Lab Recipes
Swarming Media 1% (w/v) tryptone 0.5% (w/v) yeast extract 1% (w/v) NaCl 0.6% (w/v) Eiken agar (not regular agar!) 0.5% (w/v) Glucose (add from a sterile 20% glucose solution after …
1 min
Yep Lab
Research
Literature review and explanations of my own research, for my own understanding.
12 pages
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Proposed Assay for CA Supplementation
The following tests the hypothesis that the nonswarming strain fails to swarm under an immobilizing lack of surfactant. Provided this is true, external supplementation of CA should …
2 min
Yep Lab
AAS Trial 1 / Standard Operating Procedure
Quantification of Iron in E. coli Cells by Atomic Absorption Spectroscopy PurposeThis protocol describes the use of atomic absorption spectroscopy (AAS) to quantify iron in an E. …
5 min
Lehr Lab
Colony Counting using YOLOv8n
Model used is YOLOv8n pretrained on colonies1, but optimized for our use. The process is as follows: flowchart TD A["Load image"] --> B["Find Petri dish with …
2 min
Yep Lab
Calculations for AAS
The reported amount of of iron in WT E. coli is around 10^5 to 10^6 atoms per cell 1. Converting atoms per cell to micrograms per gram of cellsUsing \[ 10^5 \,\text{atoms Fe/cell} …
3 min
Lehr Lab
Revision to the Biofilm Assay: The Bladder Cell Invasion Protocol
Since we were having issues with the biofilm formation, as expounded upon in a previous post, Dr. Yep decided to make some revisions to the protocol. This post will be a brief …
3 min
Yep Lab
Iron Quantification using Atomic Absorption Spectroscopy
Since we’re working under the assumption that we have isogenic mutants with varying intracellular iron concentrations, it would only make sense to verify this assumption by …
7 min
Lehr Lab
ASM 2025
This short informal post is long overdue, but I’ll excuse myself since this website wasn’t up and running in June, when I attended the conference—and besides, I’ve been busy with …
3 min
Yep Lab
Issues with Biofilm Formation
In the lab, Kelsey and I have been running into issues with the biofilm assay. Regardless of the incubation period, the E. coli strains that are supposed to form biofilms aren’t …
3 min
Yep Lab
LB, ∆fur, and Stationary Phase
Dr. Yep noticed how ∆fur stalled earlier than the other strains. It’s not necessarily a problem, but I’d like to understand the cause. The paper should also explain this, so we’ll …
3 min
Yep Lab