An Immovable Moving Part- That’s Just Cilia!

Biological concepts – primary cilia, sterocilia, kinocilium, Usher syndrome, actin, microtubule, signal transduction, sensory receptor, mechanoreceptor

The USS Oriskany (above) was scuttled in 2006 to

create an artificial reef off of Pensacola Florida. In

2012, the US government effectively ended its policy

of creating artificial reefs this way because of concern

for leaking toxins from the ships to the marine life. But

is was a good way to find a new job for something broken.

Naval vessels are built to move through the oceans. When they can’t, they get fixed or they get decommissioned. As broken vehicles they have no use. Or might they? Some have been re-purposed as man made reefs.

Something that seemed broken because it couldn’t move was given an important new job that didn’t require motility. Remember that analogy as we talk about today’s subject in cilia. Although the order might be reversed.

We spoke last week about how nematodes are the only animals that don’t have cilia. Eukaryotic cilia and flagella (together, the undulipodia) are organelles that move, and in turn may move cells. It turns out that cilia have some exceptions – some don’t beat, and some can’t move at all - so what good are they?

Motile cilia, the kind we have been talking about for the past couple of weeks, are also called 2˚ cilia. If there are 2˚ cilia, I think that pretty much implies that there must 1˚ cilia – and they’re what we will talk about today.

Primary cilia, while less well known, are found on many more cell types than are motile cilia. Motile cilia in mammals are located on male gametes (as flagella), on respiratory epithelium of the lower and upper respiratory tract, fallopian tubes near the ovary and epididymal cells of the testes, and the ependymal cells lining the ventricles of the brain.

Primary cilia are apparent on cells of most types, when they are quiescent (just hanging out, doing it's job). If the cell re-enters the cell cycle and starts to divide or differentiate, the primary cilium will resorb and then reappear in daughter cells once they become quiescent.

Primary cilia have basal bodies and IFT, but their

microtubule structure is different. They don’t have the

inner singlet microtubules, so the outside ones can’t slide

past one another. They do have outer dynein arms, and

those are important for retrograde IFT. See below,

kinocilium don’t even have the outer arms.

Primary cilia are 9(2) + 0 in the axoneme, which they makes them different than motile cilia (see picture and this review). Primary cilia are missing the two central microtubule singlets. They are also missing all dynein, both the inner and the outer arms. This is why they are immotile, sort of.

Another exception with primary cilia is that their microtubule axoneme can change as it goes out to the end of the cilia. It may start out as 9(2) + 0, but at the distal (far) end it's 9 + 0 in nematodes, algae, and in the nose, pancreas and kidneys of vertebrates. All of those count as exceptions too!

In addition, primary cilia are of differing lengths, but most are much shorter than motile cilia. Some don’t even extend from the surface of the cell membrane. However, they're built by IFT (intraflagellar transport) just as 2˚ cilia are, and IFT is important for their functions as well.

So, can a broken cilium have a specific job? If they don’t beat to move a cell or the environment around the cell, then what do primary cilia do? The answer is - just about everything. Primary cilia serve as mechanoreceptors, chemoreceptors, photoreceptors, as well as osmolarity, temperature, or gravity receptors. Think of primary cilia like weather balloons. They stick out into the environment and probe the conditions in the area. They send the data back and the cell can act on it.

As mechanoreceptors, primary cilia might not beat, but they can be moved. They bend in response to flow across the surface and the bend brings a pivot at the level of the basal body – yes, primary cilia have basal bodies just as motile cilia do.

Kidney cells that line the tubules have primary cilia to

sense the urine flow. The cilium is bent, and this triggers

a change in calcium influx. The change is then

transferred to the adjacent cell via calcium channels

that cross both membranes.

The kidney cells that line your urine-filled tubules have primary cilia that stick out into the urine river. As the urine flow speeds up after your third diet coke in the last hour, the primary cilia bend and transmit a signal to the cell. This then signals the cells to ramp up their filtering functions, pulling water back in or excreting urea, etc.

Primary cilia have an asymmetry so that they recognize right from left. In the kidney, the flow is based on orientation, all primary cilia bend in the same direction, toward the anterior. The anterior bend signals for increased calcium influx and then this signal is transmitted to adjacent cells. The uniform gradient (a-p) works cell to cell, and this leads to consistent a-p orientation of the mitotic spindle (which also uses basal bodies in the form of centrioles). The result is that the progeny cells of dividing renal epithelium have the same orientation as the parent they replace.

Back to our nematodes from last week. Primary cilia are the only cilia roundworms have. C. elegans, the roundworm that is used as a laboratory model, is made up of exactly 959 cells – exactly. Sixty of those cells, all sensory neurons, have primary cilia that stick out into the environment via pores called sensillae.

The left photomicrograph has labeled dendrites for sensory

neurons in C. elegans. The right cartoon shows how the

primary cilia from these neurons stick into the pore that

then helps them sense the environment around

the roundworm.

It’s through the interaction of these primary cilia with the worm's immediate environment that it senses its world. This is what passes for a roundworm brain – but your brain has them as well. Especially in the retina of your eyes.

The photoreceptors that absorb light energy and transfer it to electrical impulses are located on a single primary cilium on each retinal cell. The axoneme is used to move photosensitive pigments (like retinal in rhodopsin, see below) back and forth from the receptor to the cytoplasm.

