Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

New Software Models Immune Responses

10.10.2011
Researchers with the Virginia Bioinformatics Institute at Virginia Tech have released an upgrade to the institute's ENteric Immunity SImulator (ENISI) software, which models immune responses to beneficial and harmful bacteria that enter the gastrointestinal tract of mice, pigs, and humans.

ENISI allows users to create enteric systems such as the gut-associated mucosal immune system in silico, providing a better glimpse of how the immune system responds to pathogens that invade the bacteria-rich environment of the gut.

ENISI was initially designed by the Center for Modeling Immunity to Enteric Pathogens (MIEP) to model inflammatory bowel disease. The upgrade allows investigators to simulate immune responses in a mouse infected with Helicobacter pylori. The MIEP team plans to expand the software to simulate infection with enteroaggregative Escherichia coli and other enteric pathogens, such as Clostridium difficile and Cryptosporidium parvum. Future upgrades will allow users to run simulations via the ENISI website and eventually be able to visualize in silico cells or lesions forming in real time, rather than only seeing the outcomes of such interactions.

"ENISI is unique because it's specific to the gut, simulating each individual cell rather than creating broad mathematical models," said Kate Wendelsdorf, a Ph.D. student in the genetics, bioinformatics, and computational biology program at Virginia Tech. "Thus, it's more faithful to a living system and allows us to simulate a million individual cells, more than any other simulator. It's a powerful tool for understanding interactions between gut pathogens and the mucosal immune system."

Researchers can manipulate cells and immune processes in ENISI to determine if, for example, blocking a specific immune pathway or adding a drug can inhibit pathogen invasion and infection. The computer-generated models can, in turn, help researchers design better experiments to test the simulations in laboratory settings or in live animals. Therefore, it may be possible to test the efficacy of a novel vaccine or immune therapeutic in an ENISI model of disease, confirm the results in an animal model, and then use those results to explore the mechanisms of therapeutic efficacy in additional studies.

This feature will help immunologists and infectious disease experts immensely in understanding pathology, diagnosis, and treatment.

"ENISI is based on an interaction-based modeling approach that represents individual cells and their interactions with other cells, pathogens, and the environment. The algorithmic/procedural representation of individual agents and their interactions with other agents via an abstract interaction network is central to the modeling process. The use of high-performance computing facilitates scaling to 106 cells; we expect this number to grow 100-fold over the next two years. Such a representation yields a fundamentally different approach to understanding novel immunological processes," said Madhav Marathe, the center's modeling lead.

"ENISI runs on high-performance computers: hundreds or thousands of servers working together to produce an answer. The program shows the power of trans-disciplinary science, bringing together a team of software developers, computer scientists, immunologists, and physicists to solve problems that they wouldn't have been able to tackle on their own," said Keith Bisset, modeling expert and a key developer of the ENISI software.

A Center for Modeling Immunity to Enteric Pathogens paper entitled, "Enteric Immunity Simulator: A tool for in silico study of gut immunopathologies," has been accepted in the IEEE Bioinformatics and Biomedicine (BIBM) International conference proceedings. Preliminary ENISI modeling results that simulate bacterial-induced colitis will be presented at the conference in Atlanta in November (www.cs.gsu.edu/BIBM2011/?q=node/6).

"One of our goals is to develop user-friendly and interactive modeling tools that engage and inform the immunology and infectious disease communities, thereby enabling paradigm-shifting scientific discovery," said Josep Bassaganya-Riera, the center's principal investigator. "The release of the upgraded ENISI software by the MIEP team is a major step in allowing powerful computer simulations to uncover novel mechanisms of immunoregulation underlying immune responses to gut pathogens. The ultimate goal of such powerful simulations is to accelerate the discovery of novel drug targets and biomarkers for enteric infectious diseases. The fully integrated computational modeling, bioinformatics and immunology experimentation efforts within the MIEP program enable the generation of mechanistic evidence in silico and efficient validation in vivo," and Bassaganya-Riera, who is also director of the Nutritional Immunology and Molecular Medicine Laboratory at Virginia Bioinformatics Institute.

For more information about ENISI, visit the Center for Modeling Immunity to Enteric Pathogens at www.modelingimmunity.org.

