Homework
Weekly homework submissions:
Week 1 HW: Principles & Practices
🦠Brighter Autonomous Bioluminescence🦠 I would love to improve the intensity of the glow that is emitted from autonomous bioluminescent organisms whether natural or synthetic. There are several different organisms that produce bioluminescence through various forms of luciferases (the enzyme that catalyzes the light emitting reaction) and luciferins (the substrate). However, most of them require the addition of the substrate to the growing medium to induce bioluminescence, typically coelenterazine or D-Luciferin. This to me just does not seem like the most convenient way to do this, so I am more interested in autonomous bioluminescent systems, such as Lux (bacterial luciferase) and Luz (fungal luciferase). These systems are the only two bioluminescent systems that have been fully elucidated. This means that they are fully genetically encoded, cells express luciferase and the enzymes necessary for substrate synthesis. This enables continuous supply of substrate without having to worry about adding the substrate to the growing medium or tissues to produce a glow.
Week 2 HW: DNA Read, Write, & Edit
Benchling & In-silico Gel Art Lambda DNA Restriction Digest Gel Art (Supposed to say “Hi”) DNA Design Challenge Protein: Luciferase 💡
Lab Automation Article of Interest: Deep reinforcement learning for the control of microbial co-cultures in bioreactors This study uses an automation tool in the form of AI-based process control, deep reinforcement learning. Instead of manually tuning bioreactor conditions, the authors train an algorithm to make control decisions that regulate nutrient inputs and maintain stable microbial populations in co-culture. The novel biological application is dynamic control of multi-species microbial communities, which is a major challenge in synthetic biology and biomanufacturing because species can outcompete each other or become unstable over time. The paper shows that reinforcement learning can effectively stabilize co-cultures and optimize bioprocess performance in silico, demonstrating a promising path toward autonomous bioreactor operation. This is significant because reliable co-culture control could improve production efficiency and enable more complex engineered biological systems.
Week 4 HW: Protein Design Part I
- Why are there only 20 natural amino acids? There aren’t only 20 amino acids. There are just 20 that biology standardized early on in evolution. Proteins are built using translation. Once that system had evolved changing it was difficult because every protein in every organism depended on it. That creates evolutionary lock-in often referred to as a “frozen standard.” The current amino acids were selected due to their component atoms, functional groups, biosynthetic cost, use in a protein core or on the surface, solubility and stability. There are reasons for the selection of every amino acid. 2. Where did amino acids come from before enzymes that make them, and before life started?