Scientists create digital bacteria to forge advances in biomedical research

Jun 03, 2005

Biological assays on computer study molecular basis of cellular behavior

Scientists at the University of Chicago and Argonne National Laboratory have constructed a computer simulation that allows them to study the relationship between biochemical fluctuations within a single cell and the cell's behavior as it interacts with other cells and its environment.

The simulation, called AgentCell, has possible applications in cancer research, drug development and combating bioterrorism. Other simulations of biological systems are limited to the molecular level, the single-cell level or the level of bacterial populations. AgentCell can simultaneously simulate activity on all three scales, something its creators believe no other software can do.

"With AgentCell we can simulate the behavior of entire populations of cells as they sense their environment, respond to stimuli and move in a three-dimensional world," said Thierry Emonet, a Research Scientist in Philippe Cluzel's laboratory at the University of Chicago's Institute for Biophysical Dynamics.

Emonet and his colleagues have verified the accuracy of AgentCell in biological experiments. AgentCell now enables scientists rapidly to run test experiments on the computer, saving them valuable time in the laboratory later.

Emonet is the lead author of a paper announcing the development of AgentCell that was published in the June 1 issue of the semimonthly journal Bioinformatics. His co-authors are Argonne's Charles Macal and Michael North, and the University of Chicago's Charles Wickersham and Philippe Cluzel. The work was funded by the U.S. Department of Energy and the University of Chicago/Argonne National Laboratory Seed Grant Program.

AgentCell will be used to tackle a major goal in single-cell biology today: to document the connection between internal biochemical fluctuations and cellular behavior. "The belief is that these fluctuations are going to be reflected in the behavior of the cell as shown experimentally by John Spudich and Daniel Koshland in 1976," Emonet said. They may even reveal why cells sometimes act as individuals and sometimes as part of a community.

AgentCell was made possible by agent-based software, which researchers developed to simulate stock markets, social behavior and warfare. Argonne's Macal and North contributed their agent-based software expertise to the project. Macal and North operate Argonne's Center for Adaptive Systems Simulation.

Cluzel's laboratory began its collaboration with Macal and North following a suggestion by Robert Rosner, Argonne's Director and the William Wrather Distinguished Service Professor in Astronomy & Astrophysics at the University of Chicago. Before shifting to Cluzel's lab, Emonet worked with Rosner in devising simulations to understand how the sun reverses its magnetic field every 11 years.

Each digital cell in AgentCell is a virtual Escherichia coli, a single-celled bacterium, which is equipped with all the virtual components necessary to search for food. These digital E. coli contain their own chemotaxis system, which transmits the biochemical signals responsible for cellular locomotion. They also have flagella, the whiplike appendages that cells use for propulsion, and the motors to drive them.

Emonet and his associates have designed their digital bacterial system in modules, so that additional components may be added later.

"Right now it's a very simple model," Emonet said. "Basically the only thing those cells have is a sensory system." But additional components that simulate other biological processes--cell division, for example--can also be introduced. And the software is available to other members of the research community for the asking. "The hope is that people will modify the code or add some new capabilities. The code will soon be available for download from our Web site, www.agentcell.org," Emonet said.

AgentCell has already yielded benefits in Cluzel's laboratory, even in its current rather simple configuration. In his simulations, Emonet discovered that one type of protein controlled the sensitivity of E. coli's chemotaxis system, which helps the bacteria find food. "When you changed the level of that protein, it would change the sensitivity of the cell," Emonet said. Subsequent laboratory experiments came out exactly the same way.

Sometimes, though, conducting the actual experiment would be undesirable. Preparing for a bioterrorism attack is one example. "You can actually try to simulate dangerous experiments," said Cluzel, an Assistant Professor in Physics. "For instance, if you mix a pathogenic strain with a friendly strain, which one is going to win, and with what kind of speed?"

Source: University of Chicago

Explore further: Everglades trail surveyed for cultural artifacts

add to favorites email to friend print save as pdf

Related Stories

Tailored 'activity coaching' by smartphone

2 hours ago

Today's smartphone user can obtain a lot of data about his or her health, thanks to built-in or separate sensors. Researcher Harm op den Akker of the University of Twente (CTIT Institute) now takes this health ...

Chemists tackle battery overcharge problem

2 hours ago

Research from the University of Kentucky Department of Chemistry will help batteries resist overcharging, improving the safety of electronics from cell phones to airplanes.

Operation IceBridge turns five

2 hours ago

In May 2014, two new studies concluded that a section of the land-based West Antarctic ice sheet had reached a point of inevitable collapse. Meanwhile, fresh observations from September 2014 showed sea ice ...

A newborn supernova every night

2 hours ago

Thanks to a $9 million grant from the National Science Foundation and matching funds from the Zwicky Transient Facility (ZTF) collaboration, a new camera is being built at Caltech's Palomar Observatory that ...

Recommended for you

US state reaches deal to keep dinosaur mummy

2 hours ago

North Dakota reached a $3 million deal to keep a rare fossil of a duckbilled dinosaur on display at the state's heritage center, where it will serve as a cornerstone for the facility's $51 million expansion, officials said ...

Jerusalem stone may answer Jewish revolt questions

5 hours ago

Israeli archaeologists said Tuesday they have discovered a large stone with Latin engravings that lends credence to the theory that the reason Jews revolted against Roman rule nearly 2,000 ago was because ...

Kung fu stegosaur

5 hours ago

Stegosaurs might be portrayed as lumbering plant eaters, but they were lethal fighters when necessary, according to paleontologists who have uncovered new evidence of a casualty of stegosaurian combat. The ...

User comments : 0