Labs
Lab writeups:
Prelab Dilution Practice 1 Scenario: The stock concentration of a mystery substance (MS) is 5 M. Dilute to 100 µM (0.1 mM) using serial dilutions. 5 M = 5,000,000 µM Step 1: 500× dilution 5,000,000 µM / 10,000 µM = 500
Week 10 Lab: Mass Spectrometry
Lab 9 Work in progress check back later
Lab 2 Benchling & In-silico Gel Art: Recap This week, we made gel electrophoresis art using Lambda phage DNA and ten restriction enzymes. Gel electrophoresis uses a positive charge to pull negatively charged DNA through a conductive gel. Longer strands move slower and shorter strands move faster meaning that different lengths of DNA fragments will appear as different bars in your gel. To use this in an artistic context we take our input Lambda DNA and cut it to different lengths using different restriction enzymes which allows us to have coarse control over where these bars end up and thus we can make art with it. I have decided to really commit to my favorite animal, turtles, this semester and try to have a turtle-inspired theme to all of my projects. In an ideal world this is what I wanted my gel art to look like.
Lab 3 Lab Recap This week, we programmed the Opentrons liquid handling robot to create fluorescent protein masterpieces. I was really looking forward to this lab and even did last week homework about expressing GFP in E.Coli. Rather than using the GFP, I found we used a variety of different colors of superfluorescent proteins. Ronan’s webtool [1] made it really easy to visualize a design, and we could even upload images to serve as a template for our designs. I decided to go all in on turtles and make a turtles all the way down image featuring a turtle with a globe for its shell. This was the original image, from my collection of Turtle CADS:
Lab6 For lab this week we conducted a Gibson assembly to change the color of the purple Acropora millepora chromoprotein to a different mutant colors. I worked with Sean Murphy and Terry Luo, and we selected purple, orange, and light pink but ended up with 9 different petridishes to test our whole process, including: 4 x Purified DNA -> Gibson Assembly -> Transformation (but all mixed up and at much too low concentrations, there are four of these because one is all backbone) 3 x DNA straight from PCR -> Gibson Assembly -> Transformation (much higher concentrations but not purified) 1 x A mix of all of our purified DNA to see if we could get the concentration high enough and just see what happened 1 x A test with just the template plasmid A lot went wrong, so we really tried to troubleshoot.
Week 7 Lab: Neuromorphic Circuits
Lab7 This week we designed our own intracellular artificial neural network using plasmids from the Ron Weiss lab and human embryonic kidney cells. I worked with Sean Murphy and Terry Luo and together we designed a comet. The heatmap had a high prediction value in a square region in the bottom left corner, which then narrowed down and then expanded like the tail of a comet.
Lab9 In lab this week we learned about protein purification through a demo, then we mostly worked on our final projects. Here’s some more information about mine Final project - First DNA Twist Order For my final project, I want to make a “hydration” checking wearable device. Originally, I wanted to sense increased sodium levels insweat but that proved to be difficult so instead I’m approximating increased hydration risk by just detecting lactate. I want this to be a cell free system to make it more compatible with a safe wearable device.