Homework
Weekly homework submissions:
Week 1: 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
Benchling Gel Art 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.
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.
Conceptual Questions Why do humans eat beef but do not become a cow, eat fish but do not become fish? As we eat other materials, the proteins and molecules are broken down through our digestive system, leaving us with building blocks to support our cell replication processes. Why are there only 20 natural amino acids? These 20 amino acids were created as life was forming, and after the ‘frozen accident’, the proteins that developed at this time seem to have standardized these 20 amino acids. There were more and are more amino acids, however this connection between protein and AA during early evolution created this set of 20.
hello
DNA Assembly What are some components in the Phusion High-Fidelity PCR Master Mix and what is their purpose? This Master Mix is used to increase the speed and yield of the PCR product, with accurate DNA sequences maintained for DNA replication for testing. The HF buffer variant contains DNA polymerase, deoxynucleotides, buffer, and magnesium dichloride. source: https://www.neb.com/en-us/products/m0531-phusion-high-fidelity-pcr-master-mix-with-hf-buffer?srsltid=AfmBOoq3xHVgYXqvCn6vETXyCMTKGo4MNvB1Zs6M25yaSdNrW9j4dHWK
Intracellular Artificial Neural Networks What advantages do IANNs have over traditional genetic circuits, whose input/output behaviors are Boolean functions? IANNs allow for less prescriptive circuit method, whereas traditional genetic circuits need to be specified at each step, making it a target specific circuit by finding signalling patterns across a vast dataset. Traditional genetic circuits are limited to simpler action/reaction function simulations to create an mRNA therapy.
General Homework Questions Explain the main advantages of cell-free protein synthesis over traditional in vivo methods, specifically in terms of flexibility and control over experimental variables. Name at least two cases where cell-free expression is more beneficial than cell production. Because cell-free methods exist without the limitations of maintaining a living cell, they offer greater flexibility in exploring the details of protein synthesis without
Week 10: Advanced Imaging and Measurement Technology
Based on the older information: • m/z(n) = 824.1148 • m/z(n+1) = 800.608 • n = 34.0172 MW = (n * m/z(n)) - n MW = ((34.0172) (824.1148)) - 34.0172 MW = 28,000.06 daltons Error Rate/Accuracy = ((28006.6 - 28000.06)/28006.6)1000000 = 0.0002341000000 = 233.52ppm This value is much higher than the 50ppm threshold, indicating an issue with the tested product. Also, I think this calculation seems to actually be for inaccuracy or error rate. The sequence has 20 K’s and 6 R’s for peptide segmentation sites