Photomerge of Mural at Dali Museum

Originally uploaded by jason.stajich

stitched together from 8-10 shots, was curious to see how well PS would work, you can tell I wasn’t standing head-on but this turned out pretty good I’d say.

Wish I could go to http://awesomescience.wordpress.com/schedule/ this year. Look like fun.

Crystal Method live on KCRW http://www.k…

Crystal Method live on KCRW

brainstorming jewelry studio names for Amy and figuring out where she might host the website.

Rainbow over Berkeley

Originally uploaded by jason.stajich

Rainbow over Berkeley

I didn’t have my SLR with me so this was the best shot I could get – I took a few from home but it had faded a lot.

Was a perfect time as the golden hour light of 8PM and the very light rain shower coincided.

Just in time for the folks headed to the Death Cab for Cutie concert. I can’t believe how many people I passed on the way home jumping outside to look, point, take pictures. People were spilling out of a restaurant with their server in the lead to look at the scattered light. From some directions it was a double rainbow.

Every camping trip should begin with Fat Tire

Originally uploaded by jason.stajich

MakerFaire 2009

Kinetic Arts, originally uploaded by jason.stajich.

Had a fun day at MakerFaire 2009 – quite overwhelmed by the things to see and do. Picked up a few fun wood art+science piece for my new office. I loved what Xylocopa makes – check them out, one of the pair is a lifesciences graduate student and also an artist drawing some deliciously detailed designs.

We also saw some more fun kinetic art like this piece as well as a some more art pieces from kinetic artist and friend Benjamin Cowden.

I also really want a 3D printer now – just need to figure out how we’ll actually (i.e. in lab) the scanned micrographs turned into 3D models of fungal cells…

My Flickr album plus lots more from others with makerfaire and makerfaire2009 tags.

Day 1 JGI meeting wrapup

Jonathan and I tried our best to liveblog JGI meeting today. I ended up running out of battery during Joe Ecker’s talk (which was great, full of data!) and full of. The day continued with a talk from Dick Smith on proteomics, mostly focused on methodology. Of course these talks are supposed to be overviews and to some extent a JGI cheerleading to what interesting new projects can be addressed by the institute. Day finished with keynote from Chris Somerville from EBI (no not that EBI) and UC Berkeley on cellulosic biofuels. Some very cool stuff but to some extent showcasing the different avenues of feed stock, chemistry, and biofermentation approaches that are being explored.

Here’s a friendfeed room so we can be more organized tomorrow.

Liveblogging JGI UserMeeting: Joe Ecker

Joe Ecker, Salk institute.

Plant genomes good… Joe to talk about the importance of deep understanding of a single system. Arabidopsis is the reference plant. Still a lot of unknown. “Sequence enabled science” Systems biology for building a parts-list information. 70M genome project for Arabidopsis. Transcriptome, proteome. Couldn’t find the genes until getting expression. (The teams at TIGR really did a great job with the annotation to make this resource I will say).

Sequencing to capture information about variation, RNA, RNA degradation, alternative splicing, small RNAs, DNA methylation (epigenetic variation). (What browser is he showing, this seems like a custom view, but not sure).

Cameron Currie: ant farmers

Cameron Currie Ancient mutualism for fungi and ants – something I love to learn more about.  Great system for mutualism of animals and microbes. Showing Chapela et al figure of co-evolution.

There is also a parasite that specializes on the ant-fungal interaction. Escovopsisco-evolves with ant and fungus. So a triparte symbiosis. But Wait. The he introduces the 4th player, where the actinobacter which produces antibiotics to protect the ants. Specialized organs for culturing the bacteria which are all over the body which are specialized opening for crypts for the filamentous bacteria. 6-8 years ago, 4-way interactions.

Work in the GLBRC is currently to understanding of the breakdown of the plant biomass. The fungus that is cultured by the ants is not cellulosic. Mature colonies can produce huge amounts of biomass but it gets broken down. See if cellulose is decomposed in the fungus garden, and is being broken down. Lignin is not really getting destroyed though?

Project with the JGI is “Fungus Garden Metagenomics”. 16S metagenome. 400M bp from community sequencing. Interesting bacteria found in the fungal garden. lots of species from the gardens “Cellulomonas” sounds like it could be good hit… =)

The top hit is Klebsiella an N-fixer, cellulose-degrader and is a Gamma-proteobacteria. Gamma show up in general a lot in the top 20 hits.

What kind of enzymes are present? Beta-1,4-endoglucanase. Found several cellulase enzymes present in the garden that are of fungal origin so maybe the genes are only being expressed in the garden/dump.

Video of 10,000s of worker ants dumping the plant material dropping material into these huge dumps. The mounds have stratification as material is dumped at the top and ages and decomposes. Cellulose content at the top and bottom of dump is correlated with age, so the bottom has least amount of cellulose.

Diversity of leaf cutting ants – 210 lineages of fungus growing ant. Most are not leaf cutters. So there are different microbial associations with the different groups that should be determined.

Insect-fungal mutualisms are not unique to ants. Fungus-growing termites. May have cellulosic capabilities. Beetles and yeasts, where the beetles spread the yeast (these I presume would be Ceratocystis and Ophiostoma).

How much of the leaf material brings in the microbial community. The ants groom the leaves to remove contaminants (like spores) which directs the community composition. I wonder how many plant endophytic fungi might still come in?

Bacteria in the farm may actually induce the fungal production of cellulosic enzymes. 10k 18S sequences from different strata.