Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
First, describe a biological engineering application or tool you want to develop and why. This could be inspired by an idea for your HTGAA class project and/or something for which you are already doing in your research, or something you are just curious about. Thyroid implant for canines In the canine world, there is a very specific problem that owners face: hypothyroidism. It is a common condition that dogs develop around the ages of 2 or 3. Still, most of the time it is mistaken for other health conditions, such as intestinal problems, allergies, dermatological conditions, and so on. As this health condition has many impacts on the body of dogs, sometimes veterinarians can lead to a false positive.
Week 2 HW: DNA Read, Write & Edit
Part 1: Benchling & In-silico Gel Art See this week’s lab protocol “Gel Art: Restriction Digests and Gel Electrophoresis” for details. Overview: Make a free account at benchling.com Import the Lambda DNA. Simulate Restriction Enzyme Digestion with the following Enzymes: EcoRI HindIII BamHI KpnI EcoRV SacI SalI Restriction Enzyme Digestion made with Benchling Create a pattern/image in the style of Paul Vanouse’s Latent Figure Protocol artworks. You might find Ronan’s website a helpful tool for quickly iterating on designs! E=m*a2 EcoRV vs. EcoRI Single Enzymes Pyramid Enzymes Part 3: DNA Design Challenge
Assignment: Python Script for Opentrons Artwork — DUE BY YOUR LAB TIME! Your task this week is to Create a Python file to run on an Opentrons liquid handling robot. Review this week’s recitation and this week’s lab for details on the Opentrons and programming it. Generate an artistic design using the GUI at opentrons-art.rcdonovan.com. Star´s birth Rectangular color palette Iteration color palette 1 Iteration color palette 2 Iteration color palette 3 - Ellipse Iteration color palette 4 - Circumference 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. Iteration color palette 5 Coding done by Gemini This coding was made with Google Gemini. The steps for doing that were: first, loading the coordinates made in the GUI; second, giving instructions to the AI for what the expected outcome; finally, iterating until the idea was achieved. The given instruction given to the IA did not have any basic coding, it was all made with written instructions.
Week 4: 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) Why do humans eat beef but do not become a cow, eat fish but do not become fish? Why are there only 20 natural amino acids? Can you make other non-natural amino acids? Design some new amino acids. Where did amino acids come from before enzymes that make them, and before life started? If you make an α-helix using D-amino acids, what handedness (right or left) would you expect? Can you discover additional helices in proteins? Why are most molecular helices right-handed? Why do β-sheets tend to aggregate? What is the driving force for β-sheet aggregation? Why do many amyloid diseases form β-sheets? Can you use amyloid β-sheets as materials? Design a β-sheet motif that forms a well-ordered structure. Part B: Protein Analysis and Visualization
Week 5: Protein Design - part II
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.