Wednesday, July 31, 2013

Tough As Nails

Biology concepts – keratin, crystalline form, cornification, regeneration, stem cells

Horns are made from keratin, just as are nails, hooves, and hair. 
Believe it or not, this is a real picture of a condition called 
a cutaneous horn. It is a tumor of keratin producing cells and 
can be benign or malignant. They can be removed surgically, 
which makes me wonder why it is still on her head.
Thankfully, the cancerous ones are usually wider than they are long, 
so this example is probably benign.
The first time I remember being amazed by biology was when I found out that our fingernails and hair were made of the same thing. My hair is (was) red, but my nails are pretty much transparent and colorless. Hair is thin and is broken easily - you should see my hairbrush. But fingernails and toenails are tough. How can they be made of the same material?

Question of the Day – How do fingernails grow to be so tough and why do they grow at all?

You use your fingernails everyday, but do you take the time to think about how amazing they are? It’s true that nails are made of a protein called keratin, just like the dead layers of your skin and your hair, but there are differences too.

You’d be surprised to find out what else they do. Your fingers and toes are basically tools; they grasp, push, pull, and gather information. Switching back and forth between gross and fine movements and manipulations requires that your fingers and toes be able to take a lot of punishment, but at the same time maintain themselves for delicate work.

Your nails protect the ends of your fingers and toes during work that could injure them, this keeps them in good shape for the precise things we need to do all day long. But nails are tools as well. They can slip under surfaces and pry them up, and they can act as a hard surface against which you can apply pressure.

This idea of pressure is important for fingers especially. You push down with your fingertip to deliver a precise amount of pressure. The nail provides a flat, rigid surface against which you can measure the pressure and fine tune your work. Nerves abound beneath the nail, you know that from trimming it too short or from having a splinter driven beneath it. Ouch.

But nails have other jobs as well. Did you know that your nails can be good indicators of your overall health? Healthy nails are smooth and have no ridges, although as you get older you may notice more vertical lines. Yellow nails may indicate a malignancy or fluid in your lung spaces (called pleural effusions). Pitted nails might indicate a connective tissue disease (like psoriasis or scleroderma).

Hippocrates was a Greek physician. His importance to the
profession of medicine is evident – new physicians take the
Hippocratic Oath, promising first to do no harm. In other
words, don’t make things worse. One of his great
contributions was to make the connection between an
outward sign (clubbing) and an internal disease. In this case,
it is usually something wrong in the chest (heart, lungs,
upper GI).
Clubbing of nails as a sign of lung or heart disease was recognized by Hippocrates 2300 years ago. However, clubbing is just an anatomic variation 60% of the time and reflects no underlying disease. What you need to look out for is a change from non-clubbed to clubbed fingers and toes. For a good review, read a 2012 review by Tully et al., you’ll be surprised at what you can learn from your nails.

Even more surprising is the job your nails could do for you if you happen to get the tip of your finger or toe chopped off. Unlike starfish and lizards, we don’t generally have the ability to regenerate lost anatomical units or tissues. One exception is the ends of our digits. If you get a portion of your finger cut off, it might grow back, nail and all. But it must be just the tip, some of the nail must be left. If not, all you can do is learn a new way to type.

A 2013 study has shown that nail beds contain stem cells that can grow back the skin, muscle, and even bone of the digit. A specific signaling pathway (Wnt) is key, and when blocked, there is no regeneration. But if you stimulate the Wnt pathway, you can get regeneration beyond the nail bed. This may be huge for future regeneration of lost limbs in humans.

So these are the things your nails do for you, but we haven’t tackled the question of how they can be tough enough to carry out these tasks.

The white semicircle at the base of your nails is the lunula (luna, as in moon). This is where your nails grow from and the mass of cells that produce the nail is called the matrix. Above the matrix, but below the nail is the cuticle. This connects the nail to the finger and hurts like heck if your cut into it while trimming.

The nail and the hair are made from keratin filaments joined
together. However, in nails they are wide masses of shorter
fibrils and in hairs they are fewer but longer. You can see that
both hair and nails have a matrix that produces the keratinizing
cells, a cuticle, and the new cells push the older cells along to
make the nail or hair longer.
The cuticle and matrix are white because the melanocytes there are inactive, so there is no pigment produced. The matrix cells divide and the new cells produce a lot of keratin protein. The older cells fill with keratin and die, and the new cells push them out of the way – this means toward the end of your finger. This is how your nails grow.

