Synthetic Biology Meets Astrobiology
RedDust Reclaimer is a modular space biotech initiative that engineers Bacillus subtilis for perchlorate bioremediation under Martian regolith conditions. This project fuses multi-layered gene optimization, protein docking, metabolic modeling, and planetary bioethics — tracked at our GitHub project board:
📌 Project Board: github.com/users/Jonahnki/projects/2
Martian soil contains toxic perchlorates that threaten future habitability. This project aims to mitigate that risk using engineered B. subtilis expressing codon-optimized perchlorate reductase (pcrA/pcrB) and chlorite dismutase (cld) enzymes.
We integrate:
- 🧬 Codon optimization for high expression in B. subtilis
- 🔧 CRISPR/plasmid-based genome engineering
- ⚛️ Structural docking with AMDock & SwissDock
- 🧫 In silico metabolic modeling (COBRApy) under Mars constraints
- 🛰️ Space biosafety alignment with NASA and iGEM guidelines
- Identify optimal pcrA/pcrB and cld genes.
- Codon-optimize for B. subtilis using tools like JCat and GeneOptimizer.
- Add regulatory elements (promoters, RBS, terminators).
Tools: NCBI, UniProt, KEGG, JGI IMG, JCat, Benchling
Output: Synthesized, Mars-ready gene cassettes.
- Integrate perchlorate detox pathway into B. subtilis metabolic network.
- Simulate Mars-like metabolism using COBRApy.
Tools: COBRApy, BioCyc, KBase
Output: Simulated degradation flux map under Martian stressors.
- Dock enzymes with perchlorate/chlorite in AMDock & SwissDock.
- Run molecular dynamics (GROMACS) to confirm cold-environment stability.
Tools: PyMOL, SwissDock, AMDock, AutoDock Vina, GROMACS
Output: Structurally stable enzyme designs for Mars.
- Design plasmids or apply CRISPR editing for chromosomal integration.
- Use strong constitutive promoters (e.g., Pspac, Pveg).
Tools: Benchling, SnapGene, CHOPCHOP, Geneious
Output: Biocircuit constructs or edited B. subtilis genomes.
- Perform RNA-Seq and WGS to confirm expression and stability.
- Check for off-target effects or mutations.
Tools: Galaxy, CLC Genomics Workbench, DESeq2
Output: Omics-based validation of functional construct.
- Model system performance in low-pressure, low-temperature environments.
- Train ML models to optimize strain robustness and efficiency.
Tools: SciPy, Scikit-learn, TensorFlow, MATLAB
Output: ML-tuned performance projections under Martian constraints.
- Align project with NASA's Planetary Protection guidelines.
- Address biosafety, dual-use risks, and off-Earth release protocols.
Resources: NASA Bioethics Policies, iGEM Safety Hub, Space SynBio frameworks
Output: Compliance reports and ethical deployment pathway.
| Step | Category | Tools & Resources |
|---|---|---|
| 1 | Gene Optimization | NCBI, UniProt, KEGG, JCat, Benchling |
| 2 | Pathway Modeling | COBRApy, KBase, BioCyc |
| 3 | Enzyme Engineering | AMDock, SwissDock, AutoDock Vina, GROMACS, PyMOL |
| 4 | Genome Engineering | SnapGene, Benchling, CHOPCHOP, Geneious |
| 5 | Expression Validation | Galaxy, CLC Genomics, DESeq2 |
| 6 | Predictive Modeling | SciPy, NumPy, scikit-learn, TensorFlow, MATLAB |
| 7 | Ethics & Safety | NASA Guidelines, iGEM Safety Hub, Space Synthetic Biology Policy Documents |
🔗 Direct ZIP: Download RedDust Reclaimer
📁 Project Board: github.com/users/Jonahnki/projects/2
git clone https://github.com/Jonahnki/reddust-reclaimer.git
cd reddust-reclaimer