As Many Exceptions As Rules

Wednesday, February 4, 2015

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.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

Wednesday, January 28, 2015

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/

Wednesday, January 21, 2015

Evolving A Second Job

Biology concepts – protein moonlighting, undulipodia, evolution, basal body, centriole, GAPDH, intraflagellar transport

Today’s post is on a multitasking cell structure. This

would make Alton Brown proud, since he hates tools

that do only one thing. The University of Miami of

Florida football team runs through fire extinguisher

blasts when they enter the stadium – maybe Alton

can find a second use for his.

Alton Brown from Food Network hates a unitasker. He wants all his kitchen tools to have more than one function – I least I think it’s just his kitchen tools. But he might just as well be talking about biology. Nature hates a unitasker, that’s why some many things in our cells have multiple jobs.

This phenomenon is called protein moonlighting. The re-evaluation of the human genome (about 19,000 genes) suggests that many proteins have more than one distinct function. This would allow for a relatively small number of genes to provide a large functional proteome (the total number of protein functions). As such, a 2014 study is showing the importance of moonlighting proteins in health and biology.

There are rules for a protein to have a legitimate second job. It’s only moonlighting if the two functions are unrelated, the functions can't be carried out by two different domains of the protein either. This would suggest a gene fusion event. The two functions must be independent, so ablating one doesn’t affect the other.

There are hundreds of examples of moonlighting proteins in the literature now, and more are sure to follow. There are examples aplenty within the glycolysis pathway; you know, the breakdown of sugar for energy. No fewer than seven of the ten glycolytic enzymes are known to have other jobs.

Crystallin proteins (alpha and beta) make up the

majority of the lens and cornea of the eye. They are

transparent, but they do more than that. Recent

studies show that they have enzymatic activity in other

tissues. Aldehyde dehydrogenase and transketolase are

enzymes that turn out to be moonlight crystallins.

The king of the moonlighting proteins is glyceraldehyde -3-phosphate dehydrogenase (GAPDH). Sure, it's one of the enzymes that breaks glucose down to pyruvate, but it does so much more – like helping to maintain the ends of our chromosomes (telomeres), working to move tRNAs out of the nucleus, controlling the expression of some genes, especially those involved with gamma-interferon, repairing our DNA when it is damaged. And apparently GAPDH is crucial for helping cells to bring in particles from outside (endocytosis). That’s a full day.

But as amazing as GAPDH is, today’s example of a multitasker is even more rare, in that the moonlighter is a complete structure, made of many proteins, and has two distinctly different jobs. What’s more, each function has its own exceptions. What's our structure of interest? The basal body, or perhaps I should call it the centriole.

Let’s talk about the basal body first. This is the base of the eukaryotic undulipodia (cilia and flagella). These moving tails come in two parts; the basal body and the axoneme. We talked at length about the axoneme a few months ago, with its nine doublet microtubules surrounding two singlet microtubules (9[2]+2, see picture below). Undulipodia movement, as opposed to the motor driven prokaryotic flagella, is achieved by sliding the different doublets forward and back past one another.

But in those previous posts we didn’t talk much about the basal body. It too is a ring of microtubules, although these are shorter polymers that in the axoneme. Instead of doublets, there are almost always nine sets of triplet microtubules, and there are no center microtubules (9[3]+0). Of course, there were a couple of exceptions, and we talked about them.

The basal body has a 9(3) + 0 structure, while the

axoneme is 9(2) + 0. While this cartoon shows the

complexity of the axoneme, our post today highlights

the complexity of the basal body. One thing this cartoon

does show, the axoneme is sheathed in the plasma

membrane, it isn’t a protein structure sticking out through

the membrane.

The basal body is about 100 nm wide and 150 nm long, and serves as the base of the flagellum or cilium. If a cell has hundreds of cilia, like the male gametes of the cycads we talked about last week, then it has hundreds of basal bodies as well – one per cilium.

