🦠Dormancy & Persistence Systems
Batch Overview: This batch contains 8 fundamental M. tuberculosis processes responsible for dormancy and persistence. These processes represent the core computational systems that enable this pathogen to survive for decades within hosts, evading immune responses and antibiotic treatments.
Each process demonstrates sophisticated biological programming with metabolic adaptation, immune evasion, stress response, and dormancy regulation.
📋 Table of Contents - 8 Dormancy Processes
1. Dormancy Induction
Detailed analysis of M. tuberculosis Dormancy Induction using the Programming Framework, revealing computational logic and regulatory patterns for entering a non-replicating persistent state.
graph TD
%% Environmental Triggers
A[Oxygen Deprivation] --> B[DosR Activation]
C[Nitric Oxide Stress] --> D[NOR Activation]
E[Nutrient Limitation] --> F[RelA Activation]
G[Host Immune Pressure] --> H[Stress Response]
%% DosR Regulon
B --> I[DosR Phosphorylation]
I --> J[DosR-DNA Binding]
J --> K[Dormancy Gene Expression]
%% NOR Response
D --> L[Nitric Oxide Detoxification]
L --> M[Respiratory Protection]
M --> N[Anaerobic Adaptation]
%% Stringent Response
F --> O[ppGpp Synthesis]
O --> P[Stringent Response]
P --> Q[Growth Arrest]
%% Integration
K --> R[Dormancy Program]
N --> R
Q --> R
H --> R
R --> S[Non-Replicating State]
%% Styling - Programming Framework Colors
style A fill:#ff6b6b,color:#fff
style C fill:#ff6b6b,color:#fff
style E fill:#ff6b6b,color:#fff
style G fill:#ff6b6b,color:#fff
style B fill:#ffd43b,color:#000
style D fill:#ffd43b,color:#000
style F 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:#51cf66,color:#fff
style L fill:#ffd43b,color:#000
style M fill:#51cf66,color:#fff
style N fill:#51cf66,color:#fff
style O fill:#ffd43b,color:#000
style P fill:#51cf66,color:#fff
style Q fill:#51cf66,color:#fff
style R fill:#74c0fc,color:#fff
style S fill:#b197fc,color:#fff
Triggers & Conditions
Catalysts & Enzymes
Chemical Processing
Intermediates
Products
2. Metabolic Adaptation
Detailed analysis of M. tuberculosis Metabolic Adaptation using the Programming Framework, revealing computational logic and regulatory patterns for energy conservation and survival.
graph TD
%% Energy Source Detection
A[Glucose Depletion] --> B[Fatty Acid Metabolism]
C[Oxygen Limitation] --> D[Anaerobic Respiration]
E[Host Lipid Availability] --> F[Cholesterol Utilization]
G[Iron Limitation] --> H[Iron Scavenging]
%% Fatty Acid Metabolism
B --> I[β-Oxidation Activation]
I --> J[Acetyl-CoA Production]
J --> K[TCA Cycle Adaptation]
%% Anaerobic Respiration
D --> L[Nitrate Reduction]
L --> M[Fumarate Reduction]
M --> N[Anaerobic ATP Production]
%% Cholesterol Metabolism
F --> O[Cholesterol Uptake]
O --> P[Cholesterol Degradation]
P --> Q[Propionyl-CoA Production]
%% Integration
K --> R[Energy Conservation]
N --> R
Q --> R
H --> R
R --> S[Metabolic Dormancy]
%% Styling - Programming Framework Colors
style A fill:#ff6b6b,color:#fff
style C fill:#ff6b6b,color:#fff
style E fill:#ff6b6b,color:#fff
style G fill:#ff6b6b,color:#fff
style B fill:#ffd43b,color:#000
style D fill:#ffd43b,color:#000
style F fill:#ffd43b,color:#000
style H fill:#ffd43b,color:#000
style I fill:#ffd43b,color:#000
style J fill:#51cf66,color:#fff
style K fill:#51cf66,color:#fff
style L fill:#ffd43b,color:#000
style M fill:#ffd43b,color:#000
style N fill:#51cf66,color:#fff
style O fill:#ffd43b,color:#000
style P fill:#ffd43b,color:#000
style Q fill:#51cf66,color:#fff
style R fill:#74c0fc,color:#fff
style S fill:#b197fc,color:#fff
Triggers & Conditions
Catalysts & Enzymes
Chemical Processing
Intermediates
Products
3. Immune Evasion
Detailed analysis of M. tuberculosis Immune Evasion using the Programming Framework, revealing computational logic and regulatory patterns for avoiding host immune detection.