But our fingernail doesn’t look like individual cells. You are sloughing millions of skin cells each day, but for a nail the dead cells all mass together. Nails only wear away or must be trimmed. Individual cells are not lost. The solidity of the nail comes from the connecting of the dead cells together by junctions between the cells called desmosomes, and by the interlocking of the cells like jigsaw puzzle pieces. But there’s more.

Individual keratin protein filaments also become connected so that the entire mass of keratin becomes one solid structure. This is called cornification, like the stratum corneum (the outer, dead layers) of your skin.

One of the two main forms of keratin in your nails is crystalline keratin, which is rigid, stronger, and has an ordered structure - like a tinker toy cube. Transmitted light is less likely to strike an atom and bounce back when the atoms are all lined up, so this is why many crystalline lattices appear translucent. Precious gems have crystalline forms.

The other keratin is more gel-like and connects the different filaments of crystalline keratin together.  There are crosslinks that join glutamine and lysine amino acids in one keratin filament to those in many other filaments; the crosslinking is performed by an enzyme called transglutaminase. There are billions more of these crosslinks in nails as compared to those in dead skin or in hair.  This is why nails are much stronger than skin or hair.
Transglutaminase has become a favorite of chefs. They
can put different cuts of meat together to forma solid
mass. Also called “meat glue,” transglutaminase can be
used to fuse ground or cut meat into something sold as
a single piece. Health officials worry about this because
it takes outside surfaces that may have been
contaminated an puts them on the inside, which can
promote bacterial growth.

So if this is how nails grow, and it is the same for all your nails, why do they grow at different rates? The average rate of growth is about 3.5 mm (0.14 inch) each month (influenced by genetics, age, and health), while toenails grow about half has fast (1.5 mm or 0.06 inch/month). Toenails are thicker and more rigid, does it take longer to make their cornified structure?

Not really. The answer has more to do with the way the body responds to your behaviors and the environment. Live cells in the matrix produce the keratin before the cells die and are joined together as the nail. Being alive means that they need nutrients and oxygen – things carried in the blood.

Anything that increases the blood flow to an area will allow for faster cell grow and division. This includes heat; your superficial vessels dilate to release excess heat to the environment when your body is in a warmer environment.  Dilated vessels hold more blood, so this would mean more growth in those areas. This is why your fingernails grow faster in summer than in winter. They do – you mean you don’t keep track of how often you trim your nails?

This is pianist Liu Wei from China. He lost his arms at
the age of ten when he was electrocuted. I wonder if
his toenails now grow faster than mine. It’s amazing
what people can do with their feet. Tisha Unarmed is
a fantastic video blog where she shows you how she
all her daily chores using her feet. You should check
it out.
There are other things that increase blood flow and nail growth rate. Activity is a big determinant. This is why your fingernails grow faster than your toenails. Muscular movements of the fingers are nearly constant during the day. There is little we do that doesn’t involve moving hands and fingers. All that muscular movement requires oxygen, so blood flow is increased – and the nails grow faster.

This idea is reinforced by the fact that fingernails grow faster on your dominant hand. More use, more blood, more growth. For people that have lost the use of the their arms and learn to write, eat, brush their teeth, etc. with their toes – do their toenails grow faster than their fingernails? If they don’t have fingers, you can’t compare the growth rates of their toenails versus their fingernails, but I bet their toenails grow faster than average.

Blood flow is also increased by trauma; part of the swelling when you whack your thumb with a hammer is due to increased blood flow to the area in an effort to start the healing process. This will also make your nails grow faster. Many scientists believe that everyday uses of fingers, tapping, typing, prying, etc., are all types of microtrauma, so the more you use your fingers, the more blood flow you are inducing.

On the left is Morton’s toe, also called Greek foot. Is my big toe
short, or is my second toe long? On the right, I just decided to
show another deformity I have, called Haglund’s deformity. It
is a bony bump on my heels, and makes it hard to buy decent
hiking boots. Neither picture is my foot by the way; nobody
wants to see that mess.
The one determinant I don’t understand - fingernails and toenails on longer digits grow faster. Your index finger’s nail grows faster than your pinky nail. Is it due to usage? Maybe, but then why do longer toenails grow faster- are you using them that much more? My second toe is longer than my big toe, a condition called Morton’s Toe.  When I hike, my second toe pushes off the ground last, so maybe it is bearing more weight and doing more work. I can’t test it though, since my second toenails are always running into the front of my boots and the nails are always splitting and falling off.

