Genomes small, and getting smaller

GSAC is back, although the annual genomics meeting this year goes by the name Genomes, Medicine and the Environment Conference 2005. Now under the purview of the J. Craig Venter Institute rather than the institute for genome research (TIGR), it has returned to Hilton Head, and is slightly smaller than it?s been in past years. But that?s not a bad thing. ?It?s good to see things going back to science as usual,? said J. Craig Venter in the opening session yesterday. Sporting a black t-shirt with the cryptic logo ?I dived the lady? he appeared relaxed, but stressed vigilance.Even though much of the initial excitement over having a human genome at hand has subsided, there is still much work for genomicists. ?People are starting to feel that they don?t have the access to the data that they need, that they don?t have the tools and the know-how to use the genome sequences.? Many of science?s minions are going back to looking at their pet species, and their pet genes said Venter as he made a case for the continued relevance of genome biology. That?s not to say he wasn?t upbeat about the meeting being back in Hilton Head ? a smaller attendance meant that the meeting could commence at the cozy digs of the South Carolina shore. And the water?s still warm. Adding ?environment? to the meeting?s title reinforced an emphasis on environmental metagenomics, and yesterday?s first session featured an update on Sorcerer II (Venter?s globe trotting yacht) and the J.C. Venter Institutes? bold plan to sequence New York City?s air. A range of researchers explained their forays into metagenomics including Penny Chisholm?s investigations into Prochlorococcus, which has managed to dominate the ocean with just 1700 genes, and recent The Scientist contributor Jo Handelsman?s explorations into what she calls functional metagenomics, which basically entails cloning unknown sequences into E. coli to look for antibiotic resistance genes and antibiotics.While Handelsman was busy putting things into E. coli Fred Blattner in the afternoon session was busy taking them out. He explained his work toward creating a slimmed down version of the biotech workhorse by stripping out less than useful genes. When his group finally got to removing the so-called IS elements (which were replicating and leaping all over the place even as he was pulling out other genes), they began to notice that the organism had some really useful qualities. The altered K-12 strain bacterium which they called MDS42 (for multi deletion strain 42) had better electroporation efficiency than DH10, a common strain for transfection. It had higher DNA yields, better protein expression levels from plasmid, was more efficient at making small molecules and didn?t have the nasty IS contamination of plasmids that some researchers have had to contend with. Blattner?s talk was part of the afternoon session dealing with the nascent field of synthetic biology. Others explained their plans to slim down microbial genomes including technology doyen, George Church. Robert Holt and Nobel laureate, Hamilton Smith along not too distant lines are both working to take the genome of one organism and insert it into another. But making microbes more economic and chimeric aren?t the only goals for synthetic biology. Although the field?s definition is still progressing, the work presented here painted an impressive picture of scientists finally taking knowledge about genetic programming and starting to use it to write and edit their own code.

Genomes small, and getting smaller

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