Spaces:

garywelz
/

glmp

Running

File size: 35,830 Bytes

<!DOCTYPE html>
<html lang="en">
<head>
    <meta charset="UTF-8">
    <meta name="viewport" content="width=device-width, initial-scale=1.0">
    <title>E. coli Cellular Processes - Programming Framework Analysis</title>
    <script src="https://cdn.jsdelivr.net/npm/mermaid@10.6.1/dist/mermaid.min.js"></script>
    <style>
        body {
            font-family: 'Segoe UI', Tahoma, Geneva, Verdana, 'Arial Unicode MS', sans-serif;
            line-height: 1.6;
            margin: 0;
            padding: 0;
            background: linear-gradient(135deg, #667eea 0%, #764ba2 100%);
            min-height: 100vh;
        }
        .container {
            max-width: 1400px;
            margin: 0 auto;
            background: white;
            box-shadow: 0 0 20px rgba(0,0,0,0.1);
            border-radius: 10px;
            overflow: hidden;
        }
        .header {
            background: linear-gradient(135deg, #667eea 0%, #764ba2 100%);
            color: white;
            padding: 2rem;
            text-align: center;
        }
        .header h1 {
            margin: 0;
            font-size: 2.5rem;
            font-weight: 300;
        }
        .content {
            padding: 2rem;
        }
        .intro {
            background: #f8f9fa;
            padding: 2rem;
            border-radius: 8px;
            margin-bottom: 2rem;
        }
        .toc {
            background: #f8f9fa;
            padding: 2rem;
            border-radius: 8px;
            margin-bottom: 2rem;
        }
        .toc ul {
            list-style: none;
            padding: 0;
        }
        .toc li {
            margin: 0.5rem 0;
        }
        .toc a {
            color: #007bff;
            text-decoration: none;
            font-weight: 500;
        }
        .process-item {
            margin: 2rem 0;
            padding: 1.5rem;
            border: 1px solid #dee2e6;
            border-radius: 8px;
            background: #fafafa;
        }
        .process-item h3 {
            color: #495057;
            margin-bottom: 1rem;
        }
        .mermaid-container {
            background: white;
            padding: 1rem;
            border-radius: 8px;
            margin: 1rem 0;
            overflow-x: auto;
        }
        .footer {
            background: #f8f9fa;
            padding: 2rem;
            text-align: center;
            border-top: 1px solid #dee2e6;
            margin-top: 2rem;
        }
        .color-legend {
            display: grid;
            grid-template-columns: repeat(auto-fit, minmax(140px, 1fr));
            gap: 0.5rem 1rem;
            margin: 1rem 0 0;
            font-size: 10pt;
            color: #333;
        }
        .color-box {
            display: inline-block;
            width: 12px;
            height: 12px;
            border-radius: 2px;
            margin-right: 4px;
            border: 1px solid rgba(0,0,0,.15);
        }
    </style>
</head>
<body>
    <div class="container">
        <div class="header">
            <h1>🦠 E. coli Cellular Processes</h1>
            <p>Programming Framework Analysis - 10 Core Processes</p>
        </div>
        <div class="content">
            <div class="intro">
                <h2>🧬 Detailed Mermaid Flowcharts</h2>
                <p><strong>Important Note:</strong> This document contains detailed E. coli cellular process flowcharts rendered using embedded Mermaid code with detail-preserving configuration to demonstrate the full complexity of bacterial cellular processes as computational programs.</p>
                <p>Each flowchart uses the <strong>programming framework</strong> methodology to model biological processes as computational systems, showing how bacterial cells process information, make decisions, and execute responses through molecular networks that function like biological software.</p>
            </div>
            
            <div class="toc">
                <h2>📋 Table of Contents - 10 E. coli Processes</h2>
                <ul>
                    <li><a href="#beta-galactosidase">1. Beta-Galactosidase (Lac Operon)</a></li>
                    <li><a href="#chemotaxis">2. Chemotaxis</a></li>
                    <li><a href="#sos-response">3. SOS Response</a></li>
                    <li><a href="#tryptophan">4. Tryptophan Biosynthesis</a></li>
                    <li><a href="#iron-homeostasis">5. Iron Homeostasis</a></li>
                    <li><a href="#heat-shock">6. Heat Shock Response</a></li>
                    <li><a href="#nitrogen">7. Nitrogen Metabolism</a></li>
                    <li><a href="#cell-division">8. Cell Division</a></li>
                    <li><a href="#biofilm">9. Biofilm Formation</a></li>
                    <li><a href="#crispr">10. Phage Defense (CRISPR-Cas)</a></li>
                </ul>
            </div>
            