graph TD
%% Immune Detection
A[Host Immune Response] --> B[Antigen Masking]
C[Phagosome Recognition] --> D[Phagosome Arrest]
E[TLR Activation] --> F[TLR Inhibition]
G[Inflammatory Signals] --> H[Anti-Inflammatory Response]
%% Antigen Masking
B --> I[Cell Wall Modification]
I --> J[Antigen Concealment]
J --> K[Immune Recognition Block]
%% Phagosome Arrest
D --> L[V-ATPase Inhibition]
L --> M[Phagosome Acidification Block]
M --> N[Lysosome Fusion Prevention]
%% TLR Inhibition
F --> O[TLR Signaling Block]
O --> P[Inflammatory Response Suppression]
P --> Q[Immune Evasion]
%% Integration
K --> R[Immune System Evasion]
N --> R
Q --> R
H --> R
R --> S[Host Survival]
%% Styling - Programming Framework Colors
style A fill:#ff6b6b,color:#fff
style C fill:#ff6b6b,color:#fff
style E fill:#ff6b6b,color:#fff
style G fill:#ff6b6b,color:#fff
style B fill:#ffd43b,color:#000
style D fill:#ffd43b,color:#000
style F fill:#ffd43b,color:#000
style H fill:#ffd43b,color:#000
style I fill:#ffd43b,color:#000
style J fill:#51cf66,color:#fff
style K fill:#51cf66,color:#fff
style L fill:#ffd43b,color:#000
style M fill:#51cf66,color:#fff
style N fill:#51cf66,color:#fff
style O fill:#ffd43b,color:#000
style P fill:#51cf66,color:#fff
style Q fill:#51cf66,color:#fff
style R fill:#74c0fc,color:#fff
style S fill:#b197fc,color:#fff
Triggers & Conditions
Catalysts & Enzymes
Chemical Processing
Intermediates
Products
4. Stress Response
Detailed analysis of M. tuberculosis Stress Response using the Programming Framework, revealing computational logic and regulatory patterns for environmental adaptation.
graph TD
%% Stress Detection
A[Oxidative Stress] --> B[OxyR Activation]
C[Heat Stress] --> D[σH Activation]
E[DNA Damage] --> F[SOS Response]
G[Protein Misfolding] --> H[σE Activation]
%% Oxidative Stress Response
B --> I[Catalase Production]
I --> J[Superoxide Dismutase]
J --> K[ROS Scavenging]
%% Heat Shock Response
D --> L[Heat Shock Proteins]
L --> M[Protein Protection]
M --> N[Thermal Adaptation]
%% DNA Damage Response
F --> O[DNA Repair Enzymes]
O --> P[DNA Damage Repair]
P --> Q[Genome Stability]
%% Protein Stress Response
H --> R[Chaperone Production]
R --> S[Protein Folding]
S --> T[Proteostasis]
%% Integration
K --> U[Stress Adaptation]
N --> U
Q --> U
T --> U
U --> V[Environmental Survival]
%% Styling - Programming Framework Colors
style A fill:#ff6b6b,color:#fff
style C fill:#ff6b6b,color:#fff
style E fill:#ff6b6b,color:#fff
style G fill:#ff6b6b,color:#fff
style B fill:#ffd43b,color:#000
style D fill:#ffd43b,color:#000
style F 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:#51cf66,color:#fff
style L fill:#ffd43b,color:#000
style M fill:#51cf66,color:#fff
style N fill:#51cf66,color:#fff
style O fill:#ffd43b,color:#000
style P fill:#51cf66,color:#fff
style Q fill:#51cf66,color:#fff
style R fill:#ffd43b,color:#000
style S fill:#51cf66,color:#fff
style T fill:#51cf66,color:#fff
style U fill:#74c0fc,color:#fff
style V fill:#b197fc,color:#fff
Triggers & Conditions
Catalysts & Enzymes
Chemical Processing
Intermediates
Products
5. Drug Tolerance
Detailed analysis of M. tuberculosis Drug Tolerance using the Programming Framework, revealing computational logic and regulatory patterns for antibiotic resistance and tolerance.
