Every camping trip should begin with Fat Tire

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.

Liveblogging JGI UserMeeting: Mike Mendez on algae energy

chlamy

Sapphire energy, Mike Mendez, make fuel from the sun.

Ways to get energy. Go from sun, to corn, to fermentation, to hydrocarbons Also, you go from sun to plant to hydrocarbon.

Why algae? More biomass from algae than switchgrass, sugarcane, corn (50% vs <10%). Single-celled organism that doesn’t need to make flowers, stems, etc. How to make oil from algae? Well according to the numbers, 2-40% of the body mass is oil, so can make >5,000 gal/acre of oil… Now how to convert from POTENTIAL to ACTUAL production? Right now it doesn’t work, so how do go from algae to biodiesel?
“How to design a fuel crop – domesticate algae” (This will require wranglers I suspect to tame the wild beast!)
Example: it took 7k years to get from teosyntae to modern corn, “one of most important mutations is that corn kept kernels and didn’t drop them on the ground”

How to domesticate algae? (lots of corn examples; “algae will not be different” in terms of how to convert to agriculture)

• need to grow monoculture
• design a way to harvest and recover fuel in cost effective. Need to engineering strains that make this easier. Extract fuel from algae and get rid of water
• GMO important.

Chlamydomonas – one of largest chloroplasts – 80% of cell. Also had 60 copies of the genome in chloroplast so had engineering to fix all of them. Will require classical breeding and genetic engineering approaches to achieve end.
“Areas that can be engineered into” – so basically where can they insert genes? Mitochondria, Nucleus, and Mitochondria.
Nucleus
Harder to engineer exactly what they want as homologous recombination doesn’t work yet. (did anyone knockout Ku? – is there Ku in plants?). RNAi silencing to silence genes as well as some possibility of chromatin silencing.
chloroplast transformation
One chloroplast per cell, but has 60 copies of the genome. DNA delivery by biolistics. No silencing in the chloroplast so easier to work with. Recombinant proteins can accumulate at high levels. Can make proteins in chloroplast that can’t be made elsewhere.
What makes them special there? – Can express things that would toxic to cell since these are compartmentalized. Wasn’t clear how secretion machinery works different or better in chloroplast but it must.
Biofuel applications
Want to make highly branched alkanes since they store lots of energy. “Carbon to Carbon” from CO2 to advanced oils. So it is important to be able to control carbon length – short carbon is gasoline. Showing data that can synthesize hydrocarbon in Chlamy “gene A, SC3 product”. Show expression of a synthase, that requires two genes, to make a C30 hydrocarbon. (learning hydrocarbon lingo!)

Mmm, green crude is what comes from the algae can then be piped into refineries. Can be piped directly into fuel refinement pipeline to make in one example, gasoline. Can make 91+ octane gasoline (a premium gasoline).

Making jet fuels. 600 gallons of JP8 for turbines which works for airplanes. Fly a continental airlines flight.

How to make commercial strains a reality? Need the JGI and many many algae genomes. 20+ genomes needed. Proteomics to mine for traits and I guess the genome helps map the genes involved in the trait. So bioprospect for new producers? There are 20+ other genomes and are in the queue already, but perhaps more strains.

Now what I wonder is what are the IP issues here. How do you get public support for genome sequences but then also need patentable products I assume? Pioneering new sciences.

What percentage of the biomass is oil? 30% 1 vial of gasoline shown, cost about $10M. The algae that was used to make fuel was not Chlamy.

Has to be salt water algae so that not competing with native. Engineer them as extremophiles.

Brainstorming ideas

After a visit to Cornell visiting with Plant Pathology & Plant-Microbe Biology dept, Pseudomonas syringae groups, and SGN and also a breakfast with Tim Hubbard when he was in Berkeley I had a few ideas.

