Homework

Weekly homework submissions:

• Week 1 HW: Principles and Practices

  HW 1 First, describe a biological engineering application or tool you want to develop and why. This could be inspired by an idea for your HTGAA class project and/or something for which you are already doing in your research, or something you are just curious about. A biological engineering application I am interested in developing is biological haptic actuators. I envision a future where one can fabricate haptic systems driven by living cells to mimic touch sensations. Through some external stimulus, this device could output vibrations to mimic touch. The scenario I am presenting replaces electromechanical systems with biologically powered interfaces.

• Week 2 HW: DNA Read, Write, & Edit

  Part 1: Benchling & In-Silico Gel Art Using Benchling, I imported the Lambda DNA sequence and simulated restriction enzyme digestions with EcoRI, HindIII, BamHI, KpnI, EcoRV, SacI, and SalI. The goal was to design a gel art pattern inspired by Paul Vanouse’s Latent Figure Protocol. The design depicts a figure in a rocky victory pose with a crying face, using 5 lanes of selected enzyme combinations to form the image.

• Week 3 HW: Opentrons & Lab Automation

  Assignment 1: Python Script for Opentrons Artwork I designed an Indonesian cloud pattern called Megamendung using the Opentrons pipetting robot. The pattern uses two colors — red (mRFP1) and green (Azurite) — arranged as interlocking arcs to replicate the traditional Javanese batik motif. Simulated output of the Python script: Python script:

• Week 4 — Protein Design Part I

  Part 1: Protein Selection 1.1 Protein Choice I selected Titin (PDB: 1G1C) because it is a structural protein and acts as the “spring” in human muscle — it is the largest known protein in the human body and is responsible for the passive elasticity of muscle fibers.

• Week 5 — Protein Design Part II

  Part A: SOD1 Binder Peptide Design Superoxide dismutase 1 (SOD1) is a cytosolic antioxidant enzyme that converts superoxide radicals into hydrogen peroxide and oxygen. Mutations in SOD1 cause familial ALS — among them, the A4V mutation (Alanine → Valine at residue 4 of the mature protein) is one of the most aggressive, destabilizing the N-terminus and promoting toxic aggregation.

• Week 6 — PCR, Gibson Assembly & Genetic Circuits

  Part A: Pre-Lab Protocol Questions 1. Phusion High-Fidelity PCR Master Mix According to the NEB product page, the Phusion master mix is built around two key features of the Phusion polymerase itself: A Pyrococcus-like polymerase core with a 3’→5’ proofreading exonuclease — catches and corrects misincorporated bases in real time, giving ~50x lower error rate than Taq. An Sso7d processivity domain fused to the polymerase — a DNA-binding clamp that keeps the enzyme on the template, increasing speed and fidelity together. The master mix also includes dNTPs, MgCl₂ (essential cofactor for polymerase activity), and a reaction buffer optimized for Phusion.

• Week 7 — IANNs, Fungal Materials & DNA Design

  Part 1: Intracellular Artificial Neural Networks (IANNs) 1. Advantages of IANNs over Boolean Genetic Circuits Traditional genetic circuits implement Boolean logic — AND, OR, NOT gates — where every output is binary: a gene is either on or off. IANNs offer three key advantages over this:

• Week 9 — Cell-Free Protein Synthesis

  General Homework Questions 1. Advantages of Cell-Free Protein Synthesis Cell-free protein synthesis offers several advantages over in vivo expression: Speed — no transformation, culture growth, or induction cycle. Protein can be expressed in hours rather than days or weeks. Open system / debuggability — with no cell wall in the way, you can directly add, remove, or adjust components mid-reaction. Troubleshooting is hands-on: swap the energy system, add chaperones, tweak Mg²⁺ — all in real time. Biosafety — no live GMOs means no antibiotic resistance cassettes spreading in the environment and a lower containment burden overall. Toxic proteins — proteins that would kill a host cell can be expressed freely in lysate. Non-natural amino acids — easier to incorporate than in living cells where the genetic code is fixed. Two use cases where cell-free is preferred:

• Week 10 — Mass Spectrometry & Final Project Measurements

  Final Project: Measurements Plan What to Measure The chimeric casein project has three distinct questions that each need a different measurement approach: Stage 1 — Did the protein express? After inducing E. coli with IPTG and lysing the cells, I need to check whether the chimeric protein actually appeared. The primary tool for this is SDS-PAGE (gel electrophoresis for proteins) — the same ladder-based approach used for DNA, but with SDS added to unfold proteins and give them uniform charge so separation is purely by size. Running the pre- and post-induction lysate side by side, I’d look for a new band appearing at ~50 kDa (the expected molecular weight of the chimera). A Western blot using an anti-His antibody would then confirm the band is specifically my His-tagged chimera and not a coincidental band from the host cell.

• Week 11 — Cloud Labs & Cell-Free Protein Optimization

  Part A: Global Pixel Artwork In progress. My contribution: I added a single red pixel late in the project to correct a gap in the pattern. A small fix, but satisfying to slot into place.