Monthly Archives: December 2015

Book Excerpts – Introduction to the Cytoskeleton


Eukaryotic cytoskeleton shown using fluoresecence microscopy Actin filaments are shown in red, microtubules are green and the blue is the nucleus. Picture from

If one consults any of the standard developmental biology textbooks, the cytoskeleton will be briefly presented as the support structure of the cell and about as interesting to most biologists as the floor struts in a ballet school would be to an artistic director seeking the next prima ballerina. However, to think of cytoskeleton only as the structure on which cells do their remarkable things, leaves out a good part of the story of how cells work.

We prefer to think of the cytoskeleton as a troupe of acrobats. They run about in the cell, come together, stack to form some remarkable structure and then as rapidly as it appears, the structure falls apart and/or moves and the acrobats appear elsewhere on the stage. These acrobats are the individual proteins that make up the cytoskeleton, and the many proteins that bind to cytoskeleton, transiently hold it together, or move along it. The surface area available on the cytoskeleton filaments for molecules to electrostatically and chemically bind is huge, far exceeding that of all cell membranes in an organism. Ignoring the cytoskeleton while doing molecular biology would be like trying to choreograph a classical ballet on the same stage that has a troupe from Cirque de Soleil rehearsing.

This unfortunate attitude towards the cytoskeleton is beginning to change. For example, several of the pharmaceutical scientific supply companies have recently begun manufacturing kits designed specifically to detect the phenomenon of “cytoskeletal rearrangements” because all kinds of interesting other stuff seems to happen precisely when these rearrangements occur and therefore the rearrangements can be used to time such events. We find it ironic that only a few people seem to actually think this is more than a convenient coincidence.

The cytoskeleton is, as the name implies, the skeleton of the cell giving it shape and form. The concept goes back to Nikolai K. Koltsov in 1903. Koltsov formulated the idea that the deviation of the shape of a cell from the simple ball, that one would expect if it were a liquid drop, is caused by a stiff but elastic cytoskeleton within the cell. Cytoskeleton is nowadays more precisely defined as the various structures that are filamentous polymers of a single class of protein. These filamentous polymers have long-range order within the cell. They should have been called metapolymers, because the proteins they are made of are themselves polymers of amino acids. These cytoskeletal polymers are commonly classified as supramolecular structures. They are polymers of polymers, roughly topologically linear in their structure.

There are three types of cytoskeletal filaments, arranged in order of decreasing diameter as seen by transmission electron microscopy: microtubules (MTs, 25 nm), intermediate filaments (IFs, 11 nm), and microfilaments (MFs, 7 nm) (nm = nanometer = 10‑9 meter = 10‑3 µm). For things this small, we find it convenient to think in terms of the size of the hydrogen atom, whose diameter is 0.1 nm = 1 Å (Angstrom), so a microtubule, for instance, is 250 hydrogen atoms wide. For something so thin, microtubules can be incredibly long, with reported lengths up to 68 µm (micrometers). In Drosophila (fruit fly) species, the length of the sperm can be 5.8 cm (58000 µm), implying equally long microtubules. Such microtubules are therefore over 2 million times longer than their diameter. If we imagine a microtubule as a piece of cooked spaghetti with a width of 3 mm then the length of the spaghetti would be as long as 7 kilometers! The three cytoskeletal filaments are found throughout the cell. They are connected to each other at many points, as well as to the inner surface of the cell membrane , to the outer nuclear membrane and to the inner surface of the nucleus via specialized attachment proteins.

There is a growing awareness of other proteins that may well also be cytoskeletal in nature and deserving of addition to this triumvirate. The cytoskeleton, as a concept, can also go beyond just filaments to include structural sheets, patches and meshes. For example, septins, which are found in animals, are an example of these other cytoskeletal-like proteins. Septins use a protein called anillin to attach to microfilament rings and thereby form rings themselves. These rings line the inner surface of the cell membrane, increasing the membrane’s rigidity. Another example is CTP synthase, which forms filaments in bacteria, yeast and animals. We will nevertheless concentrate on the three best known, best characterized and universally accepted cytoskeletal components. However, the reader should keep in mind that there are likely to be more types of cytoskeletal-like structures that need to be considered in embryogenesis. We will also focus on the mechanical properties of cytoskeleton. There are poorly understood electrical and related potential memory/epigenetic properties of cytoskeleton. These properties may also become important in explaining aspects of embryogenesis.