The basal body serves as the nucleation site for mictrotubule growth into the axoneme. It’s like a skyscraper, the microtubule girders are built vertically on the basal body foundation; only here, the basal body sparks a self-assembly of the microtubules. You don’t need fearless guys climbing the beams to build an axoneme.

If we turn our attention to the centriole, we find that it’s used in mitosis. When a cell divides, each progeny cell receives one centrosome. Don’t confuse the centrosome with a centriole or a centromere (a near center point of a chromosome, it holds the two chromatids together). The centrosome is more of an area, it contains two centrioles, a mother and a daughter, and the pericentriolar matrix (PCM) amorphous group of proteins that help the centrioles do their job.

Each centriole is a complex microtubule formation in a 9(3)+0 arrangement, about 120 nm wide and 175 nm long. This is exactly the structure of the basal body – they’re the same thing! Well, almost.... a centriole has to mature into a basal body.

During S phase of the cell cycle (when the chromosome are replicated) the centrosome will duplicate. Each centriole grows another one from its side, at a right angle. The mother is a mother again, and the daughter becomes a mother for the first time. The two mother/daughter pairs then gather their own PCMs and move to the sides of the nucleus. When mitosis time comes, microtubules grow toward the chromsosomes, but from the mother centriole only. This is the spindle and will help pull the chromatids apart during cell division.

Start at the top left. During the cycle, a pair of centrioles

will separate and each will grow another from the proximal

end. The daughter centrioles then have to mature, with

proteins added toward the distal end. During mitosis, they

two pairs separate and form the spindle body, which pulls

the chromatids apart.

If you remove the centrioles after S phase, most cells can still go through mitosis just fine. In fact, there many cell types that don’t have centrioles at all (higher plants, some protists, most fungi). Even in cells that are supposed to have centrosomes, destroying centrioles with a laser after S phase doesn’t always affect mitosis negatively.

A commentary published in 2010 talks about how many cell types, including some oocytes can undergo meiosis without centrioles, while centriole numbers than are re-established after fertilization. However, in other tissues, loss of centrioles leads to genetic instability over time, even if the spindle will develop without the centrosome. To this point, we still haven’t resolved the issue of whether centrioles are necessary for proper cell division.

In the vast majority of cases, centrioles come from centrioles. One serves as a template to form the second. The process through which this occurs has just begun to be revealed in the past few years. There is a linking fiber from the proximal end of the mother centriole that acts as a seed point to start aggregation of the daughter centriole at a 90˚ angle to the first.

The process is very complicated, but is carried out spontaneously, without specific gene products to guide it. It was first believed that if centrioles were lost, then they could not be regained. Of course, they also thought that centrioles had their own DNA. Now we know that in cases where centrioles are lost, they can form de novo, and function just fine in mitosis or as basal bodies. In several studies, removal of centrioles or cells without centrioles to begin with allows for new centrioles being formed from aggregated microtubules.

Intraflagellar transport is the method by which the

axoneme grows, adding tubulin monomers to the end.

The proteins are carried up the axoneme by walking

proteins. These are important not for just cilia assembly,

but also for cell signaling and sensing that occurs in

the undulipodia.

After centriole duplication by prescribed pathways, the basal body matures. A 2011 review shows that there are many proteins involved in the process. First the distal end of the centriole is capped, then it migrates to the cell membrane and docks. A transition zone is produced that allows for selective movement of molecules up and down the inside of the axoneme (intraflagellar transport, IFT).

Finally, there is attachment of accessory bodies like rootlets to anchor it to the membrane, transition fibers to move to the axoneme and distal appendages. Only after all this maturation of the basal body can the axoneme be built by IFT. This is how the process happens in all species EXCEPT fruit fly male gametes and the microbe Plasmodium yoelii, where the axoneme grows BEFORE plasma membrane docking of the basal body.

