Featured Research

from universities, journals, and other organizations

Supercomputer Explores Biochemical Landscape To Find Memory Switches

Date:
June 24, 2008
Source:
Virginia Tech
Summary:
Cells use switches for determining what kind of cell to become -- skin or blood, for instance, in responding to stress, and in communication with other cells. Researchers have now cataloged even more templates of possible switches within a living cell than we use throughout our day.

A colorful "map" of switches within cells was created by Naren Ramakrishnan at Virginia Tech and Upinder S. Bhalla at the National Centre for Biological Sciences in India, using Virginia Tech's SystemX supercomputer. Every little square in the picture is a "switch." The lines indicate the relationship between the switches.
Credit: Created by Naren Ramakrishnan and Upinder S. Bhalla

Switches are a part of daily life, from snoozing your alarm, turning on the coffee maker, firing up your car engine, and so on until we turn off the lights at night. Researchers have now cataloged even more templates of possible switches within a living cell than we use throughout our day.

Naren Ramakrishnan, associate professor of computer science at Virginia Tech, USA, and Upinder S. Bhalla, at the National Centre for Biological Sciences (NCBS), part of the Tata Institute of Fundamental Research in India, found that cells can make use of thousands of switches to support important biological functions.

Cells use switches for determining what kind of cell to become -- skin or blood, for instance, in responding to stress, and in communication with other cells. "A switch is like a memory unit," said Bhalla. "The state of the switch -- whether it is on or off, is like a computer memory that can store a bit of 0 or 1. Although real biological switches are quite complex and regulated in many ways, we have shown the simplest possible ways in which switches could work", Bhalla said.

The researchers collaboration began during a sabbatical visit by Ramakrishnan to NCBS in Bangalore, India. Ramakrishnan is a computer scientist whose expertise is in numerical simulation and data mining. Bhalla is a computational neuroscientist with broad interests in biochemical network modeling and simulation. They decided to use Virginia Tech's System X supercomputer to search for the many ways in which cells can implement switches.

"Our exploration using System X is rather like how a tinkerer or a kid puts together things to see if they do something useful. We took a lot of 'spare parts', each spare part being one chemical reaction, connected them together every which way, and we found that a surprising number of these artificially constructed networks actually were switches," said Ramakrishnan.

"Popular opinion used to be that there are a small number of ways in which switches can be realized by biology, but we found thousands of switches in our search," Ramakrishnan said.

The researchers report in PLoS Computational Biology, "We find nearly 4,500 reaction topologies, or about 10 percent of our tested configurations, that demonstrate switching behavior."

Their research also led to a comprehensive "map" of biochemical switches. The map further revealed that most of the switches form a "family" -- that is, the switches are all related to one another. "This has important implications since it suggests how evolution might stumble upon a switch rather easily." Ramakrishnan said.

"Of course, there is more to cells than switches," Bhalla said. "But switching and memory are the most basic behaviors possible. Armed with our catalog of switches, we can now proceed to investigate more interesting behaviors like complex information processing."


Story Source:

The above story is based on materials provided by Virginia Tech. Note: Materials may be edited for content and length.


Journal Reference:

  1. Memory Switches in Chemical Reaction Space. PLoS Computational Biology, June 20, 2008

Cite This Page:

Virginia Tech. "Supercomputer Explores Biochemical Landscape To Find Memory Switches." ScienceDaily. ScienceDaily, 24 June 2008. <www.sciencedaily.com/releases/2008/06/080619203302.htm>.
Virginia Tech. (2008, June 24). Supercomputer Explores Biochemical Landscape To Find Memory Switches. ScienceDaily. Retrieved April 17, 2014 from www.sciencedaily.com/releases/2008/06/080619203302.htm
Virginia Tech. "Supercomputer Explores Biochemical Landscape To Find Memory Switches." ScienceDaily. www.sciencedaily.com/releases/2008/06/080619203302.htm (accessed April 17, 2014).

Share This



More Computers & Math News

Thursday, April 17, 2014

Featured Research

from universities, journals, and other organizations


Featured Videos

from AP, Reuters, AFP, and other news services

Heartbleed Hack Leads To Arrest

Heartbleed Hack Leads To Arrest

Newsy (Apr. 17, 2014) A 19-year-old computer science student has been arrested in relation to a data breach of 900 social insurance numbers from Canada's revenue agency. Video provided by Newsy
Powered by NewsLook.com
Apple Rumored To Introduce Song ID Service In Next iOS Build

Apple Rumored To Introduce Song ID Service In Next iOS Build

Newsy (Apr. 17, 2014) Sources close to Apple told Bloomberg the company plans to introduce an integrated song identification service during the launch of its next iOS. Video provided by Newsy
Powered by NewsLook.com
Honda's New ASIMO Robot, More Human-Like Than Ever

Honda's New ASIMO Robot, More Human-Like Than Ever

AFP (Apr. 17, 2014) It walks and runs, even up and down stairs. It can open a bottle and serve a drink, and politely tries to shake hands with a stranger. Meet the latest ASIMO, Honda's humanoid robot. Duration: 00:54 Video provided by AFP
Powered by NewsLook.com
Yahoo's Ousted COO Gets $58M Severance Package

Yahoo's Ousted COO Gets $58M Severance Package

Newsy (Apr. 17, 2014) According to SEC filings, Yahoo gave ousted COO Henrique de Castro a $58 million severance package. Video provided by Newsy
Powered by NewsLook.com

Search ScienceDaily

Number of stories in archives: 140,361

Find with keyword(s):
Enter a keyword or phrase to search ScienceDaily for related topics and research stories.

Save/Print:
Share:

Breaking News:
from the past week

In Other News

... from NewsDaily.com

Science News

Health News

Environment News

Technology News



Save/Print:
Share:

Free Subscriptions


Get the latest science news with ScienceDaily's free email newsletters, updated daily and weekly. Or view hourly updated newsfeeds in your RSS reader:

Get Social & Mobile


Keep up to date with the latest news from ScienceDaily via social networks and mobile apps:

Have Feedback?


Tell us what you think of ScienceDaily -- we welcome both positive and negative comments. Have any problems using the site? Questions?
Mobile: iPhone Android Web
Follow: Facebook Twitter Google+
Subscribe: RSS Feeds Email Newsletters
Latest Headlines Health & Medicine Mind & Brain Space & Time Matter & Energy Computers & Math Plants & Animals Earth & Climate Fossils & Ruins