The cytoskeleton is an extremely dynamic structure that can depolymerize, move and repolymerize within the cytoplasm in a matter of minutes. The three components are often interlinked in a meshwork that is required for cell movements, maintaining or altering cell shape, and for organizing and powering mitosis and meiosis. The cytoskeleton is required for transporting and sequestering proteins to specific regions of the cell. Cytoskeletal associated proteins act as levers and motors pulling cargo such as the vesicles involved in nerve transmission, chloroplasts and whole nuclei.

The cytoskeleton also serves as the host for a variety of enzymes. The cytoskeleton is directly involved in protein functioning of these enzymes by binding to (and thereby changing the functioning of) associated enzymes. The cytoskeleton can therefore direct a response to external physical or chemical signals in the form of movement of the cell towards or away from the signal by polymerizing or depolymerizing during cytoskeletal rearrangements. Due to the cytoskeleton, external signals can even travel down to and into the nucleus and trigger changes in gene expression.

The cytoskeleton found in the nucleus is also made of actin, microtubules and microfilaments but it requires special consideration. Bundles of microtubules ring the inner membrane of some nuclei. The nucleus contains additional unique protein attachments that connect it to the cytoskeleton. At the inner surface of the double nuclear membrane is a sheet of intermediate filaments called lamins, whose functions may include maintenance or change of nuclear shape, protection of the nucleus from mechanical shocks, and intranuclear rotation (rotation of the contents of the nucleus). Intranuclear rotation includes both nuclear membranes, but without causing the cytoplasm to rotate. Therefore there may be a layer just outside the outer nuclear membrane that has low viscosity, like the cell cortex. If this is the case, the motive force is occurring on the outside surface of the outer nuclear membrane. In some cells nuclear rotation and cell membrane rotation are coupled.

The cytoskeletal elements in the nucleus combine with a variety of nuclear proteins forming a “nuclear matrix” which acts like a scaffold on which the DNA is attached. For this reason the whole lot is referred to as the “nucleoskeleton”. The nucleoskeleton itself is then connected to the cytoskeleton that is outside the nucleus via proteins that bridge the two nuclear membranes.

These three filaments, tubulin, intermediate filaments and actin were once thought to be unique to eukaryotes. Many old textbooks included a table of differences between eukaryotes and prokaryotes and the presence of cytoskeletal elements figured prominently as a defining characteristic of the eukaryotic cell. This has proven to be incorrect, and as we showed in Chapter 1, many characteristics of eukaryotes are found in, if not inherited from, prokaryotes. Homologs of all three cytoskeletal proteins have been found in bacteria, albeit usually having different functions. There is a form of tubulin found in bacteria called FtsZ that is also required for cell division in most prokaryotes (but not all), which may represent the evolutionary precursor of all of the tubulins

.This book excerpt is introduction to Chapter 5, “The Cytoskeleton” in “Embryogenesis Explained”.

The Bagnold Dunes on Mars


Dick Gordon on a trip to revisit the Oregon coast in February 2013, with his back to the sea. The logs were gone. (Natalie Gordon)

When I was a graduate student in the Chemical Physics program at the University of Oregon (1963-67), I would occasionally take a break and drive with friends from Eugene to the Pacific coast. At that time huge logs that drifted in would be piled on the beach, and sometimes after we slept in an abandoned cabin up the steep cliffs, the next morning the logs would be seen totally rearranged. One does not turn one’s back on the sea.


Tide pool with typical huge anemones on the Oregon Coast near Gold Beach. Dick put his glove down for perspective. (Natalie Gordon)

Besides the tidal pools in the rocks with their anemones, snails and small fish, I was fascinated by the sand itself. For with each retreating wave dendritic patterns of darker grains atop the lighter toned majority were made. As I was (initially secretly) doing my first paper on morphogenesis:

I became fascinated by all pattern mechanisms, from rippling clouds to river deltas, and in sand. At that time Jack Carmichael was visiting my mentor, statistical mechanic Terrell Hill, working on the basic mechanism of column chromatography. That’s a strange name, because in most chromatography techniques then and now, one sees no colors. But here’s the origin of the word from an online dictionary:

  • 1930s: from German Chromatographie. The name alludes to the earliest separations when the result was displayed as a number of colored bands or spots.

The sand was doing real color chromatography, on itself.

Jack moved on, and after my first postdoc he invited me to spend the summer of 1968 with him at the Department of Polymer Science & Engineering at the University of Massachusetts in Amherst. It was a great, if hot summer, because I also met Ryan Drum there, and launched my career in diatoms. But that is another story.

Jack, his student Frank Isackson and I built a plexiglass, 6 foot long, one dimensional flume. It was 8 inches tall, and just wide enough to hold white pellet gun plastic balls so we could see every one. We ran water through it from one end to the other, slow enough so the balls were not dislodged. Then we would add one ball and photograph its bouncing motion (called saltation) as it made its way driven by the current, using a strobe light to record its motion.


