Homework
Weekly homework submissions:
Week 01 HW: Engineering a Soil Microbe to Support Short-Season Agriculture in Canada
Biological engineering application: PGPR Agriculture in northern climates, such as Canada, faces structural biological constraints, particularly short and unpredictable growing seasons, cold soil temperatures in early spring, and variable nutrient availability. These constraints limit crop maturation time and increase vulnerability to climate change. I propose developing an engineered plant growth-promoting rhizobacterium (PGPR) to enhance early-stage plant growth, nutrient uptake, and cold-stress resilience. The literature has recognized the effectiveness of PGPR in improving the growth and quality of certain crops and plants (Singh et al, 2023; Zhang et al, 2024). However, the theories have not been applied to improving the early developmental rate in cold climates. Therefore, I believe this biological engineering approach not only leverages rhizosphere ecology but also aligns agricultural productivity and ecological systems thinking.
Week 02 HW: DNA Read, White, and Edit
Part 1: Benchling & In-silico Gel Art Enzymes Cuts Temp. 1.1 2.1 3.1 4/CS BamHI 5 37°C 75* 100* 100 100* EcoRI 5 37°C 25 100* 50 50* EcoRV 21 37°C 10 50 100 10 HindIII 7 37°C 25 100 50 50 KpnI 2 — Not available for this vendor SacI 2 — Not available for this vendor SacII 4 37°C 10 100 10 100 I have difficulty creating a pattern/image in the style of Paul Vanouse’s Latent Figure Protocol artworks. I will use this image as a placeholder for now. Sorry about that.
from opentrons import types metadata = { # see https://docs.opentrons.com/v2/tutorial.html#tutorial-metadata ‘author’: ‘Scarlett Kelly’, ‘protocolName’: ‘Art’, ‘description’: ‘Making art with Opentrons’, ‘source’: ‘HTGAA 2026 Opentrons Lab’, ‘apiLevel’: ‘2.20’ } ############################################################################## Robot deck setup constants - don’t change these ############################################################################## TIP_RACK_DECK_SLOT = 9 COLORS_DECK_SLOT = 6 AGAR_DECK_SLOT = 5 PIPETTE_STARTING_TIP_WELL = ‘A1’ well_colors = { ‘A1’ : ‘Red’, ‘B1’ : ‘Green’, ‘C1’ : ‘Orange’ }
Week 04 HW: Protein Design Part 1
Part A. Conceptual Questions (the responses heavilily relied on Google) 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) It depends on the meat. If it is red meat, it is about 67.8e23 amino acid molecules. Why do humans eat beef but do not become a cow, eat fish but do not become fish?
Week 05 HW: Protein Design Part 2
Part A: SOD1 Binder Peptide Design (From Pranam) SRWDVYAGAVKWARK 10.46594, WWVPPYTAVYAWKKK 17.463782, SRWGEYVGVYKARAA 12.508359, WRVDVVVAVKKAKKK 12.361373, while FLYRWLPSRRGG shows perplexity 8.1. imTM = 0.37, seems to be a random surface and hardly binds. imTM = 0.31, a random surface and hardly binds imTM = 0.4, dimer interface imTM = 0.32, random surface imTM = 0.43, dimer interface The imTM values are small, which returns weak binding. I don’t think that any peptide matches the known binder.
Week 06 HW: Genetic Circuit Part 1
Part 1: DNA Assembly What are some components in the Phusion High-Fidelity PCR Master Mix and what is their purpose? The key components include Phusion DNA polymerase (providing extreme fidelity), optimized reaction buffer (providing the necessary environment for enzyme activity), Magnesium Chloride (supporting DNA polymerase activity), and Deoxynucleotide Triphosphates (dNTPs - building new DNA strands). The purpose of the master mix is to reduce the risk of contamination, save time, and minimize mixing errors.
Week 07 HW: Genetic Circuit Part 2
Part 1: Intracellular Artificial Neural Networks (IANNs) What advantages do IANNs have over traditional genetic circuits, whose input/output behaviors are Boolean functions? The advantages include nonlinear and adaptive processing, instead of on/off states. Describe a useful application for an IANN; include a detailed description of input/output behavior, as well as any limitations an IANN might face to achieve your goal. I will use the application I proposed in the Week 1 homework, soil microbes to optimize nitrogen release in crops in cold climates.
Part A: General and Lecturer-Specific 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. According to Biocompare “Advantages of Cell-Free Protein Expression,” Cell-free protein expression uses cellular lysates, instead of living cells as a source of components required for protein synthesis. The advantages include ease of use, speed in protein production, and minimal lab equipment and expertise requirements compared to traditional methods.
Week 10 HW: Imaging and Measurement
Homework: Final Project For your final project: Please identify at least one (ideally many) aspect(s) of your project that you will measure. It could be the mass or sequence of a protein, the presence, absence, or quantity of a biomarker, etc. a. Whether the hydrophobin gene is correctly inserted and expressed. b. the presence of a relative quantity of hydrophobin protein. Please describe all of the elements you would like to measure, and furthermore describe how you will perform these measurements. This will be measured from both the DNA and protein levels. a. DNA-level on the presence and correctness of hydrophobine gene by extracting DNA from the system, amplifying target region, and verifying size and sequence. b. Protein-level on hydrophobin expression by extracting proteins, seperate by size, and detect target protein.
HTGAA 2026 Global Pixel Artwork Cloud Lab Final projects (forms, slides, and orders are complete)
The homework requirements are posted under Week 11 homework page. Part A: The 1,536 Pixel Artwork Canvas | Collective Artwork Mine didn’t work well, and I missed the April 19 due date. Part B: Cell-Free Protein Synthesis | Cell-Free Reagents (used GenAI for answers) Referencing the cell-free protein synthesis reaction composition (the middle box outlined in yellow on the image above, also listed below), provide a 1-2 sentence description of what each component’s role is in the cell-free reaction. E. coli Lysate: