Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
Governance Assignment Biological Engineering Application Immunotherapies are a promising avenue in cancer treatment as they leverage the immune system’s innate ability to recognize and target non-self structures. However, traditional immunotherapies often result in on-target off-tumor effects, particularly in solid tumors. Synthetic biology has enabled new avenues of discovery to minimize this immunotherapy-related toxicity: engineering immune cells to target tumor-associated antigens (TAAs) or engineering genetic circuits to detect cancer disease signatures (Zhu et al., 2024). For example, modifying the traditional Chimeric Antigen Receptor (CAR) T-cell immunotherapy approach with a synthetic Notch (synNotch) receptor has demonstrated the ability to suppress off-target cytotoxicity related to organ rejection (Reddy et al., 2024) and selectively target cancerous cells in the central nervous system of mice rather than elsewhere in the body (Simic et al., 2024). Yet, while synNotch-modified CAR-T therapies show promise in their ability to reduce immunotherapy-related toxicity, additional research is needed to effectively administer these bioengineered cell systems in patients beyond pre-clinical experimentation.
Week 2 HW: DNA Read, Write, and Edit
Part 1: Benchling and In-silico Gel Art Virtual restriction enzyme digest designed with DNA from the bacteriophage Kampy (isolated at W&M!) and the restriction enzymes BstXI, KpnI, and SfiI to resemble two bacteriophages. The chosen restriction enzymes were selected because they were in stock at William & Mary, had multiple cut sites in the Kampy DNA, and could be combined to make a design resembling a bacteriophage.
Python Script for Opentrons Artwork My Opentrons design is meant to resemble a frog because I use Xenopus laevis as my model organism in my honors thesis research at William & Mary. Post-Lab Questions Find and describe a published paper that utilizes the Opentrons or an automation tool to achieve novel biological applications. In Sanders et al., 2022, the researchers use an Opentron robot to optimize a bacterial whole-genome sequencing (WGS) protocol for gut microbiota samples. The Opentron was used for DNA extraction and library preparation steps, reducing the overall cost of WGS by ~$10 per genome and eliminating the need for 16S rRNA gene-based screening.