Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
- First, describe a biological engineering application or tool you want to develop and why. This could be inspired by an idea for your HTGAA class project and/or something for which you are already doing in your research, or something you are just curious about. Inspired by the MELiSSA project (Micro-Ecological Life Support System Alternative) from ESA, this project proposes an ecosystem composed of microorganisms and higher plants using their metabolic waste products as a substrate for the next compartment. This project is designed to study the behavior of artificial ecosystems and to develop the technologies required for future regenerative life-support systems in long-duration human space missions, such as lunar bases or missions to Mars. The system comprises five different compartments, each one colonized respectively by anoxygenic thermophilic bacteria, photoheterotrophic bacteria, nitrifying bacteria, photosynthetic bacteria, higher plants, and the human crew. I would like to conceptually integrate these microorganisms and higher plants with a plasmids-based control system, through the use of reporter genes and inducible regulatory elements. This would increase the security (allowing real-time monitoring of metabolics states, for example) and predictability of the system.
week 2 HW: DNA Read, Write and Edit
Week 02 - Lecture Questions Professor Jacobson The fidelity of DNA replication is governed by DNA polymerase and its associated repair systems. The intrinsic error rate of DNA polymerase, in the absence of proofreading, is approximately 10-4 to 10-5 per nucleotide. In eukaryotes, replicative polymerases utilize 3’ —} 5’ exonuclease activity for proofreading, which enhances fidelity to an error rate of approximately 10-7. When integrated with post-replicative mismatch repair (MMR) mechanisms, the effective error rate is further optimized to roughly 10-9 to 10-10 per nucleotide.Given that the human genome comprises approximately 3.2 x 109 base pairs, replication without these multi-layered fidelity mechanisms would result in a mutational load incompatible with cellular viability. Biological systems mitigate this risk through a hierarchy of safeguards—polymerase proofreading, mismatch repair, and various DNA damage response pathways—ensuring that the mutation rate per genome remains within a range that sustains evolutionary stability and life. A typical human protein consists of approximately 300 to 400 amino acids. Due to the degeneracy of the genetic code—where 64 codons encode 20 amino acids—the theoretical number of DNA sequences capable of encoding a single protein is exceptionally high. However, functional constraints significantly restrict this theoretical diversity. Key limiting factors include:
Week 03 - Python Script for Opentrons Artwork I was not able to write the code entirely by myself. The closest I got was generating concentric circles, wich reminded me of the Argentine “Escarapela” (with the help AI). My original idea, however, was to made an Argentine Mate which I did in https://opentrons-art.rcdonovan.com/ I also did a Cherry!