Primary cilia also act as chemoreceptors. In brain proper, they work in formation of new memories – mice without primary cilia can’t remember new objects or recognize objects they have already learned. They can remember the location of the object just fine, just not the object itself. We will talk about primary cilia in the brain much more next week.

Now we can take this discussion a couple of steps further to talk about two ciliary exceptions. There are nonmotile 1˚ cilia, motile 2˚ cilia, and then a third structure called a kinocilium. From the Greek for moving eyelash, the kinocilium is poorly named. Described in guinea pigs in 1989, they don’t move like a blinking eyelash or even like a motile cilium; they lack the inner dynein arms and central microtubules that would allow them to be motile. But, they can move horizontally across a cell surface.

As this movie travels down the photoreceptor, notice the

vertical basal body/axoneme on the left. This is a primary

cilium! The microtubules help move photo pigments up and

down the cilium.

Located in humans on the hair cells the inner ear, kinocilium play a crucial role in both hearing and balance, even though they're gone by the time you hear or need to stand up straight. Their role is regulating the erection of the apparatus that allow hair cells to function.

If hair cell kinocilia are poorly named, then hair cell stereocilia are down right liars. They aren’t cilia at all. The characteristics of cilia include that they are microtubule extensions of a basal body modified from a centriole. They may be motile or nonmotile, but their functions are mediated by moving signaling, structural, or receptor molecules up and down via intraflagellar transport proteins.

None of that applies to sterocilia! They're built from actin not microtubules. They do not have an intraflagellar transport system. They have no basal body. They are very similar to the microvilli of your gut epithelium, but nothing like cilia, except for the fact that they stick up from a cell.

The hair cells work by using the sterocilia as mechanoreceptors. In the cochlea, they bend in response to fluid movement based on vibrations of sound. In the semicircular canals, they bend in response fluid movement as a result of changes in head position. When the sterocilia bend, it generates an action potential in neurons that go to the brain.

Hair cells of the cochlea can be damaged by loud noise.

The left images are the normal (top) hair cell sterocilia, and

the same sterocilia after a loud noise (bottom). The right

images show a series of hair cells in normal condition, and

after a long time exposed to loud noise. Turn down your

music – do you think the hair cells in the damaged cochlea

work well?

So that explains the sterocilia (that aren’t really cilia), but what about the kinocilium? A 2007 paper reviewed how kinocilia mediate production of sterocilia. The hair cells start out with a smooth surface and one long kinocilium in the center of the apical (top) surface. Then the sterocilia start to grow. As the sterocilia appear, the kinocilium moves laterally, to the edge of the apical surface. This defines the orientation of the hair cell – the direction the sterocilia will bend.

The sterocilia start to grow longer, with the ones closest to the kinocilium being the longest. They line up to look like a choir on risers in front of the taller kinocilium. Now they are ready to function. At this point the kinocilium disappears! If you look at working hair cells, you won't find the structure that mediated their development.

So we have two new ciliary structures - neither of which act like cilia. That’s weird enough, but it gets weirder. There is a disease that affects both hearing and vision because it messes with the primary cilia of the retina and the sterocilia of the ear. But we just learned that those are two completely different structures!

People often use "tunnel vision" to explain the field changes

in retinitis pigmentosa, the kind of progressive blindness

in Usher syndrome. But really, it’s more like backing into a

tunnel, one that never reaches the other side. Think of

running this clip backwards.

Called Usher syndrome, victims suffer from hearing loss, vision loss, and balance problems. The vision loss is due to defective maintenance of primary cilia of the retina, but the stereocilia of the cochlea and vestibular system aren’t cilia at all, how could they be affected by a 1˚ cilia protein problem?

As we said last week, nature hates a unitasker. There are at least 11 proteins that work in development and working of both sterocilia AND primary cilia, even though they look and are built completely different. A mutation in one of those proteins affects all three systems. Maybe it would be better if sometimes a protein had just one job, fewer things could get screwed up if something goes wrong with it. Would you rather have reduced vision, reduced hearing, bad balance, or all three?

All this knowledge leaves us with an unanswered question - did the sensory primary cilia develop from motile cilia, or did motile cilia develop from the primary version? Did broken motile cilia develop a new job, or did 1˚ cilia learn how to dance after they had learned their first function? Hmmmm.

We've barely touched the functions of cilia that don’t even move. In the next couple of weeks, we will see how primary cilia keep you from being fat, and how they will be crucial for long-term space travel. Then we can figure out how they give you a right and left hand.

