Rough 2/27/15 Meeting Notes

We had a meeting today on updating each other on our projects. Here are my brief notes from the meeting:

Seagrass meeting 2/27/15:

General reminders:
-Blog!
-Attend UC Berkeley Symposium? Open to any level knowledge, can also present.
—–
Hannah: Blogged about the five plants (“Biogeography 2.0”). Has cut up and taken pictures of mostly-whole roots through the ice. Planning to give to John for sequencing. Other 9 plants are frozen in plastic bags, might give to Alana to stain.
—–
Alana: Reagents mixed up. Might stain bits of roots and leaves from Hannah. Planning to stain today, Monday, and Tuesday.
—–
Ruth: Plate streaking gave 14 (hopefully different) microbes. Need to make two more media (didn’t have lactate at time of first round of media-making). Thinking about whether to sequence directly/Sanger to see what the 14 microbes are. Need to ask David and Jenna about techniques on breaking open Winogradsky columns.
—–
Bri: Redo PCR c/b neg control came out positive. No change in protocol.
—–
Laura: Been emailing Laura Parfrey in British Columbia about primers for eukaryotes. Parfrey hasn’t decided on primers yet and wants to talk to someone about sampling physically. Parfrey needs to get in contact with Jenna.
—–
Alex: Been working with Space microbes, so no progress on seagrass. So, as of right now, 4 out of 12 samples worked. Qubit readings are okay, but getting a lot of non-bacterial DNA. Haven’t done PNA blockers yet. Samples have been sitting long enough that Zymo buffer turned green.
—–
Cassie: Found out that you NEED BLAST for taxonomy assignment in Qiime, which is well known to mycologists. Not a lot of papers use QIIME to begin with. Yet another example of needed to put the workflows online. Cassie found out when writing blog on how bad ITS was and found a tutorial on the topic in the process. Coordinated with UC Berkeley’s Sydney Glassman, got a copy of her detailed methods section of her recent paper and was very helpful. Sydney is also planning to write microbe.net post on ITS. Cassie will also talk to Hawaii researcher on coral fungi symbiosis. Most of Cassie’s problems seem to be solved for now!

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