Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
Class assignment 1. First, describe a biological engineering application or tool you want to develop and why. As a CS/AI master’s student, I find it exciting that I can use AI protein design tools like AlphaFold to work on something that actually matters.
Week 11 HW: Bioproduction & Cloud Labs
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Week 2 HW: DNA Read, Write and Edit
Part 1: Benchling & In-silico Gel Art For this exercise, the full genome of Bacteriophage Lambda (GenBank accession J02459.1, 48,502 bp) was imported into Benchling from NCBI. A virtual restriction enzyme digestion was performed using seven enzymes: EcoRI, HindIII, BamHI, KpnI, EcoRV, SacI, and SalI. Each enzyme was applied individually to identify its recognition sites across the Lambda genome. The digest results were visualized using Benchling’s simulated gel electrophoresis tool. To get a nice visual, I tried different ladders and different lane orderings. The final output consisting of for each enzyme’s fragment pattern is below.
Part 1: Python Script Opentron Artwork Opentrons Colab for Source Code My Jelly Smiley Design Part 2: Post-Lab Questions Question 1: Find and describe a published paper that utilizes the Opentrons or an automation tool to achieve novel biological applications.
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Part 1: Generate Binders with PepMLM I retrieved the human SOD1 sequence from UniProt (P00441) in FASTA format. Original canonical sequence: >sp|P00441|SODC_HUMAN Superoxide dismutase [Cu-Zn] OS=Homo sapiens OX=9606 GN=SOD1 PE=1 SV=2 MATKAVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTS AGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVV HEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ I introduced the A4V mutation by changing Alanine (A) to Valine (V) at position 4 of the mature protein sequence (index 4, 0-based).
- What are some components in the Phusion High-Fidelity PCR Master Mix and what is their purpose? Phusion HF PCR Master Mix is a ready-to-use 2X solution that contains everything needed for PCR except the template, primers, and water. The most important component is Phusion DNA Polymerase, which is the enzyme that copies DNA during the reaction. The standard alternative is Taq polymerase, a widely used enzyme isolated from a heat-resistant bacterium called Thermus aquaticus. Taq survives the high temperatures of PCR but has no proofreading ability, so it cannot correct mistakes it makes while copying, resulting in a relatively high error rate. Phusion addresses this by including a proofreading domain that catches and fixes errors as they occur, making it about 50 times more accurate than Taq. This accuracy is important in a mutagenesis experiment where only the specific, intended mutations should be introduced and any unintended errors would compromise the result.
Week 7 HW: Neuromorphic Circuits
Assignment Part 1: Intracellular Artificial Neural Networks (IANNs) 1. What advantages do IANNs have over traditional genetic circuits, whose input/output behaviors are Boolean functions? Boolean genetic circuits treat signals like 0 or 1, meaning every input must pass a hard on/off threshold. However, this can lose useful information. This can be limiting because real biological signals are usually not binary. Inside cells, signals often exist as gradual changes such as in concentration level. IANNs are useful because they keep more of that analog information since they are not only asking “is this signal present or absent?”.