What’s more, you can always reverse it and go from basal body back to centriole, so their functions must somewhat overlap. The basal body and centriole both serve as microtubule organizing centers (MTOCs). So what makes it a moonlighting structure?

Prokaryotic flagella just whip around in a circle, but

eukaryotic undulipodia have more of a beating motion.

The side view shows how the flow is one direction, while

the top view indicates that the motion is circular, but not

like a propeller.

The basal body does a different job by controling the direction of movement of the cilium or flagellum! The prokaryotic flagellar motor spins the prokaryotic flagella as we have described, but eukaryotic cilia or flagella beat, rather than flop around, and the direction in which they beat is important. Cilia on a cell beat in concert in one direction, and the basal body is asymmetrical enough to drive this directional beating. Believe it or not, this is controlled by a protein called disheveled.

That’s a little weird, but what’s really weird is the kids. In a 1991 paper, part of the oviduct of a quail was reversed, so that the cilia beat toward the ovary instead of toward the uterus. When cells divided through embryo and chick development, the cilia of the progeny cells had the same orientation as those in the parent! They continued to beat in the wrong direction. Since basal bodies are duplicated from basal bodies, the mother basal bodies gave rise to daughters that beat the same direction.

The evidence presented shows that we have an ancient, yet complex, structure that has a couple of important jobs. The question for evolutionary biologists is which came first, the basal body or the centriole? The last common eukaryotic ancestor (LECA), the cell from which all eukaryotic cells descend, had undulipodia, so the basal body is an extremely old structure. But all eukaryotic cells undergo mitosis or meiosis, so the centriole must be important too.

Notice the cilia that are the upper most in the animation.

They show best the coordinated beating that pushes fluid

in one direction.

Cells without either centrioles and basal bodies suggest that basal body function came first; since you can’t have undulipodia without basal bodies, but our discussion above shows you can have mitosis without centrioles.

On the other hand, centrioles have to mature to become basal bodies, wouldn’t this suggest that they came first? Or perhaps the basal body was the primary product and nature managed to find a use for one if its precursors. What do you think, is the basal body the chicken or the egg?

Next week let’s look at one of the animal kingdoms great exceptions in terms of cilia, even though primitive and higher animals have them, round worms don’t cilia or flagella!

Henderson, B., & Martin, A. (2014). Protein moonlighting: a new factor in biology and medicine Biochemical Society Transactions, 42 (6), 1671-1678 DOI: 10.1042/BST20140273

Kobayashi, T., & Dynlacht, B. (2011). Regulating the transition from centriole to basal body The Journal of Cell Biology, 193 (3), 435-444 DOI: 10.1083/jcb.201101005

Debec, A., Sullivan, W., & Bettencourt-Dias, M. (2010). Centrioles: active players or passengers during mitosis? Cellular and Molecular Life Sciences, 67 (13), 2173-2194 DOI: 10.1007/s00018-010-0323-9

Boisvieux-Ulrich E, & Sandoz D (1991). Determination of ciliary polarity precedes differentiation in the epithelial cells of quail oviduct. Biology of the cell / under the auspices of the European Cell Biology Organization, 72 (1-2), 3-14 PMID: 1756309

For more information or classroom activities, see:

Protein moonlighting –

http://www.slideshare.net/vimalacbr/protein-moonlighting

http://www.biochemistry.org/TabId/379/MeetingNo/SA162/view/Conference

http://www.ebi.ac.uk/interpro/potm/2007_5/Page2.htm

http://www.moonlightingproteins.org/

http://www.cvent.com/events/the-biological-and-biomedical-consequences-of-protein-moonlighting/event-summary-31ba211f647f4cdda499019b008c64da.aspx

http://www.biosyn.com/tew/protein-moonlighting.aspx

http://www.petercollingridge.co.uk/blog/proteins-look-enzymes-arent

Centriole –

http://www.cellsalive.com/cells/cell_model.htm

http://www.scienceteacherprogram.org/biology/savitzky06.html