Eisen Lab Blog

10AM at #UCDavis – David Botstein “Coordination of growth rates, stress response & metabolic activity in yeast”

Special Seminar

Department of Microbiology and Molecular Genetics

*Note the special time and day

Dr. David Botstein
(Anthony B. Evnin Professor of Genomics)

"Coordination of Growth Rate, Stress Response and Metabolic Activity in Yeast"

Tuesday, May 7, 2013

10:00 am

1022 Life Sciences

Botstein 5-7-13.doc

Lab meeting May 7th 2013

Hello,
We will have our weekly lab meeting this week from 1:30 to 3pm in room 4202 of the Genome Center.
Dongying Wu is presenting.

The need for a phylogeny driven genomic encyclopedia of eukaryotes

Monday I gave a talk for the SMBE Eukaryotic Omics satellite meeting that has been going on at UC Davis.  When Holly Bik, a post doc in my lab asked me to talk at the meeting, I said, basically “Well, OK, but I don’t really do much work on eukaryotes.”  And then I came up with an idea – I could make my talk about how it might be good to have a better phylogenetic sampling of eukaryotic genome sequences.  I have been a bit obsessed for many many years about phylogenetic sampling of genomes and, well, though I have avoided eukaryotes mostly in most of my genome sequencing work, I figured, I should still get on my soap box about how phylogenetic sampling is a good thing.  So, well, I did.  And I think we (i.e., the scientific community) really needs a better sampling of eukaryotic genomes.

I have posted my talk to Slideshare and I recorded audio of my talk in synch with the slides and posted that to Youtube.  These are below.

I hereby am calling for those people interested in participating in such a phylogeny driven genomic encyclopedia of eukaryotes to make yourselves known.  We NEED to do this.

Related posts

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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I love this … "Dr. Eleanor’s Book of Common Ants" based in part on citizen science data

This is really cool:  Dr. Eleanor’s Book of Common Ants.  Free to download.  With incredible pics from Alex Wild.  And based in part on data from the School of Ants citizen science project.  You can download the PDF or the iBook from iTunes.  From the folks at “Your Wild Life” including Holly Menninger and Rob Dunn and others.  Definitely worth checking out.

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

We are getting close to sequencing!

A few of the PCRs last week didn’t work so I’m finishing up the last PCR B’s right now that we’ve had to redo and then all we have to do is Gel confirmations. If I counted correctly there are 24 confirmations to do. I would like to do one now, but I have to catch the bus in 30 minutes and I wouldn’t finish in time 😦   I plan to come in on Friday and possibly Thursday as well and hopefully as a group we can completely finished and get our samples in the sequencer by the end of the week!

 

Then comes the hard part! Data analysis. I learned a lot about this portion of the project while I was preparing my part of the lab meeting presentation a few weeks ago so hopefully that knowledge helps me understand what’s to come. Like most things, I’m sure it’s much easier said then done!

New papers from people in the lab …

A lot of new papers from people in the lab in the last month or so.  See below for details of some of them:

Zach presenting his genome project work at the Undergraduate Research Conference

Here’s a picture of Zach talking about his search for the Microbacterium genome

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Aquarium project poster at the UCD Undergraduate Research Conference

Here’s the poster that Lakshmi prepared for the conference.   The presentation went well!  Thanks to everyone who helped out.

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Lab meeting April 30th 2013

Dongying Wu will be presenting for this week’s lab meeting.
We are meeting in room 4202 of the Genome Center from 1:30 to 3pm.

Yes, the human microbiome has truly arrived: on Wait Wait Don’t Tell Me

So cool.  Yesterday on “wait wait … don’t tell me” Kai Penn (actor) was enticed to play the game “Ahhh! Get It Off Me!” in regard to microbes: Not My Job: Kal Penn Takes A Quiz On The Microbiome : NPR

Hat tip to Jenna Lang for pointing me to this.

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——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–