graph TD
%% Drug Detection
A[Isoniazid Presence] --> B[KatG Activation]
C[Rifampin Presence] --> D[RpoB Modification]
E[Ethambutol Presence] --> F[EmbB Mutation]
G[Pyrazinamide Presence] --> H[PncA Inactivation]
%% Drug Inactivation
B --> I[Isoniazid Activation]
I --> J[INH-NAD Adduct Formation]
J --> K[INH Resistance]
%% Target Modification
D --> L[RpoB Mutation]
L --> M[Rifampin Resistance]
F --> N[EmbB Mutation]
N --> O[Ethambutol Resistance]
%% Drug Efflux
H --> P[Pyrazinamide Resistance]
P --> Q[Efflux Pump Activation]
Q --> R[Drug Export]
%% Integration
K --> S[Multi-Drug Tolerance]
M --> S
O --> S
R --> S
S --> T[Treatment Failure]
%% Styling - Programming Framework Colors
style A fill:#ff6b6b,color:#fff
style C fill:#ff6b6b,color:#fff
style E fill:#ff6b6b,color:#fff
style G fill:#ff6b6b,color:#fff
style B fill:#ffd43b,color:#000
style D fill:#ffd43b,color:#000
style F fill:#ffd43b,color:#000
style H fill:#ffd43b,color:#000
style I fill:#ffd43b,color:#000
style J fill:#51cf66,color:#fff
style K fill:#51cf66,color:#fff
style L fill:#ffd43b,color:#000
style M fill:#51cf66,color:#fff
style N fill:#ffd43b,color:#000
style O fill:#51cf66,color:#fff
style P fill:#51cf66,color:#fff
style Q fill:#ffd43b,color:#000
style R fill:#51cf66,color:#fff
style S fill:#74c0fc,color:#fff
style T fill:#b197fc,color:#fff
Triggers & Conditions
Catalysts & Enzymes
Chemical Processing
Intermediates
Products
6. Granuloma Formation
Detailed analysis of M. tuberculosis Granuloma Formation using the Programming Framework, revealing computational logic and regulatory patterns for host tissue manipulation.
graph TD
%% Initial Infection
A[Macrophage Infection] --> B[Mycobacterial Replication]
C[Host Immune Response] --> D[Inflammatory Cytokines]
E[Cell Death] --> F[Caseous Necrosis]
G[Fibroblast Activation] --> H[Fibrosis Formation]
%% Granuloma Development
B --> I[Macrophage Aggregation]
D --> J[Lymphocyte Recruitment]
F --> K[Caseous Center Formation]
H --> L[Fibrotic Wall]
%% Granuloma Structure
I --> M[Epithelioid Cells]
J --> N[T-Cell Ring]
K --> O[Caseous Necrosis Center]
L --> P[Fibrotic Capsule]
%% Integration
M --> Q[Granuloma Structure]
N --> Q
O --> Q
P --> Q
Q --> R[Latent Infection]
%% Styling - Programming Framework Colors
style A fill:#ff6b6b,color:#fff
style C fill:#ff6b6b,color:#fff
style E fill:#ff6b6b,color:#fff
style G fill:#ff6b6b,color:#fff
style B fill:#ffd43b,color:#000
style D fill:#ffd43b,color:#000
style F 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:#51cf66,color:#fff
style L fill:#51cf66,color:#fff
style M fill:#74c0fc,color:#fff
style N fill:#74c0fc,color:#fff
style O fill:#74c0fc,color:#fff
style P fill:#74c0fc,color:#fff
style Q fill:#b197fc,color:#fff
style R fill:#b197fc,color:#fff
Triggers & Conditions
Catalysts & Enzymes
Chemical Processing
Intermediates
Products
7. Reactivation Signals
Detailed analysis of M. tuberculosis Reactivation Signals using the Programming Framework, revealing computational logic and regulatory patterns for exiting dormancy.
