Homework
Weekly homework submissions:
Week 1: Principles and Practices
Synthetic Bioogy in Regenerative Medicine: Drug Delivery The convergence of biology and engineering offers innovative potential to address complex healthcare challenges. More specifically, regenerative medicine has advanced enormously through inspiration from nature. Nowadays, bioengineered materials can be adapted to mimic and integrate natural designs with intricate mechanisms found in living organisms, ecosystems, and evolutionary processes. The main goal is to develop new materials, devices, and systems that can restore and enhance tissue performance and function, leading to new therapeutic approaches. Several essential synthetic biology techniques are used toward this aim, such as genetic engineering, cellular reprogramming, cellular pathway engineering, CRISPR-Cas9, delivery systems, artificial cells and organs, stem cell engineering, biomechanics, and bioinformatics.
🤖 Opentrons Liquid-Handling Artwork 🧠 Project Overview This project transforms the Opentrons OT-2 liquid handling robot into a biological plotter. Using coordinate-based programming, the robot deposits fluorescent bacterial droplets onto an agar plate to form a structured artistic pattern.
Part A. Conceptual Questions Answer any NINE of the following questions from Shuguang Zhang: (i.e. you can select two to skip) How many molecules of amino acids do you take with a piece of 500 grams of meat? For this exercise, it is necessary to assume that 20% of the meat is protein; therefore, 500 g of meat contains 100 g of protein.
Week 5: Protein design part ii
Superoxide dismutase 1 (SOD1) is a cytosolic antioxidant enzyme that converts superoxide radicals into hydrogen peroxide and oxygen. In its native state, it forms a stable homodimer and binds copper and zinc. Mutations in SOD1 cause familial Amyotrophic Lateral Sclerosis (ALS). Among them, the A4V mutation (Alanine → Valine at residue 4) leads to one of the most aggressive forms of the disease. The mutation subtly destabilizes the N-terminus, perturbs folding energetics, and promotes toxic aggregation.
Week 6: Genetic Circuits Part I - Assembly Technologies
Molecular Biology: PCR, Cloning & Transformation 1. Phusion High-Fidelity PCR Master Mix Components Phusion Hot Start II DNA Polymerase — synthesizes new DNA strands; has 3’→5’ exonuclease (proofreading) activity to correct misincorporated bases, giving very high fidelity. dNTPs (dATP, dCTP, dGTP, dTTP) — deoxynucleotide triphosphates; the building blocks incorporated into the growing DNA strand. MgCl₂ (magnesium chloride) — essential cofactor; Mg²⁺ ions stabilize the enzyme-DNA-dNTP complex and are required for catalytic activity. Optimized reaction buffer — maintains correct pH and ionic environment for efficient polymerase activity and primer annealing. Hot-start antibody/aptamer — inhibits polymerase at room temperature to prevent non-specific amplification; releases the enzyme once the initial high-temperature denaturation step is reached. 2. Factors Determining Primer Annealing Temperature GC content — G-C pairs have 3 hydrogen bonds vs. 2 for A-T; higher GC → higher Tm → higher annealing temperature. Primer length — longer primers have higher Tm due to more base-pair contributions to stability. Self-complementarity — hairpins or primer dimers reduce effective annealing temperature. Salt/ion concentration — higher Mg²⁺ or monovalent cations stabilize the duplex, raising Tm. Additives (formamide, DMSO) — destabilize base pairing, lowering effective Tm; useful for GC-rich regions. Mismatches — imperfect complementarity (e.g., mutagenic primers) requires lower annealing temperature. 💡 Rule of thumb: set annealing temperature ~5°C below the calculated Tm of the primer pair.