Eisen Lab Blog

Lake Arrowhead Microbial Genomes 2012 #Genomes #Microbes #Mountains #Lake #Fun #Wine #MustGo

Helping the organizers plan the Lake Arrowhead Microbial Genomes meeting this year (see Microbial Genomics – ARROWHEAD 2012).  In particular I organized a session on Microbiology of the Built Environment relating to the http://microbe.net project.

This session should be good

  • Session Chair: Jonathan Eisen – University of California, Davis, CA “Alfred P. Sloan Foundation Workshop”
  • Anne M. Womack – University of Oregon, Eugene, OR “Microbial Ecology of the Built Environment”
  • Jason E. Stajich – University of California, Riverside, CA “Fungi in the Built Environment”
  • Laura Sauder – University of Waterloo, Waterloo, Ontario “Archaea in the Built Environment”
  • Scott Kelley – San Diego State University, San Diego, CA “The Indoor Microbiome: Bacterial and Metagenomic Approaches for Studying the Built Environment”
  • Susanna Remold – University of Louisville, Louisville, KY “Pseudomonas as a Model for Studies of Microbes in the Home”

And the other sessions that the meeting also look good (see program here).  But whatever you think of the speaker list, the best part of the Lake Arrowhead meetings is the venue and the interactions among people.  I have been going to this meeting for many years and here are some posts of mine about previous meetings

Can food safety be fun? Not sure, but this video is OK. #microbes

Continuing with my running theme of microbe-related music videos here is another one. It has good and bad parts. But then again, don’t we all …

#UCDavis Fall2012 Intro to Bio: Principles in Ecol & Evol (BIS2B) Temp Lecturer Position

Google/ Blogger "Dynamic Views" – Fancy but limited

So – I keep switching back and forth between the current view on my blog and Google’s “Dynamic Views” system.  Right now I am annoyed with the Dynamic Views so switched it off.

To see Dynamic Views check out

Each has its benefits but the whole Dynamic Views system is incompatible with many things I would like to do with my blog – examples include embedding Storify stories (the embeds don’t work in dynamic views); jump breaks (to show only the beginning of a story with a species transition point); and much more. 
So – anyway – apologies for switching back and forth.  Still playing with what to have as a default …

Visit to Capitol Public Radio HQ & appearance on "Insight" w/ @CapRadioRuyak

Just got back from a brief visit to Sacramento (which is 15 minutes or so my where I live in Davis, CA). I had a mini 10 minute or so appearance on “Insight” a radio show on Capitol Public Radio.

My visit all started maybe a few weeks ago when I bumped into Lin Weaver in Davis.  Lin was showing some friends of hers around Davis and we chatted for a while on the sidewalk.  One of the topics was my recent fun giving a Tedmed talk.

Anyway – we chatted for 15-20 minutes or so and then I headed home.  And a few days later I got an email from Lin inviting me to be a guest on Insight.  Cool.  I love the show – and listen to it whenever I can.  So I said I had to check some details and then got back to her later and said “yes.”

Lin and the folks at Capitol Public Radio then sent me some additional details and asked for some links to use for their website.

And this AM I headed on in to town.  I was asked to get to their studio at 9:45 AM.  Their studio is on the campus of Sacramento State and I headed on in early and got their at about 9:30.  Of course – I took some pics and posted some stuff to twitter …

Got a parking permit at the desk and then was led into the back of the building to
“The Green Room” and got a look at the studio:

//platform.twitter.com/widgets.js

And of course posted to twitter 

//platform.twitter.com/widgets.js

//platform.twitter.com/widgets.js

I then relaxed in the Green room.  A few minutes before ten the host of insight Beth Ruyak came by.  She instantly made me relax about the interview (was not stressed per se, but somehow felt even more relaxed after the minute with her).  She told me I would be up second and then she left to get ready for the show. 
I took some more pictures and posted a few more tweets

//platform.twitter.com/widgets.js

I continued to hang out in the Green Room and got to listen to the interview with the previous guest – Marcos Breton – a reporter for the Sacramento Bee who’s stuff I actually know a little bit of since he covers baseball.

While listening to them chatting away on the air, I decided to add some microbes to the Insight guest book:

//platform.twitter.com/widgets.js

And then the assistant producer came out and told me it was almost time to go into the studio.  And then I was in.  Sat down and talked for 10 or so minutes with Ruyak.  We talked about diabetes, microbes, me, twitter, and more. And then it was over.