• We need to be able to put the power of annotation in the hands of more people.  Community assisted annotation at the level of just function, linking to articles, and general curation should be accessible ala-wikipedia.
• For genome annotation though, there is a more specialized need to be able to incorporate data from different sources. Git-like repository for genome annotation (in GFF) which can be served up to Gbrowse. Edits can be saved to ones own branch.  (all of this assumes the same reference genome assembly which is about the level I’m comfortable worrying about — tho some of the genome projector type tools would seem to make it easy to lift annotation from one assembly to the other).
• Would probably necessitate a GenomeAnnotationDiff tool.  This might be already accomplished by tools that the Yandell lab has produced described in publication by Eilbeck et al.
• Gene page with community annotation tools at SGN are ready to go and they have VMs to avoid having to install all the software. I even saw a cool QTL on the fly calculation.  The challenges I see in our data is always linking the data from one context to another how we make this useful. Will have to try and do a transformation of some of the different data we have here.
• The SGN approach is to use aspects of Chado for the schema that deals with ontologies/controlled vocabularies but to also have domain specific databases for annotation and related info rather than the giant “everything is a feature” that is the Chado-way and doesn’t seem to scale.
• It is about time to try out hadoop/MapReduce on our big datasets and to also earnestly start running the automated the all-vs-all ortholog prediction scripts on our genomes, there are just too many times it seems important to have an updated dataset – something to deploy on new hardware environment this summer.
• No one has figured out how to interface with NCBI/GenBank/EMBL to deal with the updating of genomes in a sensible — basically all the really complicated systems are essentially keeping the bulk of the data in their own domain-specific databases and at some appointed times feeding that data back in, but often this is a huge process and only works where there is a real effort from both NCBI/GenBank/EMBL and the group.  E.g. Ensembl has the CCDS and RefSeq projects that can take the output from Ensembl and feed that back into the system.
  What would a comparative reannotation of X fungal genomes system be able to do with the data?

On the Plant Path & fungal side of discussions

• Looking at multiple genotypes of both the host and pathogen seem like a really smart way to start to explore the effects of mutations. With so many more tools now in both systems it seems like this would be next logical arraying of experimental designs.
• I really need to get some movies made of Bd (Chytrid) zoospores swimming around, would make for better introductions to talks, I had to settle for showing oomycete zoospores which are cool but not the same.
• There needs to be new/better tools for population genetics for systems where the populations are clearly not in Hardy-Weinberg equilibrium such as newly introduced pathogens
• Closeup pictures of fungi are really cool especially through the boroscope

Excited by sharing

Reading the Xfam (Pfam & Rfam) update about Rfam and I have to say, it is a great to have the Xfam, Ensembl, and other databases blogging about what they are doing, have done, and will do. This is an important feedback mechanism for these sites and can allow users and developers to interact. It also gives users and data consumers more information. I realize there is an overhead in information sharing and most science-places prefer to have a dramatic announcement at a conference – but I mean we already know that Svante Pääbo’s group will announce the neanderthal genome project progress before the meeting. We’ve had some debates in the lab about the future of scientific meetings (or at least the number we attend) as scientists attempt to reduce costs and our carbon footprints so perhaps there will be some shift in how and when information about project progress is shared.

I’m looking forward to seeing more Blogs and information sharing about project progresses from genome centers and database providers. I’m happy that the Broad does provide a page with the current status of fungal sequencing projects for those of us who care, and the JGI has all of the project tracking available. When these things move to the realm of being RSS follow-able (or twittered!) it will be really useful.  In the same way one can track pubmed @NCBI with email updates and RSS feeds for papers from your searches  it would be nice to see more of this information from different centers beyond having to scrape the trace archive logs to see what was uploaded recently.

So more concretely I’m interested in short and simple data feeds about project progresses, not full blown press releases.  I’m also interested in the developers sharing where the projects are going and have gone.  Something the Xfam folks seem to be giving a nice try.

CiteULike Wordle

Inspired by Rod Page’s procrastination I did another Wordle of my CiteULike keywords

CiteULike keywords

Toronto fun

Enjoyed seeing many good friends and meeting bloggers. Only at ismb for first day but got to see U of Toronto and give seminar. Testing blog posts from my new ipod touch.