Homework

Growing Serratia marcescens and Bacillus sp. pigments for bio-art. Mechanotransduction experiments. Governance framework for engineered organisms in gallery settings.

Codon-optimising VioC from C. violaceum. Circadian antimicrobial system — Magainin peptide under RpaA promoter. Twist synthesis order prep.

Draft final project directions. Weighing Twist costs, remote lab availability, and UK-based ordering constraints to identify the most viable pathway.

GABARAPL2 analysis in PyMol (PDB 7LK3). ESM2 mutational scan, t-SNE latent space, ESMFold, ProteinMPNN inverse folding. Bacteriophage engineering brainstorm.

SOD1-A4V binder peptide design. PepMLM generation, AlphaFold3 evaluation, PeptiVerse property scoring, moPPIt optimisation. L-protein mutant plan for MS2 phage lysis.

DNA assembly and PCR components. Phusion High-Fidelity Master Mix, primer annealing, amilCP chromophore mutagenesis, and genetic circuit design fundamentals.

IANNs vs Boolean circuits. KaiClock + Durin parallel AND gate run at Weiss Lab. Fungal materials, mycelial pigment lightfastness. Twist DNA order review.