I've been attempting to read a lot of papers in the past week, and struggling fairly badly. Reading primary literature is hard for two reasons: you need to have enough background knowledge to understand the experiments, and you need practice at parsing the language and form of papers (a nontrivial skill). I've come a long way since high school, when it took me several days to look at all the words in a paper (and I still came out the other end with little understanding of what actually happened)... but I still have an awfully long way to go.
Which is why I love review papers. The literature search is done, the information is chewed-but-not-digested. It's just the right level for an undergrad. (Book chapters can also be good, but seem to be a bit less up to date because the publication cycle is longer.) A review paper is the best way to start a new literature search, or to get the "state of the union" on an interesting area you're not expert in.
<3 people who write review papers
Friday, August 7, 2009
Saturday, August 1, 2009
The strawberries are delicious
Today I decided to try a DIY DNA extraction. I started with Meredith Patterson's informal instructions, figured out what chemistry was actually happening, looked up some protocols from actual labs, and found what might be the original paper presenting the method of "salting out" DNA. Perhaps more research than I really needed to do, but it was pretty satisfying.
Then I went out and acquired a bunch of things: non-iodized salt, isopropanol, ethanol, papain (aka meat tenderizer), some "test tubes", a "centrifuge"... and strawberries.
For some reason, strawberries seem to be the canonical thing to extract DNA from if you're just demonstrating, so you can show your audience slimy white strands and have them go "ooh, aah". Maybe they have a lot of DNA or something. (What ploidy are generic commercial strawberries?? EDIT: they are apparently octoploid. Impressive!)
Right now, one mashed-up strawberry is sitting in a solution of salt (I should probably be using a real buffer), shampoo (disrupts cell membranes and precipitates proteins), and papain (slices up proteins). All the amounts of things were totally guessed. I put the solution in a double ziploc bag and set it on top of a hot computer case to speed up the reaction. This is the first step, where I break apart the tissue and lyse the cells to get at the DNA. I'll leave the strawberry to digest overnight, and tomorrow I'll centrifuge to try and remove as much protein and random crap as possible, then add concentrated salt and isopropanol to precipitate the DNA. If all goes well, I might even post photos.
Watching the strawberry get slowly digested is interesting by itself. The red juicy parts got digested first, turning the solution a lovely pink, and leaving behind all the white fibrous stuff from the center. Did you know each seed on the outside of a strawberry has a tract of white-fibrous-stuff connecting it to the center of the berry? Since all the red stuff surrounding those tracts has already been digested, it's a little like looking at the skeleton of a strawberry. Kind of creepy. We'll see what happens by tomorrow morning.
...Oh, a word about test tubes and centrifuges. For test tubes, I went to a florist and bought some of the plastic tubes they use to keep single flowers moist. Ten cents each, and with neat little lids. For a centrifuge, I was toying with the idea of modifying a blender or something, but then I found the lid to a salad spinner, which lots of internet people have used as a makeshift centrifuge. Unfortunately, not the whole salad spinner, which would have been brilliant; but I added some zip-ties and it became a centrifuge capable of generating about 32 Gs. This is probably good enough for a proof-of-principle DNA isolation (though of course I want to do more than prove the principle). So far, I haven't spent any money on lab equipment that's sold for the purpose of being lab equipment. I'm going to have to get fancy sometime soon, because you can't do bacterial work with a piddling little 32-G centrifuge; you need something that can get up above 10,000 Gs. (Ebay, here I come!)
Then I went out and acquired a bunch of things: non-iodized salt, isopropanol, ethanol, papain (aka meat tenderizer), some "test tubes", a "centrifuge"... and strawberries.
For some reason, strawberries seem to be the canonical thing to extract DNA from if you're just demonstrating, so you can show your audience slimy white strands and have them go "ooh, aah". Maybe they have a lot of DNA or something. (What ploidy are generic commercial strawberries?? EDIT: they are apparently octoploid. Impressive!)
Right now, one mashed-up strawberry is sitting in a solution of salt (I should probably be using a real buffer), shampoo (disrupts cell membranes and precipitates proteins), and papain (slices up proteins). All the amounts of things were totally guessed. I put the solution in a double ziploc bag and set it on top of a hot computer case to speed up the reaction. This is the first step, where I break apart the tissue and lyse the cells to get at the DNA. I'll leave the strawberry to digest overnight, and tomorrow I'll centrifuge to try and remove as much protein and random crap as possible, then add concentrated salt and isopropanol to precipitate the DNA. If all goes well, I might even post photos.
Watching the strawberry get slowly digested is interesting by itself. The red juicy parts got digested first, turning the solution a lovely pink, and leaving behind all the white fibrous stuff from the center. Did you know each seed on the outside of a strawberry has a tract of white-fibrous-stuff connecting it to the center of the berry? Since all the red stuff surrounding those tracts has already been digested, it's a little like looking at the skeleton of a strawberry. Kind of creepy. We'll see what happens by tomorrow morning.
...Oh, a word about test tubes and centrifuges. For test tubes, I went to a florist and bought some of the plastic tubes they use to keep single flowers moist. Ten cents each, and with neat little lids. For a centrifuge, I was toying with the idea of modifying a blender or something, but then I found the lid to a salad spinner, which lots of internet people have used as a makeshift centrifuge. Unfortunately, not the whole salad spinner, which would have been brilliant; but I added some zip-ties and it became a centrifuge capable of generating about 32 Gs. This is probably good enough for a proof-of-principle DNA isolation (though of course I want to do more than prove the principle). So far, I haven't spent any money on lab equipment that's sold for the purpose of being lab equipment. I'm going to have to get fancy sometime soon, because you can't do bacterial work with a piddling little 32-G centrifuge; you need something that can get up above 10,000 Gs. (Ebay, here I come!)
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