Homework

Weekly homework submissions:

• Week 1: Principles & Practices

  Week 1 HW: Principles and Practices 🌊 Biological Engineering Project Genetically waterproof mycelium surfboards from olive waste. Prior research: Polyester/pine resin coatings (6-12 months) HTGAA innovation: CRISPR hydrophobins → permanent waterproofing 📊 Governance Table Criteria Option 1 Option 2 Option 3 Biosecurity ✓ ✓ ✓ Lab Safety ✓ ✓ ✓ Environment ✓ ✓ ✓ 🎯 My Actions Beach strain registry (Environment) Skin-safe certification (Biosecurity) Open-source designs (Equity) Lab Notes: Pipetting slow → no air bubbles ✅

• Week 3: Lab Automation

  🌊 Week 3: Surf Wave Bio-Art (OT-2) 🎨 Python Script Opentrons-Art Gallery: Surf Wave Design Download Script 🧪 Protocol Setup Slot 1: P20 Single-Channel Tip Rack (20µL) Slot 3: Corning 6-Well Source Plate (16.8mL)

• 🧬 Week 4: Protein Design I

  Part A (9 Questions) 1.How many molecules of amino acids do you take with a piece of 500 grams of meat? (on average an amino acid is ~100 Daltons) 500g meat = ~5,000,000 amino acids (100 Da avg) Why are there only 20 natural amino acids? 20 natural = genetic code + tRNA efficiency If you make an α-helix using D-amino acids, what handedness (right or left) would you expect? D-amino α-helix = left-handed

• 🧬 Week 5: SOD1 A4V Peptide Binders

  HTGAA Week 5 - SOD1 A4V Peptide Binders Part A1: PepMLM Generation SOD1 A4V sequence: MATKAVCVLK… (154 aa) 4 Generated peptides (12-mers): RDGEGELLENRR (2.34) ✅ BEST WKLRHYSPQVMK (2.87) FQVTSGDKPLRI (3.12) HESLWRQPGKNT (3.45) Known: FLYRWLPSRRGG (2.98) Part A2: AlphaFold3 RDGEGELLENRR: ipTM=0.78, binds N-terminus near A4V ✅

• 🧬 Week 6: Genetic Circuits Part I: Assembly Technologies

  Week 6 HW: Gibson Assembly Questions 1. Phusion High-Fidelity PCR Master Mix Components [web:1266] Component Purpose Phusion DNA Polymerase High fidelity (52x Taq), fast extension dNTPs DNA building blocks MgCl₂ Polymerase cofactor (NH₄)₂SO₄ Stabilizes polymerase Betaine GC-rich templates DMSO Reduces secondary structure 2. Primer Annealing Temperature Factors [web:1267] Primer Tm (5°C below lowest Tm) Primer length (>20nt: +3°C above Tm) GC content (higher GC = higher Tm) Salt concentration (50mM default) Primer concentration (200-1000nM) 3. PCR vs Restriction Digest [web:1268] Feature PCR Restriction Digest Linear fragments Primers define ends Restriction sites Protocol 30 cycles (denature/anneal/extend) 1-2h 37°C digestion Advantages Scarless, any sequence Fast, cheap Gibson use Overlap primers (20-40bp) Compatible overhangs 4. Gibson Cloning Requirements [web:1269] 20-40bp overlaps between fragments No restriction sites in overlap regions High quality PCR (Phusion fidelity) Linearized vector (PCR or digest) Exonuclease chews back → Anneal → Ligate

• 🧬 Week 7: Neuromorphic Circuits & Fungal Materials

  Part 1: Intracellular Artificial Neural Networks (IANNs) 1. Advantages of IANNs over Boolean Circuits Feature Boolean Circuits IANNs Logic ON/OFF only Analog weights Complexity n inputs = 2ⁿ truth table Continuous functions Learning Fixed Trainable weights Example AND/OR gates Pattern recognition Key advantage: IANNs can learn and process continuous signals, not just digital logic.

• Week 02 - DNA Read, Write & Edit

  Week 02 Homework: DNA Read, Write & Edit Global Listener - Anastasia Ntavou Athens, Greece Project Context: Mycelium Surfboard (Ganoderma lucidum engineering) Part 0: Gel Electrophoresis Basics Watched recitation video. Gel electrophoresis separates DNA fragments by size using electric field - smaller fragments move faster through agarose gel. Visualized Lambda DNA digest patterns.