initiation</h3> |
| <p>Detailed analysis of E. coli DNA Replication Initiation using the Programming Framework, revealing computational logic and regulatory patterns.</p> |
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| |
| <div class="mermaid-container"> |
| <div class="mermaid" id="chart-1"> |
| graph TD |
| %% Initial Setup |
| A[oriC Recognition] --> B[DnaA Binding] |
| B --> C[DNA Unwinding] |
| C --> D[DnaB Helicase Loading] |
| D --> E[Primosome Assembly] |
| E --> F[DNA Polymerase III Loading] |
| F --> G[Replication Fork Formation] |
| G --> H[Bidirectional Replication] |
| %% Styling - Biological Color Scheme |
| style A fill:#ff6b6b,color:#fff |
| style B fill:#ffd43b,color:#000 |
| style C fill:#51cf66,color:#fff |
| style D fill:#ffd43b,color:#000 |
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| style F fill:#ffd43b,color:#000 |
| style G fill:#74c0fc,color:#fff |
| style H fill:#b197fc,color:#fff |
| </div> |
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| <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span> |
| <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span> |
| <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span> |
| <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span> |
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| </div> |
| </div> |
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|
| |
| <div class="process-item" id="dna-replication-elongation"> |
| <h3 id="process-2">Process 2: DNA Replication Elongation</h3> |
| <p>Detailed analysis of E. coli DNA Replication Elongation using the Programming Framework, revealing computational logic and regulatory patterns.</p> |
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| |
| <div class="mermaid-container"> |
| <div class="mermaid" id="chart-2"> |
| graph TD |
| %% Initial Setup |
| A[Leading Strand Synthesis] --> B[Lagging Strand Synthesis] |
| B --> C[Okazaki Fragment Formation] |
| C --> D[DNA Polymerase I Activity] |
| D --> E[RNA Primer Removal] |
| E --> F[DNA Ligase Activity] |
| F --> G[Fragment Joining] |
| G --> H[Continuous DNA Synthesis] |
| %% Styling - Biological Color Scheme |
| style A fill:#ff6b6b,color:#fff |
| style B fill:#51cf66,color:#fff |
| style C fill:#74c0fc,color:#fff |
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| style G fill:#51cf66,color:#fff |
| style H fill:#b197fc,color:#fff |
| </div> |
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| <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span> |
| <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span> |
| <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span> |
| <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span> |
| <span><span class="color-box" style="background:#b197fc;"></span>Products</span> |
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| </div> |
| </div> |
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| |
| <div class="process-item" id="dna-replication-termination"> |
| <h3 id="process-3">Process 3: DNA Replication Termination</h3> |
| <p>Detailed analysis of E. coli DNA Replication Termination using the Programming Framework, revealing computational logic and regulatory patterns.</p> |
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| |
| <div class="mermaid-container"> |
| <div class="mermaid" id="chart-3"> |
| graph TD |
| %% Initial Setup |
| A[Replication Fork Convergence] --> B[Tus Protein Binding] |
| B --> C[Ter Site Recognition] |
| C --> D[Fork Arrest] |
| D --> E[DNA Decatenation] |
| E --> F[Topoisomerase IV Activity] |
| F --> G[Chromosome Separation] |
| G --> H[Replication Complete] |
| %% Styling - Biological Color Scheme |
| style A fill:#ff6b6b,color:#fff |
| style B fill:#ffd43b,color:#000 |
| style C fill:#51cf66,color:#fff |
| style D fill:#74c0fc,color:#fff |
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| style G fill:#51cf66,color:#fff |
| style H fill:#b197fc,color:#fff |
| </div> |
| <div class="color-legend"> |
| <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span> |
| <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span> |
| <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span> |
| <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span> |
| <span><span class="color-box" style="background:#b197fc;"></span>Products</span> |
| </div> |
| </div> |
| </div> |
|
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| |
| <div class="process-item" id="dna-repair"> |
| <h3 id="process-4">Process 4: DNA Repair</h3> |
| <p>Detailed analysis of E. coli DNA Repair using the Programming Framework, revealing computational logic and regulatory patterns.</p> |
| |
| |
| <div class="slider-controls"> |
| <h4>🎛️ Detail Level Control</h4> |
| <div class="slider-container"> |
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| <input type="range" class="detail-slider" id="slider-4" min="1" max="5" value="1" step="1"> |
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| </div> |
| |
| <div class="mermaid-container"> |
| <div class="mermaid" id="chart-4"> |
| graph TD |
| %% Initial Setup |
| A[DNA Damage Detection] --> B[UvrA-UvrB Recognition] |
| B --> C[UvrC Recruitment] |
| C --> D[Excision Repair] |
| D --> E[DNA Polymerase I] |
| E --> F[DNA Ligase Activity] |
| F --> G[Repair Completion] |
| G --> H[Cell Survival] |
| %% Styling - Biological Color Scheme |
| style A fill:#ff6b6b,color:#fff |
| style B fill:#ffd43b,color:#000 |
| style C fill:#ffd43b,color:#000 |
| style D fill:#51cf66,color:#fff |
