Test run
Today was a productive day! I spent most of it upstairs in a laboratory for molecular biology, learning DNA extraction methods from Hanny. Since our return from Palau, she defended her thesis and received her PhD (congratulations, Dr. Rivera!). Now that the dust has settled, it's time we start processing all of the coral samples we collected.
Our first step was to test out two different methods for DNA extraction. Hanny's advisor graciously offered us some DNA extraction kits that were surplus in her lab, but the kits were a bit old and may have lost their effectiveness. We ran an experiment: using old samples from Hanny's PhD work, we extracted DNA using two different types of kits and then used a technique called electrophoresis to see if the extractions had worked (more on that later). It's highly convenient that several companies make standardized kits for DNA extraction, but I had to laugh at the instruction manuals. One of the extraction kits was meant for soils, while the other was meant to be used with animal tissue and had specific instructions for extracting DNA from rodent tails! Most of biology research is done using model organisms like fruit flies or mice, so the DNA kit market is driven by their demands. Obviously, the invertebrate animals I work with are not standardized models and probably never will be. There is no DNA extraction kit designed for corals, so the closest we can get...is rodent tails.
Most of our day was spent standing at the lab bench transferring reagants between vials with a micropipette. We then spun the vials in a centrifuge, a machine that uses centrifugal force to separate substances with different densities. Pipette, centrifuge, siphon off the liquid, repeat. Molecular biology is hard because it involves numerous monotonous steps, and you don't know if you've succeeded until the very end.
Once we had completed the DNA extraction protocol, it came time to evaluate our success using electrophoresis. This technique uses an electrical current to separate strands of DNA by size. A sample of DNA is loaded into a gel with a certain pore size, and as the strands migrate through the gel, small pieces migrate faster and large ones migrate slower. For our purposes, we were hoping to see a single, dark band of DNA, indicating a large piece - the whole genome - and a successful extraction.
You can see the results to the right here. The two rows of whitish rectangles are the wells where we loaded our samples, and the black stripes are the DNA. The tiger stripes on the very left are a DNA ladder, a series of fragments of known size that can be used as a standard. We used the ladder as a positive control - we knew there was DNA in the ladder, so if it didn't show up, something was wrong with the electrophoresis.
As you move across the picture, each column represents a different sample. On the top row, you see four dark bands. The bands are very close to their respective wells, indicating they didn't travel very far - that means they hold large pieces of DNA. That's what we were looking for! The four samples on the top were extracted using the animal tissue kit, so that kit still works! On the bottom row, you see only very, very faint bands close to the wells. Faint DNA means an ineffective extraction. The kit we used for these bottom samples was really designed for soils, so it's not surprising that it didn't work.
Moving forward, we will use the animal tissue extraction kit (rodent tails!), and we're very grateful to Hanny's advisor for offering her surplus. I'm excited to get started with the analysis!
Our first step was to test out two different methods for DNA extraction. Hanny's advisor graciously offered us some DNA extraction kits that were surplus in her lab, but the kits were a bit old and may have lost their effectiveness. We ran an experiment: using old samples from Hanny's PhD work, we extracted DNA using two different types of kits and then used a technique called electrophoresis to see if the extractions had worked (more on that later). It's highly convenient that several companies make standardized kits for DNA extraction, but I had to laugh at the instruction manuals. One of the extraction kits was meant for soils, while the other was meant to be used with animal tissue and had specific instructions for extracting DNA from rodent tails! Most of biology research is done using model organisms like fruit flies or mice, so the DNA kit market is driven by their demands. Obviously, the invertebrate animals I work with are not standardized models and probably never will be. There is no DNA extraction kit designed for corals, so the closest we can get...is rodent tails.
Most of our day was spent standing at the lab bench transferring reagants between vials with a micropipette. We then spun the vials in a centrifuge, a machine that uses centrifugal force to separate substances with different densities. Pipette, centrifuge, siphon off the liquid, repeat. Molecular biology is hard because it involves numerous monotonous steps, and you don't know if you've succeeded until the very end.
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| The results of our DNA extraction experiment |
You can see the results to the right here. The two rows of whitish rectangles are the wells where we loaded our samples, and the black stripes are the DNA. The tiger stripes on the very left are a DNA ladder, a series of fragments of known size that can be used as a standard. We used the ladder as a positive control - we knew there was DNA in the ladder, so if it didn't show up, something was wrong with the electrophoresis.
As you move across the picture, each column represents a different sample. On the top row, you see four dark bands. The bands are very close to their respective wells, indicating they didn't travel very far - that means they hold large pieces of DNA. That's what we were looking for! The four samples on the top were extracted using the animal tissue kit, so that kit still works! On the bottom row, you see only very, very faint bands close to the wells. Faint DNA means an ineffective extraction. The kit we used for these bottom samples was really designed for soils, so it's not surprising that it didn't work.
Moving forward, we will use the animal tissue extraction kit (rodent tails!), and we're very grateful to Hanny's advisor for offering her surplus. I'm excited to get started with the analysis!
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