User:James Estevez/Notebook/Summer 2010: Fungus growing social insects/2010/12/19

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<a href="leaf?id=0Bz68wO2y_AwMMjQ0YTA5YjUtNWVlNC00ZTg1LWFhNTYtMjgwMWE1NGVlYjA0&hl=en" id="jh13" title="Metagenomics Protocols">Metagenomics Protocols</a>

28 Nov 2010 

The idea that just struck me: we can search for cross feeding in all of the metagenomes sequenced to date sourced from herbivores. Whereas my original idea had been merely to look for evidence of HGT within the metagenomic data set, we can try to find the metabolic pathway by looking for genes that encode enzymes along the cellulose degradation pathway that look to be derived from different taxa. If we find them, I might be able to follow this up with isotopes and some other experimental confirmation in termites.


Alternatively, merely the difference between these two communities, if there is one would also be significant. Again, we've run into the problem of what constitutes an publishable unit of research (that's my goal).

14 Dec 2010

So I need to come up with a reasonable outline, don't I. I'm having a difficult time figuring it out. I think that trying a hidden markov model might give us something different, but there doesn't seem to be an easy way for me to get started on finding a realistically sized question in the time alloted. I could, of course, scale it back considerably. This might be the best option, but I wonder if I can really stomach another summer buried in petri dishes. So, setting aside an hour every day to chip away sounds like a decent idea. I'm guessing that finding the sequence data is a good place to start, but there might be a way to convince Frank Aylward to part with some of his data. I know he was looking at heat maps last time, so that's an idea. 
  1. Sequences for ant garden, pseudonocardia symbiont, fungual cultivar, complete klebsiella and whomever else they have published. The NSF grants... I can backtrack from those and the DOE if need be.
  2. Need some list of topics for Poulsen by the end of the year.
  3. Software-visualization, gene-trees (Dagan, Puigbo, Bapteste, Gogarten and Zhaxybraeva)
  4. Try to find a way to connect to the larger questions.
  5. Begin drafting cross-feeding letter
  6. Try to squeeze in some time with Fox-Dobbs.
Goals for tonight: 
Wrap: Not everything done, but I've started. Holy s**t.

15 Dec 2010:

Does your research involve traveling outside of the United States?         Yes                                         No                          

If yes, make an appointment with Associate Dean Lisa Ferrari to discuss your travel plans. The Associate Dean will give instructions concerning all formal documents that must be completed as part of your research grant application.. Please have the Associate Dean sign below to verify the completion of all needed documentation

Found out about CloudBioLinux. This may be necessary if the data sets I end up working with are too big. Read a bit more about how carbohydrates fit in to this. I'm leaning strongly in that direction, but I want to apply techniques from the ToL people.

19 Dec 2010
Reading a bit, need to update some annotations from my readings on the flight. One idea for CPH was looking for spatial differences in hydrolase mRNA using FISH. Also toying with SIP, but talking to Fox-Dobbs would have been helpful. SIP: We should see a difference in how these two systems, ants and termites, incorporate labeled carbon. Analysis in CPH or at UPS.