What is that? A beautiful image of deadly tumor cells

the eye

Thanks to Dr. Roberto Fiorelli of Barrow Neurological Institute for sharing this stunning image

It looks like an eye.  Perhaps a terrifying pink eye, like the Eye of Sauron, coming out of the darkness. It’s not an eye, but it is a bit terrifying. This is an image of a slice of the brain showing tumor cells (in green and red) surrounding a blood vessel.  How does this type of image get made?  How does this type of image help scientists? What does it mean that these tumor cells are near a blood vessel?

This image is created with a microscope – specifically a confocal microscope. I’m going to use a very weird analogy to explain why confocal microscopy is so cool, so stick with me. Imagine that you have a jello mold with an object it and you want to know exactly what the object looks like.  Now imagine a regular microscope is like a flashlight.  When you point the flashlight at the jello mold the whole thing lights up including what’s in front of the object, and if the object is translucent, the jello behind the object lights up too.  This gives you an idea of what the object is, but it may be kind of fuzzy because of all the jello you see in front and behind the object.  Confocal microscopy, on the other hand, is designed to turn that wide flashlight beam into a single pinpoint of light so only one part of the object is illuminated at a time.  So when you move this single pinpoint around (back and forth and up and down) over the object, you can get a clear a crisp image of what is inside the jello.


To bring this analogy back into the science-verse, the jello is a cell or a piece of human tissue with layers of many cells.  The objects inside the jello are certain proteins marked so that they light up in different colors (what we call fluorescence) when excited by the light from the laser (flashlight). When confocal microscopy is used to look at these proteins, you can see clear crisp images of exactly where the proteins are in the cells.  And if you take enough images up and down through the cells and the tissue, you can even create a 3D image of the cell or a piece of tissue. Check out this neat video of a 3D rendering of a piece of the brain called the hippocampus.

Now back to the image above.  This is a piece of tissue taken from a patient with an ependymoma, a tumor derived from brain tissue and is primarily found in younger patients.  The colors you see are:

  1. Blue: a chemical called DAPI (or 4′,6-Diamidino-2-Phenylindole, Dihydrochloride) that binds to DNA. Since DNA is found in the nucleus of every cell, staining cells with DAPI helps you to locate each cell in the image – each blue dot is one cell.
  2. Red: stains a protein called GFAP (Glial Fibrillary Acidic Protein) that is found in different cells of the brain, but is also a marker of particular brain tumors, like ependymomas
  3. Green: stains a protein called vimentin that is also found in different cells of the brain, including cells that make up large blood vessels and brain tumors like ependoymomas

So what are we able to learn from this beautiful picture?  See how there are a lot of red and green cells surrounding an empty round space.  That round space is a blood vessel. Cancer cells need food and oxygen to grow, so the green and red cancer cells are clustering around the blood vessel to get the nutrients they need. Even though this is a beautiful image, it helps scientists to understand how these deadly tumors function within the brain and how they find the resources to grow.

If you want to look at more amazing images taken using confocal microscopy and fluorescently tagged proteins, check out these links

Wellcome Image Awards 2015
The Cell: An Image Library

Thanks to Dr. Roberto Fiorelli of Barrow Neurological Institute for sharing this stunning image from his postdoctoral work in Dr. Nadar Sanai’s Laboratory, the Barrow Brain Tumor Research Center

For more “What is That?”, click here.

What does DNA look like? Like, really?

Everyone talks about DNA.  And shows those lovely double helix cartoon images of DNA. But when you’re a researcher in a lab, what does DNA actually look like?  How in the world do we see it?


  1. X-Ray crystallography.  To be fair, this is an indirect way to see DNA but it is the way that the structure of DNA was determined (as described in our book club book The Double Helix) so it’s worth mentioning.  Remember when you were a kid and you made rock candy by hanging a string or stick in water that had a ton of sugar dissolved into it?  Well scientists can do the same thing with DNA or proteins – make crystals of them.  These crystals are much smaller than the crystals in rock candy.  Think microscopic.  When molecules are all lined up in the same direction, like they are when they form a crystal, scientists can hit the crystal with X-rays and what bounces around and through the crystal can be detected (this is called a diffraction pattern), measured and transformed to determine the 3D image of the molecule – that double helix structure you see pictures of all the time.  This process is called X-Ray crystallography and for the first images of DNA, the diffraction pattern looked like the picture to the left.
  2. dna_in_cellMost scientists do not look at DNA to the atomic level like in X-Ray crystallography, but rather want to see it inside of a cell. The DNA in a cell is inside the nucleus and certain dyes (such as the Hoechst dye) bind to DNA.  Under UV light, the Hoechst dye glows, showing exactly where the DNA is in the cell.  If you look at the picture to the right, you can see the outline of three cells and the blue DNA inside the nucleus of those three cells. Why would a scientist want to see where the DNA is and what it looks like? You can learn a lot from just looking at the DNA. For example, whether or not a cell is dividing or dying, which can be really important if you want to know whether or not the cancer cells you are studying die when you treat them with a drug.
  3. Scientists don’t always look at the DNA directly inside of a cell either.  For an experiment they may want to isolate the DNA (meaning, take the DNA out of a lot of cells to dna_in_eppendorfstudy it) and then manipulate it in some way (sequence it, amplify it, modify it, etc).  Once my mom asked me how big DNA is when you take it out of cells and work with it in the lab.  Well, the answer is that you need a LOT of it to even see it.  In the lab, we may grow bacteria in 5 ml of growth media, which after growing overnight contains 10,000,000,000 cells.  We then bust these cells open with a detergent (like soap, but not soap), spin out all of the extra bits of cells, and then force the DNA to show itself by adding an alcohol like ethanol in a process called precipitation (if you want to learn more about the details, check out this article).  How much DNA do you get in the end – well it depends, but it’s not a lot, visually at least.  And what does it look like?  See the whitish smear at the bottom of that tiny tube?  That’s the DNA.

Are there other ways to see DNA?  YES!  But many of them are based on dyes like the one described in #2 above.  At some point, we’ll definitely talk about them in the context of analyzing DNA sequence and running gels.  And I’m not talking at all here about “seeing” DNA by determining it’s sequence, even though that’s important too.

strawberry_dnaSo now that you know a few ways that scientists see DNA, it’s your turn.  Grab a lab partner, and isolate DNA on your own!!  Don’t know how?  No problem!  There are a number of different ways to isolate DNA at home, the most common being from the cells of an onion or the cells of strawberries.  The experiments for extracting DNA from ONIONS or STRAWBERRIES are linked. At the end of the experiment, what will you see?  Long strands of isolated DNA from all of the onion or strawberry cells. Enjoy and please share photos and stories of your DNA isolation adventures!