Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
- First, describe a biological engineering application or tool you want to develop and why. Effective wastewater treatment is essential for clean waterways, environmental health, and safe drinking water. However, rapid urbanization and population growth have overloaded our capacity to manage aquatic waste, jeopardizing clean water access and biodiversity as pathogens, heavy metals, and algal bloom-inducing nutrients get flushed into waterways. Additionally, current water treatment strategies do not effectively remove a number of harmful compounds, including some drugs and dyes (Renganathan et al., 2025).
Week 2 HW: Read, Write, Edit DNA
DNA Design Challenge 3.1. Choose your protein. I’ve chosen PprA, a protein that contributes to radiation resistence in the extremophile bacterium Deinococcus radiodurans, which can survive exposure to space conditions, via DNA repair mechanisms. PprA and other proteins involved in D. radiodurns’s space response could have space biotechnology applications–e.g., engineering space-tolerant food sources and terraforming Martian soil for agriculture. (Note that other research groups have successfully expressed PprA in E. coli before. I’m interested in eventually engineering PprA into a different chassis with direct relevance to space travel or exploring alternative proteins that enhance space (radiation, microgravity, vacuum, etc.) tolerance.)
Python Script and Design Post-Lab Questions 1) Find and describe a published paper that utilizes the Opentrons or an automation tool to achieve novel biological applications. This paper https://pmc.ncbi.nlm.nih.gov/articles/PMC7886139/ (Lazaro-Perona et al., 2021) tests the efficacy of RNA extraction and PCR-based bulk Covid-19 testing procedures, including an Opentron method. They did not find a significant difference in the ability of the Opentron method vs. other protocols to detect Covid, however they point out that the Opentron method is cost-effective and less labor-intensive than its non-automated counterparts.