25 July 2014

collecting, Aphaenogaster, and RNA extraction

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July 21- July 25 notes


  • Collected 4 large Aphaenogaster picea colonies from Molly Bog (VT) with Grace Cosgrove. Goal of collection was to get lots of biological material for genomic DNA extraction for PacBio sequencing.
  • Helped Grace set up another experimental colony for Pogo foraging behavior


  • emails and such
  • Ran gel of Gentra Puregene genomic DNA extraction done by
  • Awesome website for searching short read archive (SRA).
  • Reviews and comments on manuscripts


  • Uploaded Evolution presentation, without Alex Wild photo, to figshare
  • Stanton-Geddes, John (2014): Patterns of thermal stress tolerance vs. resistance in genome-wide expression data of parapatric ant species. figshare. http://dx.doi.org/10.6084/m9.figshare.1115061. Retrieved 14:05, Jul 23, 2014 (GMT)
  • Tried out Dataverse beta with same presentation. From my exploring, it appears that the Dataverse is an open-source framework for data archiving. They provide the software for installation, and any group or organization can initiate their own Dataverse. For example, the Harvard Election Data Archive and the Harvard Dataverse Network, which appears to be the motivating network for the Dataverse and the largest repository for social science.
  • Advantages
    • open source
    • if an instance of dataverse goes defunct, information and data could (in theory) be transferred to a new instance
  • Disadvantages
    • still in development and lags behind figshare, dryad
    • not widely used outside of Harvard or social sciences
    • organizational inertia: who should initiate and manage a Dataverse for each field?
  • From Dataverse, (re)found the Open Science Framework which looks like a very powerful way to organize large collaborative projects
  • Comments on Yun Kang’s Medicago ms
  • Review for AmNat
  • Learned how to use VCC’s Covaris sonicator for DNA fragmentation
  • need to experiment with different times to determine appropriate time for fragmentation. check by sending sample to bioanalyzer.


  • Completed comments for Yun’s Medicago manuscript
  • Finished AmNat review
  • Following up on yesterday’s notes about Dataverse, maybe the solution is Academic Torrents for distributed archiving of datasets!
  • Set up antlab workstation to backup to ecosim in Gotelli lab.


  • preparing for DGE prep next week. setting up lab space and checking reagents.
  • ordered
  • RNAClean XP beads
  • Qubit RNA assay
  • Covaris tubes for DNA fragmentation
  • extracted from 8 samples using RNAzol as previous trials showed this give RNA with same quality as RNeasy, alone or after RNAzol
  • eluted in 22 ul
  • sent samples to Bioanalyzer to get RIN scores


Sunday JM, Bates AE, Dulvy NK (2010) Global analysis of thermal tolerance and latitude in ectotherms. Proceedings of the Royal Society B: Biological Sciences, rspb20101295.

Bérénos C, Ellis PA, Pilkington JG, Pemberton JM (2014) Estimating quantitative genetic parameters in wild populations: a comparison of pedigree and genomic approaches. Molecular Ecology, 23, 3434–3451.

Kim YB, Oh JH, McIver LJ et al. (2014) Divergence of Drosophila melanogaster repeatomes in response to a sharp microclimate contrast in Evolution Canyon, Israel. Proceedings of the National Academy of Sciences, 111, 10630–10635.

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