I had done a lot of reading about how sand moves when driven by wind and water. Much of this literature was by Sir Ralph Bagnold, and I recall reading everything he wrote on the subject. While I was visiting Lewis Wolpert in London, UK in 1969, I took a train north to meet Bagnold at his country home, where he had retired, and spent a pleasant afternoon with him. He told me how he got interested in the motion of sand while in the English foreign legion in North Africa during World War II. He spoke of saltations so high during night sandstorms that one could see nothing horizontally, but could look up and see stars. I formulated the concept that it is important to meet the grand old men and women of science while they are still with us, and have frequently done so.


The sand on the Oregon coast arranged into small dunes by the wind from the Pacific ocean. If you were to put your eye at ground level and look across sand in wind, you could watch individual grains saltating. (Dick Gordon)

I did a computer simulation of the bouncing balls, and we published the experimental and computer results in my one and only sandpaper:

acknowledging Bagnold too dryly “for discussions”. A couple of days ago I read that the Mars lander is now exploring the Bagnold Dunes  on Mars, a fitting tribute to a life well spent on shifting sands.


Bagnold Dunes on Mars courtesy of NASA/JPL-Caltech/MSSS. This image, captured by NASA’s Mars Rover Curiosity on Sept 25, 2015 shows the dark Bagnold sand dunes in the middle distance.



The Oregon Coast February 2013 (Dick Gordon)


Hagfish Slime


I was introduced to hagfish at Gulf Specimen Marine Lab after viewing the video of Joel Sartore preparing to photograph a hagfish specimen for Photoark that was graciously provided by Dean Grubb via their research vessel The Apalachee. You can see the video here.

So what’s with this slime? Hagfish are a class or marine organism that stands alone. They have skulls. They don’t have a spine. There are several species ranging in size from a few centimetres to well over a meter. They have simple light spot eyes that allow them to sense light and dark but not form any real image. If something grabs them they can literally fold themselves over in a knot while releasing copious quantities of slime as a defence. The slime deters predators and may even kill an attacker by clogging the gills until the predator suffocates.

The slime itself is fascinating stuff. It has the strength of spider silk and yet can be stretched into sheets (as the video shows). We had some people visiting who wanted information on the topic and so I decided, at Jack’s request to do some background reading. What I found was fascinating.

The cell state splitter is made of three cytoskeletal components, microfilaments, microtubules and intermediate filaments. The organelle is located in the apical end of the cell that is in a sheet epithelial cells one cell layer thick and joined by protein structures and passages like cellular rivets allowing communication with the cell. In our model of the cell state splitter we have a bistable organelle made from a microtubule mat pushing outward, a microfilament ring closing inward. The two are in a tug of war and they are in balance when a cell is competent to differentiate. There is an intermediate filament ring below that which provides stability and prevents the organelle from being influenced by random minor fluctuations. A strong mechanical perturbation starts a wave of contraction or expansion through the cell sheet propagating one of two possible signals. Those signals are sent via signal transduction pathways to the nucleus  and the pattern of gene expression changes.

While we did extensively review the role of microtubules and microfilaments we really didn’t look very hard at that intermediate filament ring. My encounter with the hagfish has me rethinking that. If you watch the individual cells as they participate in the contraction wave you see the cell contract and then return to its original shape. However the expansion wave is very different to observe. The expansion looks like a series of small jerks and then suddenly the apical end “gives” and expands rapidly. In the axolotl cells at least, the apical end spreads to double or triple the diameter and then stays that way. We knew that intermediate filament ring needs to “get out of the way” in some fashion but we never considered what the mechanism might be.

Back to hagfish slime. Hagfish have little pouches under their skin that form small hollow balls lined with a single layer of cells, an epithelial sheet. Cells within that sheet that are presumed to be stem-cell like, divide and produce two types of daughter cells. (In our book we referred to such activity as Type 5 Cell Sheet Differentiation.) One type of daughter cell begins producing a mucus and the other type fills with a specific highly modified and specialized intermediate filament. Once the cells with either slime or mucus are totally packed full, the cell undergoes a programmed cell death and this leaves sacks made of plasma membrane packed full of either mucus or the tightly coiled intermediate filaments. The intermediate filaments look like a tiny solid wasp nest only 5o um in with. This repeated cellular differentiation off the epithelial layer fills the empty space of the little pouches the hagfish have under their skin.

