How do scientists capture a virus image?

Cryo-EM technology has brought people into the tiny biological world to an atomic level.

If you see the structure of a machine, you can guess how it works. The same is true for biological structures, such as viruses. Just by seeing the virus, scientists can guess the mechanism of the disease, then prepare the vaccine to stop them.

However, seeing the virus is difficult. Some viruses also have super complex structures, along with the ability to cause extremely malignant diseases that scientists are also hard to imagine and predict. Such as Zika strains cause a global pandemic in 2015-2016.

So how can scientists take pictures of them? In fact, the animals only have a diameter of about 40 nm (as small as 1 / 2,500 times the diameter of the hair).

Cryo-EM: Revolutionary technology that helps people for the first time capture viral images.

Most likely, the battle of Zika scientists two years ago has affected the results.

Before the announcement, many people were eyeing two Li-ion battery inventors, Stanley Whittingham and John Goodenough; young talented scientist Feng Zhang at MIT with the technology to edit CRISPR genes on humans; or the trio of Tsutomu Miyasaka (Japan), Park Nam-Gyu (South Korea) and Henry Snaith (England), with the study of discovering the material of Perovskite applied to solar cells.

But in the end, the three scientists Jacques Dubochet (Switzerland), Joachim Frank (USA) and Richard Henderson (England), the names do not appear in any predictable list, the prize winner. There were surprises, but if you look back at Dubochet, Frank and Henderson's contributions to Zika and future diseases, the prize is absolutely worth it.

Three scientists have successfully developed a technology to freeze biological specimens, so that they can be seen completely under an electron microscope, called cryo-electron microscopy (Cryo-EM).

Earlier, electron microscopy helped people see each inorganic atom. But with biological molecules it is different, they will be bombarded by the electron flow of the microscope. Only when Cryo-EM was born, for the first time did humans see biological molecules, such as proteins or viruses, with the naked eye, literally.

2017 Nobel Prize in Chemistry for 3 scientists who contribute to Cryo-EM technology.

Cryo-EM has revolutionized biochemical research, bringing people into the small biological world to an atomic level. And it also helped scientists capture the shape of the Zika virus, to give accurate estimates of the virus in the heart of the pandemic.

'A lot of people used this image because it showed Zika virus', Devika Sirohi, a doctoral student at Purdue University, authored a scientific article published in 2016 that presents the Zika virus structure. said. Zika is a typical case showing the application of Cryo-EM technology.

When Zika virus began to spread and was confirmed to be associated with small head malformations in newborns, scientists were flooded with a series of questions: The structure of the virus caused this symptom. what? What is Zika different from other viruses in the same family, such as dengue fever and West Nile fever?

As early as January 2016, labs from around the world began to plunge into a competition to see who identified the Zika virus structure at the earliest. It took only 3 months for Sirohi and his team members Zhenguo Chen, Thomas Klose Lei Sun, Michael Rossmann and Richard Kuhn at Purdue University and Theodore Pierson at the US National Institute of Allergies and Infections. publish their results.

Those are the first, three-dimensional and most detailed images of the Zika virus.

A picture taken with a microscope Cryo-EM, with the structural proteins of Zika virus.

In the past, scientists used X-rays or conventional electron microscopy to photograph viruses. In particular, X-rays or electrons are fired into a sample. After they scatter and are recorded by the sensor, the virus structure will be reconstructed by the scattering data.

However, for viruses with a softer structure, this method appears to be less effective. Conversely, if the sample is solid, the resolution of the image will be much higher than the liquid sample, simply because it removes the noise signals from the water molecule.

In order to create a solid test that still preserves the biological structure, Dubochet has frozen the protein solid with liquid nitrogen, at a temperature of -196 ^o C (close to absolute zero, -273.15 ^o C, heat Theory can stop all movement of matter. Due to the fast solidification time, the ice crystals do not keep forming, leading to the preservation of protein status.

By this quick freezing, electron microscopes can capture 2D slices of biological structures. Henderson solved this problem, he found a way to handle 2D images and then combine them into 3D structures, similar to CT scans.

Frank helped create algebraic algorithms, averaging the shapes obtained to increase the resolution of complex protein structures. The results of the three scientists' work helped us capture Zika virus photographs at resolutions down to half a nanometer.

2-dimensional images of Zika virus, taken under an electron microscope.

Techniques are available, the application of it is not everyone can do. The more detailed shooting is, the more difficult it is. Sirohi's group needs to capture at least 3,000 images from an electron microscope to have enough data. Therefore, they need a high-purity virus.

"We have been working around the clock, purifying samples, collecting and processing data, and cleaning up viruses to continue collecting more data , " Sirohi said.

Recreating a 3D image from a series of 2D images is also not an easy task. Once enough images are available, they must combine them with a number of computer programs, including Relion and jspr. These two programs will analyze and build each view, averaging data on all images, and fixing and eliminating noise points that the microscope may have created. Each image is very noisy - when the electron is fired relatively light so as not to deform the virus pattern.

Each 2D image corresponds to a different direction of the Zika virus when it comes to 3D rendering in space. Math programs convert these images into abstract, easier to manipulate shapes using "Fourier transforms" , the algorithm has been learned in advanced math programs in universities.

Any pair of 2D conversion images will then share a common line. Think about slices from a ball, a vertical cut and one from the horizontal. Each slice will look like a circle, and two circles will intersect in a straight line.

The software can build these lines based on previous assumptions and convert them back to 3D images of viruses. In this case, 3D image reconstruction requires the assumption that the Zika virus has an icosahedral symmetry (in other words, it has a fairly typical shape of a spherical virus).

So the whole structure of Zika virus has appeared. But there is a note that these pictures are all black and white, because the electron microscope cannot record the color of the specimen. In order to make viruses more colorful, they are not actually more beautiful, but researchers want to color their different structural components to distinguish them.

This requires more analysis, using a number of other computer programs, including Coot, Phenix, and CNS, to delve into the molecular components of the Zika virus structure: including individual proteins odd and their amino acids.

Finally, a sophisticated, three-dimensional and colorful image of Zika has been published to help us understand and understand this dangerous virus strain.

The different structural components of Zika virus are colored differently, making it easier for scientists to study them.

Although cryo-EM was born a few decades ago, within the last five years, it has only been developed to a strong enough level. This is what Melissa Chambers, cryo-EM specialist at Harvard Electronics Microscope Center, called "resolution revolution".

Chambers assessed this revolution from a combination of many factors, including advanced electronic detectors, and new algorithms, better cooling techniques, and accurate tools and methods. than. The article on Zika virus structure is just one of many new articles using cryo-EM to find out the structure and function of the smallest pieces of life.

Now, getting these high resolution images is getting easier. Chambers said we now need a specialist to use these photography tools.

But gradually, new microscopes and devices are becoming more automated, easier to access and more user-friendly."Rather than having to become an expert using electron microscopes . this will open up opportunities for more people who do not have time to learn all this on their own (can still take a selfie). give me photos) ".

Thanks to the detailed images of Zika, Sirohi and many other research groups, there have been important steps in understanding this strain. In particular, they observed how antibodies bind to Zika to help the body's immune system attack and disable the virus.

It is not difficult to see that Cryo-EM will continue to be an important technology, allowing biologists to understand the structure of molecules that affect people's lives. Typically, learning about the pathogens capable of threatening the world like Zika and finding ways to treat them and prevent them.