Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
Week 1: Project Concept — The “Copper-Sentinel” Initiative My Vision: Why This Matters Living in the Copperbelt, we see the good and bad aspects of mining every day—it drives our economy, but it also leaves a heavy footprint on our groundwater. I want to build Copper-Sentinel, a low-cost, decentralized tool for real-time water monitoring.
Week 2 HW: DNA READ WRITE AND EDIT
Part 1: Benchling & In-silico Gel Art In-Silico Gel Art: Latent Figure Protocol Project Overview For this week’s assignment, I used Benchling to simulate restriction enzyme digests on the Lambda Phage genome (NC_001416). My goal was to move beyond simple data analysis and create “Gel Art” in the style of Paul Vanouse’s Latent Figure Protocol.
Week 3: Lab Automation & Opentrons Art Introduction This week’s focus is on the intersection of biology, robotics, and creative coding. As part of the HTGAA 2026* cohort based in Zambia, I am exploring how liquid-handling automation (specifically the Opentrons OT-2) can streamline laboratory workflows. Beyond the technical utility, this assignment challenged us to use the robot as a canvas, translating digital coordinates into physical biological art.
Homework: Protein Design I Part A. Conceptual Questions 1.# Assignment: Proteins and Amino Acids 1. Amino Acids in 500g of Meat To calculate the total molecules, we first look at the protein density. Meat is roughly 20% protein by mass.
Week 5 HW: Protein Design Part II
Week 5: Protein Design Part II SOD1 Binder Peptide Design and Evaluation Part 1: Generate Binders with PepMLM The human SOD1 sequence was retrieved from UniProt (P00441). The A4V mutation (Alanine to Valine at residue 4) was introduced to the wild-type sequence to create the target for peptide generation. Using the PepMLM-650M model, four 12-amino acid peptides were generated, and the known binder FLYRWLPSRRGG was added as a control.
Week 6 HW: Genetic Circuits Part 1
Assignment: DNA Assembly 1. What are some components in the Phusion High-Fidelity PCR Master Mix and what is their purpose? Phusion DNA Polymerase: This is the “engine.” It’s a highly thermostable enzyme that synthesizes new DNA strands. It’s “High-Fidelity” because it has $3’ \rightarrow 5’$ exonuclease activity (proofreading), making significantly fewer mistakes than standard Taq. dNTPs (Deoxynucleotide Triphosphates): These are the molecular building blocks (A, T, C, and G) used by the polymerase to construct the new DNA strand. Buffer (containing $Mg^{2+}$): Maintains the optimal pH for enzymatic activity and provides essential divalent cations. Magnesium ions act as a cofactor for the polymerase, helping it catalyze the phosphodiester bond. Stabilizers: Often includes detergents or proprietary chemicals to prevent the enzyme from denaturing or sticking to the tube walls during the high-heat cycles. 2. What are some factors that determine primer annealing temperature during PCR? Primer Length: Longer primers generally require higher temperatures to remain specific. GC Content: G-C pairs have three hydrogen bonds compared to the two in A-T pairs. Therefore, primers with higher GC content have higher melting temperatures ($T_m$). Salt Concentration: The concentration of monovalent cations (like $K^+$) in the buffer affects the stability of the DNA duplex. Primer Concentration: Higher concentrations can slightly shift the kinetics of annealing. Mismatches: If the primer isn’t a 100% match to the template, the $T_m$ will decrease. Note: The annealing temperature ($T_a$) is usually chosen to be $3-5^\circ\text{C}$ below the $T_m$ of the primers to balance specificity and yield.
Week 7 HW: GENETIC circuits II
Week 7: IANNs & Fungal Materials Part 1: Intracellular Artificial Neural Networks (IANNs) Question 1 What advantages do IANNs have over traditional genetic circuits, whose input/output behaviors are Boolean functions?
HTGAA Homework — Cell-Free Systems Part A: General & Lecturer-Specific Questions General Question 1 Explain the main advantages of cell-free protein synthesis over traditional in vivo methods, specifically in terms of flexibility and control over experimental variables. Name at least two cases where cell-free expression is more beneficial than cell production.
Week 10 HW: Advanced Imaging & Measurement Technology
Laboratory Report: Advanced Mass Spectrometric Analysis of eGFP Course: How to Grow Almost Anything (HTGAA) — Week 10 Final Project: Measurement Plan Zambia Mineral-Waste Bioremediation Predictor My final project uses a genetically engineered Bacillus subtilis strain expressing a metallothionein (MT) protein (accession WP_070466881.1) to remove copper and other heavy metals from mine-contaminated water in Zambia’s Copperbelt Province. The system also includes a copper-sensing genetic circuit (CopA-CueR), a MazF/MazE kill switch for biocontainment, and a dual-layer hydrogel encapsulation system called ZAMGEL.
Week 11 HW: Bioproduction And Cloud Labs
HTGAA Week 11 Homework — Bioproduction & Cloud Labs Part A: The 1,536 Pixel Artwork Canvas What did you contribute to the community bioart project? I contributed by correcting some of the pixel colours that appeared wrongly placed in the region slightly above and around the word “love” on the canvas, helping restore the intended colour arrangement in that section of the artwork.