graph TD
%% Reactivation Triggers
A[Immune Suppression] --> B[Immune Pressure Reduction]
C[Oxygen Availability] --> D[Aerobic Respiration]
E[Nutrient Availability] --> F[Metabolic Reactivation]
G[Host Stress] --> H[Opportunistic Growth]
%% DosR Inactivation
B --> I[DosR Dephosphorylation]
I --> J[DosR-DNA Dissociation]
J --> K[Dormancy Gene Repression]
%% Metabolic Reactivation
D --> L[Oxidative Phosphorylation]
L --> M[ATP Production]
M --> N[Growth Resumption]
%% Gene Expression
F --> O[Growth Gene Expression]
O --> P[Cell Division Activation]
P --> Q[Replication Resumption]
%% Integration
K --> R[Reactivation Program]
N --> R
Q --> R
H --> R
R --> S[Active Replication]
%% Styling - Programming Framework Colors
style A fill:#ff6b6b,color:#fff
style C fill:#ff6b6b,color:#fff
style E fill:#ff6b6b,color:#fff
style G fill:#ff6b6b,color:#fff
style B fill:#ffd43b,color:#000
style D fill:#ffd43b,color:#000
style F 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:#51cf66,color:#fff
style L fill:#ffd43b,color:#000
style M fill:#51cf66,color:#fff
style N fill:#51cf66,color:#fff
style O fill:#ffd43b,color:#000
style P fill:#51cf66,color:#fff
style Q fill:#51cf66,color:#fff
style R fill:#74c0fc,color:#fff
style S fill:#b197fc,color:#fff
Triggers & Conditions
Catalysts & Enzymes
Chemical Processing
Intermediates
Products
8. Persistence Mechanisms
Detailed analysis of M. tuberculosis Persistence Mechanisms using the Programming Framework, revealing computational logic and regulatory patterns for long-term survival.
graph TD
%% Persistence Strategies
A[Host Environment] --> B[Metabolic Flexibility]
C[Immune Pressure] --> D[Antigenic Variation]
E[Antibiotic Pressure] --> F[Drug Resistance]
G[Host Stress] --> H[Opportunistic Growth]
%% Metabolic Flexibility
B --> I[Multiple Carbon Sources]
I --> J[Energy Conservation]
J --> K[Metabolic Dormancy]
%% Antigenic Variation
D --> L[Surface Protein Variation]
L --> M[Immune Evasion]
M --> N[Host Adaptation]
%% Drug Resistance
F --> O[Resistance Gene Expression]
O --> P[Drug Efflux Systems]
P --> Q[Treatment Tolerance]
%% Integration
K --> R[Long-Term Persistence]
N --> R
Q --> R
H --> R
R --> S[Decades of Survival]
%% Styling - Programming Framework Colors
style A fill:#ff6b6b,color:#fff
style C fill:#ff6b6b,color:#fff
style E fill:#ff6b6b,color:#fff
style G fill:#ff6b6b,color:#fff
style B fill:#ffd43b,color:#000
style D fill:#ffd43b,color:#000
style F fill:#ffd43b,color:#000
style H fill:#ffd43b,color:#000
style I fill:#ffd43b,color:#000
style J fill:#51cf66,color:#fff
style K fill:#51cf66,color:#fff
style L fill:#ffd43b,color:#000
style M fill:#51cf66,color:#fff
style N fill:#51cf66,color:#fff
style O fill:#ffd43b,color:#000
style P fill:#ffd43b,color:#000
style Q fill:#51cf66,color:#fff
style R fill:#74c0fc,color:#fff
style S fill:#b197fc,color:#fff
Triggers & Conditions
Catalysts & Enzymes
Chemical Processing
Intermediates
Products