Join the Conversation on the future of science... your ideas straight to the White House

I received an announcement the other day from AAAS, soliciting ideas from the scientific community that can help shape Obama's science policy and direction in the coming years. I love the idea. Its so often, as one scientist doing your own research that is just a small piece in a large puzzle, to feel like its hard to figure out how to move what you know into the public sphere. That is why this solicitation by the white house is so exciting, they want to hear from everyone who has a good idea, and perhaps a new perspective. Of course Obama has a team of heavy hitting scientists to advise him as well as the whole AAAS and the National Academy of Science.... but with his administration's very grass roots mentality, they want to hear from a broad scope of ideas.

see: http://promo.aaas.org/expertlabs/grandchallenges.html

I am submitting a few statements on using large scale sequencing projects to study communities of eukaryotic phytoplankton (aka "algae"). They are important for controlling the carbon cycle in the oceans and they have potential as a sustainable biofuels feedstock. I believe algae could be part of distributed generation energy systems that will provide sustainable energy production on local as well as regional community scales. One thing slowing down current progress (if not holding us back) is our limited basic science knowledge about these organisms. With new genomic (DNA sequencing) and transcriptomic (RNA sequencing) methods we are able to make quick progress in understanding the basic biology of these organisms. The progress we are now making in leaps and bounds is the result of next generation sequencing technology, which is high throughput (generating hundreds of thousands and even millions of sequences in a single run) and is cost effective enough to employ it large scale. As a scientific community, we are using these new technologies for a great number of studies, but we could still do more and be more strategic. How about a new and improved, well coordinated and well funded aquatic species program. The more we learn about algal physiology, the more we learn about the ocean's biological response to climate change as well as ways to improve algae as a biofuels feedstock. Seems like a win win situation for me.

Algae Biofuels and Genomics - Where do we stand?

This week, I'm in California for the Joint Genome Institute's (JGI) Annual User's Meeting. The theme of this year is "Genomics of Energy & Environment", and there are a lot of talks in the next few days aimed at how people are using genome sequencing and bioinformatics for biofuels research.

In the algae world, we know some groups such as Saphire Energy are working to genetically engineer algal strains. People have also been working for years to try to engineer more hydrogen production from green algae, and we just learned of a group successfully genetically engineer algae to make proteins for the pharmaceutical industry.

In order to understand how to genetically engineer an organism, we need to have model genetic and genomic systems to learn from and experiment with. For a long time, very few things considered algae had a genome sequence. You hear a lot about the green algae Chlamydomonas reinhardii, because it was the first to have it's genome sequenced. In the past 10 years, only a handful of microbes that fall into the category algae have had a whole genome sequenced, including two diatoms and one of their relatives, a red alga, a coccolithophore, and two other marine green alage. Compare that to at least twice as many plant genomes and over one thousand bacterial genomes.

In my academic work, I use genomes and comparative genomics to study the evolution of algal groups and their physiological capabilities. I also use a new tool, called metagenomics, to look at the combined genome of these organisms in the environment - specifically the ocean. To do this, we go collect community samples of microbes in the ocean, extract total DNA (or RNA) from those samples and then sequence as much as we can from it. Then we identify who was there by comparing to the genomes we have already sequenced. As you might guess, this is a really hard problem when you have only a handful of genomes to compare to.

This limited genomic data also poses challenges for the algae biofuels industry. Many of the scientist doing this work would love to have genome sequence of the potential fuel producing strains. Two weeks ago, a group in Texas announced the genome project of a biofuel favorite, Botryococcus braunii.

http://www.sciencedaily.com/releases/2010/03/100312164659.htm

This will be a contribution to the industry but also to academia, where scientist looking to understand the evolution and physiology of these organism will also be able to make use of the data. B. braunii is just the beginning of sequencing for energy related organisms, that will also help to fill out our understanding of the tree of life.

(I should say that the genomes I mentioned above are the ones that are publicly available. Many labs are in the process of sequencing genomes that are not publicly available yet, and genome sequencing done through industry probably will not be shared... but we can hope.)