            <!-- Process 1: Beta-Galactosidase -->
            <div class="process-item" id="beta-galactosidase">
                <h3>1. Beta-Galactosidase (Lac Operon)</h3>
                <p>The classic bacterial gene regulation system demonstrating how E. coli processes environmental lactose and glucose signals through regulatory logic gates to control enzyme production.</p>
                <div class="mermaid-container">
                    <div class="mermaid">
graph TD
    %% Environmental Inputs
    A[Lactose in Environment] --> B[Lactose Transport]
    C[Glucose in Environment] --> D[Glucose Transport]
    E[Low Energy Status] --> F[Energy Stress Signal]
    
    %% Lactose Processing
    B --> G[Lactose Permease LacY]
    G --> H[Lactose Inside Cell]
    H --> I[Lactose Availability]
    
    %% Regulatory Logic
    I --> J{Is Lactose Present?}
    J -->|Yes| K[Lac Repressor Inactive]
    J -->|No| L[Lac Repressor Active]
    
    %% Transcription Control
    K --> M[Operator Free]
    L --> N[Transcription Blocked]
    M --> O[RNA Polymerase Binding]
    O --> P[Transcription Initiation]
    
    %% Enzyme Production
    P --> Q[Beta-Galactosidase]
    P --> R[Lactose Permease]
    P --> S[Galactoside Acetyltransferase]
    
    %% Functional Outputs
    Q --> T[Lactose Hydrolysis]
    R --> U[Lactose Transport]
    T --> V[Glucose + Galactose]
    
    %% Styling - Programming Framework Colors
    style A fill:#ff6b6b,color:#fff
    style C fill:#ff6b6b,color:#fff
    style E fill:#ff6b6b,color:#fff
    style B fill:#ffd43b,color:#000
    style D 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:#74c0fc,color:#fff
    style J fill:#74c0fc,color:#fff
    style K fill:#ffd43b,color:#000
    style L fill:#ffd43b,color:#000
    style M fill:#74c0fc,color:#fff
    style N fill:#74c0fc,color:#fff
    style O fill:#ffd43b,color:#000
    style P fill:#ffd43b,color:#000
    style Q fill:#b197fc,color:#fff
    style R fill:#b197fc,color:#fff
    style S fill:#b197fc,color:#fff
    style T fill:#b197fc,color:#fff
    style U fill:#b197fc,color:#fff
    style V 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>

            <!-- Process 2: Chemotaxis -->
            <div class="process-item" id="chemotaxis">
                <h3>2. Chemotaxis</h3>
                <p>Bacterial navigation system showing how E. coli processes chemical gradients to direct movement through sophisticated signal processing and motor control.</p>
                <div class="mermaid-container">
                    <div class="mermaid">
graph TD
    %% Environmental Inputs
    A[Chemical Attractants] --> B[Attractant Detection]
    C[Chemical Repellents] --> D[Repellent Detection]
    E[Gradient Changes] --> F[Temporal Sensing]
    
    %% Signal Transduction
    B --> G[CheA Kinase]
    D --> G
    F --> G
    G --> H[CheY Phosphorylation]
    
    %% Motor Control
    H --> I{CheY-P Level?}
    I -->|High| J[Clockwise Rotation]
    I -->|Low| K[Counterclockwise Rotation]
    
    %% Swimming Behavior
    J --> L[Tumbling]
    K --> M[Smooth Swimming]
    L --> N[Random Direction]
    M --> O[Straight Movement]
    
    %% Adaptation
    H --> P[CheZ Phosphatase]
    P --> Q[CheY Dephosphorylation]
    Q --> R[Signal Termination]
    
    %% Styling - Programming Framework Colors
    style A fill:#ff6b6b,color:#fff
    style C fill:#ff6b6b,color:#fff
    style E fill:#ff6b6b,color:#fff
    style B fill:#ffd43b,color:#000
    style D 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:#74c0fc,color:#fff
    style J fill:#b197fc,color:#fff
    style K fill:#b197fc,color:#fff
    style L fill:#b197fc,color:#fff
    style M fill:#b197fc,color:#fff
    style N fill:#b197fc,color:#fff
    style O fill:#b197fc,color:#fff
    style P fill:#ffd43b,color:#000
    style Q fill:#74c0fc,color:#fff
    style R 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>