Mathur P, & Yang J (2014). Usher syndrome: Hearing loss, retinal degeneration and associated abnormalities. Biochimica et biophysica acta, 1852 (3), 406-420 PMID: 25481835

Doroquez DB, Berciu C, Anderson JR, Sengupta P, & Nicastro D (2014). A high-resolution morphological and ultrastructural map of anterior sensory cilia and glia in Caenorhabditis elegans. eLife, 3 PMID: 24668170

Patel, A. (2014). The Primary cilium calcium channels and their role in flow sensing Pflügers Archiv - European Journal of Physiology, 467 (1), 157-165 DOI: 10.1007/s00424-014-1516-0

Fry AM, Leaper MJ, & Bayliss R (2014). The primary cilium: guardian of organ development and homeostasis. Organogenesis, 10 (1), 62-8 PMID: 24743231

For more information or classroom activities, see:

Primary cilia –

http://www.nature.com/scitable/topicpage/the-primary-cilium-an-orphan-organelle-finds-14228249

http://jcs.biologists.org/content/123/4/499

http://www.ciliopathyalliance.org/cilia/structure-and-function-of-cilia.html

http://jonlieffmd.com/blog/is-the-primary-cilium-a-cells-antenna-or-its-brain

http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/C/Cilia.html

Hair cells –

http://auditoryneuroscience.com/ear/dancing_hair_cell

http://education-portal.com/academy/lesson/the-ear-sense-of-balance-and-the-inner-ear.html

https://faculty.washington.edu/chudler/hearing.html

http://www.scholastic.com/browse/article.jsp?id=3757141

https://www.washcoll.edu/faculty/george-spilich/faculty/george-spilich/experience-biopsychology/audition.php

http://education-portal.com/academy/lesson/the-ear-hair-cells-organ-of-corti-the-auditory-nerve.html

http://bigpictureeducation.com/lesson-idea-hearing-believing

http://uthscsa.edu/shp/pa/hearing/lessonplan.html

http://highered.mheducation.com/sites/0072437316/student_view0/chapter46/index.html

http://www.sumanasinc.com/webcontent/animations/content/soundtransduction.html

http://147.162.36.50/cochlea/cochleapages/theory/hcells/hcells.htm

http://neuroscience.uth.tmc.edu/s2/chapter12.html

http://www.blackwellpublishing.com/patestas/animations/haircell.html

http://www.bbc.co.uk/science/humanbody/body/factfiles/balance/balance_animation.shtml

http://www.bbc.co.uk/science/humanbody/body/factfiles/balance/balance_animation.shtml

http://www.nebraskamed.com/health-library/3d-medical-atlas/302/balance-and-equilibrium

http://www.cengage.com/biology/discipline_content/animations/dynamic_equilibrium_m.html

http://www.slideshare.net/vacagodx/vestibular-system-3550870

Visual photoreceptors –

http://www.d.umn.edu/~jfitzake/Lectures/DMED/Vision/Retina/Phototransduction.html

https://www.khanacademy.org/test-prep/mcat/processing-the-environment/sight/v/phototransduction-cascade

https://faculty.washington.edu/chudler/eyetr.html

http://faculty.washington.edu/chudler/eyecol.html

http://www.skidmore.edu/~hfoley/Perc3.htm

http://www.physicsclassroom.com/class/light/Lesson-2/Visible-Light-and-the-Eye-s-Response

https://www.youtube.com/watch?v=6L7CDH7Jj5g

http://sciencenetlinks.com/lessons/light-3-all-those-seeing-color-say-eye/

http://education-portal.com/academy/lesson/receptors-of-the-back-of-the-eye-retina-rods-cones-fovea.html

http://askabiologist.asu.edu/rods-and-cones

https://backyardbrains.com/experiments/eye

http://howyourbrainworks.net/content/lesson-3-seeing-things-1

http://sites.sinauer.com/neuroscience5e/animations11.02.html

http://bcs.whfreeman.com/thelifewire/content/chp45/4502s.swf

http://www.sumanasinc.com/webcontent/animations/content/receptivefields.html

http://webvision.med.utah.edu/book/part-v-phototransduction-in-rods-and-cones/phototransduction-in-rods-and-cones/

Usher syndrome -

http://www.nidcd.nih.gov/health/hearing/pages/usher.aspx

http://ghr.nlm.nih.gov/condition/usher-syndrome

http://www.asha.org/aud/articles/UsherSyndrome/

http://www.usher-syndrome.org/

http://my.clevelandclinic.org/health/diseases_conditions/hic_Usher_Syndrome

Crawling To The Top

Biology concepts – characteristics of animals, undulipodia, gametes, nematodes, roundworms,

Yes, a sponge is an animal – just like a barracuda, a

platypus or a that weird nephew of yours. They are

multicellular, loosely organized into a couple tissues,

and eat other organisms. You can see how they filter

feed in this demonstration. Not so different from

that nephew.

Sponges and birds – they’re both animals, but would you know it to look at them? Sponges are sessile (except for the exceptions), and birds can’t breathe under water (no exceptions). Birds eat worms and lay eggs – most people don’t know what the heck sponges do. Yet they’re both animals. Are there characteristics that all animals have in common?

Yes there are, thanks for asking. Animals are all eukaryotic and diploid (2 of each chromosome). For the most part, our cells have nuclei and organelles and all but our gametes have two copies of each chromosome.

Animals are all multicellular - a unicellular organism that acts like an animal is still called a protist. Because they are multicellular, animals have the capability to have cells of different types that organize themselves into tissues and organs, like we have discussed before as a characteristic of life.

Another attribute of animals is that they can move. True, sponges are sessile when attached to rocks or coral reefs, but they do have motile cells and motile life cycle stages. Birds are very motile unless dead.

