Labs
Lab writeups:
Overview Materials: The following items were used in the lab: P200 Pipette: 20-200uL Pipette tips Eppendorf tubes PCR Tubes Petri dish Sharpie Tube holder invitrogen E-Gel EX: Agarose 1% Solutions I used included: Blue & Red food dye solutions DNA ladder solution (I was not able to get the exact details as the photo of the tube I took was blurry) H2O Machines I used included:
Week 10 Lab: Mass Spectrometry
This laboratory module introduces Liquid Chromatography-Mass Spectrometry (LC-MS) as a premier tool for protein characterization, focusing on enhanced Green Fluorescent Protein (eGFP). The experiment follows a logical progression from “minimally perturbative” measurements to increasingly disruptive techniques, allowing students to determine three critical pieces of information: molecular weight, protein folding/structure, and primary amino acid sequence. By moving from intact protein analysis under both native and denaturing conditions to bottom-up peptide mapping, the lab demonstrates how a protein’s physical state directly influences its behavior in a mass spectrometer.Beyond standard eGFP analysis, the curriculum highlights the biochemical nuances of the protein, such as the autocatalytic self-cyclization of its fluorophore which involves a specific $20\text{ Da}$ mass loss. As a specialized bonus, the lab introduces Charge Detection Mass Spectrometry (CDMS) to analyze macromolecular structures that are too large for conventional MS. Students will use this technology to investigate the quaternary structure of Keyhole Limpet Hemocyanin (KLH), a massive complex that exists in multiple oligomeric states within the megadalton range.
No real lab for this :D
Week 13 Lab: Golden Gate Assembly
I was in person! Impromptu so I don’t really have a lot of background information. We had like a Golden-Gate Assembly introduction
Overview Materials: The following items were used to prepare the agarose gel: Microwavable media storage bottles Agarose TAE buffer SYBR Safe DNA stain Gel tray & comb Eppendorf tubes PCR Tube rack Blue light transilluminator Imaging device Biological material I used included:
Overview Pre-Lab Process The idea of having to write my own code to create this art sounded terrifying at first given that I probably barely passed 6.100A. Then I found out a lot of it was written in Google Colab and felt relieved, until I kept running into issues so I decided to give up and just use Ronan’s code from his website: https://opentrons-art.rcdonovan.com/
Week 4 HW: Protein Design Part I
This lab is embedded into Part 3 of my Homework for Week 4
Day One Materials: The following items were used: PCR tubes Centrifuge tubes P200 pipette with 200uL tips P20 pipette with 20uL tips Nuclease-free water Sharpie Tube holder invitrogen E-Gel EX: Agarose 1% Biological material I used included:
Protocol For this section, I had to first download Neuromorphic Wizard, which was a whole process but I managed. I just filled out the Genetic Circuit Design Template with a design of my choice: My group mates decided to do something pretty similar, so we went with the same overall ERN and ERN_rec_ERNs. These were the predictions and experimental set-up that Neuromorphic Wizard came up with.
I was not here for this lab, unfortunately.