Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
Class Assignment: Biosensors for Anxiety 1. Describe a biological engineering application or tool you want to develop and why. Currently as I am working with microbiome sequencing, I have developed an interest in the relationship between the microbiome and mental health, hence my interest in using genetically modified bacteria to create biosensors for anxiety. Consider bacteria like Lactobacillus reuteri, which are specifically engineered to identify high quantities of cortisol, the hormone that human bodies release during stressful situations. GABA (gamma-aminobutyric acid), a naturally occurring substance that aids in nervous system relaxation, would be produced by the modified bacteria in response to an increase in these cortisol levels. Not everyone reacts to traditional anxiety medications equally, and they frequently have negative side effects. So my proposed strategy presents a viable substitute—a probiotic supplement that supports mental health in real time and functions organically with the body. The simplicity of this concept—using something as ubiquitous as gut microbes to create a significant impact—is what makes it beautiful and potentially innocuous.
Week 2 HW: DNA read, write and edit
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. You might find Ronan’s website a helpful tool for quickly iterating on designs! Part 3: DNA Design Challenge 3.1. Choose your protein.
Assignment: Python Script for Opentrons Artwork 1. Generate an artistic design using the GUI at opentrons-art.rcdonovan.com. I used the GUI for converting my rising phoenix image into the dot design, I loved the tool, very helpful, easy to use and to edit and perfectionate my design. The tool supplied the coordinates to add to my code, and the result looks perfect!
Week 4 HW: Protein Design Part I
Part A. Conceptual Questions Answer any of the following questions by Shuguang Zhang: Why humans eat beef but do not become a cow, eat fish but do not become fish? Proteins are made from the same 20 amino acids, and digestion breaks them down into individual amino acids, which are then reused to build proteins humans need, not cow or fish proteins. This relates to the idea that the information (DNA → proteins), not the source of amino acids, defines the organism.