            <!-- Process 3: SOS Response -->
            <div class="process-item" id="sos-response">
                <h3>3. SOS Response</h3>
                <p>DNA damage emergency response system showing how E. coli detects and responds to genetic threats through error detection and repair protocols.</p>
                <div class="mermaid-container">
                    <div class="mermaid">
graph TD
    %% DNA Damage Signals
    A[UV Radiation] --> B[DNA Damage Detection]
    C[Chemical Mutagens] --> B
    D[Replication Stress] --> B
    
    %% Damage Recognition
    B --> E[Single-strand DNA]
    E --> F[RecA Protein Binding]
    F --> G[RecA Activation]
    
    %% LexA Control
    G --> H{RecA Active?}
    H -->|Yes| I[LexA Cleavage]
    H -->|No| J[LexA Repressor Active]
    
    %% SOS Activation
    I --> K[Operator Sites Free]
    K --> L[RNA Polymerase Binding]
    L --> M[SOS Gene Transcription]
    
    %% DNA Repair
    M --> N[UvrA Expression]
    M --> O[UvrB Expression]
    M --> P[UvrC Expression]
    N --> Q[Damage Recognition]
    O --> Q
    P --> R[Damage Excision]
    Q --> R
    R --> S[DNA 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 B fill:#74c0fc,color:#fff
    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:#74c0fc,color:#fff
    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:#ffd43b,color:#000
    style R fill:#ffd43b,color:#000
    style S 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>

            <!-- Process 4: Tryptophan Biosynthesis -->
            <div class="process-item" id="tryptophan">
                <h3>4. Tryptophan Biosynthesis</h3>
                <p>Amino acid production pathway with sophisticated feedback control and transcriptional attenuation showing how E. coli regulates enzyme synthesis based on amino acid availability.</p>
                <div class="mermaid-container">
                    <div class="mermaid">
graph TD
    %% Environmental Inputs
    A[Tryptophan Availability] --> B[Tryptophan Transport]
    C[Chorismate Precursor] --> D[Pathway Initiation]
    E[Energy Status ATP] --> F[Metabolic Readiness]
    
    %% Transport and Sensing
    B --> G[TrpT Transporter]
    G --> H[Internal Tryptophan]
    H --> I[Tryptophan Pool]
    
    %% Transcriptional Control
    I --> J{Tryptophan High?}
    J -->|Yes| K[TrpR Repressor Active]
    J -->|No| L[TrpR Repressor Inactive]
    
    %% Enzyme Production
    L --> M[trp Operon Transcription]
    M --> N[TrpE Translation]
    M --> O[TrpD Translation]
    M --> P[TrpC Translation]
    M --> Q[TrpB Translation]
    M --> R[TrpA Translation]
    
    %% Biosynthetic Pathway
    D --> S[Anthranilate Synthase]
    S --> T[Anthranilate]
    T --> U[PRA Formation]
    U --> V[InGP Formation]
    V --> W[Tryptophan Synthase]
    W --> X[Tryptophan Production]
    
    %% Feedback Regulation
    X --> Y[Product Inhibition]
    Y --> Z[Pathway Slowdown]
    
    %% Styling - Programming Framework Colors
    style A fill:#ff6b6b,color:#fff
    style C fill:#ff6b6b,color:#fff
    style E fill:#ff6b6b,color:#fff
    style B fill:#ffd43b,color:#000
    style D 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:#74c0fc,color:#fff
    style J fill:#74c0fc,color:#fff
    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:#ffd43b,color:#000
    style R fill:#ffd43b,color:#000
    style S fill:#ffd43b,color:#000
    style T fill:#74c0fc,color:#fff
    style U fill:#74c0fc,color:#fff
    style V fill:#74c0fc,color:#fff
    style W fill:#ffd43b,color:#000
    style X fill:#b197fc,color:#fff
    style Y fill:#ffd43b,color:#000
    style Z 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>

            <!-- Process 5: Iron Homeostasis -->
            <div class="process-item" id="iron-homeostasis">
                <h3>5. Iron Homeostasis</h3>
                <p>Essential metal management system showing how E. coli balances iron acquisition, storage, and toxicity protection through complex regulatory networks.</p>
                <div class="mermaid-container">
                    <div class="mermaid">
graph TD
    %% Environmental Iron Status
    A[Iron Availability] --> B[Iron Sensing]
    C[Iron Limitation] --> D[Stress Signal]
    E[Iron Excess] --> F[Toxicity Risk]
    
