Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
Class Assignment Application: SoilBuddy With climate change set to disrupt global agriculture and the unsustainability of commercial monocultures threatening to render the arable land left unusable, humanity urgently needs solutions facilitating soil stewardship to fortify our food supply. Existing solutions are either too expensive for small-to-mid farms, worsening inequality in the developing world, impractical for massive commercial farms, necessitating guesswork set to be upended by the sea change wrought by climate change, or provide, at best, noisy, time-lagged feedback through remote sensing.
Week 2 HW: DNA Read, Write and Edit
Part 0 Done. Part 1 Since it’s passe to create “MIT” with the electrophoresis gel, I decided to reverse the order of the letters to spell “TIM” instead. Part 2 I don’t have in-person access to a node, so can’t perform the wet lab component.
Part 1 Find and describe a published paper that utilizes the Opentrons or an automation tool to achieve novel biological applications. The paper I’ll be analyzing is titled “Development of a high-throughput minimum inhibitory concentration (HT-MIC) testing workflow” published in Frontiers in Microbiology. In summary, the researchers used an Opentrons OT-2 robot to automate an assay used to test the safety-efficacy profile of an antibiotic. They accomplished this by programmatically preparing a serial dilution of the antibiotic candidate across multiple 96-well plates with replicates, innoculating the wells with the test bacteria, then measuring the optical density of each well with a plate reader to determine bacterial viability after the antibiotic challenge.
Week 4 - Protein Design Part I
Part A Number of amino acids = 500g/(100 Da) = 5 mol = 3.0 x 10^24 molecules of amino acids (approx). Over the course of digestion, the polynucleotides are broken down into constituent nucleobases prior to absorption. Considering the degeneracy of codons, these 20 amino acids were sufficient to produce a diversity of proteins, and were evolutionarily conserved due to a lack of strong selection pressure against them (ie. they were “good enough”). . They could’ve formed abiotically given the presence of organic precursors such as carboxylic acids, amines and small molecule side groups, catalyzed by zeolites, and triggered by lightning and heat on the primordial earth or extraterrestrial asteroids respectively. Left-handed spirals. Yes, some examples are $\pi$ helices and $3_{10}$ helices. It’s more energetically stable given L-amino acids and D-saccharides predominate natural protein helices and the sugar-phosphate backbone of polynucleotides respectively. In aqueous environments, the hydrophobic portions of beta sheets are driven together by steric interactions while the hydrophilic groups facilitate relatively strong intermolecular hydrogen bonding. Beta sheets allow for strong intermolecular bonding, in hydrophobic zippers, that renders misfolded proteins more stable than their functional conformations and facilitates the addition of more proteins to the aggregate fibril - the biochemical basis of amyloid pathogenesis. Yes, you could make materials out of amyloid beta sheets but they’d only be stable under aqueous conditions and would be potential biotoxins. . Part B I chose to investigate an antifreeze protein from an arctic bacterium as a potential solution for winter snow-clearing.