Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
Step 1. First, describe a biological engineering application or tool you want to develop and why. I am passionate about reading, as well as Biology, so I came up with an idea that could mix both and be sustainable and enjoyable for us bookworms. My idea that I would like to put into practice is a reading light powered by bioluminescent algae, combined with microbial fuel cells for supplemental energy. Instead of relying solely on electricity, the lamp is partially powered by living systems, creating a sustainable, educational, and interactive device.
Week 2 HW: DNA read, write and edit
Part 1: Benchling & In-silico Gel Art Here is a simulation with the Restriction Enzyme Digestion on Benchling.com: Part 3: DNA Design Challenge 3.1. Choose your protein. I chose the Green Fluorescent Protein (GFP) because it naturally glows green when exposed to UV light. This revolutionized cell biology by allowing scientists to see proteins inside living cells and it won the 2008 Nobel Prize in Chemistry. This protein has been isolated from the jellyfish Aequorea victoria and forms a beta-barrel structure (like a protective can). Inside the barrel is the chromophore — the light-producing part.
Opentrons Artwork Post-Lab Questions I found a published paper which describes how researchers leveraged the Opentrons OT-2 automated liquid handler to develop an automated, high-throughput proxy viscometer. The robot was programmed to dispense liquids of various viscosities and collect data for machine-learning models to predict viscosity, demonstrating a practical application of the OT-2 in fluid characterization workflows — requiring minimal human intervention while significantly increasing throughput. If I would go for my first project idea, which is the Bacterial Microplastic Sensor, there would be the following automation tools that I could apply: Automated Fluorescence Detection System The goal is to automatically quantify GFP output in response to PET degradation products. I can automate the timed fluorescence measurement (every 10 min), background subtraction, data logging (CSV), real-time plotting and threshold alert. Automated Incubation + Sampling There can be a shaking plattform automation, with 3D tube rack and/or temperature control with heat pad, temperature sensor and automated regulation. A pseudocode example can be:
Week 4 HW: Protein Design Part I
Part A. Conceptual Questions Why do humans eat beef but do not become a cow, eat fish but do not become fish? When you eat beef or fish, your body does not keep the meat intact and turn it into “cow tissue” or “fish tissue.” Instead, your digestive system breaks everything down into basic molecules, like proteins into amino acids, fats into fatty acids + glycerol, carbohydrates into simple sugars and DNA into nucleotides.