Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
source: wikimedia commons Genetically Engineered Diatoms to Bind with Building Rubble/Waste Building materials like cement and brick are difficult to reuse and natural weathering or active demolition leaves behind tons of waste material that remains under-recycled. In a previous project my team from graduate school developed a porous, bio receptive glass using glass waste and I would like to expand upon that research by bioengineering diatoms into a silica scaffold of cement and glass rubble/frits to fuse these waste materials into a new architectural material. Diatoms are an exciting prospect for architecture for their silica frustules, inherent translucency, and their lacy pore structure. I am curious to see if there would be a way to pattern their silica deposits for enhanced carbon sink and particle processing in urban spaces. It would also be beautiful to see the formation of silica deposits depending on sun patterns on site, filling in the rubble scaffold where there is more direct light. It would also be interesting to potentially engineer the directional strength of a diatom-rubble piece and the lace pattern, playing with the idea of directional bias in architecture more theoretically but also for building methods.
Week 2: DNA Read, Write, and Edit
Part 1: Benchling Gel Art Part 3: DNA Design Challenge When looking into proteins to explore further, I chose to focus on proteins related to the structure of diatom silica walls. These proteins would be exciting to understand to get a better picture of how diatoms would form the lacy micropatterns for the rubble-diatom material proposal for the final project. While there are a few different proteins key to the biosilica formation, and silaffins drive the lacy patterns and micropore structure.
Part 1: Opentrons Art When creating this GUI art I created an image of cherries with a checkered background to see how common features in traditional drawing would translate to bacterial image creation including shading, regular patterning, thinner and thicker lines, as well as curved and straight forms. I downloaded the python script for the PCR plate system from this simulator. created through Ronan’s Opentrons plate art simulator
Professor Jacobson: The error rate for polymerase is 1:10^6. Compared to the length of the human genome of around 3.2Gbp (slide 10), the error rate is minute, occurring perhaps once in one genome. Biology deals with this discrepancy by proofreading the action before it is coded into the DNA. There are 20 AA and 61 codons that specify amino acids (NHGRI), leading to different ways to code for an average human protein. Some reasons that all of these different codes don’t work for the protein of interest could be due to the physical structure of the protein, and the efficiency of each pathway. (not totally sure of this answer) Dr.Leproust