Labs
Lab writeups:
Pipetting & eGels In this week’s lab, we were tasked with familiarizing ourselves with standard pipetting equipment. We utilized P20, P200, and P2000 micropipettes, along with petri dishes and glass slides. Having prior experience in a wet lab, it was fun to explore the equipment artistically. I started by creating some “droplet art” on a glass slide using colored water. I then decided to make a smiley face and a DNA strand in the same fashion, pipetting individual droplets of colored water and “streaking” them to create lines.
Lab: DNA Gel Art Today in lab, we attempted to make DNA Gel Art using restriction enzymes and software (Benchling). In recitation, we were given an example of someone using time-controlled gel work to create an image, so I came up with a plan to use that framework to create an image of Pac-Man. I used SalI, which cuts only a single 500 bp strand from lambda DNA, for my digest to create my “blocks” that I would effectively “stack” as I pipetted them at interval times on the gel.
This week in lab, we used the Opentrons machine, giving us a taste of lab automation with an artistic twist. We pipetted flourescent, genetically engineered E.coli onto agar mixed with activated charcoal to create our design and canvas respectively. After a 16 hour incubation period, we were able to see images of our results under UV light! I decided to make two designs, one of the US Virgin Islands to pay homage to where I’m from, and the other was the Dark Side of the Moon Album Cover, as I thought it used a good variety of colors. The robot moved from top left to bottom right, which prompted a discussion with Ronan about the most optimal pathing system for the trajectory. The robot’s movement is controlled by a Python script, and Ronan created a website to generate the coordinates of each colored pixel, which the script implemented.
Week 4 Lab: Protein Design Part I
Protein Selection Briefly describe the protein you selected and why you selected it. Again, continuing with my idea for designing a carbon sequestration system, I am going to be looking at Rubisco, the most abundant protein on earth. Rubisco catalyzes photosynthesis in plants, converting atmospheric CO2 into an organic three-carbon acid that eventually is built up into sugars for plant growth. It is made of 8 large subunits and 8 small subunits.
Week 5 Lab: Protein Design Part II
Lab Option 1: L-Protein Mutational Analysis Experimental Validation & DMS This lab provides a Deep Mutational Scanning (DMS) style validation of the L-Protein. By cross-referencing experimental lysis results—where a score of 1 indicates functional lysis and 0 indicates non-functional—with the Log-Likelihood Ratio (LLR) Heatmap generated via ESM2, we can assess the predictive power of protein language models.
Day 1: Preparation of DNA Fragments Background In this two-day lab, we modified the color-generating chromophore of the purple Acropora millepora chromoprotein (amilCP) to create a variety of orange, pink, and blue mutants. We performed two sets of Polymerase Chain Reactions (PCR) to prepare for a Gibson Assembly. The insert PCR region spans the 24 base pairs before the chromophore to just beyond the gene transcription terminator. The forward primer includes an intentional mismatch for site-directed mutagenesis of the mUAV DNA plasmid. These mutants were then expressed in chemically competent E. coli cells.
Week 7 Lab: Neuromorphic Circuits
Intracellular Artificial Neural Networks (IANNs) In this two-day lab, we designed and built our very own IANN using a library of plasmids from the Ron Weiss lab and human embryonic kidney (HEK) 293 cells. IANNs differ from traditional synthetic genetic circuits because IANNs can perform analog computations, rather than being limited to digital computations. IANNs are also universal function approximators—given an adequate number of intracellular artificial neurons, you can use an IANN to achieve any input/output behavior you’d like.
Week 9 Lab: Protein Purification & Mycelium
Fungal Materials Follow-up The first thing we did was look at our mycelium molds (no pun intended). We are tracking the growth and structural integrity of the fungal networks as they colonize the substrates. Protein Purification: An Introduction To isolate our protein of interest, we first had to grow the cells and then lyse them using a combination of B-PER (Bacterial Protein Extraction Reagent) and sonication. This process breaks open the cell membranes, resulting in a lysate solution (labeled as Tube A) that contains the total protein content of the cells.