When you strike out three times in one game …

To continue with Peter Newbury’s (@polarisdotca) baseball analogy week, when you’re playing baseball, and have struck out three times in one game – you go up to bat the next time even more determined to get on base. This mentality is one of the reasons I think baseball players make good scientists – when you’re working in the lab, sometimes your procedures don’t work – again, and again, and again. Determination to get a result is sometimes all that matters.

Sometimes in the lab it’s faulty equipment. Sometimes the reagents have expired. Sometimes you don’t know what happened and have to go back and troubleshoot. After doing my DNA extractions and PCR reactions last month, my positive controls have DNA, my negative controls are free of DNA (both good things) and my Agar Gels seem to look clean of any problems. Unfortunately, my real samples aren’t showing any bands of DNA anywhere. Possibly there isn’t much DNA in the samples to begin with (they’re methanogens after all, low-biomass communities), or the oil in the samples interferes with the extraction process. Either way, I’m starting from scratch this week to get results, and not giving up – the geochem and isotope data look great in this experiment, and having some proper DNA sequencing will be the Mariano Rivera (or Tom Henke, if you prefer) of this study – providing the last bit of evidence to close out a really great story.

Baseball is life. Life is baseball. Particularly true in science, these analogies never seem to end.

~B

TomHenke

Tom Henke, closer for the Toronto Blue Jays first World Series win in 1992. Photo: http://www.rocketsports-ent.com/

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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