Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
Assignments: Class 1 Assignment Question 1 I propose a high-throughput microscopy tool to estimate intracellular PHA accumulation from granule count and size. Current standart quantification methods are slow, labor-intensive, and often require hazardous solvent-based extraction. By pairing PHA staining (e.g., Sudan Black B or Nile Red A) with automated imaging and machine-learning (ML) image segmentation, this approach could rapidly screen large libraries of environmental isolates and recombinant strains for high PHA producers.
Week 2: DNA Read, Write, & Edit
Homework Part 1: Benchling & In-silico Gel Art Opened https://benchling.com/ and signed up. Found the Lambda sequence from https://www.neb.com/en/-/media/nebus/page-images/tools-and-resources/interactive-tools/dna-sequences-and-maps/text-documents/lambdafsa.txt?rev=c0c6669b9bd340ddb674ebfd9d55c691&hash=B4188C171E5A42A1CF6FD257F98B97A1 and copied the sequence (without the header). Pasted this sequence into Benchling through “Create” > “DNA / RNA Sequence” > “New DNA / RNA Sequence”. Then I just pasted the sequence in the “Bases” field, titled it “Lambda,” and selected the topology as “Linear.”
Python Script for Opentrons Artwork Here’s my HTGAA 2026 Opentrons Art Python Script Submission. The artistic design I created using the GUI is available here. I heavily used the “Example 7 Microbial Earth” by Dominika Wawrzyniak, using pixels loaded from an external resource (a CSV file hosted on my GitHub page). I used Dominika’s well documented Notion page from HTGAA21 to understand the code and replicate it for my case. I used Gemini assistance only to debug minor typos and syntax errors, and to identify which packages to import to execute the code.
Week 4 HW: Protein Design Part 1
Homework: Protein Design I Part A. Conceptual Questions 1) 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) ~ 21% of meat is protein content (Smith et al. 2022) therefore, 500g meet contains about 105g of protein.
Week 5 HW: Protein Design Part 2
Part A: SOD1 Binder Peptide Design (From Pranam) Part 1: Generate Binders with PepMLM Question 1 This is human SOD1 sequence from UniProt (P00441) removing the initial Met ATKAVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ FASTA introducing the A4V mutant associated with the most aggressive forms of the ALS disease ATKVVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ Question 2 and 3 With the help of ChatGPT and Gemni, I generated 2 new cells ir order to generate four peptides of length 12 amino acids conditioned on the mutant SOD1 sequence.
Week 6 HW: Genetic Circuits Part 1: Assembly Technologies
Assignment: DNA Assembly Question 1: What are some components in the Phusion High-Fidelity PCR Master Mix and what is their purpose? Phusion High-Fidelity PCR Master Mix is a 2X, ready-to-use mixture where the exact formulation is partly proprietary, but the functional components are documented in the manufacturer’s manual: Component (Phusion 2X Master Mix) Purpose Phusion High-Fidelity DNA Polymerase DNA synthesis with high fidelity + proofreading dNTPs (dATP, dCTP, dGTP, dTTP) Building blocks for new DNA strands HF reaction buffer (salts + pH buffer) Maintains optimal pH/ionic strength for enzyme function Mg2+ (via buffer system; often MgCl2-derived) Essential polymerase cofactor Stabilizers / additives (partly proprietary) Improve enzyme stability and consistency Nuclease-free water Solvent to reach correct 2X working concentrations Reference: Thermo Fisher Phusion High–Fidelity DNA Polymerase Product Information Sheet, standard biochemistry manuals (e.g., Sambrook & Russell).
Week 7 HW: Genetic Circuits Part 2: Neuromorphic Circuits
Assignment Part 1: Intracellular Artificial Neural Networks (IANNs) Question 1 Traditional genetic circuits are usually implemented in Boolean logic (ON/OFF), hand-designed as fixed logic. so representing nuanced behaviors often requires many gates, sharp thresholds, and careful tuning, which can make designs bulky and brittle. As the number of inputs grows the circuit complexity can explode combinatorially, increasing burden by stacking multiple layers and adding intermediate nodes, which increases metabolic load, failure points, and sensitivity to part-to-part variability Also, adapting to new targets or shifting biological context often means redesigning the circuit architecture, not just re-tuning parameters.
Homework Part A: General and Lecturer-Specific Questions General homework questions Exercise 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.
Week 10 HW: Advanced Imaging & Measurement Technology
Homework: Final Project What to measure? I will measure visible melanin output in the material as the primary readout of the project. I want to quantify: Degree of darkening Spatial distribution of pigmentation Stability/Persistence of the pigmentation in the bacterial cellulose / after drying or storage These measurements are directly relevant because they indicate whether the melanin-producing system is functioning and whether the output is compatible with the intended material application.
Week 11 HW: Bioproduction & Cloud Labs
Part A: The 1,536 Pixel Artwork Canvas | Collective Artwork I contributed 7 pixels to the global artwork experiment, helping extend a horizontal yellow line in the top-left area (see screenshot below). At first, I was cautious and tried to understand the ongoing ideas for each section and whether there was a unifying concept. I considered introducing something new, but ultimately decided to stick with what seemed to be the area’s goal (a horizontal yellow line). For next year, it might be fun to have an in-app chat within the same domain to coordinate contributions more easily and check the current vibes.