Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
Governance 1. Bioengineering Tool Phage satellites are a diverse class of mobile genetic elements that parasitize a phage. Extracellular Prophage-Inducing Particles (EPIPs), are a novel class of phage satellite discovered by the Saha Lab that induces the extremely stable prophage, HerbertWM, in Mycolicibacterium aichiense. Due to their novelty, much of their mechanisms of action are unknown, but it is hypothesized that they contain antirepressors or partial antirepressors due to annotated genes that bear resemblance to BRO domains which have been noted to have some influence over transcription (Zemskov et al., 2000). Because of the observed ability of EPIPs to induce a stable prophage, developing a lytic-lysogenic switch from their putative antirepressors would be valuable for many applications including medical and environmental applications. This switch could ensure that a temperate phage lyses bacterial pathogens in phage therapy or control the transcription of engineered constructs in the soil.
Week 2 HW: DNA Read, Write, and Edit
DNA Design Challenge Protein chosen: tape measure protein of Alyssa1, a Mycolicibacterium phage satellite called an “Extracellular Prophage-Inducing Particle” (EPIP). Tape measure proteins are rare in phage satellites, and TEM imaging has shown that EPIPs have uniquely long tails compared to the helper phage, the phage they parasitize, suggesting the tape measure protein may contribute to a unique mechanism of parasitism.
Paper Discussion Paper: AssemblyTron: flexible automation of DNA assembly with Opentrons OT-2 lab robots This paper reports using the Opentrons robot to conduct PCR, Golden Gate assembly, and Gibson assembly. It appears that the robot was able to determine specific parameters for experiments such as annealing temperature. The paper did not go into much detail about how this occurred, but after looking at some of the supplementary materials, the script likely parses .csv files that include primer and fragement sequences.