One other thing animals have in common is how the male gamete finds the female egg. Male gametes have a flagellum that allows them to swim toward the chemical signals that show them where the egg is located. True, we have learned that protists and some lower plants also have gametes that swim with flagella or cilia, but animals characteristically have flagellated male gametes. But of course, given the nature of this blog, there must be an exception.

Nematodes are round worms; helminthes are just

one group of parasitic roundworms. They represent a

turning point in animal development. They sort of have

an internal body cavity (they are pseudocoelomates),

they sort of have a head (start of cephalization) and

they sort of have body symmetry (starting to be

bilateral).

The roundworms, phylum Nematoda, are our exception for the day. Their male gametes can’t swim! But who cares, it hasn’t seemed to slow them down. Which makes us ask why everyone else goes to the trouble of producing gametes with flagella – it’s expensive. Shall we investigate?

In every other phylum of animals, male gametes use the eukaryotic flagellum to swim their way to the egg. Using exactly the same structure that we have talked about before, male gamete flagella have basal bodies and axonemes made of microtubules. The microtubule filaments slide past one another to produce their beating movement.

Look as hard as you want, but round worms don’t have basal bodies or flagella. They do have centrioles and centrosomes used for mitosis, but none of them mature into basal bodies for flagellar assembly, In fact, the male gametes of nematodes carry one centrosome (with its centriole pair) to the egg and form the basis of all centrioles in the baby roundworm. Weird - why no basal bodies? – I have no idea, but evolution approved it.

Instead of flagella for male gamete swimming, nematodes use an amoeboid movement to crawl to the egg. O.K., so they crawl instead of swim. That’s exceptional, but is it really that weird? Well… yes, considering that they don’t contain the most important protein that most cells use to make amoeboid movements.

Actin is one of the major proteins of the cytoskeleton. Actin works mostly in protrusion and contraction of parts of the cell, while intermediate filaments hold the cell’s shape and give it rigidity and microtubules are primarily for movement of proteins and structures throughout the cell.

This short video shows you the movement of C. elegans

male gametes. They are shaped like typical animal male

gametes, they don’t move like typical male gametes, and

they don’t have the same proteins as typical ones. Yet, the

nematode is the most numerous type of animal on Earth.

Actin comes on a two main forms. G-actin is the globular form; it's the monomer. When the monomers are induced to form filaments, like tubulin monomers monomers form microtubules, it's now called F-actin. Quick assembly and disassembly of F-actin polymers from G-actin monomers allows for movement of selected parts of the cell membrane.

So amoeboid cells use F-actin as the way they extends and retracts its pseudopodia. Thus, they crawls along. Nematodes do have cells with G- and F-actin, but the male gametes don’t have any (or very little). But it’s the male gametes that need it to move! What gives?

Instead, male gametes of nematodes use the MSP protein (major sperx protein; my posts get blocked by schools if I use the whole word, so I use gamete whenever possible). A 2014 study shows that MSP proteins are abundant in the male gamete (40% of total soluble protein), and change its distribution and volume as the gamete matures and is activated. When fully activated and in the female oviduct, the MSP of the male gamete assembles and creates pseudopodia just as actin would in any other amoeboid cell. Another 2014 study shows how it then senses the egg.

Does the inability of nematode male gametes to swim to the egg cost them in terms of reproductive advantage and evolution? Heck no.

Nematodes, ie. roundworms, are the most successful animals on Earth. They live inside every other living thing, and just about everywhere on Earth. There are free living worms, parasitic worms, and worms that eat decaying tissue. There are roundworms that eat nothing but other roundworms.

Nematodes are famous for the parasitic infections they

cause. On the left is a root knot worm. Nematodes are

responsible for more than 15% of crop loss each year.

On the top is one of the filarial worms that cause river

blindness. On the bottom is a grasshopper worm (Mermis

nigrescens) that grows to fill the entire body cavity.

In strictly numerical terms, it’s amazing that we aren’t nematodes. In truth, four out of every five animals are Earth are roundworms! Long ago in classification, all the roundworms used to be lumped together; later on they were grouped according to head size. With the advent of molecular typing, there are more than 25,000 species, and estimates are for more than a million. Compare that to 5000 known mammal species.

Sure there are many species, but that number is dwarfed by the number of individuals of some species. One 2013 study from England gives us a clue. In just the city of Bristol, dogs drop about four tons of doo-doo each day. That four tons holds an astounding 3.7 billion Toxicara eggs. Every two days the dogs of that one city squat out the equivalent of the human population of the entire world. Man, is that a bizarre visual.

This isn’t useless information, considering that the eggs become worms that can cause blindness in people who accidentally eat contaminated dirt, or those who eat dirt on purpose for that matter. Indeed, many nematodes are parasites of humans and cause much disease, but this isn't our focus today. If you like that sort of weird disease stuff (and I most certainly do), I suggest you Google ascariasis, hookworm, onchocerciasis, strongyloidiasis, filariasis, or trichinosis.

Nathan Cobb of the U.S. Bureau of Plant Industry gave a very apt description of the numbers and distribution of nematodes in 1915. He said that if you eliminated every bit of matter on Earth other than nematodes, an onlooker could still recognize our world.

