My Summer Research Project: Why not?

I’m Alison, and I just finished the first year of my Environmental Science degree at U of C. When thinking about a summer job I figured I’d email my professors from first semester asking if they knew anyone who had a project that could use a newbie who likes to learn more cool stuff. Since, first years are generally regarded as the babies of academia, I didn’t really expect too much. Lucky for me, my Geology 201 prof Ben had something I could do. He met with me and briefly explained that I’d be doing work with oil core samples, by looking at isotopes from those samples. With nothing else to go on I figured, why not? I know that isotopes are atoms of the same element with a different number of neutrons, and that oil core samples probably come from the ground somewhere in Alberta… With all my previous expertise, they took me on.

Measuring samples for carbon-13 analysis on the microbalance.

My science knowledge is from high school and first year (which overlaps quite a bit). So my first week was just learning more about isotopes, like what a stable isotope actually is, and how we can use them to learn about environmental systems. My previous knowledge from physics, chemistry and geology helped give me the basics: isotopes have the same number of protons, a different number of neutrons, and different isotopes of the same element react slightly differently, because they don’t have the same mass. Makes sense right? They’re different, so they get used differently in chemical reactions. Now, a stable isotope is nonradioactive, so no radiation occurs and it exists forever through the geological record. Carbon and sulphur are two elements that have stable isotopes. By looking at what’s referred to as the isotope ratio, it’s possible to figure out how the carbon and sulphur got there in the first place! For example, having a lot less Carbon-13 (a carbon atom with 6 protons and 7 neutrons) than usual means that the carbon is most likely organic – the carbon was once alive.

So in the core samples, I’m going to take a look at the organic carbon (in the oil mucky stuff itself), some inorganic carbon (in carbonate rock that is actually pretty easy to find in the oil muck), and some sulphur (in the pyrite grains). Pyrite’s that shiny fools gold that’s so easy to recognize, but I still needed some help looking for it since the grains are so small. And the first time I thought I found something exciting, it turned out to just be some ink on the rocks from the drill cutting procedure. Things like that you just have to learn as you go. And by looking at those isotopes in those places, I’ll hopefully be able to help figure out how the rocks and oil got there in the first place. Or that’s the plan anyways.

So now that I know the plan, hanging around a lab all summer seems like a pretty good time. I have to ask about pretty much everything (like, if I wanted to weigh something, what would I weigh it in? I’d never used a weigh boat before today, but that’s how you do it). But I get to learn and see more everyday. I feel like even if I just hung around and watched I’d learn a lot more cool things about a lot more cool stuff. Which in my mind is really what science is, so why not?

-Alison

*** editor’s note: Alison will be a contributing author on the blog this summer while she works on her project. Stay tuned for more details on her work!

Extracting DNA: like baking, gotta follow the recipe

I had an interesting “out of the geologists’ box” experience last week when I started extracting DNA from the microbial enrichment cultures I’ve been growing. The goal of this experiment is to link microbial methanogenesis to the geochemical and isotopic fingerprints in oil sands cultures with variable salinity. Since the McMurray formation hosts oil sand deposits with a variety of geochemical conditions, ranging from fresh to ocean-level salinity, we hope to examine what changing chemistry does to the microbial populations that live in the sands, and degrade the oil over geological time. I started growing these enrichment cultures almost a year ago, and they have finally built up enough biomass to attempt an extraction, to see which bugs are most successful in each environment (fresh, brackish, saline).

I’m working closely with Lisa Gieg, an assistant professor in the Department of Biological sciences, and Sandra Wilson, a post-doctoral researcher in Lisa’s lab. Both have been exceptionally helpful and tolerant of my lack of biological expertise, and have shown me the ways of molecular biology. Extracting DNA from an environmental sample is a fairly straightforward procedure, but requires exceptional sterile technique to ensure human DNA doesn’t contaminate your samples. Sandra’s been super-helpful in this respect, keeping my technique proper and methodology in line. Generally the idea is to sample a bulk piece of the environment (a soil, or oil sands core), break the cells down so the DNA is exposed in solution. Proteins are then separated from the solution, and voila, DNA extract! It’s not exactly as simple as it sounds, something like an 18 step process that takes me a little over 4 hours to crunch through 4 samples (I’m getting faster every time I do it, I think). Once the DNA has been extracted from the samples, I need to run the polymerase chain reaction (PCR) to amplify the DNA enough for sequencing. The samples are then shipped off to Genome Quebec for sequencing, and I’ll know what type of bugs are in my samples in a couple months time (the isotopic results suggest dominance of acetoclastic methanogens, so I suppose that’s my hypothesis to be tested). It’s almost incredible that we (the human race, not just our research team) have the capability to determine the types of microbial populations accurately in such a short time period – and even more so that we (same “we” as above) have built an enormous database from which to interpret results. Through these types of collaborative research projects, we can build expertise across disciplines and solve the mysteries of how the world works, especially how the biological world seems to control geochemical processes so very often. Interdisciplinary science is pretty awesome.

B