Homework

Weekly homework submissions:

  1. First, describe a biological engineering application or tool you want to develop and why. I want to develop a biological engineering system for smarter nutrient liberation in agricultural soils, especially for sugarcane. The current nutrient management system depends heavily on chemical fertilizers that release nutrients in poorly timed pulses, leading to massive nutrient losses, soil degradation, and environmental damage. I do not want to sugarcoat it: the situation is bad. I am Brazilian, which also means I come from the country that exports the most sugar in the world, largely through intensive sugarcane monoculture. My goal is to explore how engineered soil microorganisms could sense plant-derived signals and release nutrients only when they are biologically needed, turning the soil from a passive substrate into an active, responsive system.

  • Week 2 HW: DNA r/w/e

    Part 1: Benchling & In-silico Gel Art: 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. It’s a smiley face!! :) Part 3: DNA Design Challenge: 3.1 Chose your protein Alkaline phosphatase. I chose this protein because it plays because it is important for nutrient sensing, as it is naturally activated under conditions of phosphate limitation. In Escherichia coli, alkaline phosphatase (PhoA) hydrolyzes organic phosphate compounds to release inorganic phosphate, directly linking environmental signals to nutrient availability. Additionally, it is a well-characterized enzyme with a resolved structure and extensively documented sequence information, making it an ideal model protein for computational and experimental analysis.

  • Week 3 HW: Lab Automation

    Part 1: Python Script for Opentrons Artwork I used the amazing Donovan’s tool to create this, then used the coordinates… It’s a homage to my cat Nico. He is a crazy cute orange cat. Part 2: Post-Lab Questions Question 1 I chose this paper: Automation of protein crystallization scaleup via Opentrons-2 liquid handling by DeRoo et al. I’m really into structural biology, and protein crystallization is a critical step in it, because it enables structure determination via X-ray crystallography. However, traditional crystallization trials are highly manual, repetitive, and sensitive to small variations in liquid handling. This paper demonstrates how the Opentrons-2 liquid handling robot can be used to automate protein crystallization experiments, specifically sitting-drop crystallization in 24-well plates.