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New software lets scientists program life


– Biochemical engineers can now download a piece of software and, with a few simple clicks, assemble the DNA for new life forms through their laptops.

“With the proper computer tools, biologists can write their own genetic code — and then turn that code into life,” said biochemist Omri Amirav-Drory, who founded Genome Compiler Corp., the company that built the software.

He demonstrated for FoxNews.com at a Starbucks early one morning by manipulating a bacteria’s genes on his MacBook.

[quote]You can send them a text file and they’ll send you back physical DNA.’ –Omri Amirav-Drory, who founded Genome Compiler Corp.[/quote]

The left side of the Genome Compiler app lists folders for known viruses, bacteria and other organisms, each storing files of genome sequences, the unique biological stamp encoded in an organism’s DNA. The software offers tools to add extra genes, mutate proteins, or toss in a few amino acids.

If a particular genetic sequence is not in the list, the compiler downloads it from a library at the National Institute of Health. Once satisfied with the results, a scientist can save her invention to a file, click the order button and ship the virtual creature’s specs to a DNA synthesizing lab such as GenScript or GeneArt, which can assemble actual physical DNA based on the specs.

“You … send them a text file and they would send you back a physical DNA,” Amirav-Drory told FoxNews.com.

The synthetic biology app is still in beta; on Jan. 15, the company added an undo feature and support for new DNA file formats. Building creatures is increasingly like word processing, it would seem. But such is the strange reality in the age of cheap genome sequencing, DNA synthesizing and “bioinformatics.”

A Fulbright Scholar with a Ph.D. from Tel Aviv University, Amirav-Drory has simply merged two fields: computer science and biochemical engineering.

“Computers understand code and living things understand the language of DNA,” he said. The software has built-in biosecurity measures to stop someone from building Ebola and other deadly agents, Amirav-Drory said, and assembling complex creatures that think is still far, far off. But it will let scientists program simple new microorganisms that can clean our air and water or produce energy just by coding their DNA in a certain way.

John Cumbers, a synthetic biologist at the NASA Ames Research Center who has been using the genome compiler, says it speeds up his DNA work approximately ten times.

“You . . . lay out all the parts of the genetic constructs that you’re working with and then reconstruct your genetic circuits just by clicking and moving things around on the screen,” he said.

Like every new technology, synthetic biology raises medical and ethical questions — from bioterrorism to creating genetically engineered humans, explained Ana Iltis, director of the Center for Bioethics, Health and Society at Wake Forest University.

“This could be put to potentially beneficial uses or dangerous and deadly uses,” Iltis told FoxNews.com. She pointed to previous controversies about microwave ovens, cars and organ transplants, noting that mankind can mitigate the risks. “As a society we have to learn as we go, monitor, establish and apply guidelines, and ensure the protection of basic rights. We’ve done it before and we can do it again.”

As the price of reading a genome has gone down, biologists have sequenced thousands of organisms. According to the National Institute of Health GenBank page, as of 2011, it accumulated about 135,440,924 sequence records, which researchers can download and experiment with. Eric Sayers, who supervises user services at the National Center for Biotechnology Information, says GenBank handles 2.2 million retrieval requests for data on a daily basis, and transfers about 3.3 terabytes of information.

The price of synthesizing new DNA also went down. “When I came to Stanford in 2007 for my post-doc research, the price was a few dollars per base pair — one DNA letter,” Amirav-Drory told FoxNews.com. “Today the price is in cents.”

DNA, or deoxyribonucleic acid, is a molecule that encodes genetic instructions necessary for development, replication and functioning of all living organisms. This information is stored in particular sequences of nucleotides, or “nucleobases” — essentially DNA units, which are written in letters A, T, G and C. The sequence of nucleotides determines the organism’s hereditary characteristics.

“Base pairs” form the two strands of the DNA’s double helix shape.The number of such pairs ranges from 600,000 for bacteria to about three billion for humans. DNA-synthesizing companies charge “per base pair.”

One leading supplier of life-science products advertises a 30 cents per pair promotion on its site, and even 28 cents in some cases. Even with these prices, it would cost a few billion dollars to write a human genome DNA, Amirav-Drory explained, but bacterial DNAs add up to tens of thousands, and the prices keep falling.

The biggest issue for biologists remains to lay out sequences for their future DNA creations.

Source from Fox News:


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