The EMBO | EMBL symposium explored how to observe true reality at all biological scales simultaneously
A recent EMBO | EMBL symposium brought together leading developers of imaging methods with cutting-edge applications that illustrate how imaging can answer biological questions. Credit: Franziska Kundel/EMBL
By Vera Janssen, PhD student, Vascular Microenvironment and Integrity Lab, Amsterdam University Medical Centers, Netherlands
A day in the life of a biologist sometimes resembles that of a detective. It is a constant quest for reality. To figure out what really happened or is happening, or even to predict what will happen, both biologists and detectives require tools that only reveal a small part of the full story. For detectives, fingerprints, forensics, and witness accounts provide different clues. For biologists, there are a variety of imaging tools to untangle molecular clues. However, none of these tools can pool the clues sufficiently on its own to solve our mysteries or obtain a complete biological picture.
This is one of the main challenges of biology today: how can we observe true reality at all biological scales simultaneously?
Observing biological reality has been limited by size, resolution, dynamics, speed, signal, identity, and function. Previously, addressing one of these problems often compromised one of the others – for example, increasing size would limit potential resolution or increasing resolution would come at the cost of dynamics.
This year’s EMBO | EMBL symposium, ‘Seeing is believing: imaging the molecular processes of life’, looked at how we can move beyond solving one problem at a time and address multiple problems simultaneously. Through interdisciplinary thinking and technology development, research groups across the world are currently allowing the movement of imaging technologies across biological scales and making them available to the research community.
Here are five topics touched upon during the symposium that explored ways to maximise what we can learn from different kinds of imaging:
1. Electron microscopy steps up sample size
Electron microscopy (EM) is known to deliver very high resolution, detailed information on very, very small samples. Multiple talks at this year’s conference showcased how volumetric EM is gaining traction in visualising increasingly larger samples without compromising on resolution. Using serial block-face scanning EM – a combination of an EM microscope and microtome that slices the sample after every image – or focused ion beam scanning EM, which combines a scanning electron microscope with a focused ion beam, scientists have been able to view the 3D ultrastructure of cells and tissues through continuous depths of at least 4 μm. By combining super-resolution fluorescence microscopy with this volumetric approach, scientists can identify large 3D EM datasets of a cell and correlate this with protein localisation. Additionally, other data processing advancements are allowing researchers to extract much faster, more meaningful parameters for these 3D models.
2. Being at the right place, right time for RNA translation
One of the challenges in microscopy is to capture molecular signals to understand biological function. RNA is a fascinating molecule that is transcribed, transported across the cell, and then translated to form a new protein. Microscopy can help us localise RNA in fixed samples and detect proteins, but it cannot observe the location and dynamics of RNA molecules during translation. In specific contexts, such as viral infections, our techniques have been too slow or the signals too dim to detect single RNA molecules before they multiply. Two labs recently harnessed the power of a molecular tagging system called SunTag, with which, they could quickly label newly translated proteins and detect RNA replication in real time. This allowed one lab to study the earliest steps of viral infection and the other to study the detailed localisation of newly translating RNA molecules.
Light-sheet microscopy, a method used for imaging relatively large living tissues, such as embryos, organoids, and even entire zebrafish, has continued to expand. This year’s talks showed how to build light sheet microscopes to image multiple samples simultaneously or to image developing zebrafish embryos at the organismal scale without losing cellular-level resolution. The latter allows scientists to visualise single-cell dynamics over time across the entire developing embryo. With this new information, we also need new ways to analyse data across enormous datasets. Consequently, other talks addressed new ways to extract meaningful information from such datasets.
4. A way to learn more about protein signalling at the membrane
Cells come in various shapes and sizes, and they have protrusions and pockets in various places, each providing different clues into cellular processes. Recent research presented at the conference showed that the specific arrangement and organisation of membrane structures and proteins within a small region of the cellular membrane can be hotspots to accumulate specific signalling proteins. The speaker used light-sheet microscopy with advanced molecular modelling to show how a cell’s surface can be mapped over time.
5. A new wave of biological sensors.
Biosensors can provide real-time or specific information about various cellular and molecular events, making them invaluable in the field of microscopy. One talk discussed a genetically encoded sensor for Piezo1, a newly discovered mechanically sensitive ion channel that has been associated with stress. This sensor is able to deduce when Piezo1 is activated, especially when cells are experiencing mechanical stress. The researchers not only used the sensor in cell cultures but also mapped the activity of the Piezo channel in the beating heart of the zebrafish, adapting its use across biological scales.
Digging deeper into cryo-EM
If you want to take a deeper dive into imaging and some of the cryo-EM imaging technologies presented in the ‘Seeing is believing’ symposium, EMBL will host the ‘Cryo-EM in academia and industry’ workshop on 29–31 January 2024.
This in-person and virtual workshop aims to bring academic and industrial cryo-EM communities together to evaluate how the cryo-EM ‘resolution revolution’ has progressed in the past 10 years and build upon a previous workshop held in 2019. Showcasing high-quality research from academia and industry, the meeting will provide updates on recent and ongoing methodological developments, such as the integration of cryo-ET and cryo-EM with complementary imaging techniques, e.g. imaging across scales as well as other omics technologies, such as proteomics, genomics, and metabolomics. The integration of cryo-EM in the drug discovery workflow will also be examined. For more information and to register, visit this link.