| style E fill:#ffd43b,color:#000 |
| style F fill:#ffd43b,color:#000 |
| style G fill:#b197fc,color:#fff |
| style H fill:#b197fc,color:#fff |
| </div> |
| <div class="color-legend"> |
| <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span> |
| <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span> |
| <span><span class="color-box" style="background:#51cf66;"></span>Chemical Processing</span> |
| <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span> |
| <span><span class="color-box" style="background:#b197fc;"></span>Products</span> |
| </div> |
| </div> |
| </div> |
|
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| |
| <div class="process-item" id="base-excision-repair"> |
| <h3 id="process-5">Process 5: Base Excision Repair</h3> |
| <p>Detailed analysis of E. coli Base Excision Repair using the Programming Framework, revealing computational logic and regulatory patterns for small DNA lesions.</p> |
| |
| |
| <div class="slider-controls"> |
| <h4>🎛️ Detail Level Control</h4> |
| <div class="slider-container"> |
| <span class="slider-label">Level:</span> |
| <input type="range" class="detail-slider" id="slider-5" min="1" max="5" value="1" step="1"> |
| <span class="level-display" id="level-5">1</span> |
| </div> |
| </div> |
| |
| <div class="mermaid-container"> |
| <div class="mermaid" id="chart-5"> |
| graph TD |
| %% DNA Damage Detection |
| A[Damaged Base] --> B[DNA Glycosylase Recognition] |
| C[Oxidative Damage] --> B |
| D[Alkylation Damage] --> B |
| E[Deamination] --> B |
| |
| %% Base Removal |
| B --> F[Glycosylase Binding] |
| F --> G[Base Excision] |
| G --> H[AP Site Formation] |
| |
| %% AP Site Processing |
| H --> I[AP Endonuclease] |
| I --> J[5' Incision] |
| J --> K[3' Incision] |
| K --> L[Gap Formation] |
| |
| %% Gap Filling |
| L --> M[DNA Polymerase I] |
| M --> N[Single Nucleotide Insertion] |
| N --> O[DNA Ligase] |
| O --> P[Repair Complete] |
| |
| %% Styling - Programming Framework Colors |
| style A fill:#ff6b6b,color:#fff |
| style C fill:#ff6b6b,color:#fff |
| style D fill:#ff6b6b,color:#fff |
| style E fill:#ff6b6b,color:#fff |
| style B fill:#74c0fc,color:#fff |
| style F fill:#ffd43b,color:#000 |
| style G fill:#ffd43b,color:#000 |
| style H fill:#74c0fc,color:#fff |
| style I fill:#ffd43b,color:#000 |
| style J fill:#ffd43b,color:#000 |
| style K fill:#ffd43b,color:#000 |
| style L fill:#74c0fc,color:#fff |
| style M fill:#ffd43b,color:#000 |
| style N fill:#ffd43b,color:#000 |
| style O fill:#ffd43b,color:#000 |
| style P fill:#b197fc,color:#fff |
| </div> |
| <div class="color-legend"> |
| <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span> |
| <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span> |
| <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span> |
| <span><span class="color-box" style="background:#b197fc;"></span>Products</span> |
| </div> |
| </div> |
| </div> |
|
|
| |
| <div class="process-item" id="nucleotide-excision-repair"> |
| <h3 id="process-6">Process 6: Nucleotide Excision Repair</h3> |
| <p>Detailed analysis of E. coli Nucleotide Excision Repair using the Programming Framework, revealing computational logic and regulatory patterns for bulky DNA lesions.</p> |
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| |
| <div class="slider-controls"> |
| <h4>🎛️ Detail Level Control</h4> |
| <div class="slider-container"> |
| <span class="slider-label">Level:</span> |
| <input type="range" class="detail-slider" id="slider-6" min="1" max="5" value="1" step="1"> |
| <span class="level-display" id="level-6">1</span> |
| </div> |
| </div> |
| |
| <div class="mermaid-container"> |
| <div class="mermaid" id="chart-6"> |
| graph TD |
| %% Damage Recognition |
| A[Bulky DNA Lesion] --> B[UvrA-UvrB Recognition] |
| C[UV-Induced Damage] --> B |
| D[Chemical Adducts] --> B |
| E[Cross-links] --> B |
| |
| %% Damage Verification |
| B --> F[UvrA Release] |
| F --> G[UvrB-DNA Complex] |
| G --> H[UvrC Recruitment] |
| H --> I[UvrBC Complex] |
| |
| %% Dual Incision |
| I --> J[3' Incision] |
| I --> K[5' Incision] |
| J --> L[Oligonucleotide Release] |
| K --> L |
| L --> M[Gap Formation] |
| |
| %% Gap Filling |
| M --> N[DNA Polymerase I] |
| N --> O[Gap Filling] |
| O --> P[DNA Ligase] |
| P --> Q[Repair Complete] |
| |
| %% Styling - Programming Framework Colors |
| style A fill:#ff6b6b,color:#fff |
| style C fill:#ff6b6b,color:#fff |
| style D fill:#ff6b6b,color:#fff |
| style E fill:#ff6b6b,color:#fff |
| style B fill:#ffd43b,color:#000 |
| style F fill:#ffd43b,color:#000 |
| style G fill:#74c0fc,color:#fff |
| style H fill:#ffd43b,color:#000 |
| style I fill:#ffd43b,color:#000 |
| style J fill:#ffd43b,color:#000 |
| style K fill:#ffd43b,color:#000 |
| style L fill:#74c0fc,color:#fff |
| style M fill:#74c0fc,color:#fff |
| style N fill:#ffd43b,color:#000 |
| style O fill:#ffd43b,color:#000 |
| style P fill:#ffd43b,color:#000 |
| style Q fill:#b197fc,color:#fff |
| </div> |
| <div class="color-legend"> |
| <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span> |
| <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span> |
| <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span> |
| <span><span class="color-box" style="background:#b197fc;"></span>Products</span> |
| </div> |
| </div> |
| </div> |
|
|
| |
| <div class="process-item" id="mismatch-repair"> |
| <h3 id="process-7">Process 7: Mismatch Repair</h3> |
| <p>Detailed analysis of E. coli Mismatch Repair using the Programming Framework, revealing computational logic and regulatory patterns for replication errors.</p> |
