X-ray Microscope: Seeing Cells in 3-D

Mark LeGros, who spent three years building the world's first x-ray microscope dedicated to cell biology, greeted me at the Lawrence Berkeley National Laboratory (LBNL) with a welcoming handshake and an accent which clips along in a musical pace, an acoustic stamp of his New Zealand roots.

I spent an hour in April talking with him about the challenges and rewards of creating a device which can capture a truer, more accurate representation of a whole cell and its organelles, or the tiny but essential cellular structures such as a cell's nucleus and its mitochondria, the latter of which supply a cell with energy.

I asked him to take me back to that moment when he and the diverse team of researchers, including biologists, physicists, chemists and computer scientists, who comprise the National Center of X-ray Tomography at LBNL powered up the microscope and waited anxiously for the first images to arrive of a yeast cell, the first biological specimen they selected for imaging.

"I wasn’t sure exactly just how well this was gonna work out. But it turned out that it was beautiful...and everybody associated with the project was stunned with the degree of detail that it revealed about the internal structure of a cell and the chromatin, which is the genetic material of the cell," he said.

It's important to note that this x-ray microscope by no means makes obsolete other imaging modalities such as light microscopy and electron microscopy. For one thing, the cell sample is frozen to hold the structures in place and protect them from the x-rays which have much greater penetrating power than visible light because x-rays have much shorter wavelengths than light rays. So it can't capture dynamic activity of cells moving in real-time, which a confocal microscope can capture. Also, while the resolution possible with the x-ray microscope is five times greater than a light microscope, an electron microscope, which uses electrons to penetrate ultra-thin sections of cells, provides better resolution than the x-ray microscope.

Nonetheless, what this x-ray microscope offers, unlike an electron microscope, is the ability to see a whole cell in its native state, with the only preparation being the freezing of the cell sample. Its worth noting that many of the images of cells people recall from their high school biology days were taken with electron microscopes which required the cells to be dehydrated and stained with heavy metals to bind the electrons to the cell and generate an image. Since a cell is 70% water, dehydration and staining can degrade delicate cellular structures and make it difficult to accurately visualize them.

Not only does the x-ray microscope therefore offer a truer representation of a cell but it also brings the world of the cell into stunning 3-D life thanks to a technique known as tomography.

Here, a sample of cells is placed in the microscope and rotated 360 degrees. While it rotates, x-rays illuminate the carbon and nitrogen present in all biological cells and rapid-fire black and white x-ray images display the absorption of the x-rays by the organic material in every part of the cell. All of this happens in about 30 seconds. Computer software then allows the team to process, in a mere five to ten minutes, the individual x-ray images and reconstruct a 3-D portrait of the cell which is possible since the cell has been imaged from every conceivable angle, allowing not only the shapes of its structures to be seen but also the amount of biological material such as the DNA packed into the cell's nucleus.

This novel form of 3-D imaging is revealing new insight into the organization of the active genes - the euchromatin - and the silenced genes - the heterochromatin - in the nucleus.

"So we can see now for the first time that the heterochromatin, or those silenced genes, are more crowded than the euchromatin regions. And we can actually quantify that and say that it’s 28% more crowded," said Carolyn Larabell, a microbiologist and the Director of the National Center for X-ray Tomography.

So why is it important to quantify the amount of active genes versus silenced genes in a cell's nucleus? For one thing, in certain diseases like cancer, previously silenced genes become active and the nucleus grows larger. So perhaps this new level of insight can shed light on the progression of cancer and perhaps even offer an early tool for its onset, well before symptoms appear. A three-dimensional window into cells may also lead to the development of better designed and consequently, more effective drug treatments.

"It’s important to see these structures in 3-D (because) you want to test drugs on cells to see if they’re having the effect that you think they are," said Larabell. "If you get a single section, you have just a very thin window on what might be happening to that cell. (So) you want to see what’s happening throughout the entire cell," she added.

Whether it's the life cycle of the deadly malaria parasite or the breakdown of sugars from plants in the production of biofuels, this exciting new imaging tool is providing a richer understanding of important biological processes.

But as ingenious as this microscope is, it can't compare to the ingenuity and complexity of the microscopic world of cells which we've strained for so long to bring into focus.