Tag Archives: microscopy

Internal cell structures revealed by powerful 3D microscopy technique

A new imaging technique called cryo-SR/EM can capture cells in unprecedented, 3D detail.

Image credits D. Hoffman et al., (2020), Science.

The insides of living cells are very cramped, busy, but fascinating places. Sadly, because they’re so small, we’ve never been able to take a proper look at what’s going on inside there.

However, a new technique that combines both optical and electron microscopy may allow us to do just that, and in very high detail to boot.

Zoomed in

“This is a very powerful method,” says Harald Hess, a senior group leader at the Howard Hughes Medical Institute’s Janelia Research Campus, US.

Cryo-SR/EM combines data captured from electron microscopy with high-resolution optical microscope imaging to create detailed 3D models of the inside of cells.

Separately, these two approaches are powerful but limited. Optical (or light) microscopes can easily differentiate between individual cell structures when fluorescent molecules are attached to them — this is known as super-resolution (SR) fluorescence microscopy. While it does provide a clear picture, SR fluorescence microscopy isn’t able to show all the proteins swishing about inside a cell at the same time, making it hard to see how different bits interact with everything else.

On the other hand, electron microscopy (EM) can ‘see’ virtually everything that’s happening inside a cell in very high detail, but it can be too powerful for its own sake. The wealth of features inside a cell, all seen in very high detail, can make it difficult to understand what you’re looking at.

The team worked to combine these two techniques into a single one that enhances their strengths while balancing out their respective limitations.

Cryo-SR/EM involves first freezing a cell or group of cells under high pressure; this step instantly freezes their internal activity without allowing for ice crystals to form (these can easily rupture cellular structures). Next, the samples are placed into a cryogenic chamber where they’re imaged in 3D using SR fluorescence microscopy. Finally, the samples are removed, embedded in resin, and viewed under an electron microscope (this paper used a powerful device developed in Hess’ lab). This step involves shooting a beam of ions at the cell, producing images of successively layers of the cell. A computer program is used to piece these images back together into a 3D reconstruction.

For the final step, all the data is pooled together, creating a very high-detail 3D model of the cell’s interior.

Techniques such as cryo-SR/EM promise to let us peek into natural systems that were previously just too tiny to spot — and they let us do so in extreme detail. One particularly-exciting possibility is that cryo-SR/EM will allow researchers to observe snapshots of cellular processes as they unfold, propelling forward basic science and its applications in fields such as genetic engineering, bioengineering, biochemistry, and medicine.

The paper “Correlative three-dimensional super-resolution and block-face electron microscopy of whole vitreously frozen cells” has been published in the journal Science.

We can now film chemical reactions on an atomic level as they unfold

Researchers manage to film a chemical process unfolding on the atomic scale for the first time in history.

The paper, lead-authored by Junfei Xing at The University of Tokyo, Department of Chemistry, shows that there are distinct stages in the process of chemical synthesis. Their work could help guide new strategies and methods for chemical synthesis with greater control and precision than ever before. Prime applications are in materials science and drug development, according to the authors.

Smile for the camera

“Since 2007, physicists have realized a dream over 200 years old—the ability to see an individual atom,” said Project Professor Eiichi Nakamura, the paper’s corresponding author.

“But it didn’t end there. Our research group has reached beyond this dream to create videos of molecules to see chemical reactions in unprecedented detail.”

Nakamura’s team specializes in the field of material synthesis, with an emphasis on the control of the processes that are used in this field. However, they’ve always been hampered by the lack of any tool to observe these processes as they unfold.

The different stages of complex chemical reactions are difficult to study as they involve multiple intermediate steps, making them very hard to model. In theory, we could just look at these steps unfolding. In practice, however, it was impossible to isolate the products at each stage and to see how these changed over time.

“Conventional analytical methods such as spectroscopy and crystallography give us useful information about the outcomes of processes, but only hints about what takes place during them,” explained Koji Harano, project associate professor in the Nakamura group and co-author of the study.

“For example, we are interested in metal-organic framework (MOF) crystals. Most studies look at the growth of these but miss the early stage of nucleation, as it is difficult to observe.”

Nakamura and the team spent over 10 years working on a solution — and finally they developed one they call molecular electron microscopy. This meant, overcoming the engineering challenge of combining a very powerful electron microscope with a fast and sensitive imaging sensor (used to record video), while at the same time finding a way to pick and hold molecules of interest in front of the lens.

For the latter, the team employed a specially-designed carbon nanotube which was held in place at the focal point of the electron microscope. This would snag up passing molecules and hold them in place, but not interfere with them chemically. The reaction could thus unfold on the tip of the nanotube, where the team could record it. Harano admits that “what surprised us very much in the beginning was that our plan actually worked.”

