Purdue cluster models Zika virus
Researchers at Purdue University are using cryo-electron microscopy and advanced computing to develop a detailed 3D image of the structure of the Zika virus.
The Purdue researchers are using the microscopy technique – where a sample is studied at very low temperatures so that it does need to be stained or fixed – to capture images of combinations of Zika virus particles or individual instances of the virus. This data is then processed using Purdue’s community cluster to turn those images into a detailed picture of the overall virus structure.
Michael Rossmann, Purdue’s Hanley distinguished professor of biological sciences, who led the research team with Richard Kuhn, director of the Purdue’s Institute for Inflammation, Immunology, and Infectious Diseases, explained why his project needed significant compute resources. ‘We have tens of thousands of pictures of the Zika virus and each one is in a different, random orientation.
'If we can find out the relative orientations of all those thousands of particles, then we can put those together to make a three-dimensional image,’ said Rossmann.
While there is some early evidence to suggest that the virus can cause microcephaly and other fetal malformations, there is still relatively little known about the Zika virus. Before any treatment or vaccine can be created, researchers need to develop an understanding of the virus structure and its method of action to infect the body.
The data analysis for this project was carried out on Purdue’s Snyder community cluster, designed for memory-intensive life science research. The cluster was used to whittle down the collection to the best images, from 60,000 to 10,000. The images were then compiled as the computer linked similarly oriented views of the virus, like pieces of a very large puzzle. Once this puzzle has been assembled by the cluster the researchers are left with a 3D image of the virus structure, at near-atomic resolution.
Rossmann stressed that treating the virus there would require further research: ‘If we’re interested in how the virus can be inhibited, neutralised, we have to do many structures of the virus complex interacting with antibodies.’
Built in collaboration with Purdue faculty, the community clusters are designed, built and operated by Information Technology at Purdue, the campus central IT organisation.
‘When we built the first community cluster in 2008, we knew the demand was there among our faculty researchers in a number of fields, for example in engineering and physical sciences,’ said Donna Cumberland, executive director for research computing at Purdue. ‘While Zika virus wasn’t on the radar then, we also could see the breadth and variety of research being done on the clusters today coming in the future.’
The Zika structure is the latest in a continuing series of notable research enabled by the Community Cluster Program. Each year since 2008 Purdue has built a research cluster, with seven of them ranked in the top 500 in the world. There are now more than 180 faculty partners and hundreds of researchers from their labs in all of Purdue’s primary colleges and schools using the community clusters for research spanning more than 30 science, engineering and social science disciplines.