https://pages.htgaa.org/2026b/ali-shirazi/index.htmlAbout me Hi! Currently MSc student in marine biotechnology Interested in synthetic biology as a mean for suistainable exploitation of natural resources Contact info ali.shirazi.mcb@gmail.comHugoenhttps://pages.htgaa.org/2026b/ali-shirazi/week-01-hw-project-ideas/index.htmlMon, 01 Jan 0001 00:00:00 +0000https://pages.htgaa.org/2026b/ali-shirazi/week-01-hw-project-ideas/index.html(1) What you would like to biomanufacture and why? The compound I’m considering as a target for biomanufacturing is Shinorine, a mycosporine-like amino acid, that’s produced by alga and it’s in consist of UV absorbing properties. It has a great potential for mass production by fermentation for commercial purposes, and the shift from conventional methods of cultivation and harvest toward biomanufacturing, make it a greener and more sustainable alternative. The reason I choose this compound comes from my background in marine biotechnology, and the whole Idea that we can leverage environmental benefits without causing ecological harm is one of my objectives.https://pages.htgaa.org/2026b/ali-shirazi/week-02-hw-dna-design/index.htmlMon, 01 Jan 0001 00:00:00 +0000https://pages.htgaa.org/2026b/ali-shirazi/week-02-hw-dna-design/index.htmlPart 0: Set up in Kernel Logged in kernel by adrian.filip@canada.ca, repository: ali-shirazi, folder name: shinorine Part 1: Define your expression target What molecule are you expressing? The compound in mind was shinorine, which is a Mycosporine like amino acid. The BGC is a set of four genes that is responsible for a biosynthetic pathway. The BGC encodes these enzymes: Ava_3858, Ava_3857, Ava_3856, Ava_3855 from cyanobacterium Trichormus variabilis. What is the sequence? https://www.kegg.jp/entry/gn:T00277 Ava_3858: KEGG, 3-dehydroquinate synthase Ava_3857: KEGG, O-methyltransferase, family 3 Ava_3856: KEGG, ATP-grasp enzyme-like protein Ava_3855: KEGG, Amino acid adenylationhttps://pages.htgaa.org/2026b/ali-shirazi/week-03-hw-cell-free/index.htmlMon, 01 Jan 0001 00:00:00 +0000https://pages.htgaa.org/2026b/ali-shirazi/week-03-hw-cell-free/index.htmlA. COMPARE CELL-FREE REACTION COMPOSITIONS Why does the concentration of potassium glutamate and magnesium glutamate differ between compositions? Which is more sensitive? The best salt concentrations are not fixed numbers. They depend on what else is in the reaction. Magnesium is the clearest example: NTPs, NMPs, phosphate and amino acids all bind Mg²⁺, so a recipe that carries more of these needs more magnesium to leave enough free Mg²⁺ for the ribosomes and T7 RNA polymerase. Potassium and glutamate mostly set the ionic strength, so a formulation that already contains many charged components can get away with less added K-glutamate. On top of that, every lysate batch and every target protein has its own tolerance, which is why published recipes land on different values.Magnesium is the more sensitive of the two. Its optimum is sharp, and a change of only 1 to 2mM can noticeably reduce yield. Too little stalls transcription and translation, and too much inhibits them and can precipitate with phosphate. Potassium has a broad plateau and tolerates changes of tens of mM. For that reason Mg is normally titrated in small steps of about 1 mM, while K is scanned more coarsely.https://pages.htgaa.org/2026b/ali-shirazi/final-project/index.htmlMon, 01 Jan 0001 00:00:00 +0000https://pages.htgaa.org/2026b/ali-shirazi/final-project/index.html