Labs
Lab writeups:
I was sick this week and missed lab.
Week 2 Lab: Gel Electrophoresis
Gel Electrophoresis Designs Our group set out to make a design with the letters “HA”, standing for the name of one of our group members, Hines Alayah. We somehow ended up with “LU” instead. Sometimes biology happens by accident, so we have decided that “LU” stands for Love U. A few photo highlights below. Loading the restriction enzymes into the lanes.
Opentrons Designs I tried to push Opentrons to the limit and chose a fairly hard design: the Mitsudomoe, a traditional Japanese family crest (Kamon) associated with my family. The result didn’t come out particularly clean, but with higher resolution and non-sequential pipetting (for speed) it would be more tractable. Reference design and Opentrons version: Lab Automation Find a published paper that uses Opentrons or another automation tool for a novel biological application. The paper I chose is AssemblyTron: flexible automation of DNA assembly with Opentrons OT-2 lab robots, by Bryant et al., published in Synthetic Biology (2023). The authors developed an open-source Python package called AssemblyTron that connects j5 DNA assembly design software to an Opentrons OT-2 liquid handling robot, allowing users to go from a digital DNA design to a physically assembled construct with minimal hands-on work.
See the Week 4 homework for this week’s writeup.
Week 5 Lab: Protein Design Part 2
See the Week 5 homework for this week’s writeup.
Week 6 Lab: Genetic Circuits Part 1
Gibson Assembly Lab This week we performed a Gibson Assembly to clone chromophore-mutant inserts into the mUAV backbone. A few photo highlights from the lab. Setting up the PCR reactions: pipetting primers, template, and master mix into tubes. Loading samples into the E-Gel EX Invitrogen cassette for gel electrophoresis.
Week 7 Lab: Genetic Circuits Part 2
This week we designed a 2-layer intracellular neural network circuit and simulated its behavior. Our team designed a comet. The heatmap of the circuit’s predicted output across X1 and X2 input space produced a comet-shaped gradient: high expression concentrated in the low-X1 / low-X2 corner, with a tail fading diagonally across the landscape. Circuit design spreadsheet. Our poly-transfection mix with Csy4, CasE, mNeonGreen, and fluorescent markers.
Writeup pending.
Lab Day at Waters Immerse Schematic of the Waters LC-MS instrument setup. Our roadmap for the day’s experiments. The team suited up in lab coats and safety goggles at the Waters facility. Benchside doodle. Someone’s artistic interpretation of the day’s science between runs.
Week 11 Lab: Bioproduction & Cloud Labs
Writeup pending.