By the way, since your nails come from the division of live cells, they only grow while you are alive. The old tale about hair and nails growing after you die is untrue. It may have started because other tissues lose water and retract after death, but proteinaceous (meaning made of protein) structures like hair and nails do not contract. Therefore, they may appear to have grown a little bit after death.

Next week - ever wonder why your grass grows back after you mow, but that tree you cut down probably won't? Believe it or not, it is related to your fingernails!

Takeo, M., Chou, W., Sun, Q., Lee, W., Rabbani, P., Loomis, C., Taketo, M., & Ito, M. (2013). Wnt activation in nail epithelium couples nail growth to digit regeneration Nature DOI: 10.1038/nature12214

Tully AS, Trayes KP, & Studdiford JS (2012). Evaluation of nail abnormalities. American family physician, 85 (8), 779-87 PMID: 22534387

Wednesday, July 24, 2013

Mildew Broke The Mold

Biology Concepts – mold, fungus, powdery mildew, downy mildew, nosocomial infection, decomposer, parasite

Bill Cosby is one of the five funniest men ever. The other four, in
no particular order, are of course, Jonathan Winters, Steve Martin,
Groucho Marx, and Benny Hill. You might sub in Robin Williams
for Benny…. maybe.
I wish I had a nickel for every time my mother told me she was “sick and tired” of picking up after me, or of telling me to clean my room. I might have a lot of nickels, but she’d still have been right. Sick always goes with tired, as if having two descriptors makes it more believable.

Mold and mildew is another example of how one problem or explanation just isn’t enough. How many commercials have you seen for products that will rid your bathroom of mold and mildew? On the other hand, ever see a commercial for something that rids you of just mildew?

Question of the Day: Is mildew different than mold?

Molds are something we can identify with, we see mold on bread, oranges, and other things left around the kitchen for too long; they’re caused by many species of fungus.

Penicillin and many antifungal drugs come from molds, so they can be useful. We get a lot of our antibiotics from fungi because they are attacked by many of the same kinds of bacteria that attack us. The difference is that they have developed specific chemical defenses while we haven’t.

Fungi are closely related to animals, much more closely related to us than they are plants. This takes many people by surprise, especially since the internet is rife with websites that call fungus a form of plant life. Many fungi are decomposers, meaning that they gather their nutrients from dead organic material, but some are parasites of living things.

Mold fungi look very different from the mushroom fruiting bodies we normally picture when someone says fungus. However, they are very similar at the cellular level. Filamentous hyphae (singular form is hypha) are the key; these are the long lines of cells (filaments) that form the structure of the fungus before it forms fruiting bodies. In mold fungi, the fruiting bodies are usually spore-forming structures that are too small to be seen.

The hyphae form chains, some of spectacular length. When the hyphae branch, cross each other, form communications, and become sufficiently dense, they are called a mycelium. This is when you can see them. Even with mushroom fungi, it is the mycelium that lies just under the surface of the dirt that gathers the nutrients and connects the mushrooms together. Sometimes the mycelium is in your bathroom.

Fungal hyphae come as septate (top left) or coenocytic
(top right). Coenocytic are really multinucleate giant cells,
while the septa may or may not divide the cells completely.
The rhizoid is the projection that anchors the hypha to a
food source, and pulls in nutrients. In decomposing fungi,
the rhizoid attaches to something dead; in parasitic fungi,
they burrow into live tissue.
The bathroom is almost always a target for people selling you things to eradicate mold and mildew. Why the bathroom – humidity is key for mold growth. This is why they sell better breads in paper packaging. The paper allows the moisture to escape and keeps the bread mold free for a longer period of time.

Bathrooms are the perfect combination of heat and humidity for promoting mold growth. All that is needed is a surface that the mold fungus can colonize. The rhizoid of the fungus is a short hyphal structure that attaches the fungus to its substrate. It also has the ability to absorb nutrients from the substrate like the rest of the hyphae.

Ceramic tile is designed to have a very smooth, flat surface with few pores. This makes it hard for mold rhizoids to attach and stick to tile. But grout and caulk are more porous and irregularly surfaced, so mold is more likely to gain an attachment and colonize these surfaces. The black mold that you see in showers is most likely going to be in vertical or horizontal lines where the tiles meet.

