Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
First, describe a biological engineering application or tool you want to develop and why. I am working on the epidemiology and development of management practices of Aster Yellows Phytoplasma (AYP) in the Plant Molecular Virology Laboratory at University of Minnesota. AYP was first detected in garlic in Minnesota in 2012, with outbreaks recorded in 2017 and 2021, and spread to planting material in 2018 and 2022. In 2024, infestations were detected throughout Minnesota. However, there are no precise data on its incidence. AYP is an obligate type of bacteria that resides in the phloem and it is transmitted by leafhoppers. AYP is a concern for production, because there are not available effective treatments for this emergent pathogen in Minnesota’s garlic crops, and current diagnostic methods are time-consuming and costly. There is a need to develop biotechnological tools for the detection and management of this plant pathogen.
Week 2 HW: DNA Read, Write, & Edit
My Homework DNA! 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 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!
My Homework DNA! Assignment: Python Script for Opentrons Artwork 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. 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.
Week 4 HW: Protein Design Part I
My homework DNA! 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? Humans do not become cows or fish after eating them because the proteins we consume are first broken down into their basic components during digestion. Although all living organisms use the same 20 standard amino acids as building blocks of proteins, these proteins are digested into individual amino acids by enzymes such as pepsin in the stomach and trypsin in the small intestine. These amino acids are then absorbed and reused by our cells to synthesize new proteins according to the instructions encoded in human DNA. Therefore, the amino acids from beef or fish are simply raw materials that our bodies use to build human proteins.
Week 5 HW: Protein Design part II
My Homework Part 1: Generate Binders with PepMLM Begin by retrieving the human SOD1 sequence from UniProt (P00441) and introducing the A4V mutation. Using the PepMLM Colab linked from the HuggingFace PepMLM-650M model card: Generate four peptides of length 12 amino acids conditioned on the mutant SOD1 sequence. To your generated list, add the known SOD1-binding peptide FLYRWLPSRRGG for comparison. Record the perplexity scores that indicate PepMLM’s confidence in the binders. sp|P00441|SODC_HUMAN Superoxide dismutase [Cu-Zn] OS=Homo sapiens OX=9606 GN=SOD1 PE=1 SV=2 MATKAVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTS AGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVV HEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ
Week 6 HW: Genetic Circuits Design part I
My Homework 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? Phusion High-Fidelity PCR master mix contains Phusion DNA polymerase, deoxynucleotides and HF reaction buffer with MgCl2. This master mix is used for long or difficult PCR amplifications and applications where high sequence fidelity is critical, such as cloning, mutagenesis, or amplicon sequencing.