It's alive!

Check it out.

Surprise, surprise

Due to the complexity and smallness of the organelles inside the cell, I thought I should devote a whole tab in the interactive to describing them visually. I decided to start with an organelle that I expected to be easy: the mitochondrion. It turns out, since the late 1990's, there has been a revolution in the way that people think of mitochondria.

In the 1950's, the transmission electron microscope became a fashionable tool for inspecting cells, and it allows extremely high resolution, but the problem is that it can only examine a very thin slice of the cell. A problem arose when trying to determine the 3D structure from 2D information. There were two cytologists who were simultaneously trying to describe mitochondria. Dr. Sjostand had a more painstaking tissue fixation technique, while Dr. Palade didn't believe that the conditions of fixation were important. Their observations led them to different conclusions about the morphology of mitochondria. Dr. Sjostand insisted that the foldings of the inner membrane (called cristae) were only continuous with the rest of the membrane in very small areas, while Dr. Palade beleived that they were like the baffles of an accordion, and were continuous with the inner membrane over large spaces.

While they both agreed that Dr. Sjostand's micrographs were better, and Dr. Sjostand's fixation method has become universally adopted, Dr. Palade's baffle model was the one to become widely accepted, and it is still in most textbooks today. It wasn't until the late 1990's, when microscopy techniques were developed that allowed the examination of thicker slices of cells, that people noticed that mitochondria look nothing like Dr. Palade's model, and Dr. Sjostand was more correct about mitochondrial internal structure. The cristae are tubular in the cells of almost all tissues, and are indeed only connected to the inner membrane by small round openings, now termed "crista junctions."

But what about the external structure and overall morphology? Better microscopy has revealed that mitochondria are not usually isolated, bean-shaped entities, floating in the cytosol, but that they form a dynamic network of interconnected mitochondria that are constantly coming together and separating, based on energy demands of the cell. Also, they associate closely with the endoplasmic reticulum.

Because this information about mitochondria took me by surprise, I have decided that a good deal of reading must be done before I can draw any organelle, because I want my interactive to have the most up-to-date and accurate pictures, and not to show the generic, formulaic representations that I have been seeing all my life. So, don't be surprised if you see something represented in a way that you are not used to seeing it.

The interactive will be online soon, although this business with the mitochondria and other organelles has slowed me down somewhat...But I think it is better to do more research and invest more time in the beginning, than to have to go back and make changes later.

What color is a cell?

Because most cells are invisible to the naked eye (with some exceptions, like the chicken egg which is all one giant cell) the scientific artist has to choose what color to make them. For the illustrations of cells in my project, I am going to use a color palette derived from pictures of cells that are stained with H & E, or hematoxylin and eosin. This combination of dyes is very often used to visualize cells for light microscopy. In fact, at a previous job, I personally spent many an hour in the lab at a microscope counting H&E-stained lung cells. Because of this tradition, it seemed like an appropriate choice for use in my project.

Click here to see a picture of cells stained with H&E. To make a long story short, hematoxylin is a dark blue-purple dye that is basic. It stains regions rich in DNA and RNA, such as the nucleus and ribosomes. Eosin is bright pink, and stains cytoplasmic protein.

For my illustrations, I created this palette by using the eye-dropper tool in Photoshop to sample the various colors from a few examples of H&E photomicrographs. The colors on the left are used for the color inside the cells, the second row is used for the stroke defining the edges of the cells, as well as organelles and details inside. The 3rd row is for the nucleus, and the last row is for highly eosinophilic structures like erythrocytes, or the bright pink spheres inside an eosinophil, which is what gives them their name.

Custom Brushes in Illustrator

As I drew the sketches of the cells that will go into my Flash site and began working in Illustrator to make them into vector art, I had a few ideas about a technique to help speed things along. Here, I want to share a tutorial on making custom brushes in Illustrator. Specifically, the ribosomes typically appear, at a scale of 10,000X, to be small 1pt dots, distributed throughout the cytoplasm or attached to the rough endoplasmic reticulum. This brush will create a regular pattern of dots that follow the path of the brush.

1. Make a 1pt dot using the ellipse tool.
2. Convert it to a symbol by selecting it, and going to the menu inside the symbols tab, and click "new symbol."
3. With the dot selected as the symbol, use the symbol sprayer to spray a bunch of dots out. Make it look natural and not too regular or patterned.
4. Select the field of dots and go to Object > Expand. The default will have "object" and "fill" selected, which is fine: say OK.
5. Remove any unwanted dots. It's probably a good idea to keep them within a square area to avoid a stamped look later. Individual dots can now be moved around to your liking.
6. With your square of dots selected, enter the menu of the brushes tab and select "new brush."
7. You will have 4 options. The first, New Calligraphic Brush, doesn't allow you to use the pattern, so forget about this one.

• New Scatter Brush - this option will create a brush that will repeat the selected pattern exactly without any distortion. The number of repeats is based on the length of the path, but it will be no fewer than one stamp of it (i.e. it will not be shrunk or cut in half). Thus it is a good option for this purpose, as long as the path is straight. Otherwise you get a tiled, stamped look. It just happens to be the first thing I tried, and it works, but lets have a look at the other choices, just out of curiosity.
  
• New Art Brush - Takes the pattern of dots and stretches it out to fit the path. This causes distortion and differences in the size and shape of the dots. Hence, it is not a good option for this purpose.
  
• New Pattern Brush - creates a brush that is like a cross between the scatter and art brushes, in that it repeats the pattern and conforms it to the path with minimal (but still present) distortion. So, not a terrible option for our purposes.
  

Now after I have drawn the cell's outline and other organelles, I can use brushes made in this way to distribute ribosomes throughout the cell in a fraction of the time it would have taken me to paste or draw them in, and with more predictability than I would have had by using the symbol sprayer. Next I hope to make a brush that can automate the drawing of the endoplasmic reticulum and golgi apparatus, which typically appear in cross-section as a series of flattened sacs or elongated ovals.

Phases of the Project

My favorite "beta-version" of the interactive got a face-lift over my Christmas break, and I have decided that I am ready to move on to the next part of my project: adding content.

My technique for drawing the cells: The first part of the interactive I will be adding content to is the "Cells" tab. I have begun drawing all of the cells that will be shown at the exact same scale, such that 1 micrometer (or micron, or um) is equal to 1 cm. This corresponds to a magnification of 10,000 X. I have a large pad of sketch paper, and on one sheet of it, I drew a 1 cm grid. This, I place underneath a blank sheet of the same paper, so that when I am drawing the cells, I can simply count off the squares to know exactly what the dimensions should be.

So far I have drawn:

• some red blood cells
• a sperm cell
• two columnar epithelial cells
• a squamous epithelial cell
• some bacteria
• some yeast

Before today, I didn't know quite how interesting-looking yeast is. Check out this link for yeast and other cool pictures from the kingdom Fungi: http://io.uwinnipeg.ca/~simmons/16cm05/1116/16fungi.htm .