Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
First, describe a biological engineering application or tool you want to develop and why. I want to develop a highly efficient bacterial chassis for rapid intracellular biosynthesis of novel PHA (polyhydroxyalkanoate) copolymers. More than 150 different hydroxyalkanoate monomers have been identified, and they can be combined into co-polymers (and potentially ter-/quad-polymers) with variable composition and sequence/microstructure, leading to an astronomical design space.
Week 2 HW: DNA Read, Write, and Edit
Part 1: Benchling & In-silico Gel Art 🦠 Create a pattern/image in the style of Paul Vanouse’s Latent Figure Protocol artworks: Part 3: DNA Design Challenge I chose poly(3-hydroxyalkanoate) polymerase / PHB synthase (PhaC) from Cupriavidus necator (UniProt accession P23608) because it is a key enzyme in microbial bioplastic production. PhaC catalyzes the polymerization of (R)-3-hydroxybutyryl-CoA monomers to form poly(3-hydroxybutyrate) (PHB), and engineered variants of PhaC are widely used to broaden substrate specificity and produce other polyhydroxyalkanoates (PHAs). I obtained the amino-acid sequence from UniProt (entry P23608) in FASTA format.
Python Script for Opentrons Artwork: https://colab.research.google.com/drive/14m54uLCM5UtsggVjU2Ucxh5hhtNELWD2#scrollTo=pczDLwsq64mk&line=4&uniqifier=1 Find and describe a published paper that utilizes the Opentrons or an automation tool to achieve novel biological applications. I found the paper ¨Opentrons for automated and high-throughput viscometry¨ very interesting. ¨The operating protocol involves measuring the amount of liquid dispensed over a set time for given dispense conditions. Data collected at different set dispense flow rates was used to train an ensemble machine learning regressor to predict Newtonian liquid viscosity¨. They demonstrated the ability of the proxy viscometer to characterize the rheological behavior of two types of power-law fluids.