Future of Data: Encoded in DNA

ORIGINAL: Professional.wsj.com

By ROBERT LEE HOTZ

In the latest effort to contend with exploding quantities of digital data, researchers encoded an entire book into the genetic molecules of DNA, the basic building block of life, and then accurately read back the text.

The experiment, reported Thursday in the journal Science, may point a way toward eventual data-storage devices with vastly more capacity for their size than today's computer chips and drives.

"A device the size of your thumb could store as much information as the whole Internet," said Harvard University molecular geneticist George Church, the project's senior researcher.

In their work, the group translated the English text of a coming book on genomic engineering into actual DNA.

DNA contains genetic instructions written in a simple but powerful code made up of four chemicals called bases: adenine (A), guanine (G), cytosine (C) and thymine (T).

The Harvard researchers started with the digital version of the book, which is composed of the ones and zeros that computers read. Next, on paper, they translated the zeros into either the A or C of the DNA base pairs, and changed the ones into either the G or T.

Then, using now-standard laboratory techniques, they created short strands of actual DNA that held the coded sequence—almost 55,000 strands in all. Each strand contained a portion of the text and an address that indicated where it occurred in the flow of the book.

In that form—a viscous liquid or solid salt—a billion copies of the book could fit easily into a test tube and, under normal conditions, last for centuries, the researchers said.

Kelvin Ma for the Wall Street Journal. Harvard biologist George Church, in his office Wednesday, recently encoded a book he wrote into the genetic molecules of DNA.

The technique likely is a long way from being commercially viable. But it highlights the potential of DNA as a stable, long-term archive for ordinary information, such as photographs, books, financial records, medical files and videos, all of which today are stored as computer code.

"It shows that the vast increase in capacity to synthesize and sequence DNA can be applied to store significant amounts of data," said pioneering synthetic biologist Drew Endy at Stanford University, who wasn't involved in the project. "If you wanted to have your library encoded in DNA, you could probably do that now."

Molecular biologists have long known that DNA is a natural information-storage system inside every cell that encodes the recipe for individual heredity.

Kelvin Ma for the Wall Street Journal.Dr. Church keeps a vial of DNA encoded with copies of his latest book.

The exact order of the DNA bases—which for the average person is a sequence of about three billion—determines the meaning of the biological instructions stored in genes and chromosomes, just as letters of the alphabet make up words and sentences.

Some scientists have been experimenting with ways to use that code to store other kinds of information.

Research groups in the U.S., Europe and Canada devised ways to use DNA to encode trademarks and secret messages in cells. And when genomics pioneer Craig Venter and colleagues created the first synthetic cell in 2010, they wrote their names into its DNA code, the way an artist might sign a painting, along with three literary quotations and a website address.

Other researchers used DNA to encode poetry and popular music inside the living cells of bacteria.

In 2003, genetic engineers at the Pacific Northwest National Laboratory in Washington state created micro-organisms that carry the tune of Disney's "It's a Small World (After All)" in their DNA.

Unlike these earlier DNA storage experiments, the DNA book reported Thursday wasn't inserted into a living cell but kept in a laboratory container. If incorporated into a living cell, the stored DNA data might be changed or erased by the normal process of cell biology.

"The cell kicks out foreign DNA," said Harvard's Dr. Church. "In a tube, it is less subject to evolution."

The Harvard effort stands out for its large scale, the scientists said. All told, the book contains 53,426 words, 11 illustrations and a JavaScript computer program. The 5.27 megabits of data are more than 600 times bigger than the largest data set previously encoded in DNA. It is the equivalent of the storage capacity of a 3.5-inch floppy computer disk.

"For some archival problems, this could be the wave of the future," said Dr. Church. The group has filed a patent on the technique.

The method requires a series of advanced laboratory procedures, microarray chips and a high-speed gene-sequencing machine to assemble the strands in the proper order, correct any errors and then read the final text.

The stored data "is sequential, like a magnetic tape, where you have to spool through stuff to get at the data," said bioengineer Sriram Kosuri at the Wyss Institute for Biologically Inspired Engineering at Harvard, who was the project's lead researcher.

It took several days to "write" the DNA form of the book, and even longer to read it back.