Along comes a predator who does something to upset the hagfish. The hagfish responds by contracting those pouches and squirting the dead cells full of slime or intermediate filaments. The opening through which the material is forced is small enough that the plasma membrane is ruptures and stripped off and a bullet of tightly coiled intermediate filament or mucus is produced. The intermediate filament and mucus take up water. The result is slime.

Intermediate filament have a neat property known as alpha/beta transition. The proteins involved can have a short tight coil or they can have a zigzag straight string and they can flip between these two configurations. Some external force has to be applied but with the right  additional force the flip can happen. If you have ever applied heat to a wool sweater and had it shrink to much smaller and denser version, you have induced the alpha/beta transition by applying heat. Hagfish intermediate filaments fill the second cell type in the highly compacted state. When they take up water they under a transition and dramatically lengthen. The tightly coiled wasp nest “skeins” spread and grow, mixing with the mucus to produce the slime. The process of changing this tight 50um ball into many threads of 150mm long fibres takes only seconds. Ions from salt water play a critical role though exactly how this works is not known. However these are the same ions so important in signal transduction during differentiation. (You can see a neat picture at the link but Nature didn’t I’ve me permission to use it.)

Temporal and spatial models of thread assembly and coiling in GTCs.

And so our adventure with the slime salty tasting hagfish slime inadvertently provided us with a valuable hypothesis on exactly how the intermediate filament of the cell state splitter “gets out of the way” of an expansion wave. That ring likely undergoes some kind of alpha/beta transition stimulated by the same ion flux that is involved in signal transduction to the nucleus.

I suppose I should not be surprised that the new clues to functioning of the organelle of differentiation can be found in a simple creature from the bottom of the sea. After, all life on earth arose from some common ancestor and the cytoskeleton goes all the way back to that common ancestor. Still, I find it amazing. When I was a child my favourite bit of verse was by Robert Louis Stevenson:

The world is so full of a number of things
I’m sure we should all be as happy as kings.

Those things include an ugly little hagfish from the bottom of the sea.

Baby Girl or Baby Boy

Today we had the pleasure of enjoying a lunch with Dr. Mark Moore and having a chance to read his wonderful and funny little book. This is basically a funny little cartoon book that lends itself to a frank and open talk about the major plague in our world of gender selection in utero, especially against girls. Nothing is fool proof and I heard the success rate for such techniques was not great, 50:50 becoming 60:40. Dr. Moore said over lunch it was more like 80:20. Those aren’t bad odds. If you are planning your pregnancy it is likely worth the effort.

The book itself is lighthearted. It talks about the things a couple can do to influence the gender of their baby. Now I am the grandmother/step-grandmother to a total of nine lovely boys and one single girl. I love all my grandchildren, boys or girl. You get what you get and you love what you get. I would not give up one single hair on the sweet head of any of my darling boys! But I do have to admit it would have been nice to have a few more granddaughters to balance things. I have to admit that the first thing I thought when the eldest grew big enough to look down on me was ‘Oh good, now I can hope for great-granddaughters!’ Princess dresses and pink frills do give me a wistful sigh before I head off to the boy’s section.

I also have done some counselling of couples and it struck me that this book gives a couple more knowledge and control. When people have more knowledge and control, I think they are more likely to accept what they end up with in all situations but especially in the gender of their baby. Working in a genetics clinic as I did, I was a party to discussions about the ethics of informing couples about the gender of their baby when we knew the result would probably be a flying trip back to old country for the termination of a healthy fetus. I think a book like this will reduce such nonsense. Given all the terrible things that can go wrong, and seeing the agony of couples who can’t conceive, or who are hoping for a specific gender to avoid a terrible sex-linked genetic illness, I must say the mere idea of terminating a healthy normal fetus just because the gender is wrong simply makes me feel ill. So I am all for anything to prevent or reduce that possibility.

I also think that the simple easy way this book is written makes it suitable for explaining this technique (and a few other things) in a clinic to a couple whose first language is not English. It has been my experience that a vehement desire for gender selection is more common in new Canadians from other cultures. I also found that some people mistakenly think that the mother determines the gender and the mother is blamed for not producing the correct desirable gender. This is, of course, incorrect. And I have seen a father take the bad news about the gender being different from expectation with much more grace when he was told it was his own doing and not his wife’s. (I also once saw a mother-in-law cuff her son-in-law not quite gently enough for it to be a joke when the new baby was the fourth child of the same gender and while I did empathize, I did not approve.)

And so we had a very nice lunch and as you would expect, given the way the book, is written, Dr. Moore was a pleasant, kind and amusing fellow in person. And having read his book I can definitely recommend it. Best of all I got to think about my wonderful grandchildren and how very blessed I have been in the grandchild department.