🌱 Photosynthesis & Development Systems
Batch Overview: This batch contains 8 fundamental A. thaliana processes responsible for photosynthesis and development. These processes represent the core computational systems that enable this model plant to convert light energy into chemical energy and coordinate complex developmental programs.
Each process demonstrates sophisticated biological programming with light sensing, energy conversion, hormone signaling, and developmental regulation.
📋 Table of Contents - 8 Plant Processes
1. Light Sensing & Photoreception
Detailed analysis of A. thaliana Light Sensing & Photoreception using the Programming Framework, revealing computational logic and regulatory patterns for light detection and signal transduction.
graph TD
%% Light Detection
A[Light Absorption] --> B[Phytochrome Activation]
C[Blue Light] --> D[Cryptochrome Activation]
E[UV Light] --> F[UVR8 Activation]
G[Red Light] --> H[Phytochrome B]
%% Phytochrome Signaling
B --> I[Pfr Formation]
I --> J[Nuclear Translocation]
J --> K[PIF Degradation]
K --> L[Light Response Genes]
%% Cryptochrome Signaling
D --> M[CRY1/2 Activation]
M --> N[COP1 Inhibition]
N --> O[HY5 Stabilization]
O --> P[Photomorphogenesis]
%% UVR8 Response
F --> Q[UVR8 Dimer Dissociation]
Q --> R[CUL4-DDB1 Complex]
R --> S[UV Response Genes]
%% Integration
L --> T[Light Response Program]
P --> T
S --> T
H --> T
T --> U[Photomorphogenic Development]
%% Styling - Programming Framework Colors
style A fill:#ff6b6b,color:#fff
style C fill:#ff6b6b,color:#fff
style E fill:#ff6b6b,color:#fff
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style I fill:#ffd43b,color:#000
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style K fill:#51cf66,color:#fff
style L fill:#51cf66,color:#fff
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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:#51cf66,color:#fff
style T fill:#74c0fc,color:#fff
style U fill:#b197fc,color:#fff
Triggers & Conditions
Catalysts & Enzymes
Chemical Processing
Intermediates
Products
2. Photosynthesis
Detailed analysis of A. thaliana Photosynthesis using the Programming Framework, revealing computational logic and regulatory patterns for light energy conversion.
graph TD
%% Light Energy Capture
A[Light Absorption] --> B[Chlorophyll Excitation]
C[PSII Activation] --> D[Water Splitting]
E[PSI Activation] --> F[NADP+ Reduction]
G[Electron Transport] --> H[ATP Synthesis]
%% Light Reactions
B --> I[Electron Transfer Chain]
I --> J[Proton Gradient]
J --> K[ATP Synthase]
K --> L[ATP Production]
%% Water Splitting
D --> M[Oxygen Evolution]
M --> N[Proton Release]
N --> O[Electron Donation]
%% NADP+ Reduction
F --> P[NADPH Production]
P --> Q[Reducing Power]
Q --> R[Calvin Cycle]
%% Integration
L --> S[Energy Production]
O --> S
R --> S
H --> S
S --> T[Carbon Fixation]
%% 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
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style Q fill:#74c0fc,color:#fff
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
3. Circadian Rhythm
Detailed analysis of A. thaliana Circadian Rhythm using the Programming Framework, revealing computational logic and regulatory patterns for time-based gene expression.
graph TD
%% Clock Components
A[Light Signal] --> B[CCA1/LHY Expression]
C[Evening Signal] --> D[TOC1 Expression]
E[Circadian Time] --> F[PRR Family]
G[Feedback Loop] --> H[Clock Regulation]
%% Morning Loop
B --> I[CCA1/LHY Proteins]
I --> J[TOC1 Repression]
J --> K[Morning Genes]
K --> L[Photosynthesis Activation]
%% Evening Loop
D --> M[TOC1 Protein]
M --> N[CCA1/LHY Repression]
N --> O[Evening Genes]
O --> P[Metabolic Regulation]
%% PRR Regulation
F --> Q[PRR7/9 Expression]
Q --> R[Clock Synchronization]
R --> S[Circadian Output]
%% Integration
L --> T[Circadian Program]
P --> T
S --> T
H --> T
T --> U[24-Hour Rhythm]
%% 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:#51cf66,color:#fff
style M fill:#ffd43b,color:#000
style N fill:#51cf66,color:#fff
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:#51cf66,color:#fff
style T fill:#74c0fc,color:#fff
style U fill:#b197fc,color:#fff
Triggers & Conditions
Catalysts & Enzymes
Chemical Processing
Intermediates
Products
4. Hormone Signaling
Detailed analysis of A. thaliana Hormone Signaling using the Programming Framework, revealing computational logic and regulatory patterns for plant hormone responses.