| |
| |
| <div class="slider-controls"> |
| <h4>🎛️ Detail Level Control</h4> |
| <div class="slider-container"> |
| <span class="slider-label">Level:</span> |
| <input type="range" class="detail-slider" id="slider-7" min="1" max="5" value="1" step="1"> |
| <span class="level-display" id="level-7">1</span> |
| </div> |
| </div> |
| |
| <div class="mermaid-container"> |
| <div class="mermaid" id="chart-7"> |
| graph TD |
| %% Mismatch Detection |
| A[DNA Mismatch] --> B[MutS Recognition] |
| C[Replication Error] --> B |
| D[Insertion/Deletion] --> B |
| E[Base Mismatch] --> B |
| |
| %% Complex Formation |
| B --> F[MutS-DNA Complex] |
| F --> G[MutL Recruitment] |
| G --> H[MutS-MutL Complex] |
| H --> I[DNA Bending] |
| |
| %% Strand Discrimination |
| I --> J[GATC Site Recognition] |
| J --> K[MutH Activation] |
| K --> L[Strand Incision] |
| L --> M[Nick Formation] |
| |
| %% Excision and Repair |
| M --> N[Helicase II Loading] |
| N --> O[Exonuclease Activity] |
| O --> P[Gap Formation] |
| P --> Q[DNA Polymerase III] |
| Q --> R[Gap Filling] |
| R --> S[DNA Ligase] |
| S --> T[Repair Complete] |
| |
| %% Styling - Programming Framework Colors |
| style A fill:#ff6b6b,color:#fff |
| style C fill:#ff6b6b,color:#fff |
| style D fill:#ff6b6b,color:#fff |
| style E fill:#ff6b6b,color:#fff |
| style B fill:#ffd43b,color:#000 |
| style F fill:#74c0fc,color:#fff |
| style G fill:#ffd43b,color:#000 |
| style H fill:#74c0fc,color:#fff |
| style I fill:#ffd43b,color:#000 |
| style J fill:#ffd43b,color:#000 |
| style K fill:#ffd43b,color:#000 |
| style L fill:#ffd43b,color:#000 |
| style M fill:#74c0fc,color:#fff |
| style N fill:#ffd43b,color:#000 |
| style O fill:#ffd43b,color:#000 |
| style P fill:#74c0fc,color:#fff |
| style Q fill:#ffd43b,color:#000 |
| style R fill:#ffd43b,color:#000 |
| style S fill:#ffd43b,color:#000 |
| style T fill:#b197fc,color:#fff |
| </div> |
| <div class="color-legend"> |
| <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span> |
| <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span> |
| <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span> |
| <span><span class="color-box" style="background:#b197fc;"></span>Products</span> |
| </div> |
| </div> |
| </div> |
|
|
| |
| <div class="process-item" id="sos-response"> |
| <h3 id="process-8">Process 8: SOS Response</h3> |
| <p>Detailed analysis of E. coli SOS Response using the Programming Framework, revealing computational logic and regulatory patterns for emergency DNA repair.</p> |
| |
| |
| <div class="slider-controls"> |
| <h4>🎛️ Detail Level Control</h4> |
| <div class="slider-container"> |
| <span class="slider-label">Level:</span> |
| <input type="range" class="detail-slider" id="slider-8" min="1" max="5" value="1" step="1"> |
| <span class="level-display" id="level-8">1</span> |
| </div> |
| </div> |
| |
| <div class="mermaid-container"> |
| <div class="mermaid" id="chart-8"> |
| graph TD |
| %% DNA Damage Detection |
| A[DNA Damage] --> B[Single-Strand DNA] |
| C[UV Radiation] --> A |
| D[Chemical Mutagens] --> A |
| E[Replication Stress] --> A |
| |
| %% RecA Activation |
| B --> F[RecA Protein Binding] |
| F --> G[RecA Nucleofilament] |
| G --> H[RecA Activation] |
| H --> I[LexA Cleavage] |
| |
| %% SOS Regulon Activation |
| I --> J[LexA Degradation] |
| J --> K[SOS Genes Derepressed] |
| K --> L[DNA Repair Genes] |
| L --> M[Error-Prone Repair] |
| |
| %% Repair Execution |
| M --> N[UmuC/UmuD Expression] |
| N --> O[Translesion Synthesis] |
| O --> P[Error-Prone Bypass] |
| P --> Q[Cell Survival] |
| |
| %% Recovery |
| Q --> R[Damage Cleared] |
| R --> S[RecA Inactivation] |
| S --> T[LexA Reformation] |
| T --> U[SOS Genes Repressed] |
| |
| %% Styling - Programming Framework Colors |
| style A fill:#ff6b6b,color:#fff |
| style C fill:#ff6b6b,color:#fff |
| style D fill:#ff6b6b,color:#fff |
| style E fill:#ff6b6b,color:#fff |
| style B fill:#74c0fc,color:#fff |
| style F fill:#ffd43b,color:#000 |
| style G fill:#74c0fc,color:#fff |
| style H fill:#ffd43b,color:#000 |
| style I fill:#ffd43b,color:#000 |
| style J fill:#ffd43b,color:#000 |
| style K fill:#ffd43b,color:#000 |
| style L fill:#ffd43b,color:#000 |
| style M fill:#ffd43b,color:#000 |
| style N fill:#ffd43b,color:#000 |
| style O fill:#ffd43b,color:#000 |
| style P fill:#ffd43b,color:#000 |
| style Q fill:#b197fc,color:#fff |
| style R fill:#74c0fc,color:#fff |
| style S fill:#ffd43b,color:#000 |
| style T fill:#ffd43b,color:#000 |
| style U fill:#b197fc,color:#fff |
| </div> |
| <div class="color-legend"> |
| <span><span class="color-box" style="background:#ff6b6b;"></span>Triggers & Conditions</span> |
| <span><span class="color-box" style="background:#ffd43b;"></span>Catalysts & Enzymes</span> |
| <span><span class="color-box" style="background:#74c0fc;"></span>Intermediates</span> |
| <span><span class="color-box" style="background:#b197fc;"></span>Products</span> |
| </div> |
| </div> |
| </div> |
| |
| |
| <div class="sources-section"> |
| <h2>📚 Academic Sources</h2> |
| <div class="sources-content"> |
| <h3>Primary References</h3> |
| <ul> |
| <li><strong>Alberts, B., et al.</strong> (2015). <em>Molecular Biology of the Cell</em>, 6th Edition. Garland Science.</li> |
| <li><strong>Berg, J.M., et al.</strong> (2015). <em>Biochemistry</em>, 8th Edition. W.H. Freeman.</li> |
| <li><strong>Lodish, H., et al.</strong> (2016). <em>Molecular Cell Biology</em>, 8th Edition. W.H. Freeman.</li> |
