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 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.
Part A. Conceptual Questions How many molecules of amino acids do you take with a piece of 500 grams of meat? (on average an amino acid is ~100 Daltons) Meat is roughly 20% protein by mass, so 500 g of meat contains about 100 g of protein. Since one Dalton equals 1 g/mol, an average amino acid at 100 Da means 100 g/mol. That gives 100 g ÷ 100 g/mol = 1 mole of amino acid residues, or about 6 × 10²³ amino acid molecules. So eating a steak hands you roughly Avogadro’s number of amino acids, a staggering count that just means “about a mole.”
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: Genetic Circuits II
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?”.
General Homework Questions 1. 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. Cell-free protein synthesis (CFPS) skips the cell membrane barrier, so the user has direct access to the reaction mixture. This means parameters like pH, redox state, magnesium and potassium concentrations, temperature, and amino acid pools can all be tuned freely without worrying about cell viability. There is also no need for cloning, transformation, or growing cultures, so the time from DNA template to protein is hours instead of days.
Week 10 HW: Imaging and Measurement
Homework: Waters Part I — Molecular Weight An eGFP standard was analyzed on a Waters Xevo G3 QTof MS system to determine the molecular weight of intact eGFP and observe its charge state distribution in the native and denatured (unfolded) states.
- What is the calculated molecular weight? eGFP Sequence:
Part A: The 1,536 Pixel Artwork Canvas | Collective Artwork Unfortunately, I missed the deadline, I guess I have to become a TA next year (hurray)! ¯(ツ)/¯ I thought the sense of community behind the project was really well designed, and I appericated the idea of many people contributing small pieces to one shared bioartwork. This also made me think about my own project on protein steganography. It could be interesting to create a message-encoding project where people enter their names, messages, or short memories, and we encode them into DNA or protein sequences. Although this would not be as immediately visual as the pixel canvas, it could still be very aligned with HTGAA. One possible version could even involve producing the encoded DNA in bacteria and sharing it with committed listeners. Adrian from the Ottawa node also suggested that it might be beautiful to encode the information into a plant seed or something similar—a living memorial for HTGAA. :')