    %% Iron Transport Systems
    D --> G[FepA Receptor]
    D --> H[FhuA Receptor]
    D --> I[Siderophore Production]
    
    %% Iron Uptake
    G --> J[Outer Membrane Transport]
    H --> J
    I --> K[Iron Chelation]
    K --> L[Fe-Enterobactin]
    J --> M[Cytoplasmic Iron]
    
    %% Fur Regulatory System
    M --> N{Iron Sufficient?}
    N -->|Yes| O[Fur-Fe Complex]
    N -->|No| P[Apo-Fur]
    O --> Q[Gene Repression]
    P --> R[Derepression]
    
    %% Iron Storage
    M --> S{Iron Excess?}
    S -->|Yes| T[Ferritin Induction]
    S -->|No| U[Normal Storage]
    T --> V[Iron Sequestration]
    
    %% Styling - Programming Framework Colors
    style A fill:#ff6b6b,color:#fff
    style C fill:#ff6b6b,color:#fff
    style E fill:#ff6b6b,color:#fff
    style B fill:#74c0fc,color:#fff
    style D fill:#74c0fc,color:#fff
    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:#74c0fc,color:#fff
    style M fill:#74c0fc,color:#fff
    style N fill:#74c0fc,color:#fff
    style O fill:#ffd43b,color:#000
    style P fill:#ffd43b,color:#000
    style Q fill:#ffd43b,color:#000
    style R fill:#ffd43b,color:#000
    style S fill:#74c0fc,color:#fff
    style T fill:#ffd43b,color:#000
    style U fill:#ffd43b,color:#000
    style V 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>

            <!-- Process 6: Heat Shock Response -->
            <div class="process-item" id="heat-shock">
                <h3>6. Heat Shock Response</h3>
                <p>Temperature stress management system showing how E. coli detects and responds to thermal damage through chaperones and recovery mechanisms.</p>
                <div class="mermaid-container">
                    <div class="mermaid">
graph TD
    %% Temperature Stress
    A[Temperature Increase] --> B[Protein Unfolding]
    C[Heat Shock] --> D[Membrane Stress]
    E[Thermal Damage] --> F[Cellular Stress]
    
    %% Stress Detection
    B --> G[Misfolded Proteins]
    D --> H[Membrane Disruption]
    F --> I[Stress Signal]
    
    %% Sigma Factor Regulation
    I --> J[σ32 Activation]
    J --> K[Heat Shock Promoters]
    K --> L[HSP Gene Expression]
    
    %% DnaK/DnaJ System
    L --> M[DnaK Chaperone]
    L --> N[DnaJ Co-chaperone]
    G --> O[Substrate Recognition]
    O --> P[Protein-DnaK Complex]
    P --> Q[Protein Refolding]
    
    %% Quality Control
    Q --> R{Refolding Success?}
    R -->|Yes| S[Native Protein]
    R -->|No| T[Repeat Cycle]
    R -->|Failed| U[Degradation Target]
    
    %% Recovery
    S --> V[Protein Function Restored]
    V --> W[Cellular Function]
    W --> X[Temperature Tolerance]
    
    %% Styling - Programming Framework Colors
    style A fill:#ff6b6b,color:#fff
    style C fill:#ff6b6b,color:#fff
    style E fill:#ff6b6b,color:#fff
    style B fill:#74c0fc,color:#fff
    style D fill:#74c0fc,color:#fff
    style F fill:#74c0fc,color:#fff
    style G fill:#74c0fc,color:#fff
    style H fill:#74c0fc,color:#fff
    style I fill:#74c0fc,color:#fff
    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:#ffd43b,color:#000
    style R fill:#74c0fc,color:#fff
    style S fill:#b197fc,color:#fff
    style T fill:#ffd43b,color:#000
    style U fill:#b197fc,color:#fff
    style V fill:#b197fc,color:#fff
    style W fill:#b197fc,color:#fff
    style X 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>

