Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
1 My artistic research project explores the phenomenon of river plumes-zones where freshwater mixes with seawater, forming unstable transitional ecosystems. These areas are understood as natural interfaces in which processes of adaptation, filtration, and redistribution of life continuously occur. The project investigates the potential of diatoms as a living adaptive mechanism capable of transitioning from freshwater to marine salinity conditions. This process is approached not only as a biological experiment, but also as a metaphor for boundaries, transformation, and survival.
Week 2 HW: DNA Read, Write, & Edit
Part 1: Benchling & In-silico Gel Art Simulate Restriction Enzyme Digestion Image in the style of Paul Vanouse’s Latent Figure Protocol artworks Part 3: DNA Design Challenge 3.1 For my homework, I chose the p53 protein because it plays a key role in regulating the cell cycle and protecting the body from tumor growth. This protein is often called the “guardian of the genome” because it is activated when DNA is damaged and can halt cell division or trigger apoptosis.
Python Script for Opentrons Artwork Post-Lab Questions Example#1 Real-time colorimetric sensing of space objects in the astronaut accommodation area - https://www.sciencedirect.com/science/article/abs/pii/S0925400523006573 In closed systems (e.g., on orbital stations):
Week 4 HW: Protein Design Part 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) Meat is ~20% protein by weight (average). So in 500 g of meat: Protein ≈ 100 g Average amino acid ≈ 100 Da ≈ 100 g/mol
Week 5 HW: Protein Design Part II
Part A: SOD1 Binder Peptide Design (From Pranam) Part 1: Generate Binders with PepMLM MATKAVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ Part 2: Evaluate Binders with AlphaFold3 HRYGAVVVELKK Structure Based on the image you provided: · ipTM score = 0.4 · pTM score = 0.86 The peptide (residues shown along the vertical axis, roughly 1–165) appears to bind along one face of the folded protein domain, but the alignment confidence (pLDDT coloring) is mixed. There is a very low confidence (dark orange/red) stretch around residues ~33–66 and again near ~132–165, suggesting the predicted binding mode may be unreliable in those regions.
Week 6 HW: Genetic Circuits Part I: Assembly Technologies
Assignment: DNA Assembly 1. What are some components in the Phusion High-Fidelity PCR Master Mix and what is their purpose? Phusion High‑Fidelity DNA Polymerase. This is the key enzyme that copies DNA during PCR. Reaction Buffer (HF Buffer). The buffer provides the chemical environment in which the enzyme works best. Deoxynucleoside Triphosphates (dNTPs). These are the building blocks of DNA (A, T, G, C). Optional Additives Water. Used to bring the reaction to the final volume and ensure proper concentrations of all components once primers and DNA template are added. 2. What are some factors that determine primer annealing temperature during PCR?
Week 7 HW: Genetic Circuits Part II: Neuromorphic Circuits
Assignment Part 1: Intracellular Artificial Neural Networks (IANNs) What advantages do IANNs have over traditional genetic circuits, whose input/output behaviors are Boolean functions? Intracellular Analog Neural Networks (IANNs) offer several advantages over traditional genetic circuits that rely on Boolean logic (ON/OFF states). First, IANNs enable graded, continuous responses rather than binary outputs. This allows cells to process varying signal intensities and produce proportional outputs, which more closely reflects natural biological systems.
General homework 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. Direct control of conditions: You can independently adjust pH, temperature, ion concentration, redox state, and cofactors without affecting cell viability. Faster optimization cycles: No need for cloning, transformation, or cell growth—results can be obtained in hours. No cellular constraints: Toxic proteins, unstable proteins, or proteins that burden cells can still be produced. Simplified system: Fewer regulatory pathways means fewer unknown biological interactions. Cases where cell-free is more beneficial:
Week 10 HW: Advanced Imaging & Measurement Technology
Homework: Final Project Fluorescent Output (GFP Expression) Intensity of fluorescence (proxy for stress-response activation. Microfluidic imaging Important: Direct readout of stress pathway activation Allows spatial mapping across salinity gradient Gene Expression Levels (mRNA) Real-time PCR systems. Important: Confirms that fluorescence reflects transcriptional activity DNA Sequence Verification DNA sequencing Important: Ensures mutations and reporter constructs are correct Protein Expression and Stability