Labs
Lab writeups:
Contents Dilution Practice Lab Practice Dilution practice 1 The stock concentration of a mystery substance (MS) is 5 M. Calculate how to dilute to 100 µM (0.1 mM).
Week 2 Lab: Gel Electrophoresis Art
Contents: Planning Lab Prep Gel Art Planning Notes: i don’t have lambda DNA, but i do have Escherichia coli BL21 genomic DNA and a small collection of various plasmids and PCR products of varying rates. we also have a handful of restriction enzymes but not a lot, and mostly not common ones. i think my strategy is going to be: sketch out a design run a restriction digest on the E. coli genomic DNA to get a bunch of different-sized fragments. doesn’t particularly matter which one i think. run the digest on a gel, and purify out the fragments of the size i want with a Qiagen or NEB kit; note: i am going to have to elute with pretty small volumes to keep them concentrated enough to show up in subsequent gels. run a new gel with the purified fragments based on the design (possibly augmenting with PCR products if desired for brightness/intensity). take photo to show off for whatever reason, neither uploading Genbank files and downloading accession files for the E. coli genomic assembly in Benchling is working for me. i suspect it probably has to do with the size of the files and speed (or lack thereof) of my internet. so i can’t do much in-silico planning and testing. but i think my plan will work without it. it just means i’ll have to do more testing during instead of thinking/planning prior. Lab Prep: Sketch out a design. I found a photo of the Portland skyline with Mt. Hood in the background from the City of Portland’s Instagram. Photo credit: @james.is.jumbled. I traced the lines of primary visual components to get a line art style drawing, and then split it into a grid of 16 columns, for the 16 wells for the largest gel comb I have available. I recreated the gridded line art, scaled to a printout of the 1kb+ gel ladder, to approximate the size DNA fragments I would need in each column.
Week 4 Lab: Protein Design Part I
No lab this week; see week 4 homework instead.
Week 5 Lab: Protein Design Part II
No lab this week; see week 5 homework instead.
Week 7 Lab: Neuromorphic Circuits
We started off our node’s discussion of the neuromorphic circuits based off of a couple example circuits developed by TA Steven with help from ClaudeAI. Because I feel like I don’t really understand the analog vs binary computing, I was most interested in the design that explored that aspect. Option C: Competing Inhibitors Concept: One dominant ERN (CasE, high dose) controls the whole network. It kills both Csy4 and the green output directly.
Unfortunately, this lab is not available for remote participation.
Week 10 Lab: Mass Spectrometetry
Unfortunately, this lab was not available for remote participation. See this week’s homework for data analysis.