Single-particle cryo-electron microscopy (Cryo-EM) enables researchers to study proteins and biomolecules at atomic resolution. With recent advancements in technology, cryo-EM is breaking barriers that imaging techniques such as x-ray crystallography could not.
Cryo-EM has had such an impact that Jacques Dubochet, Joachim Frank, and Richard Henderson were awarded the 2017 Nobel Prize in Chemistry for their work on this matter. Although work on Cryo-EM started decades ago, there have been significant breakthroughs in recent years. With this in mind, let’s take a step back and review why cryo-EM was needed.
Proteins and X-ray Crystallography
Proteins are the building blocks of our body cells. Knowing and understanding the shape of proteins and how they fit together can help researchers and scientists come up with better ways to treat pain and fight and cure diseases. In the past, an imaging technique that has made this possible has been x-ray crystallography.
X-ray crystallography is a modeling technique that helps deduce high-resolution protein structures. This technique requires proteins to be “crystallized” or packed in a stable, organized crystal. Then, an x-ray beam is directed at the crystal with the protein. Once the x-ray strikes the crystal, x-rays scatter in discernible patterns. Those patterns are analyzed to determine the position of atoms and form a 3D atomic model of the protein.
For x-ray crystallography, the crystallization process becomes a challenge and a limitation. This process is very expensive, takes lots of lab work and a very long time. For example, a protein can take weeks to many months to crystalize. Additionally, some proteins can not be crystallized, so it becomes impossible to analyze or study them using this technique.
Cryo-EM vs. X-ray Crystallography
Cryo-EM doesn’t require the samples to be crystallized. Instead, researchers need to freeze the sample. This is achieved by applying a sample to a grid, blotting the excess sample, and plunge-freezing the grid into a cryogen (usually liquid ethane kept at liquid nitrogen temperature). The sample freezes so fast with this process that ice crystals do not have enough time to form. This water state is called vitreous ice, and it helps maintain the native states of the sample. Grids with frozen samples are usually stored in “grid boxes” and are kept at liquid nitrogen temperature to prevent ice crystals from forming.
Once the sample is frozen, transmission electron microscopy (TEM) can be performed compared to x-rays. This microscopy technique transmits electron beams through the frozen sample. Then, an advanced camera captures the scattered electrons to form a high-resolution image. After collecting several images, another software is later used to generate a 3D structure from the sample.
The cryo-EM process enables researchers to explore and image a broader range of biological samples than x-ray crystallography. On top of that, the process is quicker and much simpler compared to x-ray crystallography. However, cryo-EM still faces challenges, especially on the data storage side.
Storage for Cryo-EM
Creating lots of high-resolution images also means lots of data. Thousands of images are needed for each sample. Some cryo-EM labs can easily generate about 15 TBs of data per day and need to store the data for long periods. These labs quickly start to experience capacity challenges with the significant amount of data they generate.
At the same time, optimal performance is required to process those high-resolution images. This means that both capacity and performance can be tough challenges to overcome.
Storage solutions for cryo-EM should be able to scale out to address the capacity and performance challenges. Scaling out gives the flexibility to add resources such as servers whenever more performance is needed. Or, if the cluster is running out of capacity, you should be able to add hard disks to expand your capacity. This also means that the storage solution should not require exotic hardware but work very well with commodity hardware.
Commodity hardware can provide several benefits, including cost optimization and high availability. When dealing with such delicate processes as those involved in cryo-EM, the last thing you need is a costly appliance out of stock. Also, you should be able to add resources to your cluster without any disruption. Even when performing updates, your cluster should not experience any downtime so that the workflow is not interrupted.
Another important feature for cryo-EM storage is data protection. Since researchers work with very valuable data, it is essential to have a storage solution that can provide the peace of mind that their data will be safe. This type of data can easily become a target of cybercriminals because of the monetary worth it may have. Therefore, the solution should offer features such as data encryption, access control, certificates, and more to keep the data protected.
Centralized Storage for Cryo-EM
Since cryo-EM requires a collective effort, researchers can greatly benefit from having all their data in a single platform. For that reason, the storage should be shareable and accessible from many interfaces and locations. In other words, a shared centralized storage.
A centralized storage should provide storage admins with the ability to manage and monitor the storage from a single point of access. At the same time, it should allow admins to provide the resources that every researcher needs. This improves resource utilization because resources are not wasted or are left unused. Moreover, a centralized storage would provide easier maintenance because there are no devices all over the place needed to be updated.
Cryo-EM and Cryo-ET
Another powerful cryo TEM technique similar to cryo-EM is cryo-electron tomography (cryo-ET). Cryo-ET facilitates biological structural analysis, allowing researchers to obtain 3D snapshots of proteins at work in their native environment. These snapshots give researchers a better understanding of how proteins work together in a cell.
Although sample preparation is similar to that of Cryo-EM, and the same transmission electron microscopes can be used to collect data, the data collection procedure differs. Cryo-ET requires the sample to be tilted along the electron beam axis, exposing the sample several times. This creates a challenge because biological material is extremely sensitive to radiation when it’s embedded in ice.
Storage for Cryo-ET
Additional challenges arise with storage for Cryo-ET as it creates even more data than Cryo-EM. This means that cryo-ET requires more capacity and more performance than cryo-EM. However, from a storage perspective, both techniques have to overcome the same data challenges.
As cryo-EM and cryo-ET continue to evolve, it is essential that the amount of data they generate does not become another barrier. Imaging techniques should be able to leverage storage solutions without complex configurations or expensive, exotic hardware or appliances.
Quobyte is a true scale-out file system that linearly scales capacity and performance and can help accelerate cryo-EM and cryo-ET workflows. To learn how Quobyte helps cryo-EM, check our blog: 5 Reasons Quobyte Storage Enables Stronger Cryo-EM Solutions
Originally posted on Quobyte’s blog on September 26, 2022.
