Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
Project Propalsal: A small, low-cost desktop platform that combines short DNA synthesis with cell-free expression. Users (students, community labs, small clinics) design short DNA sequences through a web interface, send them to a benchtop “DNA printer,” and immediately test them in a cell-free system. This pushes “personal fabrication” into biology and could support education and grassroots innovation, but raises serious questions about biosecurity, safety, and equity when DNA writing becomes cheap and widely accessible.
Week 2 HW: DNA Read, Write, & Edit
3.1 Choose your protein I chose Green Fluorescent Protein (GFP) from the jellyfish Aequorea victoria. Reasons: -Classic reporter protein in molecular biology and imaging -Small, monomeric, and widely used as a fusion tag sp|P42212|GFP_AEQVI Green fluorescent protein OS=Aequorea victoria OX=6100 GN=GFP PE=1 SV=1 MSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTL VTTFSYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLV NRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLAD HYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITHGMDELYK 3.2 Reverse translate (protein → DNA) reverse translation of sp|P42212|GFP_AEQVI Green fluorescent protein OS=Aequorea victoria OX=6100 GN=GFP PE=1 SV=1 to a 714 base sequence of most likely codons. atgagcaaaggcgaagaactgtttaccggcgtggtgccgattctggtggaactggatggc gatgtgaacggccataaatttagcgtgagcggcgaaggcgaaggcgatgcgacctatggc aaactgaccctgaaatttatttgcaccaccggcaaactgccggtgccgtggccgaccctg gtgaccacctttagctatggcgtgcagtgctttagccgctatccggatcatatgaaacag catgatttttttaaaagcgcgatgccggaaggctatgtgcaggaacgcaccatttttttt aaagatgatggcaactataaaacccgcgcggaagtgaaatttgaaggcgataccctggtg aaccgcattgaactgaaaggcattgattttaaagaagatggcaacattctgggccataaa ctggaatataactataacagccataacgtgtatattatggcggataaacagaaaaacggc attaaagtgaactttaaaattcgccataacattgaagatggcagcgtgcagctggcggat cattatcagcagaacaccccgattggcgatggcccggtgctgctgccggataaccattat ctgagcacccagagcgcgctgagcaaagatccgaacgaaaaacgcgatcatatggtgctg ctggaatttgtgaccgcggcgggcattacccatggcatggatgaactgtataaa
- Reference paper: HYDRA – hydrogels by robotic automation Citation Torchia, E. et al. Fabrication of cell culture hydrogels by robotic liquid handling automation for high-throughput drug testing. Communications Engineering, 4, 222 (2025). What they did This paper introduces HYDRA (HYDrogels by Robotic liquid-handling Automation), a method to fabricate thin, planar hydrogel films directly inside standard 96- and 384-well plates using liquid-handling robots.