Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
Final Project Frugal Benchtop Bioreactors: Editing the DNA of an organsim is more accessible than ever. Basic lab equipment and plasmid services like GenScript mean that you can dream up your own sequence and express it in an host for around a hundred US dollars. However to unlock the real world impact of gene edits you usually need to be able to scale the production up. The next step in scaling beyond the shaker flask is a bench-top bioreactor where you figure out how to actively manage and optimize your organisms growth and characterstics. This expense of the benchtop stage makes it less accessible than the edit stage even though in many ways the technology involved is simpler. For example a new benchtop bioreactor typically costs tens of thousands of dollars or more. Even used bioreactors costs thousands of dollars.
Week 2 HW: DNA Read, Write, and Edit
Homework Part 0: Basics Of Gel Electrophoresis Attended lecture and watched recitation video Part 1: Benchling & In-silico Gel Art Link to Benchling Project , not sure how can see this link I asked to join HTGAA group but doesn’t seem like my invite was accepted yet? My drawing of an “E Gel Person” and associated enzymes in each lane are also in screenshot below Part 2: Gel Art - Restriction Digests and Gel Electrophoresis I don’t have access to these enzymes and DNA in my local makerspace lab.
Opentron Python Script Art Basic Idea The limited pixel resolution and colors of the petri dish reminded me of the old school bitmap monitors like the IBM PC that I grew up with. Also I wasn’t looking forward to guessing/figuring out a lot of pixel locations by hand, so I took a retro route and wrote some code to provide a terminal like API that let’s you specify a cursor location to write text to using a specific bitmap font and color.
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) Why do humans eat beef but do not become a cow, eat fish but do not become fish? Why are there only 20 natural amino acids? Can you make other non-natural amino acids? Design some new amino acids. Where did amino acids come from before enzymes that make them, and before life started? If you make an α-helix using D-amino acids, what handedness (right or left) would you expect? Can you discover additional helices in proteins? Why are most molecular helices right-handed? Why do β-sheets tend to aggregate? What is the driving force for β-sheet aggregation? Why do many amyloid diseases form β-sheets? Can you use amyloid β-sheets as materials? Design a β-sheet motif that forms a well-ordered structure. Okay I am going to take a first pass through here just going off the lecture, wikipedia, and background knowledge I already have and then go back and try with AI assistance for the ones I have no answer for.