I took a few pics of the office on the way out:

//platform.twitter.com/widgets.js

And that was it.

And it seems it is already on the web.

Lab meeting July 11th 2012

Dongying Wu will be presenting for this week’s lab meeting.
We will be meeting from 1:30 to 3:30pm at the genome center in room 5206.

Extra fruit in your trees? Don’t let it rot – donate it #DavisCA #VillageHarvest

Today, one of our neighbor came over and told us that the “Village Harvest” group was at their house to collect fruit from their trees and she wanted to know if they could come into our yard as part of the collection.  I said “please … and tell them they can collect from our tree too.”  You see, we have a pluot tree that produces more fruit than I can keep up with (and I note – we get a lot of the pluots from our neighbors tree too since it leans over our yard).  I have made 40+ jars of jam, 40+ fruit rolls, froze a bunch of pulp for later projects and still there was more fruit.  So I invited people over to collect some of the pluots and still there was more fruit.  So I was very happy to see the Village Harvest folks next door.  

Village Harvest is a ” a nonprofit volunteer organization in the greater San Francisco Bay Area which harvests fruit from backyards and small orchards, then passes it along to local food agencies to feed the hungry.”

And they have a Davis chapter: http://www.villageharvest.org/davis/

And so they came over and started collecting some of the pluots and I took some pictures and video of the event …

 

Definitely going to sign up for this for all cases when we can’t use all of our fruit …

Possibly new (not sure) connection between colic and Helicobacter pylori infections

Interesting article: JAMA Network | Archives of Pediatrics & Adolescent Medicine | Helicobacter pylori and Infantile Colic.  The study basically suggests that infants with colic have a much higher incidence of Helicobacter pylori infections than do a control group of infants.  No causal relationship was established – just a correlation.

The article has been picked up by a few bloggers/news sources such as:

I was surprised that this was suggested to be a completely new connection – between HP and colic.  Given the amount of work on HP this just seemed odd.  So of course I decided to snoop around the web.  And I found a few things that were related especially:
So it seems that others have noticed a possible connection between HP and colic previously.  But in the end there is not a lot of literature out there on the topic.   If anyone out there knows anything else on this topic, please post …

Fungal parasite of caterpillars is source of "Himalayan viagra"

Photo by Nicolas Merky

Wow – never heard of this fungus before reading this CNN piece: ‘Himalayan Viagra’ taking its toll on Nepal – CNN.com. The fungus infects caterpillars (larva of a ghost moth) in the Himalayas and kills them. And the fungal coated dead caterpillars are, alas, considered to have multiple uses in various traditional Chinese medicine practices. One of the uses is as an aphrodisiac and thus these have become known as “Himalayan viagra”.

The fungus that does this is Ophiocordyceps sinensis – (it is an Ascomycota).  Not a huge literature out there if you search just for this species name but thanks to Wikipedia I found out there are some synonyms so if you search Pubmed for all the names one gets 328 papers and 56 of these have free full text including a few that seem quite useful:

So – seems that what happens here is the fungus infects larva and then kills them and then a fruiting body grows out of the caterpillars head … fun.
Snooping around led to some other news stories about this system including many that came out recently
Anyway – seems like this would be a fun organism for genome sequencing … 

Microbial music: Christine Lavin and the Amoeba Hop

Always searching for science-art-music combinations.  Especially ones that focus on some aspect of science I work on, like microbes. And, well, though this recording is less than ideal, and you need to wait a minute and a half or so, once you get to the song it is worth it.

The song is “The Amoeba Hop” and the singer is the brilliant Christine Lavin.

I have had this song in my head on and off for years and wanted to post about it for a while.  I finally remembered to Google it tonight after reading a tweet about combining music and biology.  I used to listen to Lavin all the time in college and even went to a show of hers in 1989 in Ft. Collins, CO with my brother and my friend Saul Jacobson.  As a side note – we saw Lavin at some music hall type of place the the night after seeing Killdozer at a VFW post.  As a second side note – the Killdozer show was crazy (and I even found someone else who wrote about it here).

Anyway – not only did I find the video posted above but I discovered she wrote a book in 2002 based on the song – and the book even got a review in the New York Times.   Gonna probably have to get that book at some point …