There are enough nematodes in the dirt that we could distinguish mountains and valleys. There are more in the cities, so we would know where they had been. Nematodes are numerous enough in living things that we could identify where every living thing had once stood. And yes, the onlooker could see humans, we ingest billions over our lifetime and more than two billion people are infected with Ascaris lumbricoides at any one moment.

At least 2 billion people are infected with this worm

(Ascaris lumbricoides) at any one time. The pictures of

the infection are just too gruesome, so I show his smile

instead. Look can up the pictures for yourself if you

haven’t eaten recently.

A. lumbricoides is the largest nematode by mass which infects humans. Females can be 40 cm long and the diameter of a No. 2 pencil. The worm takes quite the tour through you. From your stomach to your liver to your lung move the young larva. You cough them up and swallow them, and they mature in the gut. There they grow, fall in love, and mate. Yep—pretty gross.

The smallest nematodes are in marine sediment. Desmoscolex sp. and Greeffiella sp. are only 80 µm long, which means that if 30 of them stood on each other’s shoulders, they would only be as tall as a dime is thick.

At the other end of the spectrum, the largest known nematode is Placentonema gigantissima, which can reach around 30 feet long in the placenta of its host, the sperm whale.

The placenta of a whale, tree root balls, in water, mud, fruit, nematodes literally live everywhere except in the skies – even though they do find themselves in the sky every day - inside birds. Roundworms have been found in the crevices of South African gold mines two miles below the Earth’s surface – at 48˚ C (118.5˚ F) and 1000x atmospheric pressure. No other animal has been found living in stone at these depths and conditions.

Many roundworms live in the soil, and perhaps the greatest number live in the sediment of ocean floors. Because there are some many different kinds of nematodes, it isn’t surprising that many have very developed specific niches.

Biologist Colin Tudge stated in his book, The Variety of Life that half the animal species on Earth have a nematode that lives only in that species. Even beyond animal hosts, there is evidence of a nematode species that lives one place on Earth – in the felt of German beer coasters.

The German beer mat worm doesn’t just live on the

bottoms of beer soaked coasters. But they do like yeast

for dinner. I like this one for Apostelbrau in Germany

because the brewery has been located in Worms, a city

between Frankfort and Stuttgart, since 1713.

The German beer mat nematode, Panagrellus redivivus, was first named Chaos redivivum by none other than Linnaeus himself. Its story is told in a nice 2009 commentary. While nematologist Cobb was aware of this worm only from felt beer mats, in truth they live in rotting peaches, in book binding paste and in other places as well.

Nematodes can be political was well. The giant kidney worm, Dioctophyma renale, is found in many different mammal species, such as dogs, cats, minks, humans, etc. But the infection is almost always just in the right kidney. Since this worm is usually ingested via contaminated fish, the right kidney might be more susceptible simply because it's closer to the liver and stomach – or maybe they’re Democrats.

All this talk about undulipodia and nematodes has been perhaps a little misleading. Nematodes do have cilia on a very small subset of the their neurons, but they aren’t motile cilia. These are sensory cilia, also called primary cilia. They are our topic for next week.

Smith HE (2014). Nematode sperm motility. WormBook : the online review of C. elegans biology, 1-15 PMID: 24715710

H. Ferris (2009). The beer mat nematode, Panagrellus The beer mat nematode, Panagrellus redivivus: A study of the connectedness of scientific discovery J. Nematode Morphol. Syst., 12 (1), 19-25

McKnight, K., Hoang, H., Prasain, J., Brown, N., Vibbert, J., Hollister, K., Moore, R., Ragains, J., Reese, J., & Miller, M. (2014). Neurosensory Perception of Environmental Cues Modulates Sperm Motility Critical for Fertilization Science, 344 (6185), 754-757 DOI: 10.1126/science.1250598

Morgan, E., Azam, D., & Pegler, K. (2013). Quantifying sources of environmental contamination with Toxocara spp. eggs Veterinary Parasitology, 193 (4), 390-397 DOI: 10.1016/j.vetpar.2012.12.034

Sepsenwol S, Ris H, & Roberts TM (1989). A unique cytoskeleton associated with crawling in the amoeboid sperm of the nematode, Ascaris suum. The Journal of cell biology, 108 (1), 55-66 PMID: 2910878

For more information or classroom activities, see:

Nematodes –

https://www.youtube.com/watch?v=fmOJ0bh8le4

http://oak.ppws.vt.edu/~sforza/nematode.html

http://sznitmanlab.bm.technion.ac.il/gallery/elegans

http://cal.vet.upenn.edu/projects/merial/Nematodes/nems_5.htm

http://www.accessexcellence.org/AE/ATG/data/released/0653-SamanthaOrchard/

http://www.apsnet.org/edcenter/k-12/teachersguide/nematode/Pages/default.aspx

http://www.sciencebuddies.org/science-fair-projects/project_ideas/Zoo_p045.shtml

http://ag.arizona.edu/ento/courses/ento524/

https://www.questia.com/library/journal/1G1-180555901/malthus-under-a-microscope-using-the-soil-nematode

http://www.apsnet.org/edcenter/intropp/lessons/Nematodes/Pages/RootknotNematode.aspx

http://www.apsnet.org/edcenter/intropp/lessons/nematodes/pages/soycystnema.aspx

http://sciencenetlinks.com/science-news/science-updates/nematodes/

http://www.muhlenberg.edu/main/academics/biology/nsf/ret/ret_nematode_lesson.html