There is more than one type of black mold; one is common, and the other is toxic. Stachybotrys chartarum is one of the most toxic species. It is often associated with wet drywall conditions. Non-toxic black mold is caused by many different species and is more common on caulk and grout.

While black mold is the most common version seen in the bathroom, pink mold is probably second most common. This is our first exception of the day, since pink mold isn’t mold at all. It’s a bacterium called Serratia marcescens, which produces a red or pink pigment called prodigiosin (more about this below). The slimy film in your bathroom is the bacterial colony that feeds on fatty residues and phosphates, things found in soaps and shampoos.
Toxic black mold (Stacchbyotrys species) can cause
internal bleeding, infertility, and respiratory problems.
No wonder they call it “sick building syndrome.” I
can’t imagine how someone could let it get this bad,
but it needn't be like this for it to be causing
you trouble. It could be under the paint or wallpaper.
Thank goodness, most black mold is not the
toxic variety.

In addition, the S. marcescens bacterium was first associated with nosocomial infections in the 1950’s. Nosocomium is the Latin word for hospital, so nosocomial infections are those that you contract while in the hospital. Before the advent of hygienic and antiseptic practices in the very late 1800’s, hospitals were the last place you wanted to be if you were sick. You entered with a hangnail and left on a slab from the plague you picked up there.

Today there are many marcescens strains that are resistant to anti-bacterial drugs. It is becoming a big enough problem that some cases of necrotizing fasciitis (flesh-eating bacterial infections) are being blamed on resistant S. marcescens strains. While not common, about 25% of people who contract flesh-eating disease will die from it, and many are otherwise healthy, if you overlook the bacterial infection that is destroying large parts of their body.

Although S. marcescens is a rare cause of this horrible disease, there are about 20 cases in the literature, brought about by such diverse things as a human bite, contamination of a portal for leukemia drug injection, and immunosuppression. Makes you think about cleaning your shower better, doesn’t it.

Joseph Lister was a British surgeon who thought it
might be a good idea to keep open wounds and
operating rooms clean. Listerine was named for him,
but not invented by him. Listerine was produced by
Jordan Wheat Lambert in St. Louis, MO. He traveled
to England to get Lister’s approval to use the name.
He thought it would sell better. Lambert’s son was a
financial backer of Charles Lindbergh’s transatlantic
flight; the St. Louis airport is named for him.
It’s not all bad news, prodigiosin pigment is a potential new, antibacterial, pain, antifungal, immunosuppressive and anticancer drug. A 2013 study showed that purified S. marcescens prodigiosin kills several drug-resistant bacteria strains. The researchers determined that prodigiosin is pro-apoptotic (it makes the cell kill itself) and is not affected by the multidrug resistance transporter, so it could be a great cancer drug too. Even bad guys have good days.

So now we know that your bathroom mold is only sometimes mold. What about the mildew part of, “mold and mildew?” When it comes to your bathroom cleaning, mildew is just a throw in, an advertising ploy.

Some mildews are indeed caused by fungi. Fungal mildews usually require organic surfaces to draw nutrients from. Paper will mildew, wood will mildew, so will drywall (wallboard, plasterboard) since it is paper backed. Clothes made of cotton or other natural fibers will mildew, as will leather.  But, unless you have a cotton shower curtain, the most likely place you’ll find mildew in the bathroom is your towels.

If mildews like this are fungi, what makes them different from molds? In most cases, it is the degree of growth. Mildews are just not quite as bulky as molds. If a mildew grows for a long time and achieves greater density and mass, it is often called a mold.

However, in the vast majority of cases, mildews are problems of plants, not bathrooms. Plant mildews come in two primary types, powdery mildew and downy mildew. Neither is likely to be found in your shower unless it is so dirty that you actually have plants growing from your grout.

Mildews require living cells to parasitize; they aren’t decomposers, but obligate parasites. Both powdery and downy mildew are problems of horticulture. While they may not directly kill crops, they can reduce yields and make them more susceptible to other infections. In the great majority of cases, fungi that cause powdery mildew are plant specific, there are thousands of species, each attacking a specific plant.

