Coral crusher: part 2
Friends, I am back home in Massachusetts now and just as busy as ever. I'm corresponding with colleagues about new proposals we should write together. I'm finishing up old papers to get them ready for publication. I'm exploring new ideas for projects I want to do this summer. And I'm busy crushing corals.
Truth be told, I'm making a lot of progress. In fact, Hanny and I have now successfully extracted DNA from each of the coral samples we collected in Palau - 260 of them in all. Our next step is to decide which technique we want to use to analyze the DNA. There are two options - microsatellites and RAD. Microsatellites are commonly used in forensic analysis and paternity tests, but RAD is a newer technique that gives more precise results. Both can answer the same question - to what extent populations of corals are connected - but they go about it in different ways.
The decision to use one technique over the other will come down to budget, time, and the quality of the DNA we were able to extract. How does one measure the quality of extracted DNA, you ask? There are (you guessed it) two possible methods. They give the same information (sound familiar?) in different ways. Oh, the multiplicity of molecular methods.
The first quality-measurement method is called NanoDrop, and it essentially involves putting a small (nano-)drop of my extracted DNA solution in the machine, which then measures the transmittance of light through the liquid. Based on how much light of different wavelengths is absorbed or transmitted, the machine can tell how concentrated the DNA is. You'll see an example output to the right here. The blue curve in the front represents the transmittance of the current sample, and the gray ones behind show the transmittance of earlier samples I measured. The shape of all the curves is exactly what you would expect from high-quality, high-concentration DNA.
The second technique we used to measure our extracted DNA was called Qubit. For this technique, we mixed small sub-samples of the DNA with fluorescent reagents and then measured how much the sub-sample fluoresced. Qubit is slightly more precise than NanoDrop, but as you will see in the screenshot to the left here, we maxed out the machine. The DNA we extracted was too concentrated to measure!
It is immensely exciting for us to have such good results from our DNA extraction. I've shown you the best results here, but over half of our samples look like this - concentrated, high-quality DNA. Because our results are so promising, we will probably be able to use the RAD technique for our population genetic analysis. Exciting times are ahead!
Truth be told, I'm making a lot of progress. In fact, Hanny and I have now successfully extracted DNA from each of the coral samples we collected in Palau - 260 of them in all. Our next step is to decide which technique we want to use to analyze the DNA. There are two options - microsatellites and RAD. Microsatellites are commonly used in forensic analysis and paternity tests, but RAD is a newer technique that gives more precise results. Both can answer the same question - to what extent populations of corals are connected - but they go about it in different ways.
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| The NanoDrop data output |
The first quality-measurement method is called NanoDrop, and it essentially involves putting a small (nano-)drop of my extracted DNA solution in the machine, which then measures the transmittance of light through the liquid. Based on how much light of different wavelengths is absorbed or transmitted, the machine can tell how concentrated the DNA is. You'll see an example output to the right here. The blue curve in the front represents the transmittance of the current sample, and the gray ones behind show the transmittance of earlier samples I measured. The shape of all the curves is exactly what you would expect from high-quality, high-concentration DNA.
 |
| The Qubit data output |
It is immensely exciting for us to have such good results from our DNA extraction. I've shown you the best results here, but over half of our samples look like this - concentrated, high-quality DNA. Because our results are so promising, we will probably be able to use the RAD technique for our population genetic analysis. Exciting times are ahead!
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