Bio Saga Blog - A Chronicle of Life Sciences & Informatics

Abstract Whole genome amplification by the multiple displacement amplification (MDA) method allows sequencing of DNA from single cells of bacteria that cannot be cultured. Assembling a genome is challenging, however, because MDA generates highly nonuniform coverage of the genome. Here we describe an algorithm tailored for short-read data from single cells that improves assembly through the use of a progressively increasing coverage cutoff. Assembly of reads from single  Escherichia coli  and  Staphylococcus aureus  cells captures >91% of genes within contigs, approaching the 95% captured from an assembly based on many  E. coli  cells. We apply this method to assemble a genome from a single cell of an uncultivated SAR324 clade of Deltaproteobacteria, a cosmopolitan bacterial lineage in the global ocean. Metabolic reconstruction suggests that SAR324 is aerobic, motile and chemotaxic. Our approach enables acquisition of genome assemblies for individual uncu...

To design cells to spec, researchers still need better tools. MONDAY, JUNE 20, 2011 BY KATHERINE BOURZAC Last July , scientists created the first " synthetic cell ," an organism that's controlled by a chemically synthesized genome edited on a computer and stitched together in the lab. One year later, biologists at the  Fifth Annual Synthetic Biology  conference at Stanford University are still struggling to take the next step in the field. Holding them back are the vagaries of biology itself, and the expense and time needed to get from idea to engineered organism. While the creation of the synthetic cell, at the J. Craig Venter Institute , hints at a future in which synthetic biologists can redesign living cells to perform whatever tasks they dream up, that goal is still distant. Most research has focused on coaxing microbes to perform tasks that are similar to what they already do, such as transforming sugar into fuels using processes and materials that resemble the on...

A team of researchers from the J. Craig Venter Institute has created the first synthetic organellar genome, using a method called isothermal DNA assembly to construct a synthetic mouse mitochondrial genome from hundreds of overlapping oligonucleotides. The work, published online yesterday in   Nature Methods , is the latest in a series of synthetic biology achievements by the group. JCVI researchers reported in  Science  in 2008  that they had put together four Mycoplasma genitalium  quarter genomes in  Escherichia coli  and yeast to create the first synthetic genome, dubbed  M. genitalium  JCVI-1.0. They later tweaked this process, showing that they could assemble the  synthetic  M. genitalium  genome in a single step in yeast. And earlier this year the team took another step toward synthetic life when they made a synthetic  M. mycoides  genome, transplanted it into another bacterial species,  M. capricolum , ...