Homework
Weekly homework submissions:
- Describe an application Identify a biological engineering tool or application you wish to develop and explain your motivation. I would like to develop a way to make plants grow 100x faster. I find this a very interesting and ambitious question. Perhaps you reverse-engineer the genome, morphological development and constraints, proteins/enzymes/catalysts for growth. Perhaps you design a separate organism (two bacterium?) which produces biomass - a combination of a carbon sequester and a cellulose printer. Perhaps you attempt to design a minimal artificial cell, like a Xenobot / JCVI minimal cells - using new AI design software, you create a minimal genome/DNA, design your own morphological topology through simulation, which is compiled down to gene regulatory networks (GRN’s), transcription factors/thresholds, and DNA.
Week 1 HW.2: Lecture prep for W2
Answer prep questions from three faculty members: Homework Questions from Professor Jacobson: Nature’s machinery for copying DNA is called polymerase. What is the error rate of polymerase? How does this compare to the length of the human genome. How does biology deal with that discrepancy? Error rate refers to errors per nucleotide added per replication. An error could be a misincorporation (wrong base expressed for a pair), for example.
Week 1 HW.3: Setup your website
CHECK IT OUT https://pages.htgaa.org/2026a/liam-edwards-playne/
Week 2 HW.1: Benchling & In-silico Gel Art
Make a free account at benchling.com, Import the Lambda DNA. Simulate Restriction Enzyme Digestion with the following Enzymes: EcoRI HindIII BamHI KpnI EcoRV SacI SalI Create a pattern/image in the style of Paul Vanouse’s Latent Figure Protocol artworks. Benchling screenshots. Experimental design for Gel art.
Week 2 HW.2: Gel Art - Restriction Digests and Gel Electrophoresis
In the wet-lab perform the lab experiment you designed in Part 1 and outlined in this week’s lab protocol “Gel Art: Restriction Digests and Gel Electrophoresis”. N/A - no access to BioClub Tokyo Lab.
Week 2 HW.3: DNA Design Challenge
3.1. Choose your protein. In recitation, we discussed that you will pick a protein for your homework that you find interesting. Which protein have you chosen and why? Using one of the tools described in recitation (NCBI, UniProt, google), obtain the protein sequence for the protein you chose. Miraculin - https://rest.uniprot.org/uniprotkb/P13087.fasta https://rest.uniprot.org/uniprotkb/P13087.txt >sp|P13087|MIRA_SYNDU Miraculin OS=Synsepalum dulcificum OX=3743 PE=1 SV=3 MKELTMLSLSFFFVSALLAAAANPLLSAADSAPNPVLDIDGEKLRTGTNYYIVPVLRDHG GGLTVSATTPNGTFVCPPRVVQTRKEVDHDRPLAFFPENPKEDVVRVSTDLNINFSAFMP CRWTSSTVWRLDKYDESTGQYFVTIGGVKGNPGPETISSWFKIEEFCGSGFYKLVFCPTV CGSCKVKCGDVGIYIDQKGRRRLALSDKPFAFEFNKTVYF 3.2. Reverse Translate: Protein (amino acid) sequence to DNA (nucleotide) sequence. Using https://www.bioinformatics.org/sms2/rev_trans.html:
Week 2 HW.4: Twist DNA Synthesis Order
Prepare a Twist DNA Synthesis Order This is a practice exercise, not necessarily your real Twist order! 4.1. Create a Twist account and a Benchling account click through for Twist signup click through for Twist signup click through for Benchling signup click through for Benchling signup 4.2. Build Your DNA Insert Sequence For example, let’s make a sequence that will make E. coli glow fluorescent green under UV light by constitutively (always) expressing sfGFP (a green fluorescent protein):
Week 2 HW.5: DNA Read/Write/Edit
DNA Read (i) What DNA would you want to sequence (e.g., read) and why? This could be DNA related to human health (e.g. genes related to disease research), environmental monitoring (e.g., sewage waste water, biodiversity analysis), and beyond (e.g. DNA data storage, biobank). No idea. Possibly my basil plant.
Week 3 HW.1: Python Script for Opentrons Artwork
Review recitation materials and lab documentation. Design artwork using the GUI at opentrons-art.rcdonovan.com. Write a Python script using coordinates from the GUI via the “HTGAA26 Opentrons Colab”. Sign up for a robot time slot and run the script on the Opentrons robot. Submit Python file via provided form. Artwork Design Python Script
Week 3 HW.2: Post-Lab Reflection
2.1. Find and describe a published paper utilizing Opentrons or similar liquid handling automation tools. Paper: Description: 2.2. Describe your intended automation use for your final project, including pseudocode, scripts, or implementation plans.
Week 3 HW.3: Final Project Ideas
Submit 1–3 slides with three individual project concept ideas. Idea 1 Idea 2 Idea 3