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 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 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.