http://urbanext.illinois.edu/soil/SoilBiology/nematodes.htm

https://www.youtube.com/watch?v=6okurk9O1ow

http://www.ucmp.berkeley.edu/phyla/ecdysozoa/nematoda.html

http://www.nematodes.com/

http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=14&ved=0CDYQFjADOAo&url=http%3A%2F%2Fwww.austincc.edu%2Fmlt%2Fclin3%2FParasitNematodesSummer2012.ppt&ei=k2nBVLi1K8aAygSwo4G4Cw&usg=AFQjCNHttLL3VjOpHSiZpAWr7UMxnf67ww&sig2=Oo4yxTDFNit6YDKQALmDRg

http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&ved=0CB4QFjAA&url=http%3A%2F%2Ffaculty.plattsburgh.edu%2Fneil.buckley%2FInvertebrate%2520Zoology%2FNematodes.ppt&ei=q2nBVNGdN4-3yAS2ioDYAw&usg=AFQjCNH659z_DIHYqzgPcrnbLJMbqsJp5Q&sig2=uhsI36kewUFAcy9FO_AgQA

http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=11&ved=0CFAQFjAK&url=http%3A%2F%2Fwww.pleasanton.k12.ca.us%2Favhsweb%2Fturner%2Fwebdoc%2FZoology%2FNotes%2Fch18Nematoda09_files%2Fch18Nematoda09.ppt&ei=q2nBVNGdN4-3yAS2ioDYAw&usg=AFQjCNHTuBnXJvsOSoz9PviF6DsKQfoqhw&sig2=BKoXUJfZLAKj6MnLRg8Nqg

Characteristics of animals –

http://animals.about.com/od/animal-facts/a/animal-characteristics.htm

http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=4&ved=0CC4QFjAD&url=http%3A%2F%2Fwww.paec.org%2Fbiologypartnership%2Fassets%2FCharacteristics%2520of%2520animals%2FLesson%2520Plan%25205%2520-%2520Animals%2520-%2520REVISED.docx&ei=PmrBVI6-FcOvyAS4woAI&usg=AFQjCNEZbv5-X2pu694tl6t1tG7eqfUNrQ&sig2=ffeM4AQDqKQA_PVOeip3Uw

http://www.yale.edu/ynhti/curriculum/units/1996/5/96.05.04.x.html

http://www.prometheanplanet.com/en-us/products/PublisherCreatedResources/Item/90402/core-life-science-i-lesson-2-2-physical-characteristics-of-animals#.VMFqe4Vf13I

http://schoolworkhelper.net/kingdom-animalia-general-characteristics-of-animals/

https://www.youtube.com/watch?v=UmpTARZKyvc

Cytoskeleton –

http://biology.kenyon.edu/HHMI/Biol113/cytoskeleton.htm

http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/C/Cytoskeleton.html

http://www.nature.com/scitable/topicpage/microtubules-and-filaments-14052932

http://www.biology.arizona.edu/cell_bio/tutorials/cytoskeleton/page1.html

http://oregonstate.edu/instruction/bi314/summer09/cytoskel.html

http://www.dls.ym.edu.tw/ol_biology2/ultranet/Cytoskeleton.html

http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=14&ved=0CDAQFjADOAo&url=http%3A%2F%2Fweb.pdx.edu%2F~kstedman%2FCell%2520Biology%2FCarternotes%2520II.pdf&ei=rmvBVOqTD9OsyASb14G4BQ&usg=AFQjCNGYF5_OuXF-OZoG_JORPbUHWxIAFA&sig2=816hfCq-DzGATydB1rvc4g

http://www.wiley.com/college/pratt/0471393878/student/animations/actin_myosin/actin_myosin.swf

http://education-portal.com/academy/lesson/the-cytoskeleton-microtubules-and-microfilaments.html

https://www.youtube.com/watch?v=5rqbmLiSkpk

http://www.sparknotes.com/biology/cellstructure/intracellularcomponents/section1.rhtml

http://www.cureffi.org/2013/03/02/cell-biology-05-the-cytoskeleton-part-i-actin/

A Tale Of Two Tails

Biology concepts – flagella, bacteria, prokaryotes, eukaryotes, undulipodia, axoneme, basal body, centriole

Everyone has the dream where you show up for a class

that you didn’t know was on your schedule, only to be

having a test. But in second place is the dream where you

are back in elementary school, or maybe the principal’s

office. Above is a picture of every teacher I had in

elementary school.

You find yourself transported back to sixth grade grammar class. You barely fit in the desk and your clothes are out of style.... again. You don’t know how you got there, but the immediate problem is that Mrs. Belcher has just called your name to answer the next question. What are homonyms?! You stare back at her with terror in your eyes.

But your study of word roots may help you survive. Homo- means same, while -nym means word. OK, it’s coming back to you. Homonyms can be words that are spelled but have different meanings and origins (called homographs) or words that are pronounced the same but have different spellings and meanings (called homophones).  Yes! The class cheers, and Mrs. Belcher is more than mildly surprised. Crisis averted.

