Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
Class Assignment A Wearable or At-Home Androgen Biosensing Platform for PCOS Diagnosis and Management I am interested in developing an easy-to-use biosensor/microfluidic kit that can detect and quantify androgen levels from blood or sweat to support the diagnosis and personalized management of Polycystic Ovary Syndrome (PCOS).
Week 2 HW: DNA Read, Write, and Edit
Predicted structure of Pro-resilin (Drosophila melanogaster), generated by AlphaFold and retrieved from UniProt (UniProtKB: Q9V7U0). *You can find parts 1 and 2 in the week 2 lab section! Part 3: DNA Design Challenge My protein choice: Pro-resilin! Pro-resilin is a highly elastic, rubber-like structural protein found in insects that enables efficient energy storage for jumping, flight, and sound production. About seven years ago, my biotechnology teacher in high school showed us an article about a very cool leading professor in Israel, who was doing things that seemed almost impossible. I vividly remember one of the projects he was working on: scientists had identified a protein that enables a particular spider species to jump remarkably high relative to its body size, and this scientist wanted to give humans the same ability by creating shoes with soles made from some protein similar to Pro-resilin.
*You can find the Python Script for Opentrons Artwork part in the Week 3 Lab section! Post-Lab Questions 1. Find and describe a published paper that utilizes the Opentrons or an automation tool to achieve novel biological applications.
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) Answer: On average, raw meat is ~20–25% protein by weight. If we assume 20%, then in a 500 g sample we have:
Week 5 HW: Protein Design Part II
Part A: SOD1 Binder Peptide Design Part 1: Generate Binders with PepMLM Searching the human SOD1 (P00441) page on UniProt, I found its amino acid sequence: 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 Part I
DNA Assembly Questions What are some components in the Phusion High-Fidelity PCR Master Mix and what is their purpose? The Phusion High-Fidelity PCR Master Mix contains several key components that enable accurate and efficient DNA amplification. First, it includes the Phusion DNA polymerase, which is responsible for synthesizing new DNA strands. This enzyme has both 5’→3’ polymerase activity and 3’→5’ exonuclease (proofreading) activity, which allows it to correct mistakes during DNA replication and results in very high fidelity compared to standard polymerases like Taq. The mix also contains deoxynucleotides (dNTPs), which are the building blocks used by the polymerase to construct the new DNA strands. In addition, it includes an optimized reaction buffer with MgCl₂, which provides the proper chemical environment for the enzyme to function. Because all of these components are already included in the master mix, only the template DNA, primers, and water need to be added to perform the PCR.
Week 7 HW: Genetic Circuits Part II
Part 1: Intracellular Artificial Neural Networks What advantages do IANNs have over traditional genetic circuits, whose input/output behaviors are Boolean functions? Answer: The main advantage of IANNs over traditional genetic circuits is their ability to operate with analog (continuous) inputs and outputs, rather than being limited to Boolean (ON/OFF) behavior. This allows cells to respond more precisely to different signal levels instead of only detecting their presence or absence.
General homework questions 1. 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. Answer: Cell-free protein synthesis offers greater flexibility and control compared to traditional in vivo methods because the reaction occurs outside of living cells. This allows precise control over experimental variables such as temperature, pH, ion concentrations, and the addition of specific components (e.g., cofactors, inhibitors, or non-natural amino acids), without being constrained by cellular viability or stress responses. Additionally, cell-free systems are not time-dependent on cell growth, making them faster and more consistent. DNA constructs can also be prepared and stored for long periods and used on demand.
Week 10 HW: Imaging and Measurement
Final Project Please identify at least one (ideally many) aspect(s) of your project that you will measure. It could be the mass or sequence of a protein, the presence, absence, or quantity of a biomarker, etc. Please describe all of the elements you would like to measure, and furthermore describe how you will perform these measurements. What are the technologies you will use (e.g., gel electrophoresis, DNA sequencing, mass spectrometry, etc.)? Describe in detail. My final project is inherently related to measurement, as it is going to be a measurement instrument. The main aspect that I will measure for my final project is therefore its core purpose — measuring testosterone levels in sweat. To do that, I will use either cell-free systems, bacterial expression, or an aptamer-based method to create a fluorescent or electrical signal that correlates with the levels of testosterone in the sample.
Week 11 HW: Bioproduction and Cloud Labs
Part A: The 1,536 Pixel Artwork Canvas | Collective Artwork My Contribution My involvement in the community bioart project started right at the beginning. I found myself in a “digital battle” with other users over whether the top row on the left plate would be blue or yellow - I was on Team Yellow! No particular reason, just a gut feeling:) After a few minutes, others joined me: