Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
First, describe a biological engineering application or tool you want to develop and why. This could be inspired by an idea for your HTGAA class project and/or something for which you are already doing in your research, or something you are just curious about. I am curious aboutI the develop of engineered biological decoys systems designed to reduce infections by preventing bacteria or viruses from attaching to human cells. Instead of destroying pathogens these systems would work by mimicking the cellular receptors that microorganisms need to initiate infection. It would consist of synthetic type of cells that display molecules similar to those found on real cell surfaces. Pathogens would bind to these decoys rather than to human tissues, thereby reducing the likelihood of infection and lowering the initial pathogen load. This is inspired by natural protective mechanisms such as mucosal barriers and could help reduce antibiotic use. By not directly killing microorganisms, it would reduce evolutionary pressure and potentially slow the development of antimicrobial resistance.
HW 3: Lab automation Assignment: Python Script for Opentrons Artwork Generate an artistic design using the GUI at opentrons-art.rcdonovan.com. Using the coordinates from the GUI, follow the instructions in the HTGAA26 Opentrons Colab to write your own Python script which draws your design using the Opentrons. You may use AI assistance for this coding — Google Gemini is integrated into Colab (see the stylized star bottom center); it will do a good job writing functional Python, while you probably need to take charge of the art concept. If you’re a proficient programmer and you’d rather code something mathematical or algorithmic instead of using your GUI coordinates, you may do that instead.
Week 4 HW: Protein Design Part 1
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) The calculation would be to use an equation like moles = mass / molar mass, then multiply by Avogadro’s number. Roughly ~3 × 10²⁴ molecules. Why do humans eat beef but do not become a cow, eat fish but do not become fish? We absorb the nutrients, don’t imitate the animal, and slowly turn them into our own molecules.
Week 5 HW: Protein Design Part 2
Part A: SOD1 Binder Peptide Design (From Pranam) Part C: Final Project: L-Protein Mutants
Week 2 HW: DNA Read, Write, & Edit
HW 2: DNA Read, Write, & Edit Part 1: Benchling & In-silico Gel Art Own experience on: Make a free account at benchling.com Import the Lambda DNA. The first view of Benchling workspace Then i transfered de Lambda DNA, here we have two option for DNA document type, either we can use Genbank or, but Benchlink does have more options. Upload to Benchling So we can now view it on Benchling and start exploring the different options available