Notebook This page logs the notes, thoughts, brainstorming, and planning associated with my individual final project.
Links to section Idea brainstorming Quorum-sensing based killswitch PHA synthase enzyme engineering Feb 24, 2026 Brainstorming: Identification of PhaC analog in Cyanobacterium aponium UTEX 3222 and overproducing or engineering for increased efficiency BLAST/align with known PHA-synthases Compare efficiency / mutations that improved turnover in other PhaC - test analogous mutations (aligned location, similar or different AAs). improved substrate specificity? Site-specific saturation mutagenesis? Would be good use for automation Quorum sensing based killswitch (i.e. cell dies if it escapes bioreactor) Has to have some kind of inducible element or won’t grow after initial transformation What’s good at quorum sensing already? Something else??? Something in E coli that can be done on Opentron Because it’s more convenient for a final project to be executed in Victoria remotely Cyanobacterial expression plasmid across multiple cyano species needs to include E coli machinery for manipulation and production (and conjugation, for relevant species) Ideas: PhaC protein engineering Short term aim: Design small library of PhaC variants with expected improvement Medium term aim: Generate library and test in chassis strain Long term aim: Develop PHB bio-manufacturing cyanobacterial strain for carbon-neutral/carbon-negative plastic (depending on biodegradation). Quorum sensing based circuit for biocontainment Short term aim: Design killswitch with genetic circuit to trigger based on quorum sensing. Medium term aim: Build genetic circuit with expression based on quorum sensing with a measureable output; test circuit in E. coli. Long term aim: Optimize circuit sensitivity and test with killswitch expression; integrate into bio-manufacturing chassis strains for population-linked biocontainment. Broad cyanobacterial expression plasmid Short term aim: Design plasmid backbone based off native cyanobacterial plasmids and established E. coli machinery. Medium term aim: Test expression in multiple cyanobacterial strains (including some previously considered genetically intractable with classic broad-host-range vectors). Long term aim: Establish protocol for domestication of newly prospected, wild-type cyanobacterial strains using the cyanobacterial plasmid. Mar 31, 2026 Leaning towards quorum sensing killswitch because it’s more aligned with my prior experience and knowledge, so i think it will take less research on my behalf. since i’m already falling behind on homeworks, i’m worried about how much time it would take to optimize a protein since i have no prior machine learning experience.