AI helps in the discovery of a hidden virosphere

Using AI, an international team of researchers has shed light on a diverse and fundamental branch of life living all around us, essentially, a huge hidden virosphere.

Published in October in Cell, the study categorised 1,61,979 new species of RNA virus using a machine learning tool that researchers believe will vastly improve the mapping of life on the earth and could aid in the identification of many millions of other viruses yet to be characterised.

“We have been offered a window into an otherwise hidden part of life on earth, revealing remarkable biodiversity,” the senior author Edwards Holmes from the School of Medical Sciences at the University of Sydney was quoted in a university release. “To find this many new viruses in one fell swoop is mind-blowing…. There are millions more to be discovered, and we can apply this same approach to identifying bacteria and parasites.”

Although RNA viruses are commonly associated with disease, they are also found in extreme environments around the world. In this study they were found living in the atmosphere, in hot springs, and in hydrothermal vents.

“That extreme environments carry so many types of viruses is just another example of their phenomenal diversity and tenacity to live in the harshest settings, potentially giving us clues on how viruses and other elemental life-forms came to be,” Holmes said.

The researchers built a deep learning algorithm, LucaProt, to compute vast troves of genetic sequence data, including lengthy virus genomes of up to 47,250 nucleotides and genomically complex information that enabled the massive discovery.

According to Holmes, the vast majority of these viruses had been sequenced already and were on public databases, but they were so divergent that no one knew what they were. “They comprised what is often referred to as sequence ‘dark matter’. Our AI method was able to organise and categorise all this disparate information, shedding light on the meaning of this dark matter for the first time,” he said. However, the new discovery also included about 70,500 viruses that were previously unknown.

LucaProt was trained to compute the dark matter and identify viruses on the basis of sequences and the secondary structures of the protein that all RNA viruses use for replication. It was able to significantly fast-track virus discovery, which would have been time-intensive using traditional methods.

CERN plans to transport antiprotons from one lab to another for the first time

Considering that antimatter and matter annihilate themselves upon contact, the Baryon Antibaryon Symmetry Experiment (BASE) at CERN is the only place in the world where scientists can even store antiprotons—which the CERN Antiproton Decelerator produces and traps every day—for more than a year. But now with a newly designed apparatus, BASE’s sub-project BASE-STEP hopes to be able to transport the stored antimatter.

Recently, a research team took an important step towards this by transporting a cloud of 70 protons in a truck across CERN’s main site. “If you can do it with protons, it will also work with antiprotons,” said Christian Smorra, the leader of BASE-STEP. “The only difference is that you need a much better vacuum chamber for the antiprotons.”

This is the first time that loose particles have been transported in a reusable trap that scientists can then open in a new location and transfer the contents into another experiment. The end goal is to create an antiproton delivery service from CERN to experiments located at other laboratories.

Antimatter is almost identical to ordinary matter except that the charges and magnetic properties are reversed. According to the laws of physics, the big bang should have produced equal amounts of matter and antimatter. These equal-but-opposite particles would have quickly annihilated each other, leaving behind a simmering but empty universe. So what is baffling is that the universe exists and predominantly contains matter, but there are antiparticles as well that are produced in natural and laboratory subatomic phenomena.

The BASE experiment aims to answer this question by precisely measuring the properties of antiprotons, such as their intrinsic magnetic moment, and then comparing these measurements with those taken with protons. However, the precision the experiment can achieve is limited by its location.

The goal of BASE-STEP is to trap antiprotons and then transfer them to a facility where scientists can study them with a greater precision. To be able to do this, they need a device that is small enough to be loaded onto a truck and can resist the bumps and vibrations that are inevitable during ground transport. The current apparatus includes a superconducting magnet, cryogenic cooling, power reserves, and a vacuum chamber that traps the particles using magnetic and electric fields. Although it weighs a tonne and needs two cranes to be lifted out of the experimental hall and onto the truck, BASE-STEP is the most compact existing system used to study antimatter.

During the rehearsal, the scientists used trapped protons as a stand-in for antiprotons. But storing protons as loose particles and then moving them onto a truck is a challenge because any tiny disturbance will draw the unbonded protons back into an atomic nucleus.

“When it’s transported by road, our trap system is exposed to acceleration and vibrations, and laboratory experiments are usually not designed for this,” Smorra said. “We needed to build a trap system that is robust enough to withstand these forces, and we have now put this to a real test for the first time.” However, Smorra noted that the biggest potential hurdle is not currently the bumpiness of the road but traffic jams. “If the transport takes too long, we will run out of helium at some point,” he said. Liquid helium keeps the trap’s superconducting magnet at a temperature below 8.2 kelvin: its maximum operating temperature. If the drive takes too long, the magnetic field will be lost and the trapped particles will be released and vanish as soon as they touch ordinary matter.

“Eventually, we want to be able to transport antimatter to our dedicated precision laboratories at the Heinrich Heine University in Düsseldorf, which will allow us to study antimatter with at least 100-fold improved precision,” Smorra said. “In the longer term, we want to transport it to any laboratory in Europe. This means that we need to have a power generator on the truck. We are currently investigating this possibility.”

After this successful test, which included ample monitoring and data taking, the team plans to refine its procedure with the goal of transporting antimatter next year. “This is a totally new technology that will open the door for new possibilities of study, not only with antiprotons but also with other exotic particles, such as ultra-highly-charged ions,” Stefan Ulmer, the BASE spokesperson, said.