I have no idea how you got transported back to grammar school, but your question and answer is very timely to our discussion today. Homographs, like minute (min-it, a short time) and minute (my-noot, a small amount), look the same, but have different meanings. Homophones, like to, too, and two sound the same but mean different things and have different origins.  This is very much like the differences in prokaryotic flagella and eukaryotic undulipodia. Too much of a stretch for you... maybe.

We have seen that bacterial flagella are long, whip-like structures protruding from the cell that can aid in motility. So are eukaryotic undulipodia. They look very similar, yet we are going to see they have very different structures, mechanisms of function, and origins – just like homophone and homonyms.  So maybe the analogy wasn’t so far off.

Both flagella and undulipodia extend from the cell surface with a long tail. But in the prokaryote, this was made of small subunits of flagellin proteins. In the undulipodia, the structure is called the axoneme, and is made of long microtubules of tubulin protein. Already we have significant differences between two things that look very similar.

A cross section of an undulipodium axoneme looks like

this – although I’m not sure they’re color coded in the

cell. Notice how the inner are connects the nested tubule

of one doublet to the outside tubule of the next doublet.

The inner arms are responsible for the degree of bend,

the outer arms are involved in the rate of movement. There

are other proteins involved, but we aren’t getting that

detailed. Maybe you want to do that on your own.

The axoneme (axo = axis, and neme = thread) of the undulipodia has a very distinct structure which is best appreciated when you look at it in cross section. The long microtubles appear as small circles in the cross cut, but they are arranged very precisely (see picture). They come in doublets, and there are nine sets of them surrounding a central doublet (called 9 + 2 or 9(2) + 2). This is very different from the single hollow tube of the prokaryotic flagellum.

The way the axoneme is built is also the key to how it works. The different microtubule doublets are cross-linked by protein complexes called dynein arms. There are inner arms and outer arms. An inner arm connects one microtubule from one doublet to another microtubule of the adjacent doublet. When one doublet slides further out from the cell body and the connected adjacent doublet doesn’t, this creates stress and the whole thing must bend to maintain the connections.

So, walking proteins are how the undulipodia create their whip-like action. There is a walking system analogous to dynein arm movement that has developed in many animals. We have looked at muscle contraction before. Just like myosin heads walking along actin filaments that are anchored to the muscle cell membrane, the dynein arms on some doublets start to crawl up or down the adjacent microtubule of an undulipodia creating a bend and then they can reverse to whip back the other direction. This is very different from the spinning motor of the bacterial flagellum.

Pay attention to these cartoons, they show how the undulipodia

bend. ATP powers the sliding of the dynein arms. As they move

down one tubule, that filament moves up. If the filaments are

anchored in the membrane, as they are in undulipodia, the

movement creates tension and a bend. The cartoon on the

right is a good summary.

The motions the two different mechanisms produce is different too (a homophone). While the prokaryotic flagellum spins like a propeller, the sliding of the microtubules makes the undulipodium wave back and forth, like a field of wheat on a breezy day, or how a snake might thrash if you held his head down (don’t just hold his tail down, he’ll bite you).

The undulipodium motion often occurs in just one plane, back and forth instead of all around, but that doesn’t mean it has too limit itself to that. It can spin too; it just takes a very coordinated sliding back and forth of microtubules.

Another difference between prokaryotic flagella and eukaryotic undulipodia is in how they are powered. We saw that flagella in bacteria get their force from the spinning motor, and the motor gets its energy from an ion gradient across the membrane. But in eukaryotes, it was seen early on that if you strip the membrane off of an undulipodium, and added ATP, they start to move.

Yes, all undulipodia are held within the membrane. Some bacterial flagella are membrane covered, but all eukaryotic versions are sheathed in plasma membrane. But back to the ATP. Exposing the naked undulipodium to ATP, even on a dead cell, can initiate the dynein walking and microtubule sliding, so it is definitely ATP powered.

Also, this points out that the power for the bacteria movement comes from the motor in the base, but the eukaryotic movement is in the axoneme, not the base. The basal body that anchors the eukaryotic undulipodium into the cell membrane is amazing in its own way. The basal body is actually a centriole, the same structure that helps to move the chromosomes apart in the spindle apparatus during mitosis. We’ll come back to this double duty organelle in a a few weeks.

Chlamydomonas algae species have a double flagella

for swimming. A single stroke as shown above. The

power strokes on top is followed by the recovery stroke

below. Put all the numbers together and looks like

someone swimming underwater. The picture of the

organism is there because it’s always better to see the

real thing as compared to a cartoon.

Our two systems still look similar, but we see how they are not so similar in structure and action. Since eukaryotic cells are so much bigger than prokaryotes, the first flagella to be examined and found to have the 9(2) + 2 structure were in sperm tails.

But soon after that, the protozoans were discovered to have undulipodia as well. Organisms from the algae genus Chlamydomonas have two long undulipodia that they use for motility. Located at the front of the cell, their movement pulls the alga through the water. But protozoans are just as likely to have undulipodia that push them through water. They can work both ways.

Amazingly, when a Chlamydomonas finds itself out of water, the undulipodia resorb in short order. Nature hates to waste energy, so why maintain a boat motor if you’re not in the water. But place them back in a liquid environment and the two structures will reassemble with in an hour – with the same structure 9(2) + 2 and working the same exact way.