The center is funded by the National Institute of Allergy and Infectious Diseases under the Modeling Immunity for Biodefense program.

About the Virginia Bioinformatics Institute

The Virginia Bioinformatics Institute at Virginia Tech is a premier bioinformatics, computational biology, and systems biology research facility that uses transdisciplinary approaches to science, combining information technology, biology, and medicine. These approaches are used to interpret and apply vast amounts of biological data generated from basic research to some of today's key challenges in the biomedical, environmental, and agricultural sciences. With more than 240 highly trained multidisciplinary, international personnel, research at the institute involves collaboration in diverse disciplines such as mathematics, computer science, biology, plant pathology, biochemistry, systems biology, statistics, economics, synthetic biology, and medicine. The large amounts of data generated by this approach are analyzed and interpreted to create new knowledge that is disseminated to the world's scientific, governmental, and wider communities.

Tiffany Trent | Newswise Science News
Further information:
http://www.vbi.vt.edu

More articles from Life Sciences:

nachricht How brains surrender to sleep
23.06.2017 | IMP - Forschungsinstitut für Molekulare Pathologie GmbH

nachricht A new technique isolates neuronal activity during memory consolidation
22.06.2017 | Spanish National Research Council (CSIC)

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

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

Im Focus: Can we see monkeys from space? Emerging technologies to map biodiversity

An international team of scientists has proposed a new multi-disciplinary approach in which an array of new technologies will allow us to map biodiversity and the risks that wildlife is facing at the scale of whole landscapes. The findings are published in Nature Ecology and Evolution. This international research is led by the Kunming Institute of Zoology from China, University of East Anglia, University of Leicester and the Leibniz Institute for Zoo and Wildlife Research.

Using a combination of satellite and ground data, the team proposes that it is now possible to map biodiversity with an accuracy that has not been previously...

Im Focus: Climate satellite: Tracking methane with robust laser technology

Heatwaves in the Arctic, longer periods of vegetation in Europe, severe floods in West Africa – starting in 2021, scientists want to explore the emissions of the greenhouse gas methane with the German-French satellite MERLIN. This is made possible by a new robust laser system of the Fraunhofer Institute for Laser Technology ILT in Aachen, which achieves unprecedented measurement accuracy.

Methane is primarily the result of the decomposition of organic matter. The gas has a 25 times greater warming potential than carbon dioxide, but is not as...

Im Focus: How protons move through a fuel cell

Hydrogen is regarded as the energy source of the future: It is produced with solar power and can be used to generate heat and electricity in fuel cells. Empa researchers have now succeeded in decoding the movement of hydrogen ions in crystals – a key step towards more efficient energy conversion in the hydrogen industry of tomorrow.

As charge carriers, electrons and ions play the leading role in electrochemical energy storage devices and converters such as batteries and fuel cells. Proton...

Im Focus: A unique data centre for cosmological simulations

Scientists from the Excellence Cluster Universe at the Ludwig-Maximilians-Universität Munich have establised "Cosmowebportal", a unique data centre for cosmological simulations located at the Leibniz Supercomputing Centre (LRZ) of the Bavarian Academy of Sciences. The complete results of a series of large hydrodynamical cosmological simulations are available, with data volumes typically exceeding several hundred terabytes. Scientists worldwide can interactively explore these complex simulations via a web interface and directly access the results.

With current telescopes, scientists can observe our Universe’s galaxies and galaxy clusters and their distribution along an invisible cosmic web. From the...

Im Focus: Scientists develop molecular thermometer for contactless measurement using infrared light

Temperature measurements possible even on the smallest scale / Molecular ruby for use in material sciences, biology, and medicine

Chemists at Johannes Gutenberg University Mainz (JGU) in cooperation with researchers of the German Federal Institute for Materials Research and Testing (BAM)...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

Plants are networkers

19.06.2017 | Event News

Digital Survival Training for Executives

13.06.2017 | Event News

Global Learning Council Summit 2017

13.06.2017 | Event News

 
Latest News

Quantum thermometer or optical refrigerator?

23.06.2017 | Physics and Astronomy

A 100-year-old physics problem has been solved at EPFL

23.06.2017 | Physics and Astronomy

Equipping form with function

23.06.2017 | Information Technology

VideoLinks
B2B-VideoLinks
More VideoLinks >>>