Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

LIAI finding gives boost to bioinformatics use in fighting disease

19.06.2006
Researchers prove 95 percent accuracy in extremely complex virus

The use of computers to advance human disease research – known as bioinformatics -- has received a major boost from researchers at the La Jolla Institute for Allergy & Immunology (LIAI), who have used it to successfully predict immune response to one of the most complex viruses known to man – the vaccinia virus, which is used in the smallpox vaccine. Immune responses, which are essentially how the body fights a disease-causing agent, are a crucial element of vaccine development.

"We are excited because this further validates the important role that bioinformatics can play in the development of diagnostic tools and ultimately vaccines," said Alessandro Sette, Ph.D., an internationally known vaccine expert and head of LIAI's Emerging Infectious Disease and Biodefense Center. "We've shown that it can successfully reveal – with a very high degree of accuracy -- the vast majority of the epitopes (targets) that would trigger an effective immune response against a complex pathogen."

Bioinformatics holds significant interest in the scientific community because of its potential to move scientific research forward more quickly and at less expense than traditional laboratory testing.

The findings were published this week in a paper, "A consensus epitope prediction approach identifies the breadth of murine TCD8+-cell responses to vaccinia virus," in the online version of the journal Nature Biotechnology. LIAI scientist Magdalini Moutaftsi was the lead author on the paper.

While bioinformatics – which uses computer databases, algorithms and statistical techniques to analyze biological information -- is already in use as a predictor of immune response, the LIAI research team's findings were significant because they demonstrated an extremely high rate of prediction accuracy (95 percent) in a very complex pathogen – the vaccinia virus. The vaccinia virus is a non-dangerous virus used in the smallpox vaccine because it is related to the variola virus, which is the agent of smallpox. The scientific team was able to prove the accuracy of their computer results through animal testing.

"Before, we knew that the prediction methods we were using were working, but this study proves that they work very well with a high degree of accuracy," Sette said.

The researchers focused their testing on the Major Histocompatibility Complex (MHC), which binds to certain epitopes and is key to triggering the immune system to attack a virus-infected cell. Epitopes are pieces of a virus that the body's immune system focuses on when it begins an immune response. By understanding which epitopes will bind to the MHC molecule and cause an immune attack, scientists can use those epitopes to develop a vaccine to ward off illness – in this case to smallpox.

The scientists were able to find 95 percent of the MHC binding epitopes through the computer modeling. "This is the first time that bioinformatics prediction for epitope MHC binding can account for almost all of the (targeted) epitopes that are existing in very complex pathogens like vaccinia," said LIAI researcher Magdalini Moutaftsi. The LIAI scientists theorize that the bioinformatics prediction approach for epitope MHC binding will be applicable to other viruses.

"The beauty of the virus used for this study is that it's one of the most complex, large viruses that exist," said Moutaftsi. "If we can predict almost all (targeted) epitopes from such a large virus, then we should be able to do that very easily for less complex viruses like influenza, herpes or even HIV, and eventually apply this methodology to larger microbes such as tuberculosis."

The big advantage of using bioinformatics to predict immune system targets, explained Sette, is that it overcomes the need to manufacture and test large numbers of peptides in the laboratory to find which ones will initiate an immune response. Peptides are amino acid pieces that potentially can be recognized by the immune system. "There are literally thousands of peptides," explained Sette. "You might have to create and test hundreds or even thousands of them to find the right ones," he said. "With bioinformatics, the computer does the screening based on very complex mathematical algorithms. And it can do it in much less time and at much less expense than doing the testing in the lab."

The LIAI scientific team verified the accuracy of their computer findings by comparing the results against laboratory testing of the peptides and whole infectious virus in mice. "We studied the total response directed against infected cells," Sette said. "We compared it to the response against the 50 epitopes that had been predicted by the computer. We were pleased to see that our prediction could account for 95% of the total response directed against the virus."

Bonnie Ward | EurekAlert!
Further information:
http://www.liai.org

More articles from Life Sciences:

nachricht Warming ponds could accelerate climate change
21.02.2017 | University of Exeter

nachricht An alternative to opioids? Compound from marine snail is potent pain reliever
21.02.2017 | University of Utah

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

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

Im Focus: Breakthrough with a chain of gold atoms

In the field of nanoscience, an international team of physicists with participants from Konstanz has achieved a breakthrough in understanding heat transport

In the field of nanoscience, an international team of physicists with participants from Konstanz has achieved a breakthrough in understanding heat transport

Im Focus: DNA repair: a new letter in the cell alphabet

Results reveal how discoveries may be hidden in scientific “blind spots”

Cells need to repair damaged DNA in our genes to prevent the development of cancer and other diseases. Our cells therefore activate and send “repair-proteins”...

Im Focus: Dresdner scientists print tomorrow’s world

The Fraunhofer IWS Dresden and Technische Universität Dresden inaugurated their jointly operated Center for Additive Manufacturing Dresden (AMCD) with a festive ceremony on February 7, 2017. Scientists from various disciplines perform research on materials, additive manufacturing processes and innovative technologies, which build up components in a layer by layer process. This technology opens up new horizons for component design and combinations of functions. For example during fabrication, electrical conductors and sensors are already able to be additively manufactured into components. They provide information about stress conditions of a product during operation.

The 3D-printing technology, or additive manufacturing as it is often called, has long made the step out of scientific research laboratories into industrial...

Im Focus: Mimicking nature's cellular architectures via 3-D printing

Research offers new level of control over the structure of 3-D printed materials

Nature does amazing things with limited design materials. Grass, for example, can support its own weight, resist strong wind loads, and recover after being...

Im Focus: Three Magnetic States for Each Hole

Nanometer-scale magnetic perforated grids could create new possibilities for computing. Together with international colleagues, scientists from the Helmholtz Zentrum Dresden-Rossendorf (HZDR) have shown how a cobalt grid can be reliably programmed at room temperature. In addition they discovered that for every hole ("antidot") three magnetic states can be configured. The results have been published in the journal "Scientific Reports".

Physicist Dr. Rantej Bali from the HZDR, together with scientists from Singapore and Australia, designed a special grid structure in a thin layer of cobalt in...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

Booth and panel discussion – The Lindau Nobel Laureate Meetings at the AAAS 2017 Annual Meeting

13.02.2017 | Event News

Complex Loading versus Hidden Reserves

10.02.2017 | Event News

International Conference on Crystal Growth in Freiburg

09.02.2017 | Event News

 
Latest News

Impacts of mass coral die-off on Indian Ocean reefs revealed

21.02.2017 | Earth Sciences

Novel breast tomosynthesis technique reduces screening recall rate

21.02.2017 | Medical Engineering

Use your Voice – and Smart Homes will “LISTEN”

21.02.2017 | Trade Fair News

VideoLinks
B2B-VideoLinks
More VideoLinks >>>