Integrating Biology

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Article: Tracking Bacteria in the Blood

Article: Modeling for New Research

Article: Engineering an Ecosystem

Identifying all the parts of a cell or organism won't necessarily tell you how those parts work together to make the system run. To do this, scientists have turned to a relatively new field called systems biology that combines experimental data and computational models to diagram everything from how cells move to how hearts beat. With the diagrams, the researchers can tinker with different parts and begin to explore questions nearly impossible to answer through traditional lab experiments.

»  Bacteria Blast Off
»  Connected Worlds
»  On the Move

Bacteria Blast Off

In this computer model simulation, a Listeria bacterium propels itself through an infected cell by stimulating the growth of cellular filaments (yellow and red) at the cell's surface.
Credit: Jonathan Alberts, Susanne Rafelski, and Garrett Odell

Ten, nine, eight, seven, six, five, four, three, two, one . . . BLAST OFF!

While this object might look like a rocket blasting through space, it's really a fake bacterium jetting around a virtual cell. It represents Listeria, a type of bacteria best known for causing food poisoning.

Computational biologist Jonathan Alberts and mathematical biologist Garrett Odell at the University of Washington's Center for Cell Dynamics in Friday Harbor created it to study how the bacterium moves around the cells it infects, ultimately making you sick to your stomach.

By combining experimental data with computer-based approaches, Alberts and Odell have created virtual models of Listeria that show it moving through time. This more complete picture may enable the researchers to identify new ways to prevent foodborne illnesses.—AD

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Connected Worlds

Each spot on this globe represents a city, and each color corresponds to a community of easily connected cities.
Luis A.N. Amaral and Roger Guimerà

This sphere represents all the known chemical reactions in the E. coli bacterium.
Luis A.N. Amaral

For scientists, the Internet is more than an information superhighway and airports aren't just places where planes take off and land. They are examples of complex networks that can help researchers study even more complicated ones in the body.

Networks, whether social or cellular, share a number of features. Each one is a system made up of different elements that connect through important centers of activity called hubs. Hubs could be Web pages linked to many other sites or major airports that route passengers to additional cities. Communication occurs within the network, letting it organize itself and even change over time.

Any network can serve as a model for understanding another because all these systems operate by a similar set of rules, says physicist Luis Amaral at Northwestern University in Evanston, Illinois.

Amaral models the networks of the Internet and air travel, but he also maps metabolic networks—the intricate pathways by which cells generate the energy needed to carry out biological processes spanning the production of proteins to the breakdown of drugs. He creates simple computational models that show how the paths of these complicated networks connect and communicate.

Knowing all the details about the body's networks may help scientists learn to rewire them to prevent certain diseases, just like air traffic controllers re-route planes to avoid thunderstorms.—AD

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On the Move

Like us, cells rely on transportation to do their daily activities. But while we can choose to take cars, busses, bikes, and even Segways®, cells take the pedestrian approach: They move themselves.

A cell moves by grabbing onto something, like the wall of a blood vessel, and then pulling itself forward. This mobility is an essential part of wound healing. When you cut yourself, your white blood cells speed to the wound like paramedics.

This image, taken with a microscope-camera, shows the intricate network of fibers that builds a cell's structure. These fibers are called microtubules (yellow) and actin filaments (blue).
Clare Waterman-Storer

But cellular movement can also cause health problems, like when cancer cells spread to other parts of the body.

Scientists want to understand how cells move so they can develop new drugs that can rev up or stop cell migration altogether. But like most biological processes, cell movement hasn't been easy to figure out because it involves hundreds of proteins.

Cell biologist Clare Waterman-Storer and bioengineer Gaudenz Danuser, both at the Scripps Research Institute, take a systems biology approach to studying cell movement. They use mathematical equations and computer software to piece together the various components that make cells motor along.—AD

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