            <!-- Process 7: Nitrogen Metabolism -->
            <div class="process-item" id="nitrogen">
                <h3>7. Nitrogen Metabolism</h3>
                <p>Nitrogen assimilation and regulation system showing how E. coli processes various nitrogen sources for amino acid and nucleotide synthesis.</p>
                <div class="mermaid-container">
                    <div class="mermaid">
graph TD
    %% Nitrogen Sources
    A[Ammonia NH3] --> B[Ammonia Transport]
    C[Nitrate NO3] --> D[Nitrate Transport]
    E[Amino Acids] --> F[Amino Acid Transport]
    
    %% Transport Systems
    B --> G[AmtB Transporter]
    D --> H[NarK Transporter]
    F --> I[General Amino Acid Permease]
    
    %% Nitrogen Assimilation
    G --> J[NH4+ Pool]
    H --> K[NO3- Reduction]
    I --> L[Amino Acid Pool]
    K --> M[NH4+ Production]
    M --> J
    
    %% Glutamine Synthetase System
    J --> N{NH4+ Concentration?}
    N -->|High| O[Direct Assimilation]
    N -->|Low| P[GlnA Activation]
    P --> Q[Glutamine Synthetase]
    Q --> R[Glutamine Formation]
    
    %% GOGAT System
    R --> S[Glutamine Pool]
    S --> T[GltBD GOGAT]
    T --> U[2 Glutamate]
    U --> V[Amino Acid Biosynthesis]
    
    %% Styling - Programming Framework Colors
    style A fill:#ff6b6b,color:#fff
    style C fill:#ff6b6b,color:#fff
    style E fill:#ff6b6b,color:#fff
    style B fill:#ffd43b,color:#000
    style D 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:#ffd43b,color:#000
    style J fill:#74c0fc,color:#fff
    style K fill:#ffd43b,color:#000
    style L fill:#74c0fc,color:#fff
    style M fill:#ffd43b,color:#000
    style N fill:#74c0fc,color:#fff
    style O fill:#ffd43b,color:#000
    style P fill:#ffd43b,color:#000
    style Q fill:#ffd43b,color:#000
    style R fill:#b197fc,color:#fff
    style S fill:#74c0fc,color:#fff
    style T fill:#ffd43b,color:#000
    style U fill:#b197fc,color:#fff
    style V 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>

            <!-- Process 8: Cell Division -->
            <div class="process-item" id="cell-division">
                <h3>8. Cell Division</h3>
                <p>Bacterial cell division machinery showing how E. coli coordinates chromosome segregation, septum formation, and daughter cell separation.</p>
                <div class="mermaid-container">
                    <div class="mermaid">
graph TD
    %% Division Initiation Signals
    A[Cell Size Critical] --> B[Division Signal]
    C[DNA Replication Complete] --> D[Chromosome Signal]
    E[Nutrient Availability] --> F[Growth Signal]
    
    %% Cell Cycle Checkpoints
    B --> G{Size Adequate?}
    D --> H{DNA Segregated?}
    F --> I{Resources Available?}
    G -->|Yes| J[Division Permitted]
    H -->|Yes| J
    I -->|Yes| J
    
    %% FtsZ Ring Assembly
    J --> K[FtsZ Polymerization]
    K --> L[Z-ring Formation]
    L --> M[FtsZ-ring Positioning]
    M --> N[Mid-cell Localization]
    
    %% Divisome Assembly
    N --> O[FtsA Recruitment]
    O --> P[ZipA Recruitment]
    P --> Q[FtsK Assembly]
    Q --> R[Divisome Complete]
    
    %% Chromosome Segregation
    D --> S[Chromosome Duplication]
    S --> T[ParAB System]
    T --> U[oriC Separation]
    U --> V[Nucleoid Segregation]
    
    %% Peptidoglycan Synthesis
    R --> W[Septum Initiation]
    W --> X[FtsW Lipid II Transport]
    X --> Y[FtsI Transpeptidase]
    Y --> Z[Peptidoglycan Cross-linking]
    Z --> AA[Septum Formation]
    
    %% Cell Separation
    AA --> BB[Cell Wall Constriction]
    BB --> CC[Septum Completion]
    CC --> DD[Daughter Cell Formation]
    DD --> EE[Cell Separation]
    
