Homework

Weekly homework submissions:

  1. First, describe a biological engineering application or tool you want to develop and why. I want to develop a biological engineering system for smarter nutrient liberation in agricultural soils, especially for sugarcane. The current nutrient management system depends heavily on chemical fertilizers that release nutrients in poorly timed pulses, leading to massive nutrient losses, soil degradation, and environmental damage. I do not want to sugarcoat it: the situation is bad. I am Brazilian, which also means I come from the country that exports the most sugar in the world, largely through intensive sugarcane monoculture. My goal is to explore how engineered soil microorganisms could sense plant-derived signals and release nutrients only when they are biologically needed, turning the soil from a passive substrate into an active, responsive system.

  • Week 2 HW: DNA r/w/e

    Part 1: Benchling & In-silico Gel Art: 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. It’s a smiley face!! :) Part 3: DNA Design Challenge: 3.1 Chose your protein Alkaline phosphatase. I chose this protein because it plays because it is important for nutrient sensing, as it is naturally activated under conditions of phosphate limitation. In Escherichia coli, alkaline phosphatase (PhoA) hydrolyzes organic phosphate compounds to release inorganic phosphate, directly linking environmental signals to nutrient availability. Additionally, it is a well-characterized enzyme with a resolved structure and extensively documented sequence information, making it an ideal model protein for computational and experimental analysis.

  • Week 3 HW: Lab Automation

    Part 1: Python Script for Opentrons Artwork I used the amazing Donovan’s tool to create this, then used the coordinates… It’s a homage to my cat Nico. He is a crazy cute orange cat. UPDATE (THE RESULT!) And… here is the result! I’m so happy, this is so cool! Thank you so much, USFQ node :) Oh, and here is the real Nico haha

  • Week 4 HW: Protein Design Part I

    Part A. Conceptual Questions All of the questions are so interesting, so c :D 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) To answer this question, we first need to know how much of meat is made of proteins (therefore, aminoacids). A quick search on Google returned that in 100g of meat we have ~26g of protein (this, of course, changes based on what type of meat we’re talking about, but let’s use this number). Then we have 130g of protein in 500g of meat. If on average an aminioacid is ~100 Daltons (equivalent to 100g/mol) then we have 1.3 mol in 500 grams of meat. Therefore 1.3 x 6 x 10^23 molecules.

  • Week 5 HW: Protein Design Part II

    Part A: SOD1 Binder Peptide Design (From Pranam) Part 1: Generate Binders with PepMLM I first generated the mutated sequence: SOD1 A4V MATKVVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ I then used the PepMLM-650M notebook to generate peptide binders conditioned on the mutant SOD1 sequence. I set the peptide length to 12 amino acids and generated candidate binders from the model output. The resulting peptides and their pseudo-perplexity values are shown below.

  • Week 6 HW: Genetic Circuits Part I

    Assignment: DNA Assembly 1. 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 Phusion DNA polymerase, a enzyme that synthesizes DNA (this one also has proofreading activity). It also includes HF buffer, which provides the optimal pH and salt concentration (MgCl2) required for enzyme activity, as well as dNTPs, which are the nucleotide building blocks used to synthesize the new DNA strands. Glycerol helps stabilize the enzyme, and DMSO may be added to improve amplification of GC-rich regions by reducing secondary structure formation.

  • Week 7 HW: Genetic Circuits Part II: Neuromorphic Circuits

  • Week 9 HW: Cell-Free Systems

    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. Cell-free protein synthesis (CFPS) offers much greater flexibility and experimental control than in vivo expression because protein production occurs outside living cells, typically in a test tube using cellular extracts. This means variables such as DNA concentration, ion composition, temperature, cofactors, chaperones, and energy substrates can be precisely adjusted without worrying about cell viability, metabolism, or toxicity. Another notable example is time, as to perform CFPS takes 1 –2 days, whereas in vivo protein expression may take 1–2 weeks. Here are two examples of when CFPS can be efficiently used:

  • Week 10 HW: Advanced Imaging & Measurement Technology

    Final Project For my final project I would like to measure a few things: whether the biosensor can detect carbon monoxide (CO) in a reliable and quantifiable way. The main readout will be the signal generated after CO binding, such as fluorescence, or a visible color change, depending on the final design. By exposing the system to known CO concentrations, I can build a calibration curve and evaluate sensitivity, detection range, and response time. also if the protein sensor itself is being produced correctly and remains functional. For this, I would use SDS-PAGE to confirm protein size and purity, and UV-visible spectroscopy to verify heme incorporation and observe spectral changes upon CO binding. To test specificity, I would compare the response to CO with other gases or environmental factors such as CO2 and humidity. Waters Part I — Molecular Weight Question 1 Using the online calculator, the calculated molecular weight (unmodified) is 28006.60

  • Week 11 HW: Bioproduction & Cloud Labs

    Part A: The 1,536 Pixel Artwork Canvas | Collective Artwork Unfortunately, I didn’t have a chance to contribute because I never received the personalized URL. I guess I’ll have to make up for it by becoming a TA this fall :) That said, I really loved the idea of collaborative bioart. My favorite part was the upper right section with the gene expression, it looks so cool. For next year, I think it could be even more engaging if there were multiple canvases or themes (for example, one per node or topic), so more people could contribute and explore different ideas within the same project.