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 Unique genome architectures after fertilisation in single-cell embryos
30.03.2017 | IMBA - Institut für Molekulare Biotechnologie der Österreichischen Akademie der Wissenschaften GmbH

nachricht Transport of molecular motors into cilia
28.03.2017 | Aarhus University

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

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

Im Focus: A Challenging European Research Project to Develop New Tiny Microscopes

The Institute of Semiconductor Technology and the Institute of Physical and Theoretical Chemistry, both members of the Laboratory for Emerging Nanometrology (LENA), at Technische Universität Braunschweig are partners in a new European research project entitled ChipScope, which aims to develop a completely new and extremely small optical microscope capable of observing the interior of living cells in real time. A consortium of 7 partners from 5 countries will tackle this issue with very ambitious objectives during a four-year research program.

To demonstrate the usefulness of this new scientific tool, at the end of the project the developed chip-sized microscope will be used to observe in real-time...

Im Focus: Giant Magnetic Fields in the Universe

Astronomers from Bonn and Tautenburg in Thuringia (Germany) used the 100-m radio telescope at Effelsberg to observe several galaxy clusters. At the edges of these large accumulations of dark matter, stellar systems (galaxies), hot gas, and charged particles, they found magnetic fields that are exceptionally ordered over distances of many million light years. This makes them the most extended magnetic fields in the universe known so far.

The results will be published on March 22 in the journal „Astronomy & Astrophysics“.

Galaxy clusters are the largest gravitationally bound structures in the universe. With a typical extent of about 10 million light years, i.e. 100 times the...

Im Focus: Tracing down linear ubiquitination

Researchers at the Goethe University Frankfurt, together with partners from the University of Tübingen in Germany and Queen Mary University as well as Francis Crick Institute from London (UK) have developed a novel technology to decipher the secret ubiquitin code.

Ubiquitin is a small protein that can be linked to other cellular proteins, thereby controlling and modulating their functions. The attachment occurs in many...

Im Focus: Perovskite edges can be tuned for optoelectronic performance

Layered 2D material improves efficiency for solar cells and LEDs

In the eternal search for next generation high-efficiency solar cells and LEDs, scientists at Los Alamos National Laboratory and their partners are creating...

Im Focus: Polymer-coated silicon nanosheets as alternative to graphene: A perfect team for nanoelectronics

Silicon nanosheets are thin, two-dimensional layers with exceptional optoelectronic properties very similar to those of graphene. Albeit, the nanosheets are less stable. Now researchers at the Technical University of Munich (TUM) have, for the first time ever, produced a composite material combining silicon nanosheets and a polymer that is both UV-resistant and easy to process. This brings the scientists a significant step closer to industrial applications like flexible displays and photosensors.

Silicon nanosheets are thin, two-dimensional layers with exceptional optoelectronic properties very similar to those of graphene. Albeit, the nanosheets are...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

International Land Use Symposium ILUS 2017: Call for Abstracts and Registration open

20.03.2017 | Event News

CONNECT 2017: International congress on connective tissue

14.03.2017 | Event News

ICTM Conference: Turbine Construction between Big Data and Additive Manufacturing

07.03.2017 | Event News

 
Latest News

'On-off switch' brings researchers a step closer to potential HIV vaccine

30.03.2017 | Health and Medicine

Penn studies find promise for innovations in liquid biopsies

30.03.2017 | Health and Medicine

An LED-based device for imaging radiation induced skin damage

30.03.2017 | Medical Engineering

VideoLinks
B2B-VideoLinks
More VideoLinks >>>