Research Experience for Community College Students in Critical Zone Science

June 9^th, 2016

I showed up to the lab happy to find out that the peptidoglycan extraction hadn’t happened yet! I was excited that I would be able to see how to go from having a concentrated solution of bacteria cells to only having fragments of their peptidoglycan leftover.

Although I was ecstatic for learning the process, I was a bit saddened that I was not able to help with the extraction at all. I walked around the lab following Tess and Paul, another laboratory technician, like a duckling following its mother. I still made a point to ask questions when I didn’t understand what was happening, or if I wasn’t sure what was next in the procedure, but I didn’t have the chance to touch or use any laboratory equipment at all. It was an interesting process to observe, nonetheless; the bacteria cells were killed with the addition of trichloroacetic acid and by boiling them in glass tubes submerged in a water bath – this ensured that the cells burst and their innards spilled out into a glob at the bottom of the tube, leftover DNA was digested with the addition of DNase and proteins were digested with the addition of trypsin. All that was left of the bacteria was some peptidoglycan fragments and peptides.

Although I wasn’t able to do any lab work, one particularly useful part of today was sitting down with Tess and scheduling a work plan. We discussed what was left to do for the experiment and set reasonable due dates for completing each task. We then made sure to keep a few weeks in July freed up just in case the experiment doesn’t go exactly as planned. The last few weeks of my time in the laboratory will be spend processing data and prepping for the poster session and presentation.

Part of our experiment is to subject the soil bacteria to 5 different resuscitation substances; substances that cause dormant bacteria cells to “wake-up” and start actively growing again. We’ve already determined three that we can test: the peptidoglycan fragments, N-acyl homoserine lactones (AHLs), and volatile organic compounds (VOCs) from leaf litter. Tess assigned me to come up with 2 more by tomorrow – if the substance requires some sort of extraction procedure, and especially by Monday when we need to start testing the resuscitation substances. The pressure is on! I’m feeling a little lost since I don’t know what to look for and my understanding of the physiology of microbes and the availability of supplies in the lab is painfully novice. I’m hoping that I can come up with something… I will definitely read some articles and look through some textbooks to hopefully have 2 ideas for substances to try that have a relatively reasonable validation behind choosing them.