The physical difference between powdery and downy
mildew is seen above. Powdery is well, more powdery.
It looks fuzzier because it grows higher off the surface.
Downy mildew usually turns the leaf yellow or brown.
There are often plant specific, but in both cases above,
it's a grape leaf that is infected.
There are wheat mildews, grape mildews, melon mildews etc. and each may require a different treatment. The hyphae attach to the leaf or the fruit and suck out the nutrients they need. This can’t be good for the plant.

If powdery mildew is a fungus, but only grows on living organisms, what does this make fungal infections of humans; are they more like molds or mildews? There was an incident in Maine in 2005 after it rained for many days in a row. Doctors started seeing fungal growths in the ears of inhabitants (would they be called Maineiacs?), primarily in their outer ears. This was fungal and was a form of human mildew, and overgrowth of normal fungal flora.

What about athlete’s foot? Is athlete’s foot, toenail fungus, or trench foot really just foot mildew? I suppose it just wouldn’t be polite to tell someone they were mildewing, so we call them fungal infections.

Another exception - downy mildew isn’t even a fungus. The causative organisms are oomycetes, a type of false fungus. Having “mycete” in the name makes it sound like they are fungi, and they used to be categorized with the fungi. New naming systems have altered what is or isn’t a fungus based on shared DNA.

This is a coccolithophore, a member of the chromalveolata, the
supergroup that also includes downy mildew oomycetes. They
live in the oceans and die in the trillions each day. The plates
are made from calcium carbonate, so they fall to the bottom
and become limestone or chalk. They might end up as
drywall that could mildew. It’s a circle of life sort of thing.
Now the fungi have been joined to animals in the supergroup Unikonta (one flagellum). You see now why some many fungal drugs are useful for us, fungi are more closely related to us than they are to plants.

Under some new phylogeny schemes, downy mildew organisms are completely unrelated to fungal powdery mildew organisms, which are only distantly related to the organisms that cause some molds. The Tilex people have no idea what a box of worms they’ve opened.

Next week, let's examine your fingernails and toenails. If they are made from the same thing as hair, why are they so tough?

Elahian, F., Moghimi, B., Dinmohammadi, F., Ghamghami, M., Hamidi, M., & Mirzaei, S. (2013). The Anticancer Agent Prodigiosin Is Not a Multidrug Resistance Protein Substrate DNA and Cell Biology, 32 (3), 90-97 DOI: 10.1089/dna.2012.1902
Rehman, T., Moore, T., & Seoane, L. (2012). Serratia marcescens Necrotizing Fasciitis Presenting as Bilateral Breast Necrosis Journal of Clinical Microbiology, 50 (10), 3406-3408 DOI: 10.1128/JCM.00843-12


Wednesday, July 17, 2013

A Linnaeus For The Biomes

Biology concepts – ecosystem, biome, naming systems, climate, chaparral, taiga, pyrophyte

Clint Eastwood was already a minor film star when he made the spaghetti westerns 
for director Sergio Leone. It is a genre he would return to as a director, with the
Oscar winning, Unforgiven. Notice the sparse landscape behind him. This was 
probably in Spain even though the film had an Italian director 
and crew. Chaparral biome is found throughout the Mediterranean region.
Clint Eastwood made a series of westerns in the mid-1960’s; nothing surprising about that. The Good The Bad, and The Ugly, For A Few Dollars More, A Fistful of Dollars; these were all directed by Sergio Leone, an Italian director.

Filmed on location, the landscapes were barren. There were rocks and dirt, bushes and the rare tree, buttes and canyons, coyotes and lizards – typical American southwest. But the movies were filmed in Italy and Spain! These were the spaghetti westerns.

The stories took place in the American southwest and northwestern Mexico, but they were actually half a world away. How can the countryside around the Mediterranean Sea look like the desert southwest in America? The climate, flora, and fauna of very different places can look very similar because they are the same biome, sooo…..

Question of the Day: What makes biomes the same or different and who decides which biome it is?

First of all, some of the desert southwest isn’t desert. It is a biome called chaparral (chapa = scrub in Spanish). Chaparral is the smallest of all the world’s biomes. A biome is a major ecosystem with a single climate, but perhaps more than one habitat or community. It’s a huge ecosystem, which in turn is made up of several smaller habitats. The major idea is that it is housed within a single climatic region.

In North America, the chaparral is found in California and maybe Arizona, at about 40˚ North latitude. In Spain and Italy, chaparral is found at just about the same latitude. In fact, all around the edge of the Mediterranean is very chaparral-like, including North Africa and much of Israel.

