User:Tara K. Luckau/Notebook/Team ConGen/2011/09/13

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Rulon Meeting

rodent species ID

  • Stephen joined meeting
  • paper that Stephen found? Stephen will email the articles he's been looking at
  • next steps for Stephen are:
ordering stock DNA of each species from the website, or from MVP
see if published flanking primers will amplify across species
aligning Cyt b sequences to develop internal species-specific primers
  • send download link of CLC Sequence Viewer to Stephen

SCOC microsats

  • multiplex still developing
shipment in the mail
have 6 loci working well (won't have to throw out), and 5-ish more to play with
stay open to the idea of needing a couple multiplexes to include all loci (not gunna fit it all in one reaction)
  • go ahead and use AB proprietary NED if that's what's needed (PET, too)
not a huge cost for a necessary component, especially since will only need to order once or twice
  • look up Mol Ecol µsat guidelines
doesn't look like Molecular Ecology states any minimum number of microsatellites to be considered for publication
Molecular Ecology Author Guidelines
Guichoux et al 2011, Molecular Ecology Resources
survey of the most recent Molecular Ecology journal articles (2009-2010) that used microsatellites
average of 564 individuals surveyed at 11.6 nuclear microsatellite loci
in studies that didn't multiplex, 11.1 microsats
in studies that did multiplex, 12.3 microsats, 3.9 loci per multiplex (13.9 microsats, 5 loci per multiplex if using a multiplexing kit)

general lab stuff

  • log-ins and ordering info to Stephen
set up a meeting with Stephen to go over vendor log-ins and
  • primer order and quote request
follow-up with Daniela
  • pipet calibration: 10 pipets @ $25 each (
Rulon says do it
  • FedEx shipment charges
quoted as ~$85 on FedEx site
I have a feeling it's much less
Rulon sees these charges:
(post date - $charge)
July 22 - $9.32 ... probably from June's shpiment
Aug 19 - $12 and $7.80 ... probably from July's shipment (when I messed up the paperwork and FedEx sent it back and charged a bit)
no record from March's shipment
so, looks like shipping to UAGC ranges from $0-$12 - nice!
maybe we'll see yesterday's shipment charges in another month - check back?

Next Week:

  • nail down target primer number for our species, based on guidelines from review papers or journal standards
I think 12 is good! (ugh, got some more to check out)
Graduate Research Affairs - Graduate Program Forms
    • this semester, file official Program of Study (POS) - fill out form (don't know where it is, but Bio website above has a worksheet for it), have Rulon and Todd sign it, and give to Biology Graduate Coordinator. You should file this document by the middle of 3rd semester, even if you have not yet proposed
    • this semester, assemble thesis committee - done!
    • this semester, propose - written and oral proposal for approval by your thesis committee and the EPA faculty; at least 3 members of the EPA faculty must be present and approve of the oral presentation
    • this semester, file Thesis Proposal Form - will document completion of your thesis proposal for Advancement to Candidacy; form must be signed by Rulon and Todd before giving to Biology Graduate Coordinator.