So far, the cost of synthesizing and sequencing such very long strands of data-rich DNA as from the book remains too high to make the technique a practical commercial data-storage medium for the foreseeable future.

But Dr. Church is confident those costs will drop dramatically, and the speeds increase, as more advanced technology becomes available.

"The cost of both synthesis and sequencing [of DNA] are plummeting in an unprecedented way," Dr. Church said.

Already, the production costs of generating raw, unassembled DNA sequence data, such as might be used to archive data, have dropped from $10,000 per million base pairs of DNA in 2001 to about 10 cents per million base pairs in 2012, according to the National Human Genome Institute.

"This new work demonstrates that there is a whole new market for these technologies, to synthesize DNA for people who want to store information," said Dr. Endy.

The experiment also set a milestone of sorts in the techniques of book marketing—Dr. Church wrote the book that was turned into DNA. Called "Regenesis," it is scheduled for conventional publication in October.

Dr. Church said he first considered encoding the novel "Moby Dick," but then chose to use his own manuscript because its combination of words, pictures and JavaScript code would better showcase DNA's capacity to handle different ki

Artificial jellyfish created from heart cells

ORIGINAL: BBC

The artificial jellyfish replica is made from silicone polymer and rat heart cells

Scientists in the US have created a free swimming artificial jellyfish.

The team members built the replica using silicone as a base on which to grow heart muscle cells that were harvested from rats.

They used an electric current to shock the Medusoid into swimming with synchronised contractions that mimic those of real jellyfish.

The advance, by researchers at Caltech and Harvard University, is reported in the journal Nature Biotechnology.

The finding serves as a proof of concept for reverse engineering a variety of muscular organs and simple life forms.

Because jellyfish use a muscle to pump their way through the water, the way they function - on a very basic level - is similar to that of a human heart.

"I started looking at marine organisms that pump to survive," said Kevin Kit Parker, a professor of bioengineering and applied physics at Harvard.

"Then I saw a jellyfish at the New England Aquarium, and I immediately noted both similarities and differences between how the jellyfish pumps and the human heart.

"The similarities help reveal what you need to do to design a bio-inspired pump."

Mechanical movement

The work also points to a broader definition of "synthetic life" in an emerging field of science that has until now focused on replicating life's building blocks, say the researchers.

Prof Parker said he wanted to challenge the traditional view of synthetic biology which is "focused on genetic manipulations of cells". Instead of building just a cell, he sought to "build a beast".

The two groups at Caltech and Harvard worked for years to understand the key factors that contribute to jellyfish propulsion, including the arrangement of their muscles, how their bodies contract and recoil, and how fluid dynamics helps or hinders their movements.

The swimming behaviour of the Medusoid closely mimics that of the real thing

Once these functions were well understood, the researchers began to reverse engineer them.

They used silicone to fashion a jellyfish-shaped body with eight arm-like appendages.

Next, they printed a pattern made of protein onto the "body" that resembled the muscle architecture of the real animal.

They grew the heart muscle cells on top, with the protein pattern serving as a road map for the growth and organisation of the rat tissue. This allowed them to turn the cells into a coherent swimming muscle.

When the researchers set the Medusoid free in a container of electrically conducting fluid, they shocked the Medusoid into swimming with synchronised contractions. The muscle cells even started to contract a bit on their own before the electrical current was applied.

"I was surprised that with relatively few components - a silicone base and cells that we arranged - we were able to reproduce some pretty complex swimming and feeding behaviours that you see in biological jellyfish," said John Dabiri, professor of aeronautics and bioengineering at Caltech.

"I'm pleasantly surprised at how close we are getting to matching the natural biological performance, but also that we're seeing ways in which we can probably improve on that natural performance. The process of evolution missed a lot of good solutions."

Lead author Janna Nawroth from the California Institute of Technology (Caltech) in Pasadena commented that the field of tissue engineering was "still a very qualitative art".

She said researchers tried to copy a tissue or organ "based on what they think is important or what they see as the major components without necessarily understanding if those components are relevant to the desired function or without analysing first how different materials could be used".

The team aims to carry out further work on the artificial jellyfish. They want to make adjustments that will allow it to turn and move in a particular direction.

They also plan to incorporate a simple "brain" so it can respond to its environment and replicate more advanced behaviours like moving towards a light source and seeking energy or food.