    %% Styling - Programming Framework Colors
    style A fill:#ff6b6b,color:#fff
    style C fill:#ff6b6b,color:#fff
    style E fill:#ff6b6b,color:#fff
    style B fill:#74c0fc,color:#fff
    style D fill:#74c0fc,color:#fff
    style F fill:#74c0fc,color:#fff
    style G fill:#74c0fc,color:#fff
    style H fill:#74c0fc,color:#fff
    style I fill:#74c0fc,color:#fff
    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:#ffd43b,color:#000
    style R fill:#ffd43b,color:#000
    style S fill:#ffd43b,color:#000
    style T fill:#ffd43b,color:#000
    style U fill:#ffd43b,color:#000
    style V fill:#ffd43b,color:#000
    style W fill:#ffd43b,color:#000
    style X fill:#ffd43b,color:#000
    style Y fill:#ffd43b,color:#000
    style Z fill:#ffd43b,color:#000
    style AA fill:#ffd43b,color:#000
    style BB fill:#ffd43b,color:#000
    style CC fill:#ffd43b,color:#000
    style DD fill:#b197fc,color:#fff
    style EE 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>

            <!-- Process 9: Biofilm Formation -->
            <div class="process-item" id="biofilm">
                <h3>9. Biofilm Formation</h3>
                <p>Multicellular community formation system showing how E. coli transitions from planktonic to sessile lifestyle through quorum sensing and matrix production.</p>
                <div class="mermaid-container">
                    <div class="mermaid">
graph TD
    %% Environmental Triggers
    A[Surface Contact] --> B[Adhesion Signal]
    C[Nutrient Limitation] --> D[Stress Signal]
    E[Cell Density] --> F[Quorum Signal]
    
    %% Initial Attachment
    B --> G[Flagellar Contact]
    G --> H[Surface Recognition]
    H --> I[Reversible Attachment]
    I --> J{Surface Suitable?}
    J -->|Yes| K[Attachment Commitment]
    J -->|No| L[Detachment]
    
    %% Adhesion Mechanisms
    K --> M[Type I Pili Expression]
    M --> N[FimA Assembly]
    N --> O[Mannose-specific Binding]
    O --> P[Irreversible Attachment]
    
    %% Curli Fiber Production
    P --> Q[csg Operon Activation]
    Q --> R[CsgA Monomer]
    Q --> S[CsgB Nucleator]
    R --> T[Curli Assembly]
    S --> T
    T --> U[Amyloid Fibers]
    U --> V[Strong Adhesion]
    
    %% Biofilm Development
    V --> W[Microcolony Formation]
    W --> X[Coordinated Development]
    X --> Y[Cell-Cell Adhesion]
    Y --> Z[Multilayer Structure]
    
    %% Matrix Maturation
    Z --> AA[EPS Production]
    AA --> BB[Extracellular DNA]
    AA --> CC[Protein Secretion]
    BB --> DD[Matrix Integration]
    CC --> DD
    DD --> EE[Biofilm Architecture]
    
    %% Styling - Programming Framework Colors
    style A fill:#ff6b6b,color:#fff
    style C fill:#ff6b6b,color:#fff
    style E fill:#ff6b6b,color:#fff
    style B fill:#74c0fc,color:#fff
    style D fill:#74c0fc,color:#fff
    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:#74c0fc,color:#fff
    style K fill:#ffd43b,color:#000
    style L fill:#b197fc,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
    style Q fill:#ffd43b,color:#000
    style R fill:#ffd43b,color:#000
    style S fill:#ffd43b,color:#000
    style T fill:#ffd43b,color:#000
    style U fill:#b197fc,color:#fff
    style V fill:#b197fc,color:#fff
    style W fill:#ffd43b,color:#000
    style X fill:#ffd43b,color:#000
    style Y fill:#ffd43b,color:#000
    style Z fill:#b197fc,color:#fff
    style AA fill:#ffd43b,color:#000
    style BB fill:#ffd43b,color:#000
    style CC fill:#ffd43b,color:#000
    style DD fill:#ffd43b,color:#000
    style EE 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>

            <!-- Process 10: CRISPR-Cas -->
            <div class="process-item" id="crispr">
                <h3>10. Phage Defense (CRISPR-Cas)</h3>
                <p>Adaptive immune system showing how E. coli acquires, stores, and uses genetic memory to defend against phage infections through targeted defense responses.</p>
                <div class="mermaid-container">
                    <div class="mermaid">
graph TD
    %% Phage Infection
    A[Phage Attachment] --> B[DNA Injection]
    C[Phage Replication] --> D[Foreign DNA Signal]
    E[Viral Proteins] --> F[Infection Detection]
    
