Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
- Describe a biological engineering application or tool you want to develop and why. Throughout my previous research as a new biodesigner, I have been particularly drawn to two themes: the intricate relationship between the gut microbiota and its effects on human physical and mental health, and the fascinating world of fungi and their broader implications for planetary health. I have deepened my research into psilocybin and related tryptamine alkaloids (substances that activate serotonin 5-HT receptors), which are already being investigated clinically for neuropsychiatric conditions (Xi et al., 2023), but what especially interests me is emerging evidence that some of their effects may be mediated by the gut microbiota rather than the brain alone (Caspani et al., 2024). There is still a lack of research on the precise impact that serotonergic psychedelics have on the structure and composition of the gut microbiota, even though animal studies suggest possible links (Császár-Nagy et al., 2022). A survey of wild‑type rats has shown changes in the abundance of spore‑forming gut bacteria following oral administration of serotonin, suggesting that serotonergic compounds such as psilocybin could directly or indirectly reshape microbial communities (Fung et al., 2019).
Week 2 HW: Dna-Read-Write-and-Edit
Part 1: Benchling & In-silico Gel Art I simulated the Restriction Enzyme Digestion in Benchling to create a design. I found it initially difficult to visualise patterns or images with the 7 restriction enzymes. I therefore decided to mix certain enzymes in the same wells to generate more DNA fragments and explore shapes further. Part 3: DNA Design Challenge 3.1 Which protein have you chosen and why? Using one of the tools described in the recitation (NCBI, UniProt, Google), obtain the protein sequence for the protein you chose. Name of protein: psiH (tryptamine 4-monooxygenase)
Assignment: Python Script for Opentrons Artwork 1) Generate an artistic design using the GUI at opentrons-art.rcdonovan.com. My OpenTron design is inspired by the nudibranch (sea slug) from the Mollusca phylum. Image source: Siewert, I. (2014). Nudibranch - Marine Life in Thailand. [online] Diving in Phuket Thailand. Available at: https://www.diving-thailand-phuket.com/nudibranch-marine-life-thailand/. Using the coordinates from the GUI, follow the instructions in the HTGAA26 Opentrons Colab to write your own Python script which draws your design using the Opentrons.