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Bio-boffins create world's first digital STD

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A bacterium that in humans can cause genital pain, itching, and a burning sensation while urinating has become the subject of the first-ever complete software simulation of an entire organism, the New York Times reports.

The simulation is the work of a team of boffins from Stanford University and the J. Craig Venter Institute, headed by Stanford's Markus Covert. Their research was published on Friday in the journal Cell.

The bacterium in question, known by the snicker-inducing name Mycoplasma genitalium, is a parasite that lives in the genital and respiratory tracts of humans and other primates, and we're sorry to report that it can be transmitted sexually.

It was chosen for the computer simulation project not for its charm, however, but for its simplicity. The M. genitalium genome contains just 525 genes, making it the world's smallest free-living bacterium.

By comparison, E. coli, another bacterium that's often used in laboratory experiments, contains 4,288 genes. Humans have upwards of 20,000.

But even modeling an organism as tiny as M. genitalium was challenging. The simulation was designed to model a whole cell, including all of its molecular components and their interactions.

"Right now, running a simulation for a single cell to divide only one time takes around 10 hours and generates half a gigabyte of data," Covert told the paper.

Developing the model hasn't been easy, either. In February 2010, Covert announced that he hoped to have it completed "in a matter of months." No such luck.

The researchers hail their breakthrough as an important steppingstone in the use of computer-aided design for bioengineering and medicine.

Most biological experiments are aimed at figuring out the function of a single gene at a time, Covert said, but that approach isn't sufficient to gain insight into more complex biological processes, such as cancer.

"Many of the issues we're interested in these days aren't single-gene problems. They're the complex result of hundreds or thousands of genes interacting," Covert said.

While the current research falls far short of simulating such a complex system, it's a step in the right direction. The hope is that in the future, digital models of cells will be used for experimentation, drug discovery, and even the creation of new organisms.

Covert and his team aren't shy about spreading the digital bacteria around. Anyone who might be interested in observing the nasty bug on their own can access the project's website to read further information and download the data and source code used in the research.

"You don't really understand how something works until you can reproduce it yourself," said Jayodita Sanghvi, one of the co-authors of the research paper. ®

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