Jonathan Eisen's Lab

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.

The need for a phylogeny driven genomic encyclopedia of eukaryotes #SMBEEuks from Jonathan Eisen

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.

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:

PLOS ONE: Phylogeny of Bacterial and Archaeal Genomes Using Conserved Genes: Supertrees and Supermatrices from Jenna Morgan Lang, Aaron E. Darling, Jonathan A. Eisen
Global marine bacterial diversity peaks at high latitudes in winter in ISME where Guillaume Jospin in the lab is a co-author
An Introduction to Social Media for Scientists in PLOS Biology by Holly Bik and Miriam Goldstein
Some genome announcement papers from our undergraduate genome sequencing project (with more coming).
- Draft Genome Sequence of Microbacterium sp. Strain UCD-TDU (Phylum Actinobacteria) with Zachary Bendiks (undergraduate) as first author.
- Draft genome sequence of an Actinobacterium, Brachybacterium muris strain UCD-AY4 with Jonathan Lo (undergraduate) as the first author.

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

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.

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.

Via @nprnews: Not My Job: Kal Penn Takes A Quiz On The Microbiome n.pr/10hVj0J @jessicaleegreen @phylogenomics
— Jenna Morgan Lang (@jennomics) April 27, 2013

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Trying to sort out all the STEM and STEM related departments, graduate programs , at #UCDavis

Well, I was in a meeting yesterday for the UC Davis ADVANCE program. This program is an NSF funded project to improve presence of women and underrepresented minorities on the faculty in Science, Technology, Engineering and Math (STEM). So I decided to see – how many departments at UC Davis might participate in such an initiative. And, well, wow. I knew there were a lot of STEM or STEM-related departments at UC Davis but I did not know there were this many.

Here is a list I compiled of UC Davis STEM or STEM-related Departments. I included medical departments here since many people in such departments do medical/science research. But clearly this is a broad definition of STEM. But nevertheless, this gives some picture of the scope of science and medicine and related departments at UC Davis.

Vet School departments in Yellow
Med School departments in Red
College of Biological Sciences Departments are In Green
College of Agricultural and Environmental Sciences in Orange
College of Letters and Science in Light Blue
College of Engineering in Grey

And then of course UC Davis has a TON of graduate groups and almost all of these are separate from departments. They do not hire faculty but they are a key part of the atmosphere and academics at UC Davis. And there are an enormous number of these in STEM or STEM-related fields. See below

Graduate Groups

Agricultural and Environmental Sciences Graduate Programs

Biological and Life Sciences Graduate Programs

Engineering Graduate Programs

Health Sciences Graduate Programs

Physical Sciences and Mathematics Graduate Programs

Social Sciences Graduate Programs

And then there are the Undergraduate Majors of which many are in STEM or STEM-related fields

So – lots and lots of STEM stuff at Davis and lots of chances / opportunities to improve the presence / treatment / life of women and underrepresented minorities.

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