Homework

Weekly homework submissions:

  • Class Assignment 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.
  • Part 1: Benchling & In-silico Gel Art Attempt Result Description 1 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. 2 Finally got success with all of the listed enzymes, separately. 3 Some experimentation on Ronan’s website got me this pattern that sort of looks like a pair of pants. In hindsight I should’ve definitely explored results from a combination of enzymes (e.g. EcoRI and HindIII together), which would’ve given me a bigger range of visual results. 4 Replicated “sort-of pants” on Benchling, and my final result. Part 3: DNA Design Challenge 3.1. Choose your protein.
  • Python Script for Opentrons Artwork Generate an artistic design using the GUI at opentrons-art.rcdonovan.com. I used https://ginkgoartworks.com/ to draw a mushroom and imported the program into Colab. Since the bacteria names don’t register as RGB colors, I had to “color-correct” well_colors to get the visualization to show up (but I assume both versions will work as long as the PCR tubes are physically in order).
  • 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) The Dalton is an atomic mass unit that converts from mass using Avogadro’s number. So 500 grams = 500 * 6.022 * 1023 Daltons / 100 Daltons/amino acid = 5 * 6.022 * 1023 amino acids = 3.011 * 1024 amino acids.
  • Part A: SOD1 Binder Peptide Design Part 1: Generate Binders with PepMLM Begin by retrieving the human SOD1 sequence from UniProt (P00441) and introducing the A4V mutation. P00441 can be found on the UnitProt site here. It has the following sequence: sp|P00441|SODC_HUMAN Superoxide dismutase [Cu-Zn] OS=Homo sapiens OX=9606 GN=SOD1 PE=1 SV=2 MATKAVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTS AGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVV HEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ
  • Part 1: 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? The master mix can be found here and contains “Phusion DNA Polymerase, nucleotides, and optimized reaction buffer including MgCl2”. The polymerase is an essential part of PCR, nucleotides are the base materials needed to form new DNA sequences, and reaction buffer lowers the energy needed to start the process.
  • Part 1: Intracellular Artificial Neural Networks (IANNs) What advantages do IANNs have over traditional genetic circuits, whose input/output behaviors are Boolean functions? Increased complexity in what it can process. Genetic circuits are capable of digital logic, but neural networks can fine tune connections and weights to represent a nuanced system with a set of many inputs and outputs. This is in particular in a cell’s ability to contain a “weighted summation” dependent on the situation it gets trained on.
  • Part A: General and Lecturer-Specific Questions General homework questions 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. Cell-free systems have an advantage in “extreme” situations, while in-vivo occurs within cells that have to be kept alive. In taking the process outside of the cell, you can handle it more roughly i.e. freeze drying the system for long-distance transport, or making a system that can be kickstarted just by adding water (in remote locations). Cell-free systems also have more control because they’re synthetic, so you can determine how big the cell is and what exactly goes in it.
  • Final Project For your 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. Waters Part I — Molecular Weight We will analyze an eGFP standard on a Waters Xevo G3 QTof MS system to determine the molecular weight of intact eGFP and observe its charge state distribution in the native and denatured (unfolded) states. The conditions for LC-MS analysis of intact protein cause it to unfold and be detected in its denatured form (due to the solvents and pH used for analysis).
  • Part A: The 1,536 Pixel Artwork Canvas | Collective Artwork Contribute at least one pixel to this global artwork experiment before the editing ends on Sunday 4/19 at 11:59 PM EST. A personalized URL was sent to the email address associated with your Discourse account, and you can discuss the artwork on the Discourse. If you did not have a chance to contribute, it’s okay, just make sure you become a TA this fall! 😉 Make a note on your HTGAA webpages including: what you contributed to the community bioart project (e.g., “I made part of the DNA on the bottom right plate”) what you liked about the project, and what about this collaborative art experiment could be made better for next year. Unfortunately, I did not get to contribute this year, but I did discuss the project with friends in the class. I really like the concept of a collaborative (and also competitive, occasionally) project with an end result that is artistic (while also leading to the lesson next week). I think the process was very lovely, with people’s ideas growing and shifting until it reaches a fully developed design. I’m not too sure if this would lose the spirit of the assignment, but coordinating within nodes or between people might better guide us towards a final design. I feel like the end result, with the four different designs on each well, was a little lucky.