| <li><strong>Nelson, D.L. & Cox, M.M.</strong> (2017). <em>Lehninger Principles of Biochemistry</em>, 7th Edition. W.H. Freeman.</li> |
| </ul> |
| <h3>E. coli DNA Replication & Repair Research</h3> |
| <ul> |
| <li><strong>Bell, S.P. & Kaguni, J.M.</strong> (2013). Helicase loading at chromosomal origins of replication. <em>Cold Spring Harbor Perspectives in Biology</em>, 5(6), a010124.</li> |
| <li><strong>Modrich, P.</strong> (2016). Mechanisms in E. coli and human mismatch repair. <em>Annual Review of Biochemistry</em>, 85, 843-867.</li> |
| <li><strong>Sancar, A., et al.</strong> (2004). Molecular mechanisms of mammalian DNA repair and the DNA damage checkpoints. <em>Annual Review of Biochemistry</em>, 73, 39-85.</li> |
| <li><strong>Friedberg, E.C., et al.</strong> (2014). <em>DNA Repair and Mutagenesis</em>, 2nd Edition. ASM Press.</li> |
| </ul> |
| </div> |
| </div> |
|
|
| |
| <div class="scientific-disclosure"> |
| <h2>🔬 Scientific Accuracy & Educational Purpose</h2> |
| <div class="disclosure-content"> |
| <h3>Educational Framework</h3> |
| <p><strong>Purpose:</strong> These interactive flowcharts are designed for educational visualization of E. coli DNA replication and repair processes using the Programming Framework methodology developed by Gary Welz (1995).</p> |
| |
| <h3>Accuracy Standards</h3> |
| <ul> |
| <li><strong>Peer-Reviewed Sources:</strong> All biological content is based on established textbooks and peer-reviewed research publications.</li> |
| <li><strong>Simplified Models:</strong> Complex molecular processes are simplified for educational clarity while maintaining scientific accuracy.</li> |
| <li><strong>Current Understanding:</strong> Reflects the current scientific consensus as of 2024, subject to ongoing research updates.</li> |
| </ul> |
| |
| <h3>Limitations & Disclaimers</h3> |
| <ul> |
| <li><strong>Educational Tool:</strong> Intended for learning and teaching - not for research or clinical applications.</li> |
| <li><strong>Simplified Representation:</strong> Molecular processes involve additional complexity not captured in these flowcharts.</li> |
| <li><strong>Species-Specific:</strong> Information specifically applies to <em>E. coli</em> systems and may differ in other organisms.</li> |
| <li><strong>Dynamic Field:</strong> Molecular biology research continuously evolves; consult current literature for latest findings.</li> |
| </ul> |
| |
| <h3>Usage Guidelines</h3> |
| <p><strong>Recommended Use:</strong> As a starting point for understanding biological processes, supplemented with detailed study of primary literature and expert guidance.</p> |
| </div> |
| </div> |
|
|
| <div class="footer"> |
| <p><strong>Generated using the Programming Framework methodology</strong></p> |
| <p>This batch demonstrates the computational nature of E. coli DNA replication and repair systems</p> |
| <p>Each flowchart preserves maximum detail through optimized Mermaid configuration</p> |
| <p><em>Batch 01 of 25: DNA Replication & Repair</em></p> |
| </div> |
| </div> |
| </div> |
| |
| <script> |
| |
| const allProcesses = { |
| 1: { |
| levels: { |
| 1: `graph TD |
| A[oriC Recognition] --> B[DnaA Binding] |
| B --> C[Replication Fork] |
| |
| style A fill:#ff6b6b,color:#fff |
| style B fill:#ffd43b,color:#000 |
| style C fill:#b197fc,color:#fff`, |
| |
| 2: `graph TD |
| A[oriC Recognition] --> B[DnaA Binding] |
| B --> C[DNA Unwinding] |
| C --> D[DnaB Helicase Loading] |
| D --> E[Replication Fork Formation] |
| |
| style A fill:#ff6b6b,color:#fff |
| style B fill:#ffd43b,color:#000 |
| style C fill:#51cf66,color:#fff |
| style D fill:#ffd43b,color:#000 |
| style E fill:#b197fc,color:#fff`, |
| |
| 3: `graph TD |
| A[oriC Recognition] --> B[DnaA Binding] |
| B --> C[DNA Unwinding] |
| C --> D[DnaB Helicase Loading] |
| D --> E[Primosome Assembly] |
| E --> F[DNA Polymerase III Loading] |
| F --> G[Replication Fork Formation] |
| |
| style A fill:#ff6b6b,color:#fff |
| style B fill:#ffd43b,color:#000 |
| style C fill:#51cf66,color:#fff |
| style D fill:#ffd43b,color:#000 |
| style E fill:#74c0fc,color:#fff |
| style F fill:#ffd43b,color:#000 |
| style G fill:#b197fc,color:#fff`, |
| |
| 4: `graph TD |
| A[oriC Recognition] --> B[DnaA Binding] |
| B --> C[DNA Unwinding] |
| C --> D[DnaB Helicase Loading] |
| D --> E[Primosome Assembly] |
| E --> F[DNA Polymerase III Loading] |
| F --> G[Replication Fork Formation] |
| G --> H[Bidirectional Replication] |
| |
| style A fill:#ff6b6b,color:#fff |
| style B fill:#ffd43b,color:#000 |
| style C fill:#51cf66,color:#fff |
| style D fill:#ffd43b,color:#000 |
| style E fill:#74c0fc,color:#fff |
| style F fill:#ffd43b,color:#000 |
| style G fill:#74c0fc,color:#fff |
| style H fill:#b197fc,color:#fff`, |
| |
| 5: `graph TD |
| A[oriC Recognition] --> B[DnaA Binding] |
| B --> C[DNA Unwinding] |
| C --> D[DnaB Helicase Loading] |
| D --> E[Primosome Assembly] |
| E --> F[DNA Polymerase III Loading] |
| F --> G[Replication Fork Formation] |
| G --> H[Bidirectional Replication] |
| |
| style A fill:#ff6b6b,color:#fff |
| style B fill:#ffd43b,color:#000 |
| style C fill:#51cf66,color:#fff |
| style D fill:#ffd43b,color:#000 |
| style E fill:#74c0fc,color:#fff |
| style F fill:#ffd43b,color:#000 |
| style G fill:#74c0fc,color:#fff |
| style H fill:#b197fc,color:#fff` |
| } |
| }, |
| 2: { |
| levels: { |
| 1: `graph TD |
| A[Leading Strand] --> B[Lagging Strand] |
| B --> C[DNA Synthesis] |
| |
| style A fill:#ff6b6b,color:#fff |
| style B fill:#51cf66,color:#fff |
| style C fill:#b197fc,color:#fff`, |
| |
| 2: `graph TD |
| A[Leading Strand Synthesis] --> B[Lagging Strand Synthesis] |
| B --> C[Okazaki Fragment Formation] |
| C --> D[DNA Ligase Activity] |
| D --> E[Continuous DNA Synthesis] |
| |
| style A fill:#ff6b6b,color:#fff |
| style B fill:#51cf66,color:#fff |
| style C fill:#74c0fc,color:#fff |
| style D fill:#ffd43b,color:#000 |
| style E fill:#b197fc,color:#fff`, |
| |
| 3: `graph TD |
| A[Leading Strand Synthesis] --> B[Lagging Strand Synthesis] |
| B --> C[Okazaki Fragment Formation] |
| C --> D[DNA Polymerase I Activity] |
| D --> E[RNA Primer Removal] |
| E --> F[DNA Ligase Activity] |
| F --> G[Continuous DNA Synthesis] |
| |
| style A fill:#ff6b6b,color:#fff |
| style B fill:#51cf66,color:#fff |
| style C fill:#74c0fc,color:#fff |
| style D fill:#ffd43b,color:#000 |
| style E fill:#51cf66,color:#fff |
| style F fill:#ffd43b,color:#000 |
| style G fill:#b197fc,color:#fff`, |
| |
| 4: `graph TD |
| A[Leading Strand Synthesis] --> B[Lagging Strand Synthesis] |
| B --> C[Okazaki Fragment Formation] |
| C --> D[DNA Polymerase I Activity] |
| D --> E[RNA Primer Removal] |
| E --> F[DNA Ligase Activity] |
| F --> G[Fragment Joining] |
| G --> H[Continuous DNA Synthesis] |
| |
| style A fill:#ff6b6b,color:#fff |
| style B fill:#51cf66,color:#fff |
| style C fill:#74c0fc,color:#fff |
| style D fill:#ffd43b,color:#000 |
| style E fill:#51cf66,color:#fff |
| style F fill:#ffd43b,color:#000 |
| style G fill:#51cf66,color:#fff |
| style H fill:#b197fc,color:#fff`, |
| |
| 5: `graph TD |
| A[Leading Strand Synthesis] --> B[Lagging Strand Synthesis] |
| B --> C[Okazaki Fragment Formation] |
| C --> D[DNA Polymerase I Activity] |
| D --> E[RNA Primer Removal] |
| E --> F[DNA Ligase Activity] |
| F --> G[Fragment Joining] |
| G --> H[Continuous DNA Synthesis] |
| |
| style A fill:#ff6b6b,color:#fff |
| style B fill:#51cf66,color:#fff |
| style C fill:#74c0fc,color:#fff |
| style D fill:#ffd43b,color:#000 |
| style E fill:#51cf66,color:#fff |
| style F fill:#ffd43b,color:#000 |
| style G fill:#51cf66,color:#fff |
| style H fill:#b197fc,color:#fff` |
| } |
| }, |
| 3: { |
| levels: { |
| 1: `graph TD |
| A[Fork Convergence] --> B[Termination] |
| B --> C[Chromosome Separation] |
| |
| style A fill:#ff6b6b,color:#fff |
| style B fill:#74c0fc,color:#fff |
| style C fill:#b197fc,color:#fff`, |
| |
| 2: `graph TD |
| A[Replication Fork Convergence] --> B[Tus Protein Binding] |
| B --> C[Fork Arrest] |
| C --> D[DNA Decatenation] |
| D --> E[Chromosome Separation] |
| |
| style A fill:#ff6b6b,color:#fff |
| style B fill:#ffd43b,color:#000 |
| style C fill:#74c0fc,color:#fff |
| style D fill:#51cf66,color:#fff |
| style E fill:#b197fc,color:#fff`, |
| |
| 3: `graph TD |
| A[Replication Fork Convergence] --> B[Tus Protein Binding] |
| B --> C[Ter Site Recognition] |
| C --> D[Fork Arrest] |
| D --> E[DNA Decatenation] |
| E --> F[Topoisomerase IV Activity] |
| F --> G[Chromosome Separation] |
| |
| style A fill:#ff6b6b,color:#fff |
| style B fill:#ffd43b,color:#000 |
| style C fill:#51cf66,color:#fff |
| style D fill:#74c0fc,color:#fff |
| style E fill:#51cf66,color:#fff |
| style F fill:#ffd43b,color:#000 |
| style G fill:#b197fc,color:#fff`, |
| |
| 4: `graph TD |
| A[Replication Fork Convergence] --> B[Tus Protein Binding] |
| B --> C[Ter Site Recognition] |
| C --> D[Fork Arrest] |
| D --> E[DNA Decatenation] |
| E --> F[Topoisomerase IV Activity] |
| F --> G[Chromosome Separation] |
| G --> H[Replication Complete] |
| |
| style A fill:#ff6b6b,color:#fff |
| style B fill:#ffd43b,color:#000 |
| style C fill:#51cf66,color:#fff |
| style D fill:#74c0fc,color:#fff |
| style E fill:#51cf66,color:#fff |
| style F fill:#ffd43b,color:#000 |
| style G fill:#51cf66,color:#fff |
| style H fill:#b197fc,color:#fff`, |
| |
| 5: `graph TD |
| A[Replication Fork Convergence] --> B[Tus Protein Binding] |
| B --> C[Ter Site Recognition] |
| C --> D[Fork Arrest] |
| D --> E[DNA Decatenation] |
| E --> F[Topoisomerase IV Activity] |
| F --> G[Chromosome Separation] |
| G --> H[Replication Complete] |
| |
| style A fill:#ff6b6b,color:#fff |
| style B fill:#ffd43b,color:#000 |
| style C fill:#51cf66,color:#fff |
| style D fill:#74c0fc,color:#fff |
| style E fill:#51cf66,color:#fff |
| style F fill:#ffd43b,color:#000 |
| style G fill:#51cf66,color:#fff |
| style H fill:#b197fc,color:#fff` |
| } |
| }, |
| 4: { |
| levels: { |
| 1: `graph TD |
| A[DNA Damage] --> B[Repair Mechanism] |
| B --> C[Cell Survival] |
| |
| style A fill:#ff6b6b,color:#fff |
| style B fill:#51cf66,color:#fff |
| style C fill:#b197fc,color:#fff`, |
| |
| 2: `graph TD |
| A[DNA Damage Detection] --> B[UvrA-UvrB Recognition] |
| B --> C[Excision Repair] |
| C --> D[DNA Ligase Activity] |
| D --> E[Cell Survival] |
| |
| style A fill:#ff6b6b,color:#fff |
| style B fill:#ffd43b,color:#000 |
| style C fill:#51cf66,color:#fff |
| style D fill:#ffd43b,color:#000 |
| style E fill:#b197fc,color:#fff`, |
| |
| 3: `graph TD |
| A[DNA Damage Detection] --> B[UvrA-UvrB Recognition] |
| B --> C[UvrC Recruitment] |
| C --> D[Excision Repair] |
| D --> E[DNA Polymerase I] |
| E --> F[DNA Ligase Activity] |
| F --> G[Cell Survival] |
| |
| style A fill:#ff6b6b,color:#fff |
| style B fill:#ffd43b,color:#000 |
| style C fill:#ffd43b,color:#000 |
| style D fill:#51cf66,color:#fff |
| style E fill:#ffd43b,color:#000 |
| style F fill:#ffd43b,color:#000 |
| style G fill:#b197fc,color:#fff`, |
| |
| 4: `graph TD |
| A[DNA Damage Detection] --> B[UvrA-UvrB Recognition] |
| B --> C[UvrC Recruitment] |
| C --> D[Excision Repair] |
| D --> E[DNA Polymerase I] |
| E --> F[DNA Ligase Activity] |
| F --> G[Repair Completion] |
| G --> H[Cell Survival] |
| |
| style A fill:#ff6b6b,color:#fff |
| style B fill:#ffd43b,color:#000 |
| style C fill:#ffd43b,color:#000 |
| style D fill:#51cf66,color:#fff |
| style E fill:#ffd43b,color:#000 |
| style F fill:#ffd43b,color:#000 |
| style G fill:#b197fc,color:#fff |
| style H fill:#b197fc,color:#fff`, |
| |
| 5: `graph TD |
| A[DNA Damage Detection] --> B[UvrA-UvrB Recognition] |
| B --> C[UvrC Recruitment] |
| C --> D[Excision Repair] |
| D --> E[DNA Polymerase I] |
| E --> F[DNA Ligase Activity] |
| F --> G[Repair Completion] |
| G --> H[Cell Survival] |
| |
| style A fill:#ff6b6b,color:#fff |
| style B fill:#ffd43b,color:#000 |
| style C fill:#ffd43b,color:#000 |
| style D fill:#51cf66,color:#fff |
| style E fill:#ffd43b,color:#000 |
| style F fill:#ffd43b,color:#000 |
| style G fill:#b197fc,color:#fff |
| style H fill:#b197fc,color:#fff` |
| } |
| }, |
| 5: { |
| levels: { |
| 1: `graph TD |
| A[Damaged Base] --> B[Glycosylase] |
| B --> C[Repair Complete] |
| |
| style A fill:#ff6b6b,color:#fff |
| style B fill:#ffd43b,color:#000 |
| style C fill:#b197fc,color:#fff`, |
| |
| 2: `graph TD |
| A[Damaged Base] --> B[DNA Glycosylase] |
| B --> C[AP Site Formation] |
| C --> D[AP Endonuclease] |
| D --> E[Repair Complete] |
| |
| style A fill:#ff6b6b,color:#fff |
| style B fill:#ffd43b,color:#000 |
| style C fill:#74c0fc,color:#fff |
| style D fill:#ffd43b,color:#000 |
| style E fill:#b197fc,color:#fff`, |
| |
| 3: `graph TD |
| A[Damaged Base] --> B[DNA Glycosylase Recognition] |
| B --> C[Base Excision] |
| C --> D[AP Site Formation] |
| D --> E[AP Endonuclease] |
| E --> F[Gap Formation] |
| F --> G[DNA Polymerase I] |
| G --> H[Repair Complete] |
| |
| style A fill:#ff6b6b,color:#fff |
| style B fill:#ffd43b,color:#000 |
| style C fill:#ffd43b,color:#000 |
| style D fill:#74c0fc,color:#fff |
| style E fill:#ffd43b,color:#000 |
| style F fill:#74c0fc,color:#fff |
| style G fill:#ffd43b,color:#000 |
| style H fill:#b197fc,color:#fff`, |
| |
| 4: `graph TD |
| A[Damaged Base] --> B[DNA Glycosylase Recognition] |
| B --> C[Glycosylase Binding] |
| C --> D[Base Excision] |
| D --> E[AP Site Formation] |
| E --> F[AP Endonuclease] |
| F --> G[5' Incision] |
| G --> H[Gap Formation] |
| H --> I[DNA Polymerase I] |
| I --> J[DNA Ligase] |
| J --> K[Repair Complete] |
| |
| style A fill:#ff6b6b,color:#fff |
| style B fill:#74c0fc,color:#fff |
| style C fill:#ffd43b,color:#000 |
| style D fill:#ffd43b,color:#000 |
| style E fill:#74c0fc,color:#fff |
| style F fill:#ffd43b,color:#000 |
| style G fill:#ffd43b,color:#000 |
| style H fill:#74c0fc,color:#fff |
| style I fill:#ffd43b,color:#000 |
| style J fill:#ffd43b,color:#000 |
| style K fill:#b197fc,color:#fff`, |
| |
| 5: `graph TD |
| A[Damaged Base] --> B[DNA Glycosylase Recognition] |
| C[Oxidative Damage] --> B |
| D[Alkylation Damage] --> B |
| E[Deamination] --> B |
| |
| B --> F[Glycosylase Binding] |
| F --> G[Base Excision] |
| G --> H[AP Site Formation] |
| |
| H --> I[AP Endonuclease] |
| I --> J[5' Incision] |
| J --> K[3' Incision] |
| K --> L[Gap Formation] |
| |
| L --> M[DNA Polymerase I] |
| M --> N[Single Nucleotide Insertion] |
| N --> O[DNA Ligase] |
| O --> P[Repair Complete] |
| |
| style A fill:#ff6b6b,color:#fff |
| style C fill:#ff6b6b,color:#fff |
| style D fill:#ff6b6b,color:#fff |
| style E fill:#ff6b6b,color:#fff |
| style B fill:#74c0fc,color:#fff |
| style F fill:#ffd43b,color:#000 |
| style G fill:#ffd43b,color:#000 |
| style H fill:#74c0fc,color:#fff |
| style I fill:#ffd43b,color:#000 |
| style J fill:#ffd43b,color:#000 |
| style K fill:#ffd43b,color:#000 |
| style L fill:#74c0fc,color:#fff |
| style M fill:#ffd43b,color:#000 |
| style N fill:#ffd43b,color:#000 |
| style O fill:#ffd43b,color:#000 |
| style P fill:#b197fc,color:#fff` |
| } |
| }, |
| 6: { |
| levels: { |
| 1: `graph TD |
| A[Bulky Lesion] --> B[UvrABC System] |
| B --> C[Repair Complete] |
| |
| style A fill:#ff6b6b,color:#fff |
| style B fill:#ffd43b,color:#000 |
| style C fill:#b197fc,color:#fff`, |
| |
| 2: `graph TD |
| A[Bulky DNA Lesion] --> B[UvrA-UvrB Recognition] |
| B --> C[UvrC Recruitment] |
| C --> D[Dual Incision] |
| D --> E[Gap Filling] |
| E --> F[Repair Complete] |
| |
| style A fill:#ff6b6b,color:#fff |
| style B fill:#ffd43b,color:#000 |
| style C fill:#ffd43b,color:#000 |
| style D fill:#ffd43b,color:#000 |
| style E fill:#51cf66,color:#fff |
| style F fill:#b197fc,color:#fff`, |
| |
| 3: `graph TD |
| A[Bulky DNA Lesion] --> B[UvrA-UvrB Recognition] |
| B --> C[UvrA Release] |
| C --> D[UvrC Recruitment] |
| D --> E[UvrBC Complex] |
| E --> F[3' Incision] |
| E --> G[5' Incision] |
| F --> H[Oligonucleotide Release] |
| G --> H |
| H --> I[DNA Polymerase I] |
| I --> J[Repair Complete] |
| |
| style A fill:#ff6b6b,color:#fff |
| style B fill:#ffd43b,color:#000 |
| style C fill:#ffd43b,color:#000 |
| style D fill:#ffd43b,color:#000 |
| style E fill:#ffd43b,color:#000 |
| style F fill:#ffd43b,color:#000 |
| style G fill:#ffd43b,color:#000 |
| style H fill:#74c0fc,color:#fff |
| style I fill:#ffd43b,color:#000 |
| style J fill:#b197fc,color:#fff`, |
| |
| 4: `graph TD |
| A[Bulky DNA Lesion] --> B[UvrA-UvrB Recognition] |
| C[UV-Induced Damage] --> B |
| D[Chemical Adducts] --> B |
| |
| B --> E[UvrA Release] |
| E --> F[UvrB-DNA Complex] |
| F --> G[UvrC Recruitment] |
| G --> H[UvrBC Complex] |
| H --> I[3' Incision] |
