Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
- Biological engineering application or tool to develop and why Idea Mi idea its a biological biosensor designed to detect early changes in dependence on the molecular chaperone HSP90 in KIT mutant gastrointestinal stromal tumors (GIST), as functional indicators of cellular adaptation preceding the development of resistance to imatinib. Figure 1. Conceptual schematic of the proposed biological biosensor. Image generated using AI for graphical representation purposes only.
Part A: The 1,536 Pixel Artwork Canvas | Collective Artwork what you contributed to the community bioart project what you liked about the project, and what about this collaborative art experiment could be made better for next year. R/: I contributed one pixel in the upper right area of the collaborative canvas. It was a small but meaningful contribution to a collective bioart piece created by students from around the world.
Week 2 HW:DNA read write and edit
Part 1: Benchling & In-silico Gel Art Figure 1. Simulated agarose gel showing the LAMCG plasmid digested with different restriction enzymes. Figure 2. Screenshot of the online tool used to simulate restriction digests and generate the virtual gel pattern for LAMCG.
Generate an artistic design using the GUI at opentrons-art.rcdonovan.com. Using the coordinates from the GUI, follow the instructions in the HTGAA26 Opentrons Colab to write your own Python script which draws your design using the Opentrons. You may use AI assistance for this coding — Google Gemini is integrated into Colab (see the stylized star bottom center); it will do a good job writing functional Python, while you probably need to take charge of the art concept. If you’re a proficient programmer and you’d rather code something mathematical or algorithmic instead of using your GUI coordinates, you may do that instead. Google colab link: https://colab.research.google.com/drive/1CuzPdG5pSYIgSalc1o3C1FA-yUbnaW0_?usp=sharing
Week 4 HW: Protein design part I
Protein design part i Part A. Conceptual Questions Answer any NINE of the following questions from Shuguang Zhang: (i.e. you can select two to skip) 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) R/: Meat is approximately 20% protein by mass, so 500g of meat contains roughly 100g of protein. Since the average amino acid has a molecular weight of ~100 Daltons (100 g/mol), 100g of protein equals 1 mole of amino acids. Multiplying by Avogadro’s number gives approximately 6 × 10²³ molecules = 600 sextillion amino acid molecules in a single piece of meat.
Week 5 HW: Protein design part II
week-05-hw-protein-design-part-ii Part A: SOD1 Binder Peptide Design (From Pranam) Part 1: Generate Binders with PepMLM Begin by retrieving the human SOD1 sequence from UniProt (P00441) and introducing the A4V mutation. original sequence: sp|P00441|SODC_HUMAN Superoxide dismutase [Cu-Zn] OS=Homo sapiens OX=9606 GN=SOD1 PE=1 SV=2 MATKAVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTS AGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVV HEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ A4V mutation: MATKVVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTS AGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVV HEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ Using the PepMLM Colab linked from the HuggingFace PepMLM-650M model card: https://colab.research.google.com/drive/1tOhdz-ZO91A0u--wk65WY69CSMcL0e70?usp=sharing Generate four peptides of length 12 amino acids conditioned on the mutant SOD1 sequence.
Week 6 HW: Genetic Circuits part I
Assignment: DNA Assembly Answer these questions about the protocol in this week’s lab: What are some components in the Phusion High-Fidelity PCR Master Mix and what is their purpose? R/The Phusion HF PCR Master Mix contains several key components. The Phusion DNA Polymerase is a high-fidelity polymerase with 3’→5’ exonuclease (proofreading) activity, which significantly reduces errors during amplification. dNTPs (dATP, dTTP, dCTP, dGTP) serve as the building blocks for the new DNA strand. The HF Buffer stabilizes pH and ionic conditions optimal for standard templates, while the GC Buffer is used for GC-rich sequences. MgCl₂ acts as an essential cofactor for polymerase activity. Additional stabilizers and additives improve enzyme stability and overall reaction efficiency.
🧬 General Homework Questions Cell-Free Protein Synthesis Explain the main advantages of cell-free protein synthesis over traditional in vivo methods, specifically in terms of flexibility and control over experimental variables. R/: The main advantage of cell-free protein synthesis over traditional in vivo methods is the greater flexibility and control over experimental variables. In living cells, there are many uncontrollable factors the cell may degrade the target protein through proteolysis, compete for resources, or respond unpredictably to foreign sequences. Cell-free systems eliminate the cell itself as a variable, allowing direct manipulation of reaction conditions such as temperature, pH, and component concentrations.
week-07-hw-genetic-circuits-part-ii
< Assignment Part 1: Intracellular Artificial Neural Networks (IANNs) Assignment Part 1: Intracellular Artificial Neural Networks (IANNs) 1. Advantages of IANNs over Traditional Boolean Genetic Circuits Continuous Input/Output Behavior Traditional genetic circuits operate as Boolean functions a gene is either ON or OFF (0 or 1). IANNs instead process continuous values, meaning inputs and outputs can exist across a full range (like protein concentrations or expression levels). This is much closer to how biological systems actually work, where gene expression is rarely all or nothing but rather graded and proportional to stimuli.
week-10-hw-imaging-and-measurement
Homework: Final Project Please identify at least one (ideally many) aspect(s) of your project that you will measure. R/: I would like to measure the expression levels of mutant p53 protein across different cancer types. High accumulation of mutant p53 (due to MDM2 being unable to degrade it) would indicate a GOF mutation, making those cancers more susceptible to p53 GOF-driven oncogenesis.