Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
Class Assignment 1. First, describe a biological engineering application or tool you want to develop and why. Endometriosis is an inflammatory disease characterized by the endometrial-like tissue growth outside of the uterine cavity. This ectopic growth leads to hormonal imbalances, systemic inflammation, and debilitating pain during menstruation, sexual intercourse, and bodily functions . Although it affects 10–15% of reproductive age women, there is currently no cure and the diagnosis of this diseases remains a clinical challenge [1]. Current clinical management is limited to hormonal suppression, pain control and surgical excision [2]. Consequently, there is a critical need for non-invasive, targeted therapies that can modulate the immune response and minimize recurrence rates without compromising the patient’s reproductive health.
Week 2 HW: DNA READ, WRITE AND EDIT
Part 1: Benchling & In-silico Gel Art This DNA gel art was designed in the style of Paul Vanouse’s Latent Figure Protocol. I chose to create the letter “P” as it is the initial of my name, Paula. To achieve this, I used Ronan’s website, which was a helpful tool for quickly iterating on the designs and determining the best enzyme combinations to form the silhouette of the letter.
Your task this week is to Create a Python file to run on an Opentrons liquid handling robot. 1. Generate an artistic design using the GUI at opentrons-art.rcdonovan.com. 2. 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. Link to cell: https://colab.research.google.com/drive/1-f-vpwBCOx1gmlD5qXbW5z-7sLun1xwP?authuser=2#scrollTo=pczDLwsq64mk&line=1&uniqifier=1
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) The average composition of muscle without external fat cover is composed of approximately 70% water, 20% protein, and 9% fat (The exact values vary depending on the animal source) [1]. Therefore 500 g of meat provides 100 g of protein. Since proteins are chains of amino acids, once digested they break down into individual amino acid molecules. We are told the average molecular weight of an amino acid is ~100 Daltons, which means its molar mass is 100 g/mol.
Week 5 HW: 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 7 HW: Genetic circuits part II
Assignment Part 1: Intracellular Artificial Neural Networks (IANNs) 1. What advantages do IANNs have over traditional genetic circuits, whose input/output behaviors are Boolean functions? Boolean functions are limited to discrete on/off states while IANNs are capable of processing analogue signals and, because of that, carry more information. Real world phenomena are analog, inside a cell there is inherent molecular noise, and Boolean circuits are fragile to this, especially at low signal concentrations.