21 May 2010

What Use is a New-Born Baby?

On a Friday in March, scientists inserted over 1 million base pairs of synthetic DNA into Mycoplasma capricolum cells before leaving for the weekend. When they returned on Monday, their cells had bloomed into colonies.

“When we look at life forms, we see fixed entities,” said J. Craig Venter, president of the Institute, in a recent podcast. “But this shows in fact how dynamic they are. They change from second to second. And that life is basically the result of an information process. Our genetic code is our software.” _Wired

"Impressive!", you may say, "but what good is it?" Yes, what good is a newborn baby? Only time can tell. Here is a look at the coverage of the Venter Institute's achievement from a few prominent websites:
The cell was created by stitching together the genome of a goat pathogen called Mycoplasma mycoides from smaller stretches of DNA synthesised in the lab, and inserting the genome into the empty cytoplasm of a related bacterium. The transplanted genome booted up in its host cell, and then divided over and over to make billions of M. mycoides cells.

Venter and his team have previously accomplished both feats – creating a synthetic genome and transplanting a genome from one bacterium into another – but this time they have combined the two.

"It's the first self-replicating cell on the planet that's parent is a computer," says Venter, referring to the fact that his team converted a cell's genome that existed as data on a computer into a living organism. _NewScientist

"It is a big deal," geneticist and technology developer George Church of Harvard Medical School says of the achievement. "It's not incremental, but it's not final either," noting that other groups are already delivering useful products from partially reengineered genomes, such as biofuels from engineered E. coli.

Biological engineer Drew Endy of Stanford University clarified how to think of this creation. "It's not genesis, it's not as if mice are coming from a pile of dirty rags in a corner," he says. "The correct word is poesis, human construction. We can now go from information and get a reproducing organism. It lays down the gauntlet for us to learn how to engineer genomes." _SciAm

Using a method developed in 2008, the researchers, led by genomics pioneer Craig Venter, synthesized the genome of a tiny bacterium called Mycoplasma mycoides, containing just over a million DNA base pairs. Next they transplanted the synthetic genome into a related bacterium, Mycoplasma capricolum, in a process they had previously perfected using nonsynthetic chromosomes.

Once the recipient cells incorporated the synthetic genome, they immediately began to carry out the instructions encoded within the genome. The cells manufactured only M. mycoides proteins, and within a few rounds of self-replication, all traces of the recipient species were gone. The results were published Thursday in the online edition of the journal Science.

To distinguish their synthetic genome from the naturally occurring version, the researchers encoded a series of watermarks into the sequence. They began by developing a code for writing the English alphabet, as well as punctuation and numbers, into the language of DNA--a decoding key is included in the sequence itself. Then they wrote in their names, a few quotations, and the address for a website people can visit if they successfully crack the code. _TechnologyReview

This publication represents the construction of the largest synthetic molecule of a defined structure; the genome is almost double the size of the previous Mycoplasma genitalium synthesis. With this successful proof of principle, the group will now work on creating a minimal genome, which has been a goal since 1995. They will do this by whittling away at the synthetic genome and repeating transplantation experiments until no more genes can be disrupted and the genome is as small as possible. This minimal cell will be a platform for analyzing the function of every essential gene in a cell. _GCC

What we now need are ways to construct and test billions of genome combinations using protein and RNA biosensors for many or all metabolic intermediates and cell-signalling states. In combination with the sort of techniques that the JCVI has just demonstrated — but at much lower cost — this would enable researchers to select for important products such as pharmaceuticals, fuels, chiral chemicals and novel materials.

Ever since Watson and Crick, biologists and biochemists have known that it was only a matter of time before humans learned to bend biological mechanisms to the will of humans. The journey has just barely begun. It is likely to be a very wild ride.


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