By Tom Farnell, 4th year, Chemistry
Bristol researchers are making use of cloud computing, a powerful new tool that is rapidly transforming the computational power available to researchers in the age of big data.
A new type of vaccine for the mosquito-borne virus Chikungunya was synthesised by a collaboration of researchers from the University of Bristol and the French National Centre for Scientific Research (CNRS), with help from tech giant Oracle. The article, published in Science Advances on September 25th, revealed a promising Chikungunya vaccine candidate engineered using a synthetic protein scaffold which could revolutionise the way vaccines are made.
Chikungunya is a virus transmitted through the bite of mosquitos carrying the disease. it is similar to Zika and Dengue fever, causing crippling headache, vomiting, swelling of limbs and sometimes death. Chikungunya causes 3 million infections a year and although historically it was confined to Africa, deforestation and climate change have allowed the host mosquitoes to spread worldwide, with outbreaks reported in over a quarter of countries so far.
The inspiration for the research was explained by Imre Berger, Director of the Max Planck-Bristol Centre for Minimal Biology, who said that the team ”figured that we could insert small, harmless bits of Chikungunya to generate a virus-like mimic we could potentially use as a vaccine." This was done using a scaffold named ADDomer to build up the vaccine molecule, which looks like the Chikungunya virus on the outside and prmopts the immune system to create antibodies to remove it. However, unlike the actual virus, ADDomer contains no genetic information so will not infect human cells and self-replicate.
Vaccination is an extremely powerful tool for preventing the spread of infectious diseases, with the most successful cases such as smallpox being completely eradicated due to vaccination. One of the problems with many current vaccines is that they require constant refrigeration to remain stable. This is especially problematic in developing countries, where most outbreaks occur, as they don’t have the infrastructure for transporting refrigerated vaccines en masse. However, this is not the case for ADDomer.
"Viruses are waiting to strike, and we need to have the tools ready to tackle this global threat. Our vaccine candidate is easy to manufacture, extremely stable and elicits a powerful immune response,” said Berger, adding that "it can be stored and transported without refrigeration to countries and patients where it is most needed. Intriguingly, we can now rapidly engineer similar vaccines to combat many other infectious diseases just as well."
The structure of ADDomer was determined using a powerful new technique called cryo-electron microscopy, recently installed at Bristol’s state-of-the-art microscopy facility. Cryo-EM produces very large datasets from which the structure of a molecule can be determined near-atomic resolution, requiring massive computing power. Using Oracle's high-performance cloud infrastructure, an accurate 3D model of the synthetic vaccine was created in record time and at a minimal cost.
Phil Bates, leading cloud architect at Oracle commented that "researchers have had a long tradition of building and installing their own supercomputers on-premises, but cloud computing is allowing them to run large data sets in record time, with fast connectivity and low latency. This is helping them crunch data and make scientific breakthroughs much faster.”
A Bristol biotech start-up, Imophoron Ltd. is developing new vaccines derives from the present work. The founder, Fred Garzoni added "Many challenges in the industry require innovative solutions, to bring powerful new vaccines to patients. Matching cutting-edge synthetic biology with cloud computing turned out to be a winner."
In recent years, cloud computing has become increasingly important in many areas of science. Any research which generates large amounts of raw data can benefit from using cloud computing as a cheaper, quicker alternative to custom building a supercomputer on site. Cloud computing has recently been used in seismology research to process data collected from a continent-scale survey of seismic signatures.
According to Jonathan MacCarthy of the Earth and Environmental Sciences Division at Los Alamos National Laboratory, "using a traditional workflow…this work would've taken more than 40 days to do. Using the cloud service, it took just under 7 hours." Cloud computing is also being used in theoretical physics, mathematical research and has great potential for future work in all these fields and beyond.
Featured image: Flickr / Chris Potter, ccPix.com
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