Homework
Weekly homework submissions:
Week 1 HW: Principles & Practices
Project: Physarum-on-a-Chip Environmental Sensor The tool I want to develop is a Physarum-on-a-Chip environmental sensor – a microfluidic device that confines the plasmodium of Physarum polycephalum (slime mold!!) within a controlled chemotactic gradient array, and reads out the organism’s foraging behavior as a chemical-environment signal. Why Physarum Physarum is a single multinucleated cell that solves problems no single cell “should” be able to solve. With no neurons and no central controller, it:
Week 2 HW: DNA Read, Write, & Edit
My protein this week is rhodopsin (RHO, UniProt P08100) Iti is a photon-sensing G-protein-coupled receptor in rod cells of the retina. As someone who works professionally in photography, this protein is basically my biological counterpart: a single 11-cis-retinal molecule sits in the middle of a 7-transmembrane GPCR and isomerizes to all-trans on absorbing one photon, triggering the entire phototransduction cascade. It is the sensor in the world’s oldest and most refined camera.
- Published Paper Using Opentrons for a Novel Biological Application Paper: Bryant, J. A., Kellinger, M., Longmire, C., Miller, R., & Wright, R. C. (2023). AssemblyTron: flexible automation of DNA assembly with Opentrons OT-2 lab robots. Synthetic Biology, 8(1), ysac032. https://doi.org/10.1093/synbio/ysac032 What they built AssemblyTron is an open-source Python package that turns the ~$10k Opentrons OT-2 (with a thermocycler module) into a hands-free DNA-assembly workstation. It plugs into existing assembly-design tools (j5, Cello, Benchling) and executes the resulting build plans directly on the robot, covering three of the most common synbio assembly chemistries:
Week 4 HW: Protein Design Part I
Part A — Conceptual Questions 1. How many molecules of amino acids are in 500 g of meat? Assume meat is roughly 20% protein by weight. The mass of protein is: 500 × 0.20 = 100 grams of protein. Let’s assume the average molecular weight of a protein is 100 g/mol. Therefore:
Week 5 HW: Protein Design Part II
Part 1: Generate Binders with PepMLM The original sequence of SOD1 is: MATKAVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ Mutate the 4th amino acid A to V (A4V): MATKVVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ Generate four peptides of length 12 amino acids conditioned on the mutant SOD1 sequence: index Binder Pseudo Perplexity 0 HLYYAVALELKX 13.299815648347872 1 WRSYAVVLELWK 17.97100111129112 2 WRYYPVAAAWKK 11.081842724779028 3 WHYGAVGLRHKX 13.983770011694478 Part 2: Evaluate Binders with AlphaFold3 We submitted each peptide paired with the mutant SOD1 (A4V) sequence to the AlphaFold Server as separate chains to model the protein–peptide complex. All runs used seed 2026616022 for reproducibility.
Week 6 HW: Genetic Circuits Part I
Part 1. Questions 1. Phusion High-Fidelity PCR Master Mix Components Phusion DNA Polymerase — high-fidelity polymerase with 3′→5′ proofreading exonuclease activity; ~50× lower error rate than Taq dNTPs — nucleotide building blocks (dATP, dCTP, dGTP, dTTP) incorporated during strand synthesis HF Buffer + Mg²⁺ — provides optimal pH and ionic conditions; Mg²⁺ is an essential cofactor for polymerase activity Stabilizers — maintain enzyme activity during storage and reaction setup 2. Factors That Determine Primer Annealing Temperature GC content — G·C pairs have 3 H-bonds vs. 2 for A·T, raising T_m Primer length — longer primers = higher T_m Salt/Mg²⁺ concentration — stabilizes duplexes, increases T_m Primer secondary structure — hairpins or self-dimers reduce effective T_m Polymerase used — Phusion tolerates higher T_a than Taq; use NEB Tm Calculator for Phusion Rule of thumb: T_a ≈ T_m of the lower-melting primer (for Phusion)
Week 7 HW: Genetic Circuits Part II
Part 1. Intracellular Artificial Neural Networks Q1. Advantages of IANNs over Traditional Boolean Genetic Circuits A traditional genetic circuit works like a panel of on‑off light switches. Each gene is either fully expressed or completely silent, and the circuit’s output is a strict Boolean function of those binary inputs. An IANN, by contrast, behaves more like a set of dimmer switches connected through a mixing board. Each input can take any value within a continuous range, the connections have adjustable weights, and the final output is a smooth, graded signal instead of a hard 0 or 1.
##Part 1 1.Advantages of Cell-Free Over In Vivo Expression Cell-free protein synthesis (CFPS) removes the cell as a “black box” and allows you directly control and observe every variable in real time: pH, redox potential, ionic strength, and cofactor concentration. 2.Main Components and Their Roles Component Role Cell extract Provides ribosomes, tRNA, synthetases, chaperones, and machinery DNA/mRNA template Encodes the target protein (plasmid or linear) RNA polymerase Transcribes DNA → mRNA (T7 RNAP is most common) Amino acids Raw building blocks for translation Energy system Supplies and recycles ATP/GTP to power translation Salts and buffer Maintains pH (~7.5) and ionic strength (Mg²⁺, K⁺ critical) Additives Chaperones, detergents, etc., added based on target needs 3.Energy Provision and ATP Regeneration
Week10 HW: Imaging and Measurement
What to measure: Identity, mass, purity, and post-translational modifications of the target protein; concentration of a biomarker; oligomeric state. How: Intact mass by LC-MS (QTof) → confirms overall MW and detects unexpected modifications. Peptide mapping by tryptic digest + LC-MS/MS → confirms primary sequence and identifies PTM sites. Native MS / CDMS → reveals folded state and oligomeric assembly. SDS-PAGE / Western blot → quick purity and identity check before MS. UV-Vis (A280) → concentration. Part I — Molecular Weight of Intact eGFP Q1. Theoretical MW from sequence Sequence length: 247 residues (includes LE linker + HHHHHH His-tag).
Week11 HW: BIOPRODUCTION AND CLOUD LABS
Unfortunately I was away at CHI 2026 during the contribution window, so I didn’t get to commit a pixel in time. Part B – Cell-Free Protein Synthesis B1. Role of each component E. coli Lysate BL21 (DE3) Star Lysate (with T7 RNAP): The “factory floor” – a crude cytoplasmic extract carrying ribosomes, tRNAs, aminoacyl-tRNA synthetases, translation factors, and the T7 RNA polymerase needed to transcribe T7-promoter templates. The DE3 Star background also lacks RNase E activity, so mRNAs last longer. Salts / Buffer