graph TD
%% Hormone Detection
A[Auxin Presence] --> B[TIR1/AFB Receptors]
C[Cytokinin Presence] --> D[AHK Receptors]
E[Gibberellin Presence] --> F[GID1 Receptors]
G[Abscisic Acid] --> H[PYR/PYL Receptors]
%% Auxin Signaling
B --> I[Aux/IAA Degradation]
I --> J[ARF Activation]
J --> K[Auxin Response Genes]
%% Cytokinin Signaling
D --> L[AHK Phosphorylation]
L --> M[ARR Phosphorylation]
M --> N[Cytokinin Response]
%% Gibberellin Signaling
F --> O[DELLA Degradation]
O --> P[PIF Activation]
P --> Q[Growth Promotion]
%% ABA Signaling
H --> R[PP2C Inhibition]
R --> S[SnRK2 Activation]
S --> T[Stress Response]
%% Integration
K --> U[Hormone Response Program]
N --> U
Q --> U
T --> U
U --> V[Developmental Control]
%% 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
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style O fill:#ffd43b,color:#000
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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. Stress Response
Detailed analysis of A. thaliana Stress Response using the Programming Framework, revealing computational logic and regulatory patterns for environmental adaptation.
graph TD
%% Stress Detection
A[Drought Stress] --> B[ABA Accumulation]
C[Salt Stress] --> D[SOS Pathway]
E[Oxidative Stress] --> F[ROS Scavenging]
G[Pathogen Attack] --> H[SA Signaling]
%% Drought Response
B --> I[PYR/PYL Activation]
I --> J[SnRK2 Activation]
J --> K[Stomatal Closure]
%% Salt Response
D --> L[SOS1 Activation]
L --> M[Na+ Efflux]
M --> N[Salt Tolerance]
%% Oxidative Response
F --> O[Catalase Production]
O --> P[SOD Activation]
P --> Q[ROS Detoxification]
%% Pathogen Response
H --> R[NPR1 Activation]
R --> S[PR Gene Expression]
S --> T[Systemic Resistance]
%% 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:#51cf66,color:#fff
style K fill:#51cf66,color:#fff
style L fill:#ffd43b,color:#000
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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:#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
6. Development & Growth
Detailed analysis of A. thaliana Development & Growth using the Programming Framework, revealing computational logic and regulatory patterns for plant development.
graph TD
%% Developmental Signals
A[Meristem Activity] --> B[Cell Division]
C[Auxin Gradients] --> D[Cell Elongation]
E[Cytokinin Signals] --> F[Cell Differentiation]
G[Light Signals] --> H[Organ Development]
%% Meristem Function
B --> I[Stem Cell Maintenance]
I --> J[Organ Initiation]
J --> K[Pattern Formation]
%% Cell Elongation
D --> L[Cell Wall Loosening]
L --> M[Expansin Activation]
M --> N[Cell Growth]
%% Cell Differentiation
F --> O[Fate Specification]
O --> P[Tissue Formation]
P --> Q[Organ Development]
%% Integration
K --> R[Developmental Program]
N --> R
Q --> R
H --> R
R --> S[Plant Architecture]
%% 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:#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
7. Nutrient Uptake
Detailed analysis of A. thaliana Nutrient Uptake using the Programming Framework, revealing computational logic and regulatory patterns for mineral nutrition.
graph TD
%% Nutrient Detection
A[Nitrate Availability] --> B[NRT1/NRT2 Transporters]
C[Phosphate Limitation] --> D[PHT Transporters]
E[Iron Deficiency] --> F[IRT1/FRO2]
G[Potassium Need] --> H[AKT1/KAT1]
%% Nitrate Uptake
B --> I[Nitrate Transport]
I --> J[Nitrate Reduction]
J --> K[Nitrogen Assimilation]
%% Phosphate Uptake
D --> L[Phosphate Transport]
L --> M[Phosphate Storage]
M --> N[Phosphate Utilization]
%% Iron Uptake
F --> O[Iron Chelation]
O --> P[Iron Transport]
P --> Q[Iron Storage]
%% Integration
K --> R[Nutrient Homeostasis]
N --> R
Q --> R
H --> R
R --> S[Plant Nutrition]
%% 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
8. Flowering Control
Detailed analysis of A. thaliana Flowering Control using the Programming Framework, revealing computational logic and regulatory patterns for floral transition.
graph TD
%% Flowering Signals
A[Photoperiod] --> B[CO Expression]
C[Vernalization] --> D[FLC Repression]
E[Gibberellin] --> F[GA Signaling]
G[Autonomous Pathway] --> H[FCA/FVE]
%% Photoperiod Pathway
B --> I[FT Expression]
I --> J[Floral Meristem]
J --> K[Flower Development]
%% Vernalization
D --> L[FLC Silencing]
L --> M[Vernalization Response]
M --> N[Spring Flowering]
%% Gibberellin Pathway
F --> O[DELLA Degradation]
O --> P[Flowering Promotion]
P --> Q[Flower Initiation]
%% Integration
K --> R[Flowering Program]
N --> R
Q --> R
H --> R
R --> S[Reproductive Success]
%% 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
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style H fill:#ffd43b,color:#000
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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