Grant writing and DNA barcoding

No, I'm not writing an NSF grant (yet!). The National Science Foundation is one of the premiere grant funding agencies in the US for basic science research. From what I know, the competition is brutal, so I'm probably in need of some skin-thickening before I apply for anything there. Some preliminary results might also be helpful!

What I've been working on are some more specialized grants. The American Arachnological Society provides a small amount of funding for research supplies, and I submitted my grant about 3 weeks ago. It's too early to feel any waiting pressure, but I am getting anxious!

I'm currently working on a grant funded through OSU which is their SEEDS program. I've written up my master's research proposal and will be requesting $3000. Somehow my research ideas are proving to be expensive! One of my goals is to molecularly analyze the gut contents of some of the spiders I will collect in three urban greenspaces in Cleveland: vacant lots, community gardens, and lots redesigned as natural areas.

Most gut-content analysis frames the question as "Who is eating this particular pest species?" Then, DNA tags which are specific to the pest species are used to find that tag within different potential predators' guts. This is helpful when researchers and farmers want to know which predator populations to invest support for conservation within particular crops.

But my question is "What are these spiders eating?" This is a hard question to answer for spiders because they are difficult to watch for long periods of time (not because they're boring, you just don't know when they're going to eat!). But there are ways to analyze gut contents without previous knowledge or species-specific DNA tags. What I plan to do is identify a "universal" sequence region of DNA within each spider gut. This region is within the COI gene which is found within mitochondria (the power supplies within cells). In fact, all animals (and other eukaryotes) contain mitochondria, so they all have a COI sequence. This sequence mutates relatively quickly, so in theory is quite different between species but consistent within a species. Ultimately, this region (other regions are used for plants) is used for"DNA barcoding," where you can identify a DNA sequence by comparing it to a database with already identified sequences. Using these methods, I can recover COI sequences from each spider gut and then run them through a database and viola, the database tells me what animal each sequence comes from.

It's sort of like if you have a word to translate from a language you don't know, so you put it through an online translator. My high school German is a little rusty, so when I type in "schreibe" I find it means "to write." And that's its only meaning. That would be a species-specific identification.

However, the result is only as good as the translator's dictionary, but you may come close. So if I look up the Finnish word "kirjoittaa" the translation results are: "write, type, compose, spell, print, author, put, etc etc etc". I'm in the neighborhood of what the word means, but it's not precise. For my COI identification, that's similar to the database telling me this particular sequences comes from the fly genus Brachyopa but that's it. My dictionary doesn't have anything more specific, but I'm close. Hopefully I can come at least this close in my research with all my sequences.

What makes this process expensive is how I plan to recover my sequences. First, the spiders will be ground up (sorry guys!) and all their DNA and the DNA in their guts will be amplified so I have a bunch of sequences to work with. Then, this recovered DNA needs to be sequenced (CAATTAAGGA etc. - I need to know which letters make up my "word"). A new fancy (read expensive) method of sequencing involves adding a specific tag to each "word" so I know which spider it came from ("schreibe-Spider1" vs "schreibe-Spider2" and "kirjoittaa-Spider2").

And then I'll know what these spiders are eating. This first summer I'm focusing on a wolf spider Pardosa milvina which from what Mary has found is pretty common in all the sites she's looked at so far. Later on I hope to identify sequences from a few different spiders and compare how their diets may overlap or complement one another.

What did you eat today?