Homework

Weekly homework submissions:

  • Week 1 HW: Principles and Practices

    1. First, describe a biological engineering application or tool you want to develop and why. I’m passionate about both food and biotechnology and seek to combine the two discipline together for my future career. A biological engineering application that I would love to work on is precision fermentation production for alternative sustainable protein sources, specifically β-Lactoglobulin (BLG) protein for recombinant milk production. I was inspired by a PhD student’s publication at Wageningen University & Research while I was searching for a university to earn my Master’s degree. Indonesia’s demand for milk and dairy products has been increasing over the years, and our climate isn’t suited for dairy cattle farming compared to other countries with a more appropriate climate and productive dairy cows. Not to mention the environmental impact of dairy farming, along with the scarcity of arable land, are also factors to be considered to supplement part of the industry with precision fermentation (Hoppenreijs, 2024).

  • Week 1 HW: Week 2 Lecture Prep

    Questions from Professor Jacobson: Nature’s machinery for copying DNA is called polymerase. What is the error rate of polymerase? How does this compare to the length of the human genome? How does biology deal with that discrepancy? How many different ways are there to code (DNA nucleotide code) for an average human protein? In practice what are some of the reasons that all of these different codes don’t work to code for the protein of interest? Answer:

  • Week 2 HW: DNA Read, Write, & Edit

    Part 1: Benchling & In-silico Gel Art For this week’s Part 1 homework, students are tasked with doing several tasks. First, create a Benchling account. Second, simulate restriction enzyme digestion of a predetermined sequence using several enzymes. Third, once students are able to simulate the restriction enzyme digestion, they can create a simple art form named the Latent Figure Protocol. For the first part of the task, I would need to create an account for Benchling. It was a relatively simple process of using my Gmail account to sign up for Benchling. A few minutes later, after entering my details, I am now the proud owner of a Benchling account.

  • Week 3 HW: Lab Automation

    Python Script for Opentrons Artwork For my Opentrons artwork, I went through several designs I found interesting. Instead of drawing the art from scratch, I decided to add the images I wanted as templates for the artwork. The first is a photorealistic picture of a cat, but due to it being too detailed and the Opentrons pixel/well limitations, I wasn’t able to recreate it. The same happened when I inserted a picture of Vincent van Gogh’s painting, Starry Night. In the first few tries, I failed to account for the pixel/well limitations for the Opentron art. Because of this, I decided to pick a simpler design for my final image in the form of a Costco logo. I chose this particular design because I liked Costco’s business model and products from watching reviews of Costco products, and I would love for the company to open a branch store here in Indonesia.

  • Week 4 HW: Protein Design Part I

    Shuguang Zhang Questions Answers:

  1. Why do humans eat beef but do not become cows, eat fish but do not become fish? The human body only digests the fish into its nutritional constituents, such as amino acids. Humans lack the biological capacity to reverse translate the amino acid sequence back into the mRNA sequence and reverse transcribe it back into DNA. Basically, humans aren’t able to do the Central Dogma in reverse. Humans also do not have the natural ability to incorporate dietary genes of the consumed animals into their genome.

  • Week 5 HW: Protein Design Part II

    Part A. SOD1 Binder Peptide Design (From Pranam) Part 1: Generate Binders with PepMLM This homework starts by opening the protein database UniProt to copy the FASTA format of the AA sequence of Superoxide dismutase (SOD1). According to UniProt, Superoxide dismutase functions as a catalyst for the oxidation of hydrogen sulfide (H2S) to sulfate, playing a crucial role in detoxifying H2S and limiting the accumulation of reactive sulfur species (RSS). It is an enzyme critical for destroying free radicals produced within cells, which are toxic to biological systems. As such, mutations to the gene that encodes the enzyme come with their own potential health complications. One such mutation is the alanine to valine mutation at codon 4 (A4V) of SOD1. It is a mutation that causes a rapidly progressive dominant form of amyotrophic lateral sclerosis (ALS). ALS is a terminal disease that causes the progressive loss of motor neurons, which leads to paralysis and death (Saeed et al., 2009). The images below show the AA sequence of the normal SOD1 protein along with its mutated counterpart.