https://pages.htgaa.org/2026b/ahmed-hussain-shah/index.htmlI am a final-year Biomedical Sciences student at PAF-IAST passionate about synthetic biology and biomanufacturingHugoenTue, 06 Oct 2026 00:00:00 +0000https://pages.htgaa.org/2026b/ahmed-hussain-shah/week-02-hw-dna-design/index.htmlMon, 01 Jan 0001 00:00:00 +0000https://pages.htgaa.org/2026b/ahmed-hussain-shah/week-02-hw-dna-design/index.htmlPart 0: Kernel Setup My work is located in the HTBAA 2026 workspace, in the repository ahmed-synbio-ink under the folder shah-hw2. Part 1: Define your expression target Molecule: LbCas12a (CRISPR-Cas effector nuclease) engineered as a fusion protein with an Elastin-Like Polypeptide (ELP) tag and a mutated Mxe GyrA Intein. This is the core diagnostic engine for the “SynBio-Ink” multiplexed biosensor. Sequence: Lachnospiraceae bacterium Cas12a (UniProt Accession: A0A182DWE3). Host/Chassis: E. coli Cell-Free Protein Synthesis (CFPS) extract. Destination: The protein is expressed directly into the open in vitro diagnostic matrix (the “ink”). Therefore, no signal peptides or cellular secretion tags are required. Part 2: Design your genetic parts To eliminate the massive cost of downstream affinity chromatography for the bio-ink, I designed a self-cleaving thermal purification cassette.https://pages.htgaa.org/2026b/ahmed-hussain-shah/final-project/index.htmlMon, 01 Jan 0001 00:00:00 +0000https://pages.htgaa.org/2026b/ahmed-hussain-shah/final-project/index.htmlhttps://pages.htgaa.org/2026b/ahmed-hussain-shah/week-03-hw-cell-free/index.htmlTue, 06 Oct 2026 00:00:00 +0000https://pages.htgaa.org/2026b/ahmed-hussain-shah/week-03-hw-cell-free/index.htmlPart 3A: Formulation Analysis Potassium vs. Magnesium Glutamate Dynamics Potassium glutamate supplies bulk ionic strength to maintain general protein solubility, requiring high physiological concentrations (e.g., 130–273 mM) with a wide tolerance window (Smith et al., 2026). Conversely, magnesium is a highly sensitive catalytic cofactor essential for stabilizing mRNA-tRNA-ribosome complexes; optimal concentrations are drastically lower (8–20 mM), and slight deviations rapidly induce ribosomal aggregation (Smith et al., 2026). Glutamate is preferred over acetate or chloride as it optimizes protein-nucleic acid interactions under osmotic stress.https://pages.htgaa.org/2026b/ahmed-hussain-shah/week-01-hw-project-ideas/index.htmlMon, 01 Jan 0001 00:00:00 +0000https://pages.htgaa.org/2026b/ahmed-hussain-shah/week-01-hw-project-ideas/index.htmlBiomanufacturing the “Universal Bio-Ink” for Autonomous Lab-on-a-Chip Diagnostic Sentinels (1) What you would like to biomanufacturer and why? I would love to biomanufacturer “SynBio-Ink,” a programmable, cell-free diagnostic matrix containing lyophilized LAMP (Loop-mediated isothermal amplification) reagents, CRISPR-Cas effectors, and biosensor reporters. My motivation is to be the part in solving global health and pandemic preparedness over the next 10 years. It will be based on decentralized and autonomous bio-surveillance. I dream a future where robotic “sentinel” devices homes use a near to universal cheap microfluidic Lab-on-a-Chip (LoC). For achieving that we need to bio-manufacture a bio-ink that can be printed directly onto these chips. We can create a universally deployable diagnostic fabric. This ink would allow a single chip to perform multiplexed LAMP amplification and CRISPR-based nucleic acid detection for hundreds of pathogens simultaneously.