Research

Literature review and explanations of my own research, for my own understanding.

Lab Recipes

1 min 148 words
Yep Lab

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

2 min 394 words
Yep Lab

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

5 min 1014 words
Lehr Lab

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. …

Colony Counting using YOLOv8n

2 min 400 words
Yep Lab

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

3 min 427 words
Lehr Lab

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} …

ASM 2025

3 min 595 words
Yep Lab

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

3 min 533 words
Yep Lab

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

3 min 492 words
Yep Lab

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 …