Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
Part I 1. First, describe a biological engineering application or tool you want to develop and why. I am interested in the development of engineered bee gut bacteria or similar that help bees resist viral infections, pesticide stress but especially harmful varroa mites. The presence of varroa mites in bee colonies place an important pressure on bee health since they attack and feed on them in a parasitism relationship. 1 Instead of genetically modifying bees themselves, I aim to modify their symbiotic bacteria to strengthen colony resilience while minimizing ecological risks. Bees are increasingly threatened by habitat loss, unsustainable agricultural practices, climate change and pollution. Their decline jeopardizes food production, increases costs and exacerbates food insecurity, particularly for rural communities. I am convinced that supporting pollinators will get more and more critical for global food systems and biodiversity and this approach could offer a scalable and ecologically sensitive alternative to chemical treatments currently used in agriculture. Even if it needs human intervention into nature to keep our ecosystem in balance, I think supporting these small often unnoticed pollinators could make a real difference.
Week 2 HW: DNA read/write/edit
Part I: Benchling & In-silico Gel Art Create a pattern/image in the style of Paul Vanouse’s Latent Figure Protocol artworks. Part III: DNA Design Challenge 1. Choose your protein. Since my project proposal from last week focuses on honeybee health, I searched for relevant proteins in Apis mellifera. During this process, I identified three candidates that seemed particularly interesting: Defensin-1, Hymenoptaecin and Vitellogenin. Working with Twist Bioscience’s codon optimization tool, I learned that the tool only accepts sequences within a specific length range — proteins that are too short or too long cannot be optimized. After several iterations, vitellogenin was the only protein for which I could successfully perform codon optimization. Vg, a phospholipoglycoprotein synthesized and stored in the honey bee fat body, is an ancient reproduction-associated protein that provides nutrients to eggs in most oviparous animals. Honey bee queens, who produce hundreds of eggs each day, have high levels of Vg gene expression. It is involved in nutrient storage, immune regulation and longevity in honeybees. Its expression is closely linked to colony health and higher vitellogenin levels are associated with improved immune responses and tolerance to Varroa destructor infestation. 1
Part I: Python Script for Opentrons Artwork Your task this week is to Create a Python file to run on an Opentrons liquid handling robot. Firstly, I used Ronan’s Automation Art Interface to translate my logo into a pixelated biological artwork. The software converted the image into a set of coordinate outputs, where each tuple (x, y) represents the precise millimeter offset from the calibrated center of the agar plate. Each of these coordinate pairs defines the placement of a single 1 µL droplet, allowing the robot to reconstruct the digital logo physically on the plate.