Homework

Weekly homework submissions:

• Week 1 HW: Principles and Practices

  First, describe a biological engineering application or tool you want to develop and why. This could be inspired by an idea for your HTGAA class project and/or something for which you are already doing in your research, or something you are just curious about. I have worked with the concept of CA before within design and 3d space generative making through creating tools for generating patterns and environments, so it was really fascinating to see it being brought up during class. So, for my idea I’d like to merge my previous digital experience with CA and synthetic biology tooling in a form of a computer aided design tool for spatial synthetic biology

• Week 2 HW: DNA Read, Write, & Edit

  Part 1: Benchling & In-silico Gel Art Enzyme Number of Cuts Number of Fragments Fragment Sizes (bp) EcoRI 5 6 21,226 / 7,421 / 5,804 / 5,643 / 4,878 / 3,530 HindIII 6 7 9,416 / 6,682 / 4,361 / 3,130 / 2,322 / 2,027 / 564 BamHI 5 6 16,841 / 7,233 / 6,770 / 6,527 / 5,626 / 5,505 KpnI 2 3 29,942 / 17,057 / 1,503 EcoRV 21 22 5,765 / 5,376 / 4,613 / 3,873 / 3,744 / 3,595 / 2,884 / 2,674 / 1,921 / 1,679 / 1,434 / 1,403 / 1,377 / 1,313 / 738 / 655 / 618 / 597 / 588 / 268 / 52 / 35 SacI 2 3 24,776 / 22,621 / 1,105 SalI 2 3 32,745 / 15,258 / 499 Restriction Enzymes Used EcoRI EcoRV HindIII KpnI BamHI SacI SalI Restriction Digest Setup Lane Water CutSmart Buffer λ DNA Enzyme(s) M (Ladder) 14 μL 2 μL 3 μL - 1 13 μL 2 μL 3 μL 1 μL EcoRI 2 13 μL 2 μL 3 μL 1 μL KpnI + 1 μL BamHI 3 14 μL 2 μL 3 μL 1 μL EcoRI + 1 μL HindIII 4 14 μL 2 μL 3 μL 1 μL EcoRV 5 13 μL 2 μL 3 μL 1 μL EcoRI + 1 μL KpnI 6 13 μL 2 μL 3 μL 1 μL SacI + 1 μL HindIII 7 13 μL 2 μL 3 μL 1 μL SacI + 1 μL SacI 8 13 μL 2 μL 3 μL 1 μL SalI + 1 μL KpnI 9 14 μL 2 μL 3 μL 1 μL SacI + 1 μL SacI 10 13 μL 2 μL 3 μL 1 μL HindIII + 1 μL SacI Total volume per tube: 20 μL

• Week 3 HW: Principles and Practices

  Post-Lab Questions Find and describe a published paper that utilizes the Opentrons or an automation tool to achieve novel biological applications. https://www.nature.com/articles/s41598-024-64938-0 This study by Norton-Baker et al. (2024) used an Opentrons OT-2 liquid-handling tool to efficiently characterise a large number of proteins. They also described a generalizable pipeline for high-throughput protein purification using small-scale expression in E. coli and an affordable liquid-handling robot. As a result, the automation significantly increased throughput, reduced manual labour, and improved consistency across samples, demonstrating how accessible robotics can accelerate biological research workflows. It also allowed to confirm the validity of previous findings.