Modeling the Cell

The first full computer model of a single-celled organism mimics the bacterium’s behaviors and paves the way to more complete disease models.

By | July 23, 2012

Wonderlane" > Digital DNA, Art in Public Places, Palo Alto, CaliforniaFlickr, Wonderlane

Mycoplasma genitalium, a bacterium known to cause urethritis, made headlines in 2008 when J. Craig Venter and colleagues announced that they had manufactured and assembled the organism’s 600,000 base pair genome. Now, the microbe is in the news again—this time for becoming the first organism to be fully modeled by a computer program.

Bioengineering professor Markus Covert of Stanford University and colleagues scoured some 1,000 papers in the scientific literature to glean the information needed about the functions of M. genitalium proteins and genes to model how the bacterium behaves in the real world. In the end, they constructed a computer simulation that incorporates every known gene function. The team published its results last week (July 19) in Cell.

"So far, it all works great," Covert told The Chronicle of Higher Education. "We were able to recapitulate a lot of the behaviors of the cell." Running hundreds of simulations, the researchers identified key factors involved in processes such as cell growth. They also were able to test the effects of knocking out individual genes—an exercise that proved "extremely predictive," Covert said.

Past modeling studies have created programs that reflected certain functions of cells, such as the metabolism of E. coli, but this is the first to model an entire organism. But with only 460 genes, however, M. genitalium is a relatively simple. (By comparison, the metabolic E. coli model involved about 1,300 genes.) Still, the new model is an important first step."He did this for the entire cell," bioengineer Bernhard Palsson of the University of California at San Diego told The Chronicle. "So that's the achievement here."

Such models could help uncover mechanisms involved in cancers and other diseases, Covert added. "The simple fact is, there's no way we are going to wrap our heads around cancer or any complex disease without a computer model, and so I see this as definitely a big start," he told The Chronicle.

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Avatar of: sirvijay111


Posts: 1

July 24, 2012

the struggle to synthesize life continues.

Avatar of: alexandru


Posts: 1457

July 26, 2012

The big problem for life syntheses is that the scientists forgot the Adam mtDNA in their research.

I developed five years ago a new theory: "Mitochondrial Adam DNA data transmissions theory - ISBN 978-606-92107-1-0"

On my calculation the resonance frequency of the Adam mtDNA QCLs is 30-33 THz

Abstract: Brain and soul storming -
The necessary and sufficient processes to a well function of the human body are
meticulous arranged by specific organizational cells, so called process bio-managers, using interconditioned procedures, transmitted through three ways
of communication: chemical or “protein channelâ€쳌, electrical or “ion channelâ€쳌
and mitochondrial or “EMF wireless channelâ€쳌. The third type is out of the
visible and measurable spectrum and raises a new challenge to the scientist.
For this type of bio communication we bring a new theoretical hypothesis, based
on the managerial multidisciplinary analysis of a cybernetic model proposed by
us, by simulating the human body function with the virtual computerized system
based on the management of its total knowledge and its perfect quality way of
function. The main bricks used for this virtual construction are: the brain, as
main bio-processor, and Eve mtDNA and Adam mtDNA, as bio-antennas. This
assembly of the total knowledge, build with “brain reasoning, biological
feeling, and unlimited soul feelingâ€쳌, is called by us “main decision triangle,
IQ-EQ-CQâ€쳌. The main principle of the management of the total knowledge imposes
us to not neglect the information produced by man during the time, even if it
seems creasy at the beginning (see brainstorming definition). Because in the
natural fertilisation the spermatozoids are naturally equipped with the
paternal mtDNA (it looks like reflex klystron power amplifier, KPA = a
veritable main bio-GPS), we consider that the paternal mitochondria DNA have a
very important role in the evolution of the human being life quality and we
have developed a new hypothesis, “Adam mtDNA theoryâ€쳌, in addition to “Eve mtDNA theoryâ€쳌.

Keywords: brain, mitochondria, maternal, paternal

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