20.20(S10):Notebook/BEI/2010/04/15

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Grant's research
Strains of Shewanella Directory

http://img.jgi.doe.gov/cgi-bin/pub/main.cgi?section=TaxonList&page=lineageMicrobes&genus=Shewanella

Article Confirming the Ability of Shewanella Putrefaciens to Putrify Fish

http://www3.interscience.wiley.com/cgi-bin/fulltext/119836999/PDFSTART

Nancy's research (avoid edit conflicts

 * http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TCW-4SM7RJW-1&_user=501045&_coverDate=07%2F31%2F2008&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_searchStrId=1296529033&_rerunOrigin=scholar.google&_acct=C000022659&_version=1&_urlVersion=0&_userid=501045&md5=f8d6907fb75949725953a454771e64b5

"For success in the production of alternative biofuels, similar metabolic engineering strategies will be necessary; for example, the development of targeted and efficient transport systems, the improvement of the resistance of biofuels producers to the toxic effects of accumulating biomolecules, the optimization of carbon flux to the desired products, and the construction of strains that are robust under industrial process conditions"

Good overview of sythn bio. "Perhaps the best studied of these is Botryococcus braunii (Metzger & Largeau 2005), which has been reported to produce high levels (up to 60% of dry weight) of both long-chain alkenes and branched-chain isoprenoid hydrocarbons. Considerable research has gone into the development of processes for the large-scale growth of such algae for hydrocarbon production (Chisti 2007), with a number of companies established specifically for this purpose, but to date, very little genetic work appears to have been done with such algae, meaning that transfer of the hydrocarbon synthesis pathway to a more convenient host would not be possible without a great deal more research. Given the level of interest in this area and the decreasing costs of sequencing, B. braunii would seem to be a strong candidate for a genome sequencing project. "
 * http://rsif.royalsocietypublishing.org/content/6/Suppl_4/S547.full

OVerall thoughts
So far: Algae: b. braunii, assume they are secreting the oil or otherwise output is taken care of (in actuality, still unclear how much secrete, most articles still mention dry algae and chemical extraction) Thus cannot design tank around the algae output (because don't know it), so just pick one and specify it

Bacteria: Algae and daphnia have a kind of cycle we want, bacteria? Possib schwenalla

NEed to find out how to key bacteria to dead algae (what is different about dead vs live algae, what exactly dead algae composed of) to figure out bacterial pathway that we need, and then to search for that pathway sequenced, either import into E. Coli or modify existing bacteria with that pathway, or find a bac with that pathway

Tasks
By wednesday have list of reactions Wednesday try to simulate


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