Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
Class Assignment 1. First, describe a biological engineering application or tool you want to develop and why. I want to develop a membraneless organelle within plant cells that is able to detect breakage of the cell membrane by a foreign organism. This organelle, which is comprised of intrinsically disordered proteins (IDPs), would trigger immune system responses upon detection. The purpose of this organelle is to detect and shut down fungal plant pathogens that infect through breaching cell membranes. This novel application would lower yield loss in rice plants (primarily Oriza Sativa) from fungal diseases like Rice Blast (Magnaporthe grisea) which is responsible for 10%-30% yield losses every year for rice, preventing the possibility of feeding about 60 million people.
Week 2 HW: DNA Read, Write, & Edit
Part 1: Benchling & In-silico Gel Art Info This is a picture of the gel art I designed on Benchling. The bands in the 1-6 ladders create the word “Hi” on completion. The restriction enzymes used on the Lambda DNA are listed above the diagram.
Assignment: Python Script for Opentrons Artwork This is a link to the code for my Opentrons Artwork. AI Contributions: I used AI to generate large portions of my code as I am largely unfamiliar with python programming. I used Gemini AI and asked it to integrate my coordinates for my artwork into the code in Colab.
Week 4 HW: Protein Design Part I
Part A. Conceptual Questions 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) Assuming that meat contains about 20% protein, 500 grams of meat translates to ~100 grams of protein. If an amino acid weighs 100 Daltons, this will translate to 100 grams per mole of amino acids. Knowing this, we calculate 500 grams of meat to have one mole of amino acids. Using Avogadro’s constant, we can calulate the number to be 6 x 1023 molecules of amino acids in 500 grams of meat.
Week 5 HW: Protein Design Part II
Part A: SOD1 Binder Peptide Design (From Pranam) Part 1: Generate Binders with PepMLM This is the human SOD1 sequence containing the A4V mutation: MATKVVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ Binder Pseudo Perplexity 0 WHYYATGARWGE 16.929015 1 WRYGAVALELKK 12.714672 2 WRSPAAAARWWK 9.155765 3 WRYPATAAALKX 4.843841 4 FLYRWLPSRRGG N/A Info The table generated by PepMLM detailing possible peptides to bind to mutant SOD1 along with their pseudo perplexity scores. Peptide 4 is an already known SOD1-binding peptide.
Week 6 HW: Genetic Circuits Part I: Assembly Technologies
Assignment: DNA Assembly What are some components in the Phusion High-Fidelity PCR Master Mix and what is their purpose? The Phusion High-Fidelity PCR Master Mix consists of Phusion DNA Polymerase, deoxynucleotides, and a reaction buffer (including MgCl2). The Phusion DNA Polymerase is a high-fidelity enzyme that is used to synthesize new, complementary nucleotides to the 3’ end of a DNA strand. Deoxynucleotides are present within the master mix to be added to the cloned DNA strand. The reaction buffer facilitates enzymatic function and stabilizes the DNA polymerase, allowing the PCR reaction to proceed smoothly.
Week 7 HW: Genetic Circuits Part II
Assignment Part 1: Intracellular Artificial Neural Networks (IANNs) What advantages do IANNs have over traditional genetic circuits, whose input/output behaviors are Boolean functions? Intracellular Artificial Neural Networks (IANNs) have several advantages over traditional Boolean genetic circuits. Traditional genetic circuits usually operate in an ON/OFF manner where genes are either expressed or not expressed. In contrast, IANNs can process inputs in a continuous and graded manner similar to biological systems. This allows IANNs to respond to multiple inputs at once with varying strengths instead of simple binary outputs. IANNs are also more capable of pattern recognition, noise tolerance, and complex decision making. These systems can integrate many molecular signals simultaneously and produce more flexible cellular behaviors than standard Boolean logic gates.
General homework questions/answers 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 has several advantages over traditional in vivo protein expression methods. In cell-free systems, researchers have direct control over experimental conditions such as pH, ion concentrations, temperature, substrate availability, and DNA concentration without needing to maintain living cells. This allows for rapid optimization and easier manipulation of gene expression conditions. Cell-free systems also avoid problems associated with cellular toxicity, metabolic burden, and membrane transport limitations. In addition, proteins can be produced much more quickly because there is no need for cell growth or transformation. Cell-free expression is especially beneficial when producing toxic proteins that would kill living cells and when rapidly prototyping genetic circuits for synthetic biology applications.
Week 10 HW: Advanced Imaging & Measurement Technology
Homework: Final Project Measurement Draft 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. For the experimental validation of Project Aero-Sentry, several distinct biological and biochemical components must be measured to ensure the engineered probiotic nasal spray functions as intended. First, the transcriptional activity and expression level of the chimeric EnvZ receptor must be quantified to confirm successful membrane integration. Second, the binding affinity and kinetic interaction between this engineered receptor and the target allergen, Bet v 1, must be measured to verify the precision of the sensory mechanism. Third, the transcriptional output of the sense-and-respond genetic circuit must be monitored, specifically tracking the induction of the Nb32ILZ nanobody gene under the control of the osmolarity-responsive pOmpF promoter. Finally, the total concentration of the secreted Nb32ILZ fusion nanobody in the extracellular environment must be measured alongside its ultimate neutralization efficiency when bound to Bet v 1, confirming that the therapeutic countermeasure is produced in effective quantities.
Week 11 HW: Bioproduction & Cloud Labs
Part A: The 1,536 Pixel Artwork Canvas | Collective Artwork For the artwork, I contributed to four pixels on the DNA strand. I really liked how the whole community came together to work on this one project. It was nice to interact with all the other students in the HTGAA course.
Week 13 HW: AI, SynBio, and Scaling Health Innovation (ARPA-H)
Info No Homework. . . Working on final project.
Week 14 HW: Bio Design & Bio Fabrication
Info No Homework. . . Working on final project.