| H --> J[5' Incision] |
| I --> K[Oligonucleotide Release] |
| J --> K |
| K --> L[Gap Formation] |
| L --> M[DNA Polymerase I] |
| M --> N[DNA Ligase] |
| N --> O[Repair Complete] |
| |
| style A fill:#ff6b6b,color:#fff |
| style C fill:#ff6b6b,color:#fff |
| style D fill:#ff6b6b,color:#fff |
| style B fill:#ffd43b,color:#000 |
| style E fill:#ffd43b,color:#000 |
| style F fill:#74c0fc,color:#fff |
| style G fill:#ffd43b,color:#000 |
| style H fill:#ffd43b,color:#000 |
| style I fill:#ffd43b,color:#000 |
| style J fill:#ffd43b,color:#000 |
| style K fill:#74c0fc,color:#fff |
| style L fill:#74c0fc,color:#fff |
| style M fill:#ffd43b,color:#000 |
| style N fill:#ffd43b,color:#000 |
| style O fill:#b197fc,color:#fff`, |
| |
| 5: `graph TD |
| A[Bulky DNA Lesion] --> B[UvrA-UvrB Recognition] |
| C[UV-Induced Damage] --> B |
| D[Chemical Adducts] --> B |
| E[Cross-links] --> B |
| |
| B --> F[UvrA Release] |
| F --> G[UvrB-DNA Complex] |
| G --> H[UvrC Recruitment] |
| H --> I[UvrBC Complex] |
| |
| I --> J[3' Incision] |
| I --> K[5' Incision] |
| J --> L[Oligonucleotide Release] |
| K --> L |
| L --> M[Gap Formation] |
| |
| M --> N[DNA Polymerase I] |
| N --> O[Gap Filling] |
| O --> P[DNA Ligase] |
| P --> Q[Repair Complete] |
| |
| style A fill:#ff6b6b,color:#fff |
| style C fill:#ff6b6b,color:#fff |
| style D fill:#ff6b6b,color:#fff |
| style E fill:#ff6b6b,color:#fff |
| style B fill:#ffd43b,color:#000 |
| style F fill:#ffd43b,color:#000 |
| style G fill:#74c0fc,color:#fff |
| style H fill:#ffd43b,color:#000 |
| style I fill:#ffd43b,color:#000 |
| style J fill:#ffd43b,color:#000 |
| style K fill:#ffd43b,color:#000 |
| style L fill:#74c0fc,color:#fff |
| style M fill:#74c0fc,color:#fff |
| style N fill:#ffd43b,color:#000 |
| style O fill:#ffd43b,color:#000 |
| style P fill:#ffd43b,color:#000 |
| style Q fill:#b197fc,color:#fff` |
| } |
| }, |
| 7: { |
| levels: { |
| 1: `graph TD |
| A[DNA Mismatch] --> B[MutS Recognition] |
| B --> C[Repair Complete] |
| |
| style A fill:#ff6b6b,color:#fff |
| style B fill:#ffd43b,color:#000 |
| style C fill:#b197fc,color:#fff`, |
| |
| 2: `graph TD |
| A[DNA Mismatch] --> B[MutS Recognition] |
| B --> C[MutL Recruitment] |
| C --> D[MutH Activation] |
| D --> E[Strand Incision] |
| E --> F[Repair Complete] |
| |
| style A fill:#ff6b6b,color:#fff |
| style B fill:#ffd43b,color:#000 |
| style C fill:#ffd43b,color:#000 |
| style D fill:#ffd43b,color:#000 |
| style E fill:#ffd43b,color:#000 |
| style F fill:#b197fc,color:#fff`, |
| |
| 3: `graph TD |
| A[DNA Mismatch] --> B[MutS Recognition] |
| B --> C[MutS-DNA Complex] |
| C --> D[MutL Recruitment] |
| D --> E[MutS-MutL Complex] |
| E --> F[GATC Site Recognition] |
| F --> G[MutH Activation] |
| G --> H[Strand Incision] |
| H --> I[Gap Formation] |
| I --> J[DNA Polymerase III] |
| J --> K[Repair Complete] |
| |
| style A fill:#ff6b6b,color:#fff |
| style B fill:#ffd43b,color:#000 |
| style C fill:#74c0fc,color:#fff |
| style D fill:#ffd43b,color:#000 |
| style E fill:#74c0fc,color:#fff |
| style F fill:#ffd43b,color:#000 |
| style G fill:#ffd43b,color:#000 |
| style H fill:#ffd43b,color:#000 |
| style I fill:#74c0fc,color:#fff |
| style J fill:#ffd43b,color:#000 |
| style K fill:#b197fc,color:#fff`, |
| |
| 4: `graph TD |
| A[DNA Mismatch] --> B[MutS Recognition] |
| C[Replication Error] --> B |
| D[Base Mismatch] --> B |
| |
| B --> E[MutS-DNA Complex] |
| E --> F[MutL Recruitment] |
| F --> G[MutS-MutL Complex] |
| G --> H[DNA Bending] |
| H --> I[GATC Site Recognition] |
| I --> J[MutH Activation] |
| J --> K[Strand Incision] |
| K --> L[Nick Formation] |
| L --> M[Helicase II Loading] |
| M --> N[Exonuclease Activity] |
| N --> O[Gap Formation] |
| O --> P[DNA Polymerase III] |
| P --> Q[DNA Ligase] |
| Q --> R[Repair Complete] |
| |
| style A fill:#ff6b6b,color:#fff |
| style C fill:#ff6b6b,color:#fff |
| style D fill:#ff6b6b,color:#fff |
| style B fill:#ffd43b,color:#000 |
| style E fill:#74c0fc,color:#fff |
| style F fill:#ffd43b,color:#000 |
| style G fill:#74c0fc,color:#fff |
| style H fill:#ffd43b,color:#000 |
| style I fill:#ffd43b,color:#000 |
| style J fill:#ffd43b,color:#000 |
| style K fill:#ffd43b,color:#000 |
| style L fill:#74c0fc,color:#fff |
| style M fill:#ffd43b,color:#000 |
| style N fill:#ffd43b,color:#000 |
| style O fill:#74c0fc,color:#fff |
| style P fill:#ffd43b,color:#000 |
| style Q fill:#ffd43b,color:#000 |
| style R fill:#b197fc,color:#fff`, |
| |
| 5: `graph TD |
| A[DNA Mismatch] --> B[MutS Recognition] |
| C[Replication Error] --> B |
| D[Insertion/Deletion] --> B |
| E[Base Mismatch] --> B |
| |
| B --> F[MutS-DNA Complex] |
| F --> G[MutL Recruitment] |
| G --> H[MutS-MutL Complex] |
| H --> I[DNA Bending] |
| |
| I --> J[GATC Site Recognition] |
| J --> K[MutH Activation] |
| K --> L[Strand Incision] |
| L --> M[Nick Formation] |
| |
| M --> N[Helicase II Loading] |
| N --> O[Exonuclease Activity] |
| O --> P[Gap Formation] |
| P --> Q[DNA Polymerase III] |
| Q --> R[Gap Filling] |
| R --> S[DNA Ligase] |
| S --> T[Repair Complete] |
| |
| style A fill:#ff6b6b,color:#fff |
| style C fill:#ff6b6b,color:#fff |
| style D fill:#ff6b6b,color:#fff |
| style E fill:#ff6b6b,color:#fff |
| style B fill:#ffd43b,color:#000 |
| style F fill:#74c0fc,color:#fff |
| style G fill:#ffd43b,color:#000 |
| style H fill:#74c0fc,color:#fff |
| style I fill:#ffd43b,color:#000 |
| style J fill:#ffd43b,color:#000 |
| style K fill:#ffd43b,color:#000 |
| style L fill:#ffd43b,color:#000 |
| style M fill:#74c0fc,color:#fff |
| style N fill:#ffd43b,color:#000 |
| style O fill:#ffd43b,color:#000 |
| style P fill:#74c0fc,color:#fff |
| style Q fill:#ffd43b,color:#000 |
| style R fill:#ffd43b,color:#000 |
| style S fill:#ffd43b,color:#000 |
| style T fill:#b197fc,color:#fff` |
| } |
| }, |
| 8: { |
| levels: { |
| 1: `graph TD |
| A[DNA Damage] --> B[SOS Response] |
| B --> C[Cell Survival] |
| |
| style A fill:#ff6b6b,color:#fff |
| style B fill:#ffd43b,color:#000 |
| style C fill:#b197fc,color:#fff`, |
| |
| 2: `graph TD |
| A[DNA Damage] --> B[RecA Activation] |
| B --> C[LexA Cleavage] |
| C --> D[SOS Genes Activated] |
| D --> E[DNA Repair] |
| E --> F[Cell Survival] |
| |
| style A fill:#ff6b6b,color:#fff |
| style B fill:#ffd43b,color:#000 |
| style C fill:#ffd43b,color:#000 |
| style D fill:#ffd43b,color:#000 |
| style E fill:#51cf66,color:#fff |
| style F fill:#b197fc,color:#fff`, |
| |
| 3: `graph TD |
| A[DNA Damage] --> B[Single-Strand DNA] |
| B --> C[RecA Protein Binding] |
| C --> D[RecA Nucleofilament] |
| D --> E[LexA Cleavage] |
| E --> F[SOS Genes Derepressed] |
| F --> G[DNA Repair Genes] |
| G --> H[Error-Prone Repair] |
| H --> I[Cell Survival] |
| |
| style A fill:#ff6b6b,color:#fff |
| style B fill:#74c0fc,color:#fff |
| style C fill:#ffd43b,color:#000 |
| style D fill:#74c0fc,color:#fff |
| style E fill:#ffd43b,color:#000 |
| style F fill:#ffd43b,color:#000 |
| style G fill:#ffd43b,color:#000 |
| style H fill:#ffd43b,color:#000 |
| style I fill:#b197fc,color:#fff`, |
| |
| 4: `graph TD |
| A[DNA Damage] --> B[Single-Strand DNA] |
| C[UV Radiation] --> A |
| D[Chemical Mutagens] --> A |
| |
| B --> E[RecA Protein Binding] |
| E --> F[RecA Nucleofilament] |
| F --> G[RecA Activation] |
| G --> H[LexA Cleavage] |
| H --> I[LexA Degradation] |
| I --> J[SOS Genes Derepressed] |
| J --> K[DNA Repair Genes] |
| K --> L[UmuC/UmuD Expression] |
| L --> M[Error-Prone Repair] |
| M --> N[Cell Survival] |
| |
| style A fill:#ff6b6b,color:#fff |
| style C fill:#ff6b6b,color:#fff |
| style D fill:#ff6b6b,color:#fff |
| style B fill:#74c0fc,color:#fff |
| style E fill:#ffd43b,color:#000 |
| style F fill:#74c0fc,color:#fff |
| style G fill:#ffd43b,color:#000 |
| style H fill:#ffd43b,color:#000 |
| style I fill:#ffd43b,color:#000 |
| style J fill:#ffd43b,color:#000 |
| style K fill:#ffd43b,color:#000 |
| style L fill:#ffd43b,color:#000 |
| style M fill:#ffd43b,color:#000 |
| style N fill:#b197fc,color:#fff`, |
| |
| 5: `graph TD |
| A[DNA Damage] --> B[Single-Strand DNA] |
| C[UV Radiation] --> A |
| D[Chemical Mutagens] --> A |
| E[Replication Stress] --> A |
| |
| B --> F[RecA Protein Binding] |
| F --> G[RecA Nucleofilament] |
| G --> H[RecA Activation] |
| H --> I[LexA Cleavage] |
| |
| I --> J[LexA Degradation] |
| J --> K[SOS Genes Derepressed] |
| K --> L[DNA Repair Genes] |
| L --> M[Error-Prone Repair] |
| |
| M --> N[UmuC/UmuD Expression] |
| N --> O[Translesion Synthesis] |
| O --> P[Error-Prone Bypass] |
| P --> Q[Cell Survival] |
| |
| Q --> R[Damage Cleared] |
| R --> S[RecA Inactivation] |
| S --> T[LexA Reformation] |
| T --> U[SOS Genes Repressed] |
| |
| style A fill:#ff6b6b,color:#fff |
| style C fill:#ff6b6b,color:#fff |
| style D fill:#ff6b6b,color:#fff |
| style E fill:#ff6b6b,color:#fff |
| style B fill:#74c0fc,color:#fff |
| style F fill:#ffd43b,color:#000 |
| style G fill:#74c0fc,color:#fff |
| style H fill:#ffd43b,color:#000 |
| style I fill:#ffd43b,color:#000 |
| style J fill:#ffd43b,color:#000 |
| style K fill:#ffd43b,color:#000 |
| style L fill:#ffd43b,color:#000 |
| style M fill:#ffd43b,color:#000 |
| style N fill:#ffd43b,color:#000 |
| style O fill:#ffd43b,color:#000 |
| style P fill:#ffd43b,color:#000 |
| style Q fill:#b197fc,color:#fff |
| style R fill:#74c0fc,color:#fff |
| style S fill:#ffd43b,color:#000 |
| style T fill:#ffd43b,color:#000 |
| style U fill:#b197fc,color:#fff` |
| } |
| } |
| }; |
| |
| |
| function updateChart(processId, level) { |
| const chartDiv = document.getElementById(`chart-${processId}`); |
| const levelSpan = document.getElementById(`level-${processId}`); |
| |
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| levelSpan.textContent = level; |
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| |
| if (allProcesses[processId] && allProcesses[processId].levels[level]) { |
| chartDiv.innerHTML = ''; |
| const mermaidCode = allProcesses[processId].levels[level]; |
| chartDiv.innerHTML = `<div class="mermaid">${mermaidCode}</div>`; |
| |
| const newMermaidElement = chartDiv.querySelector('.mermaid'); |
| if (newMermaidElement) { |
| try { |
| mermaid.init(undefined, newMermaidElement); |
| } catch (error) { |
| console.error('Mermaid error:', error); |
| } |
| } |
| } |
| } |
| |
| |
| mermaid.initialize({ |
| startOnLoad: true, |
| theme: 'default', |
| flowchart: { |
| useMaxWidth: false, |
| htmlLabels: true, |
| curve: 'linear', |
| nodeSpacing: 30, |
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| lineColor: '#333333', |
| secondaryColor: '#feca57', |
| tertiaryColor: '#4ecdc4' |
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| |
| document.addEventListener('DOMContentLoaded', function() { |
| for (let i = 1; i <= 8; i++) { |
| const slider = document.getElementById(`slider-${i}`); |
| if (slider) { |
| slider.addEventListener('input', function() { |
| updateChart(i, this.value); |
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| updateChart(i, 1); |
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| } |
| }); |
| </script> |
| </body> |
| </html> |