Of course, saying they all have the same 9(2) + 2 structure is an invitation to find exceptions, and science has found them. A 2006 study found that rabbits are quite the rule breakers. Sure, they have 9(2) + 2 axonemes, but they don’t stop there. Some rabbit embryo undulipodia show a 9(2) + 0 structure, where the central doublet is completely missing, yet the structure functions just as other motile undulipodia.

What’s more, rabbits can also have 9(2) + 4 axonemes, with double the number of central microtubules. Again, they function just fine. Is there a reason for these variations – maybe, but maybe they are just mutations that didn’t have a negative impact, so they were retained.

You know how annoying it is when you touch a cactus

and those little bristles get stuck in your skin? Well,

don’t touch a bristleworm. They’re lined with those painful

bristles – hence the name. Somebody studied these worms,

and found out they have parasitic protozoans in their gut.

Then someone studied those parasites and found that they

have sperm. And someone studied the sperm and found

that they have unique axoneme structures. I love science.

A couple of parasitic protozoans that live in bristle worm guts show differences in their axonemes. Lecudina tuzetae sperm tails have a 6(2) + 0 structure, while the Diplauxis hatti protozoan sperm has a 3(2) + 0 axoneme. Described in a 1980 paper, this is the simplest motile undulipodium known – as of now.

The undulipodium basal body (born as a centriole) can have exceptions as well. The vast majority have a structure of 9(3) + 0, where instead of doublets, they have triplets. This makes sense since they need to be strong to support the axoneme.

But diatoms, very small algae cells protected by a silica shell, can have sperm that look very different, according to a 2013 study. Their basal bodies have been observed to have doublet microtubules, and are very similar to the axoneme. Even weirder, a couple of insects feel the need to go big with their basal bodies. Acerentomonon microrhinus, a primitive hexapod insect has sperm tail basal bodies with 14 microtubule doublets, while Sciara coprophila, a fungus gnat (see picture), has up to 90 singlet microtubules in its sperm basal body.

We have talked a lot about sperm tails and protozoan motility structures, and these undulipodia look the most like bacterial flagella. But undulipodia come in a couple of flavors; those longer than 40 m or so are called flagella while the shorter ones are called cilia. See the naming problem and why Lynn Margulis came up with undulipodia?

This is a fungus gnat – it sounds like they eat fungus,

but nope. Only the larval form feeds; the adults never

eat. That’s OK, they don’t live very long at all. They

overwinter in their adult form because they are unique

in that they can both tolerate freezing weather and freeze

themselves without damage. It must be important, since

their sperm tails are loaded with 90 microtubules in the

basal body – everyone knows that massive numbers of

microtubules is the best way to avoid cold damage.

Both eukaryotic flagella and cilia have the microtubule and dynein arm structure, with centrioles for their basal bodies. There are exceptions to the cilia that we will look at in a few weeks, but the biggest difference between them, besides their length, is that cilia occur in groups, while flagella are usually found in ones or twos. You could say that cilia and flagella are like synonyms, they have almost the same meaning (and structure), although they are two different things.

Next week – Halloween is coming, so what better time to have a discussion of genetically modified foods and an 19th century teenage girl who wrote the best science fiction book ever.

Prensier, G., Vivier, E., Goldstein, S., & Schrevel, J. (1980). Motile flagellum with a "3 + 0" ultrastructure Science, 207 (4438), 1493-1494 DOI: 10.1126/science.7189065

Idei, M., Osada, K., Sato, S., Nakayama, T., Nagumo, T., & Mann, D. (2012). Sperm ultrastructure in the diatoms Melosira and Thalassiosira and the significance of the 9 + 0 configuration Protoplasma, 250 (4), 833-850 DOI: 10.1007/s00709-012-0465-8

Feistel K, & Blum M (2006). Three types of cilia including a novel 9+4 axoneme on the notochordal plate of the rabbit embryo. Developmental dynamics : an official publication of the American Association of Anatomists, 235 (12), 3348-58 PMID: 17061268

For more information or classroom activities, see:

Undulipodia –

http://alevelnotes.com/Organelles-Working-Together/115?tree=

http://prezi.com/ymmso_3aisul/cell-movement-structures-cilia-flagella-and-undulipodia/

http://books.google.com/books?id=9IWaqAOGyt4C&pg=PA15&lpg=PA15&dq=undulipodia&source=bl&ots=1EtV0cSi1D&sig=bOUiVnepg2oxW46_nIczDs5DBSQ&hl=en&sa=X&ei=tEcaVPnOD4KMyATRuoHIBw&ved=0CD4Q6AEwBTgK#v=onepage&q=undulipodia&f=false

http://www.ciliopathyalliance.org/cilia/structure-and-function-of-cilia.html

http://www.ncbi.nlm.nih.gov/books/NBK21698/

http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/C/Cilia.html

http://www.nature.com/scitable/topicpage/the-primary-cilium-an-orphan-organelle-finds-14228249

http://www.microbiologybytes.com/video/cilia.html

http://phys.org/news/2014-07-artificial-cilia-scientists-nano-structured.html

https://news.brown.edu/articles/2014/01/cilia

http://biology.about.com/od/cellanatomy/a/aa050208a.htm