You win some, you lose some

Our project is starting to pick up! After our initial sampling/sequencing period, we realized that there is actual DNA we can work with from the tanks. This past week, we started our actual sample collecting from the tropical tank. We collected 3 sets of samples from the sediment, walls, and water. Throughout the week, we extracted the DNA and ran PCR on all 9 samples (plus one negative control). Today, we completed the gel electrophoresis and got some unpleasant results. Unfortunately, we couldn’t see the primer bands and the DNA bands didn’t show up like we thought they would. This means something went wrong in our PCR, but we don’t know if it was during PCR16SA or PCR16SB. Well, it’s back to the drawing board! Starting next week, we will be re-running the PCR on the 9 samples and possible collecting more samples from other tanks.

Although this week’s results were a bust, we know that there is definitely some DNA present that we can work with. I’m sure we’ll be finding some pretty cool things as we continue sampling and sequencing. 🙂

Sampling, DNA extraction, and PCR, OH MY!

For the past week, we’ve been doing preliminary sampling, as well as some DNA extractions and PCR on samples from the saltwater and freshwater flasks of water that we filtered and the wall and protein skimmer from the saltwater tank. Those four samples have now been through PCR. Although we found DNA, but the gel prepared after the PCR failed. We also went back to the tanks to gather samples from a saltwater tank that is soon to be broken up to create two coral ponds.

Hi There!

I’m Sabreen Aulakh, one of the undergraduates working on the Undergraduate Aquarium Project! I’m a third year Microbiology major, and my plan is to go to medical school some time in the near future. I’m from San Jose, and I love to dance, specifically Bhangra, which is a traditional North Indian dance from Punjab, India. For those who are curious as to what it looks like, here’s a video of my team. (Nope, I’m not in this video because I was still in school.)

There’s just something about how those teeny tiny microbes have huge impacts on their environment that’s so darn interesting to me! I’m very excited to be a part of this lab, and can’t wait to see how this project unfolds. 🙂

Introductory Post

Yes, a boring title, but that’s exactly what this is. I am Alex Alexiev, second year biological sciences major. I’ve been thinking about a microbiology major for the past year or so, and this lab seems like a step in the right direction. I love aquatic systems and I think microbes are awesome, so I am extremely excited to research the two. Who knows what results the data will yield, but at the very least, it should be interesting.

New undergraduate research project: Aquarium Biogeography

Last year we undertook an undergraduate research program to isolate bacteria and sequence reference genomes from the built environment.  That work is still ongoing, and can be found here.

This year we’re going to take a look at the biogeography and succession of microbial communities in aquariums.  We’re fortunate to have access to several aquariums here on campus that we can examine.  We’ll be looking at a number of different questions, more detail will be forthcoming in student posts.

We had our first meeting yesterday and will begin sampling aquariums starting this coming Monday.  Watch this space for information on our progress.