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

  • Week 3 HW: Lab Automation

    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.

  • Week 6: 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? Elements: Pyrococcus-like enzyme fused with a processivity-enhancing domain that increases fidelity and speed. 53 polymerase activity, 35exonuclease activity, and generates blunt-ended products. Phusion DNA Polymerase, deoxynucleotides, and reaction buffer that has been optimized and includes MgCl2 Requirements to be added: template, primers, and water. Purpose:

  • Week 7 HW: Genetic Circuits - part II

    Assignment Part 1: Intracellular Artificial Neural Networks (IANNs) What advantages do IANNs have over traditional genetic circuits, whose input/output behaviors are Boolean functions? In-vivo Artificial Neural Networks provide an analog approach to computation within biological systems, enabling cells to process continuous inputs and generate a gradient and a non-binary output. IANNs can integrate multiple signals and capture more complex, non-linear relationships through distributed gene regulation. IANNs have the ability to capture patterns and complex inputs.

  • Week 9 HW: Cell Free Systems

    Part A: General and Lecturer-Specific Questions 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. Cell-free protein synthesis: is a protein expression approach that enables the production of a target protein without the use of living cells. In vivo methods: it is also a protein expression approach that uses living cells such as bacteria (e. coli, most common), yeast, insect cells, and mammalian cells. Here is a chart that makes a summary about differences between both methods:

  • Week 10 HW: Imagin and Measurement

    Waters Part I — Molecular Weight We will analyze an eGFP standard on a Waters Xevo G3 QTof MS system to determine the molecular weight of intact eGFP and observe its charge state distribution in the native and denatured (unfolded) states. The conditions for LC-MS analysis of intact protein cause it to unfold and be detected in its denatured form (due to the solvents and pH used for analysis).

  1. Based on the predicted amino acid sequence of eGFP (see below) and any known modifications, what is the calculated molecular weight? You can use an online calculator like the one at https://web.expasy.org/compute_pi/
  1. Contribute at least one pixel to this global artwork experiment before the editing ends on Sunday 4/19 at 11:59 PM EST. A personalized URL was sent to the email address associated with your Discourse account, and you can discuss the artwork on the Discourse. If you did not have a chance to contribute, it’s okay, just make sure you become a TA this fall! 😉 2. Make a note on your HTGAA webpages including: