Homework
Weekly homework submissions:
Week 1 HW: Principles + Practices
1.1 A Neighborly Bio-literacy Learning System for Non-Scientists, Living in a Disaster-Prone World Full disclosure: My house burned down in the Palisades, California fire last year with 5,000 other homes and it inspired me to see neighborhood disaster as a rich opportunity for study. Rather than treating bio-literacy as isolated content mastery, this project frames bio-literacy as ethical sense-making within one’s own community and around community-based problems. Bio-literacy is understood as the ability to know ourselves and our world by asking questions, interpreting uncertainty, engaging responsibly, and building trust with biological systems. These capacities become more meaningful—and more powerful—when grounded in local concerns and lived experience. There is no shortage of biology-based shared community challenges: food security, extreme weather and fire, infectious disease, and environmental instability.
Week 02 Homework: DNA Read, Write and Edit
Part 1: Benchling & In-silico Gel Art Part 2: Gel Art - Restriction Digests and Gel Electrophoresis No lab access Part 3: DNA Design Challenge 3.1. Choose your protein.
Week 03 Homework: Lab Automation
1/Create a Python file to run on an Opentrons liquid handling robot. This is what I want to do, but I am still working on it. Happy Late Valentines Day! 2/ Find and describe a published paper that utilizes the Opentrons or an automation tool to achieve novel biological applications. Bryant Jr. et al., 2023 — “AssemblyTron: Automated DNA Assembly Using the Opentrons OT-2.” Synthetic Biology (Oxford University Press). This paper describes an automated workflow that connects DNA design software to the Opentrons OT-2 liquid-handling robot. Rather than manual pipetting, the robot executes highly standardized molecular biology workflows.The innovation is novel because it is integration of design software and robotic execution. This reduces human error and makes it easier to reproduce experiements. Although this is challening information for me, I can see how it might lower the bar for entry into syn bio experiements and and speed up design cycles. If HTGAA’s mission is to democratize access to cutting-edge bioengineering and synthetic biology education and foster global “biological literacy” by equipping diverse, distributed participants with the skills and laboratory knowledge to design, experiment, and create with living organisms, then this Opentron is a gamechanger. 3/ Write a description about what you intend to do with automation tools for your final project. You may include example pseudocode, Python scripts, 3D printed holders, a plan for how to use Ginkgo Nebula, and more. You may reference this week’s recitation slide deck for lab automation details. In my wildfire soil project, automation might add rigor to the process of detecting subtle microbial differences in post-fire environments. My samples might be: Burned soil, Unburned soil, Sunflower rhizosphere soil, Adjacent burned soil away from roots. For each sample I will need to: Create standardized slurry. Perform serial dilutions. Plate onto defined media, Record colony morphology and counts, Measure pH 4/ Three Final Project Ideas What if post-fire soil holds a molecular archive of both hope + disturbance, and we could build biological instruments that translate that archive into visible signals — making ecological memory perceptible to communities rebuilding after disaster?
A protein created by RFdiffusion3, a newly released protein design tool from Nobel laureate David Baker’s lab, interacting with DNA. (UW Institute for Protein Design / Ian C. Haydon Image) Protein Design I Objective: Learn basic concepts: amino acid structure 3D protein visualization the variety of ML-based design tools Part A. Conceptual Questions 1/ How many molecules of amino acids do you take with a piece of 500 grams of meat? 2/ Why do humans eat beef but do not become a cow, eat fish but do not become fish? 3/ Why are there only 20 natural amino acids? 4a/ Can you make other non-natural amino acids? Design some new amino acids. 4b/ Design some new amino acids. 5/ Where did amino acids come from before enzymes that make them, and before life started? Ran out of time. Will return!
Week 5 HW: Protein Design Part Two
Superoxide dismutase 1 (SOD1) is a cytosolic antioxidant enzyme that converts superoxide radicals into hydrogen peroxide and oxygen. In its native state, it forms a stable homodimer and binds copper and zinc. Mutations in SOD1 cause familial Amyotrophic Lateral Sclerosis (ALS). Among them, the A4V mutation (Alanine → Valine at residue 4) leads to one of the most aggressive forms of the disease. The mutation subtly destabilizes the N-terminus, perturbs folding energetics, and promotes toxic aggregation.
Week 6 HW: Genetic Circuits Pt 1
https://kernel.asimov.com/ hello@biopunklab.com Biopunk2026! Part 1 — Concept Questions 1. Components of Phusion High-Fidelity PCR Master Mix Phusion PCR master mix typically contains: High-fidelity DNA polymerase • enzyme that synthesizes new DNA strands • has proofreading ability, reducing mutation errors dNTPs (deoxynucleotide triphosphates) • building blocks used to create new DNA strands