Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Using Computers, Scientists Successfully Predict Evolution of E. Coli Bacteria

15.11.2002


For more than a decade, researchers have been trying to create accurate computer models of Escherichia coli (E. coli), a bacterium that makes headlines for its varied roles in food poisoning, drug manufacture and biological research.


Photomicrograph of E. coli.

Credit: Image courtesy of National Institute of Allergy and Infectious Diseases, National Institutes of Health



By combining laboratory data with recently completed genetic databases, researchers can craft digital colonies of organisms that mimic, and even predict, some behaviors of living cells to an accuracy of about 75 percent.

Now, NSF-supported researchers at the University of California at San Diego have created a computer model that accurately predicts how E. coli metabolic systems adapt and evolve when the bacteria are placed under environmental constraints. Bernhard Palsson, Rafael Ibarra (now at GenVault Corporation in Carlsbad, California) and Jeremy Edwards (now at the University of Delaware at Newark) report their findings in the November 14 issue of Nature.


"Ours is the only existing genome-scale model of E. coli," says Palsson. In addition, while many approaches to genetics experiments "knock out" individual genes and track the results, the new model takes a whole-system approach. Changing one aspect of a genetic code could be irrelevant if an organism adapts and evolves, says Palsson. The constraints-based models allow the E. coli to evolve more naturally along several possible paths.

Scientists may use the approach to design new bacterial strains on the computer by controlling environmental parameters and predicting how microorganisms adapt over time. Then, by recreating the environment in a laboratory, researchers may be able to coax living bacteria into evolving into the new strain.

The resulting strains may be more efficient at producing insulin or cancer-fighting drugs than existing bacterial colonies engineered by researchers using standard techniques.

"Now we have a better tool to predict how bacteria evolve and adapt to changes," says National Science Foundation program director Fred Heineken. "As a result, this constraints-based approach could lead to better custom-built organisms," he says.

The researchers based their digital bacteria on earlier laboratory studies and E. coli genome sequences, detailed genetic codes that have been augmented with experimental information about the function of every gene.

Such digital models are known as "in silico" experiments -- a play on words referring to biological studies conducted on a computer.

In the first days of testing on living organisms, the bacteria did not adapt into the strain predicted by the simulation. Yet, with more time (40 days, or 500-1000 generations), the E. coli growing in the laboratory flasks adapted and evolved into a strain like the one the in silico model predicted.

"The novelty of the constraints-based approach is that it accounts for changes in cellular properties over time," says Palsson. "Fortunately," he adds, "the other advantage is that it actually works surprisingly often."

For many years, drug manufacturers have manipulated the genetic code in E. coli strains, creating species that can produce important substances, such as the hormone insulin for use by people with diabetes or the experimental cancer drug angiostatin.

Using the new constraints-based techniques Palsson and his colleagues developed, drug manufacturers and bioprocessing companies could use computers to determine the genetic code that could yield the most efficient and productive versions of E. coli, and then use adaptive evolution to create bacterial strains that have the desired properties.

Says Palsson, "This development potentially opens up a revolutionary new direction in the design of new production strains." In addition, says Palsson, "now that we have gained a greater understanding of this process in E. coli, developing similar simulations of other organisms should take less time."

Josh Chamot | EurekAlert!
Further information:
http://www.nsf.gov/
http://www.nsf.gov/od/lpa/news/02/pr0292.htm

More articles from Life Sciences:

nachricht Navigational view of the brain thanks to powerful X-rays
18.10.2017 | Georgia Institute of Technology

nachricht Separating methane and CO2 will become more efficient
18.10.2017 | KU Leuven

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: Neutron star merger directly observed for the first time

University of Maryland researchers contribute to historic detection of gravitational waves and light created by event

On August 17, 2017, at 12:41:04 UTC, scientists made the first direct observation of a merger between two neutron stars--the dense, collapsed cores that remain...

Im Focus: Breaking: the first light from two neutron stars merging

Seven new papers describe the first-ever detection of light from a gravitational wave source. The event, caused by two neutron stars colliding and merging together, was dubbed GW170817 because it sent ripples through space-time that reached Earth on 2017 August 17. Around the world, hundreds of excited astronomers mobilized quickly and were able to observe the event using numerous telescopes, providing a wealth of new data.

Previous detections of gravitational waves have all involved the merger of two black holes, a feat that won the 2017 Nobel Prize in Physics earlier this month....

Im Focus: Smart sensors for efficient processes

Material defects in end products can quickly result in failures in many areas of industry, and have a massive impact on the safe use of their products. This is why, in the field of quality assurance, intelligent, nondestructive sensor systems play a key role. They allow testing components and parts in a rapid and cost-efficient manner without destroying the actual product or changing its surface. Experts from the Fraunhofer IZFP in Saarbrücken will be presenting two exhibits at the Blechexpo in Stuttgart from 7–10 November 2017 that allow fast, reliable, and automated characterization of materials and detection of defects (Hall 5, Booth 5306).

When quality testing uses time-consuming destructive test methods, it can result in enormous costs due to damaging or destroying the products. And given that...

Im Focus: Cold molecules on collision course

Using a new cooling technique MPQ scientists succeed at observing collisions in a dense beam of cold and slow dipolar molecules.

How do chemical reactions proceed at extremely low temperatures? The answer requires the investigation of molecular samples that are cold, dense, and slow at...

Im Focus: Shrinking the proton again!

Scientists from the Max Planck Institute of Quantum Optics, using high precision laser spectroscopy of atomic hydrogen, confirm the surprisingly small value of the proton radius determined from muonic hydrogen.

It was one of the breakthroughs of the year 2010: Laser spectroscopy of muonic hydrogen resulted in a value for the proton charge radius that was significantly...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

ASEAN Member States discuss the future role of renewable energy

17.10.2017 | Event News

World Health Summit 2017: International experts set the course for the future of Global Health

10.10.2017 | Event News

Climate Engineering Conference 2017 Opens in Berlin

10.10.2017 | Event News

 
Latest News

Osaka university researchers make the slipperiest surfaces adhesive

18.10.2017 | Materials Sciences

Space radiation won't stop NASA's human exploration

18.10.2017 | Physics and Astronomy

Los Alamos researchers and supercomputers help interpret the latest LIGO findings

18.10.2017 | Physics and Astronomy

VideoLinks
B2B-VideoLinks
More VideoLinks >>>