Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
IDEA Through art, design, biology, and apparel, I am interested in exploring how wearers can become more attuned to their identity by expressing their unique microbial genomes and ecosystems that make up their bodies through a bio-engineered second-skin-like textile. This project explores clothing as a custom, an expression, and a living interface that evolves with the body, offering an alternative to the rapid cycles of novelty and replacement characteristic of fashion today. The garment becomes a second skin that is not consumed or discarded, but lived with, every day, shifting gradually and meaningfully over time (National Institutes of Health).
Week 2 HW: DNA Read Write & Edit
Part 1: Benchling & In-silico Gel Art https://benchling.com/s/seq-B1mFk0Oh2ZF9coVeqBMH?m=slm-ySVijsqZThHxK3Qq6kwq Part 2: Gel Art - Restriction Digests and Gel Electrophoresis I am interested in the protein Reflectin. This protein is common in Cephalopods and is responsible for their structural colour as their skin changes with the environment. I am interested in the potential applications of Reflectin in smart materials/textiles. Reflectins’ optical properties can be reversibly engineered to change colour under different conditions. There is one study in which Reflecin was used in this way in a thin film substrate, and responsive to hydration or dehydration of the material.
OPENTRON GEL ART Figure 1 I tried creating a butterfly using the OpenTron drawing tool, with 4 different colours, dark blue, light blue, red and purple, which are some of the available colours in Lifefabs. I also tried to create an Iris in the style of Van Gogh. As this is a more fluid and asymmetrical design, it would be harder to achieve, given the complexity of the multiple colours in organic scaddered shades, rather than in small units. Moreover, the dots and spaces are quite compact, which would make it harder to achieve a clean result.
Week 4 HW: Protein Design Part I
(American Chemical Society, 2023) Protein Design Google Collab Part A. Conceptual Questions Answer any NINE of the following questions from Shuguang Zhang: (i.e. you can select two to skip) Why do humans eat beef but do not become a cow, eat fish but do not become fish? Even though some may like to say you are what you eat, this really isn’t the case when it comes to eating an organism. Even though we consume its parts and convert protein into energy we are transforming energy into energy that we can use. One may argue we embody that organism to a degree, but we dont fully transform into that being. Your cells follow a genetic blueprint, and while other DNA enters your body, you do not absorb its genome, nor does it integrate into yours.
Week 5 HW: Protein Design Part II
(Carnaroli et al.,2025) PART A: SOD1 Binder Peptide Design (From Pranam) Superoxide dismutase 1 (SOD1) is a cytosolic antioxidant enzyme that converts superoxide radicals into hydrogen peroxide and oxygen. In its native state, it forms a stable homodimer and binds copper and zinc. Mutations in SOD1 cause familial Amyotrophic Lateral Sclerosis (ALS). Among them, the A4V mutation (Alanine → Valine at residue 4) leads to one of the most aggressive forms of the disease. The mutation subtly destabilizes the N-terminus, perturbs folding energetics, and promotes toxic aggregation.
Week 6 HW: Genetic Circuits Part I: Assembly Technologies
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? The Phusion High-Fidelity PCR Master Mix is a pre-mix solution used to amplify DNA during PCR. There are a few components that make the master mix efficient and accurate.
Week 7 HW: Genetic Circuits Part II: Neuromorphic Circuits
ASSIGNMENT PART 1: Intracellular Artificial Neural Networks (IANNs) IANN ADVANTAGES VS GENETIC CIRCUITS Intracellular Artificial Neural Networks, are genetic circuits designed with the same framework as neural networks taking from the most intelligent systems of communication that exist in our inner worlds. In traditional genetic circuits the outpus are boolean ON(1)OFF(0), however IAANs have outputs with continous analog, rather 0.2,0.5,0.75,1… The advantages of Iann vs genetic circuit logic, is the complexity of the analogue captured, combining many inputs as well as nonlinear relationships, and thus work better with biological systems with gradual changes and growth (Nilsson et al., 2022).
- 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. The first advantage of cell-free protein synthesis (CFPS) over traditional in vivo methods is that it avoids the ethical concerns associated with modifying living cells; CFPS uses cellular machinery such as ribosomes and enzymes. The second advantage of CFPS is the time and cost. CFPS takes around 1-2 hours while cell-based expressions, such as in E. coli, take around a few days to a week, depending on the expression. Third, there is increased biosafety and controllability with CFPS. CFPS are more controllable and programmable. Unlike using living cells which can escape into the environment and potentially cause harm depending on the organism. Lastly