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. There is currently an urgent research focus on the biodegradation of plastics, due to the extremely long life cycle of synthetic polymers. Prior work has focused on a mix of exploring bacterial and microbial processes (e.g. anaerobic digestion) to break down plastics, and developing compositions that can be commercial compostable (e.g. for single use plastics). My personal interest is in fiber arts and sustainability, so I’d like to tackle this problem from a textile perspective. Fast fashion has exacerbated the volume of cheap, low quality clothes produced everyday. These clothes are often made with synthetic fibers and not for long term use (although the two are not necessarily interchangeable). I believe it’s incredibly important to find a way to biodegrade polyester, one of the most common synthetic polymers in fast fashion clothing.
Week 2 HW: DNA Read, Write, & Edit
Part 1: Benchling & In-silico Gel Art Had an initial mess-up where I tried to “speedrun” the process and ended up with a ladder packed with the effects of multiple restriction enzymes. Finally got success with all of the listed enzymes, separately.
Python Script for Opentrons Artwork Opentrons Art I tried to play around with math functions to create a design, like the Mathematical Heart sample. I drew up a cute fox in Desmos graphing calculator using the following functions, making sure to scale them to the 40 mm limit. Transferring that to Colab was a bit more difficult, and I had to play around with the functions, ranges, and dispense volume to find something that looked good.
Week 4 HW: Protein Design Part I
Part A. Conceptual Questions Answer any NINE of the following questions from Shuguang Zhang: 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? The natural amino acids are determined by codons, which are determined by three nucleotides (of which can be adenine, uracil, guanine, cytosine). This gives 4 x 4 x 4 = 64 total codons, but redundancy among codons produces only 20 unique amino acids.
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 6 HW: Genetic Circuits Part I
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? What are some factors that determine primer annealing temperature during PCR? There are two methods from this class that create linear fragments of DNA: PCR, and restriction enzyme digests. Compare and contrast these two methods, both in terms of protocol as well as when one may be preferable to use over the other. How can you ensure that the DNA sequences that you have digested and PCR-ed will be appropriate for Gibson cloning? How does the plasmid DNA enter the E. coli cells during transformation? Describe another assembly method in detail (such as Golden Gate Assembly) Explain the other method in 5 - 7 sentences plus diagrams (either handmade or online). Model this assembly method with Benchling or Asimov Kernel! Asimov Kernel Create a Repository for your work Create a blank Notebook entry to document the homework and save it to that Repository Explore the devices in the Bacterial Demos Repo to understand how the parts work together by running the Simulator on various examples, following the instructions for the simulator found in the “Info” panel (click the “i” icon on the right to open the Info panel) Create a blank Construct and save it to your Repository Recreate the Repressilator in that empty Construct by using parts from the Characterized Bacterial Parts repository Search the parts using the Search function in the right menu Drag and drop the parts into the Construct Confirm it works as expected by running the Simulator (“play” button) and compare your results with the Repressilator Construct found in the Bacterial Demos repository Document all of this work in your Notebook entry - you can copy the glyph image and the simulator graphs, and paste them into your Notebook Build three of your own Constructs using the parts in the Characterized Bacterials Parts Repo Explain in the Notebook Entry how you think each of the Constructs should function Run the simulator and share your results in the Notebook Entry If the results don’t match your expectations, speculate on why and see if you can adjust the simulator settings to get the expected outcome