Research
Literature review and explanations of my own research, for my own understanding.
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 …
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 …
AAS Trial 1 / Standard Operating Procedure
Quantification of Iron in E. coli Cells by Atomic Absorption Spectroscopy Purpose This protocol describes the use of atomic absorption spectroscopy (AAS) to quantify iron in an E. …
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 …
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 cells Using \[ 10^5 \,\text{atoms Fe/cell} …
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 …
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 …
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 …
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 …
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 …