“It was a complex challenge, but we first visualized these molecular videos in 2013,” he adds. “Between then and now, we worked to turn the concept into a useful tool.”

“Our first success was to visualize and describe a cube-shaped molecule, which is a crucial intermediate form that occurs during MOF synthesis. It took a year to convince our reviewers what we found is real.”

The team says their work is the first step towards gaining control over chemical synthesis in a precise and controlled manner — a term they call “rational synthesis.” If we know what goes on along every step of a chemical reaction, we can better control the outcome.

In time, the team hopes their work will lead to things like synthetic minerals for construction, or even new drugs.

The paper “Atomistic structures and dynamics of prenucleation clusters in MOF-2 and MOF-5 syntheses” has been published in the journal Nature.

The world’s tiniest game of Pac-Man is both awesome and educational

Studying microorganisms is hard work — and sometimes it can get a bit dull. To stave off the tedium of a day’s work in the lab, researchers from the Univeristy College of Southeast Norway now rely on watching games of Pac-Man, with a twist: the team re-created the iconic maze in tiny proportions to better understand the predator and prey behaviours of protozoans and rotifers.

Led by Professor Erik Andrew Johannessen of the Institute of Micro and Nano System Technology, a team of Norwegian scientists created the “Mikroskopisk Pacman” project, a nano-structure maze of under one millimeter in diameter. The role of Pac-Man is assumed by protozoans euglena and ciliate, with pseudocoelomate (in this case rotifers) acting as the Ghosts. While undeniably awesome, the project wasn’t put together for its fun factor alone, the team reports.

The maze forms a 3D environment that allows microorganisms to interact more naturally than the artificial medium of a 2D petri dish. The tiny canals inside the maze also resemble the structures these creatures navigate to in the wild.

To make it more accessible to the public, film director Adam Bartley lyslagt was brought in to create the Pac-Man themed map and film the “gameplay” between euglena and rotifers. Using micro scenography, Iyslagt captured the video above. The little creatures can be seen darting around for dear life — or a tasty meal.

The team behind the project says that it not only helped with their research but also with relaying their findings in a way people can understand better and are more engaged with, raising awareness of science. I’d say they hit the nail on the head here — I’m definitely engaged and aware.

We can also look forward to a sequel. The team said they’re focusing on creating more Pac-Man style levels in future projects, as well experiments based on other games.

I’m gonna need a smaller controller.


Underwater Atomic Force Microscopy opens new frontiers for biologists

To fully understand the processes and mechanisms that work at a cellular level, biologists should study them in their native, watery environments. But how would you go on doing this? Well, leave it to engineers to solve everyone’s problems – they have now deviced a kind of atomic force microscopy that works on samples sitting in water and that is gentle enough to analyze fragile biological surfaces.


An elevated silicon hexagon. The colors designate the relative height of the surface from high (red) to low (yellow). The image on the left is a scanning electron micrograph of the same silicon hexagon. Right is with new technique.

Atomic force microscopy (AFM) or scanning force microscopy (SFM) is a very high-resolution type of scanning probe microscopy, which works at incredibly large resolutions, on the order of fractions of a nanometer – there’s nanometers in a meter.

In an AFM experiment, a sharp tip scans over a surface, producing an image based on the forces the tip experiences as it interacts with molecules or atoms on the surface. It then generates images which reveal information about the topographic and electrical properties of a surface. But AFM is not suitable for cells and proteins; cells and proteins are wet, squishy – not really what you want for this technique.

Seong H. Kim, a chemical engineer at Pennsylvania State University, wanted to develop something that works for those kinds of environments as well. He developed a method called scanning polarization force microscopy. Whoa! That sounds really fancy – and it is. In this method, which was first developed in the 90s, physical contact with the surface being imaged is not required. Instead, static charges on the surface either attract or repel the tip, creating a measurable force.

Most people working in the field thought this method wouldn’t work underwater – and they were right, initially; dissolved ions coated the AFM tip, interfering with how the tip interacted with a sample’s surface. But by oscillating the voltages, they were able to overcome this hurdle.

To prove that this method works, Kim’s group imaged a gold surface covered with self-assembled monolayers of charged polymers. With the AFM technique, the team could make a map of the surface’s topography and distinguish between positive and negative charges.

“The fact that you can truly operate in a liquid with this method could make it interesting for biological researchers,” says Adam Z. Stieg of the California NanoSystems Institute at the University of California, Los Angeles. If Kim’s group can demonstrate it with actual biological samples and can make a user-friendly version, he says, the method could offer something unique for biologists. No technique currently used could match the spatial resolution possible with AFM, Stieg says.