BISC413 Lab 1, August 30: Collecting trips
Your biggest project this semester will be to collect a few hundred individuals of your assigned species and run allozyme gels on them. I'll tell you more about allozymes in class; the important thing to know for today's trip is that you'll look at genetic variation by running native proteins on a gel, then staining for one particular enzyme. A "native" protein is one that is folded up into its natural, functional shape. Proteins in a living organism are in their native state. After the organism dies, the proteins are oxidized, broken into smaller peptides, or unfolded, and they no longer have enzyme activity and can't be used for allozyme gels.
To keep the proteins in their native form, you will collect live organisms and either keep them alive until you come back to the lab, or you will freeze them on dry ice as soon as you collect them. Once you get back to the lab, you will put the organisms (or small parts of them) into a -20°C freezer along with some molecular sieve desiccant. The desiccant will absorb the water from the specimens even though they are frozen, and in a week or so, they'll be freeze-dried. The proteins in a freeze-dried organism are very stable, so you'll be able to collect and freeze-dry a bunch of organisms in September, then run gels on them in October and November.
Here are some general rules for collecting and handling your organisms:
- Collect as many as you need for the project, but don't collect a lot more. All of your species are very common, but it's still wrong to kill them unnecessarily.
- For most of the projects, you should try to collect about 60 individuals from each location. Keep count as you're collecting, so you know when to stop. (For walnut flies, webworms, and bagworms, you'll want to collect 12 individuals per walnut, per web, or per bush.)
- After you turn over a log or rock to collect what's underneath, put it back in its original position; otherwise you will destroy the cool, moist habitat that the species you are collecting lives in. Likewise, if you dig in the soil for something, put the dirt back in the hole when you're done; if you scrape aside dead leaves, push the leaves back over the bare spot.
- Those of you turning over logs in the woods may find a salamander. Salamanders are extremely cool, so make sure you show it to your teammates. But do NOT take it home to be a "pet"; it will almost certainly die, and then you'll be haunted by salamander nightmares for the rest of your life. Instead, put the log back, then put the salamander next to the log so it can crawl back under. Don't leave the salamander where it was and drop the log onto it!
- You'll be working in teams of three or four, so you might each have a container to collect organisms in. Combine them all into one container for each location.
- If you're taking the organisms back to the lab alive, keep the container cool, out of direct sun. You do NOT need to poke air holes in the container; invertebrates don't use oxygen very fast, especially if kept cool, so they'll have plenty of oxygen in the container to last them until they get back to the lab.
- Put a piece of tape on the side of the container and label it. Do NOT put the label on the lid, because that makes it too easy to mix up different containers.
- The label should include:
- your full name (first and last)
- the species (common name or scientific name, either is okay for this project; but pick one and stick to it, don't switch back and forth). You can abbreviate the genus, such as "P. platensis" instead of "Platorchestia platensis."
- the collection location. I recommend that you give each location a short, descriptive name, like "North end of Pomeroy trail", rather than something like "Site 1." Experience has shown that it's too easy to forget where Site 1 was. Of course, if your collection locations are close together (like each location is a different branch on a single tree), your may be stuck with something like "California Tortilla, branch 1."
- The date. Write the month, don't use numbers; "9/1/2016" means Sept. 1 in the United States but means Jan. 9 in the rest of the world, so using numbers can be confusing.
- If it's your species, draw a clear map of your collection location in your lab notebook. This does not need to be artistic, but it should be detailed enough, with enough clearly labelled landmarks, that a student next year could look at your map and go to the exact location.
You should also record the latitude and longitude of the location. The easiest way is to take a photo with your phone, then use an "EXIF Viewer" app on your phone to show the latitude and longitude of the photo. For iPhone, I recommend Koredoko for iPhone and Koredoko for Android. Install the app, go to Settings (the plus mark in the lower right) and change "Coordinate Format" from DMS to Decimal. Then when you open the app, you can look at your photos and see their latitude and longitude:
In the lab
Back in the lab, freeze your organisms to kill them (if they're not already frozen). Label two microtiter plates by putting a piece of tape across the bottom two rows, then put your name, species, collection location, and collection date on the tape. Label one microtiter plate "Sample A" and the other plate "Sample B." You'll run a gel on Sample A, then if some parts of the gel don't work, you can rerun the same individuals using Sample B.
Thaw out your organisms and sort them into the microtiter plates. For small organisms, rip the organism in half and put one half in each plate. For larger organisms, cut off a small piece to put in each well, about the size of a peppercorn, and discard the rest. Write down how many individuals you have. Put the microtiter plates in a larger plastic container with some desiccant, and put it in the freezer.
The procedures above apply to all of your organisms. For today, you'll be collecting the following. You can lock up your stuff in the lab while you're out collecting.
- Team Bagworm (Alex, Rachel, Suthep) should bring their bikes. You'll be riding around Newark and collecting bagworms for Alex. You can bring them back to the lab alive. If you run out of places to find bagworms, you'll look for walnut trees and record whether they're English or black walnuts, for Suthep's project.
- Team Isopod (Morgan, Marisa, Emily E., Erik) will be driving around the area around Newark, collecting Caecoidotea for Emily E. You should wear old sneakers so you can go wading in shallow streams. Marisa will be the driver. You will bring the isopods back to the lab frozen on dry ice.
- Team Honeyee (Katie, Christine, Daniel, Geno) will be driving around Newark, collecting bees for Daniel. Katie will be the driver. You will bring the bees back to the lab frozen on dry ice.
- Team Webworm (Peter, Meghan, Emily D., Taylor) will drive around Newark, looking for webworms. Taylor will be the driver. Remind me to give you the pole lopper before we leave the lab. You'll bring the webworms back to the lab frozen on dry ice.
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