Individual Final Project

Mindmap

mindmap
  root((Natural Indigo - bacterially derived))
    Audience - Funding and Implementation
      Lab spaces + backing → fibersheds
        Community biolabs 
        Indirect pulls from DBs; NCBI, UniProt, KEGG, Reactome
      AI protein/peptide design
        PepMLM from HuggingFace for peptide generation
        Structure prediction + docking/MD
        Binder design: AfDesign / RFdiffusion / EvoBind / BindCraft
      Automation & coding
        Google Colab protocols → Opentrons robots
        Scale experiments, iterate fast
    Protein Science & Design
      Amino acids & stereochemistry
        L vs D amino acids, helix handedness
      Secondary structure
	        α-helices & variants, β-sheets → aggregation
        Amyloids as stable materials
      Model protein
        eGFP: primary→tertiary structure characterization
    Genetic Engineering Methods
      DNA read/write/edit basics
        Gel electrophoresis, Benchling workflows
      PCR chemistry
        Phusion HF Master Mix components/purpose
      Assembly
        Gibson Assembly
      Cloning & expression
        Vector design → E. coli expression
    Regulatory Logic & Circuits
      Post-transcriptional vs post-translational control
        Endoribonucleases for RNA cleavage vs proteases for protein degradation
    Cell-Free Systems
      Why cell-free?
        Speed - no culturing!
        Open control of DNA, amino acids, energy, enzymes
        Toxic proteins OK; supports UAAs
    Bioproduction & Pathways
      Carotenoids in E. coli
        crtE + crtI + crtB → lycopene
        + crtY → β-carotene
      Automation mindset
        What new questions when everything is automated?
    Phage Engineering: MS2
      Lysis protein L
        N- vs C-terminal roles; C-term TM drives lysis
        33-nt non-overlapping window
        Introduce stop codon to split N from C → DnaJ-independent lysis
        Preserve overlaps with cp/rep genes
    Mitochondrial Therapeutics
      Target: Cyclophilin D "CypD"
        Block mPTP opening in I/R injury
        Design peptide inhibitor; plan in vitro/in vivo validation
    Knowledge Sources
      NCBI GenBank • UniProt • KEGG • Reactome