    %% Spacer Acquisition
    B --> G[Cas1-Cas2 Complex]
    D --> G
    F --> G
    G --> H[Foreign DNA Recognition]
    H --> I[PAM Sequence Identification]
    I --> J[Protospacer Selection]
    J --> K[DNA Cleavage]
    K --> L[Spacer Processing]
    
    %% CRISPR Array Integration
    L --> M[Leader Sequence Targeting]
    M --> N[Array Integration]
    N --> O[New Spacer Addition]
    O --> P[Genetic Memory Storage]
    P --> Q[Inherited Immunity]
    
    %% Transcription and Processing
    Q --> R[CRISPR Transcription]
    R --> S[pre-crRNA Synthesis]
    S --> T[Cas6 Endonuclease]
    T --> U[crRNA Processing]
    U --> V[Mature crRNA]
    V --> W[Guide RNA Ready]
    
    %% Surveillance Complex
    W --> X[Cas3 Recruitment]
    X --> Y[Cascade Complex]
    Y --> Z[crRNA Loading]
    Z --> AA[Surveillance Mode]
    
    %% Target Recognition
    AA --> BB[DNA Scanning]
    BB --> CC{PAM Present?}
    CC -->|Yes| DD[PAM Recognition]
    CC -->|No| EE[Continue Scanning]
    DD --> FF[R-loop Formation]
    FF --> GG[Target Validation]
    
    %% Sequence Matching
    GG --> HH{Perfect Match?}
    HH -->|Yes| II[Target Confirmed]
    HH -->|No| JJ[Mismatch Detected]
    II --> KK[Cas3 Activation]
    KK --> LL[DNA Degradation]
    
    %% Immune Response
    LL --> MM[Phage DNA Destruction]
    MM --> NN[Infection Clearance]
    NN --> OO[Cell Survival]
    OO --> PP[Immunity Acquired]
    
    %% Styling - Programming Framework Colors
    style A fill:#ff6b6b,color:#fff
    style C fill:#ff6b6b,color:#fff
    style E fill:#ff6b6b,color:#fff
    style B fill:#74c0fc,color:#fff
    style D fill:#74c0fc,color:#fff
    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:#ffd43b,color:#000
    style O fill:#ffd43b,color:#000
    style P fill:#ffd43b,color:#000
    style Q fill:#b197fc,color:#fff
    style R fill:#ffd43b,color:#000
    style S fill:#b197fc,color:#fff
    style T fill:#ffd43b,color:#000
    style U fill:#ffd43b,color:#000
    style V fill:#b197fc,color:#fff
    style W fill:#b197fc,color:#fff
    style X fill:#ffd43b,color:#000
    style Y fill:#74c0fc,color:#fff
    style Z fill:#b197fc,color:#fff
    style AA fill:#b197fc,color:#fff
    style BB fill:#ffd43b,color:#000
    style CC fill:#74c0fc,color:#fff
    style DD fill:#ffd43b,color:#000
    style EE fill:#ffd43b,color:#000
    style FF fill:#ffd43b,color:#000
    style GG fill:#ffd43b,color:#000
    style HH fill:#74c0fc,color:#fff
    style II fill:#ffd43b,color:#000
    style JJ fill:#ffd43b,color:#000
    style KK fill:#ffd43b,color:#000
    style LL fill:#ffd43b,color:#000
    style MM fill:#b197fc,color:#fff
    style NN fill:#b197fc,color:#fff
    style OO fill:#b197fc,color:#fff
    style PP 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="footer">
                <p><strong>Generated using the Programming Framework methodology</strong></p>
                <p>These detailed flowcharts demonstrate the full complexity of E. coli cellular processes as computational programs</p>
                <p>Each flowchart preserves the intricate detail through optimized Mermaid configuration and shows the computational nature of biological systems</p>
            </div>
        </div>
    </div>
    
    <script>
        mermaid.initialize({
            startOnLoad: true,
            theme: 'default',
            flowchart: {
                useMaxWidth: false,
                htmlLabels: true,
                curve: 'linear',
                nodeSpacing: 30,
                rankSpacing: 40,
                padding: 10
            },
            themeVariables: {
                fontFamily: 'Arial, sans-serif',
                fontSize: '14px',
                primaryColor: '#ff6b6b',
                lineColor: '#333333',
                secondaryColor: '#feca57',
                tertiaryColor: '#4ecdc4'
            }
        });
    </script>
</body>
</html>