The distance from the equator with the tilt of the Earth means that 40˚ South latitude might have much the same climate, and we see that the Chilean chaparral, as well as similar biomes in South Africa and Australia are close to 40˚S.

Also called a Mediterranean scrub biome, chaparral is hot, dry, and liable to catch fire. Many of it plants depend on fire to disperse or activate their seeds (pyrophytes = fire-loving). Others have below ground growth that sprouts after a fire. We will have to do some posts on pyrophytes soon. However, lots of fire doesn’t mean chaparral is lifeless; it has 20% of the world’s plant species and many are endemic (only found in that climate).

A 2013 study in PNAS shows that fire is essential for regrowth
of habitats. The study found that a chemical is produced by
plants when they catch fire, called karrikins. This signaling
molecule settles in the soil after the fire and binds to the seeds
that are there. The binding protein was discovered to be KA12,
which then alters its shape and promotes germination of the
seeds right after the fire is over. Amazing.
One exception to the endemic nature of chaparral flora is the tumbleweed. Tumbleweed is known as any small round shrub that, when sufficiently tall, will be caught by the wind, torn off its roots and blown across the forbidding landscape. You can hardly watch a western without encountering at least one rolling tumbleweed.

But it’s all a lie! The tumbleweed proper is known as Russian thistle (Salsola tragus, probably several species). It doesn’t roll along because of the harsh and destructive nature of the chaparral; this is how it disperses it seeds. After flowering, the plant dries up and disengages from its roots on purpose. As it rolls, it drops seeds, like a trail of breadcrumbs never to be used to find a way home.

Heck, Russian thistle isn’t even from the chaparral biome. It's native to the steppe grasslands of Russia, a different biome altogether. Russian steppe is cold, and is wet, but it is windy, so it’s mechanism of seed dispersal works in chaparral. Therefore, it can survive in California, and Spain, and Italy, and Morocco, and Israel. Here we have a plant that is identified closely with one climate that comes from another.

Indecision and overlap abound when it comes to naming and defining biomes. For instance, what makes a chaparral a chaparral and not a desert? What makes it a chaparral and not a grassland?

For many ecologists, the difference is precipitation. Deserts get less rain, snow, fog, or humidity than chaparrals, which in turn get less of these things than grasslands. But others divide grasslands into tall and moist versus short and wet. So does the dry grassland still get more rain than the chaparral?

In the chaparral of Israel, different biomes can come as close together as different slopes of a canyon. A 2012 study has proposed that these canyon faces with completely different flora and climate should be used as “evolution canyons” where global warming can be monitored and changes in many different ecosystems can be tracked in a small place. And this is all supposed to be within the world's smallest biome?

This is one of the proposed “evolution canyons” in the Israeli
chaparral. Notice the different vegetation on one slope as
compared to the other. There are differences in rain,
temperature, and animal life – and yet it is all supposed to
be chaparral?
At the other extreme, the taiga is the world’s largest terrestrial biome (11% of land) and is quite wet. In North America, taiga is found north of 50˚ N latitude, and tundra begins as far south as 60˚ N. England and Scotland are situated at 50-58˚ N latitude, but they are nothing like taiga or tundra. Even though they are located at similar points on the Earth, they have a different climate because they benefit from the Atlantic Conveyor, an extension of the Gulfstream. This current pulls warm air up from the tropics and keeps Great Britain warmer than it would otherwise be.

At 50-60˚ S latitude, there is very little land. Almost all the way around the Earth at those latitudes there is nothing but ocean. So latitude isn’t everything when it comes to defining biomes. Tierra del Fuego and the southern part of Patagonia are located south of 50˚ S, but they are defined as neither taiga nor tundra.

As water travels around the world through the upper and lower
currents of the ocean, it picks up and releases heat. When it is
shallow and in the tropics, it arms and travels close to the
surface. As it cools and releases its heat to the atmosphere, it
drops deeper. The gulfstream ends in the Atlantic conveyor,
which keeps Great Britain warm. The warm water moves
faster, which is why it takes less time to sail from the US to
Europe but longer to go west.
You can tell by the descriptions above that many places around the world share general descriptions, so where does one biome end and a different one begin? This is a serious point of vagueness for me. Many people publish maps showing the biomes of the Earth, and no two of them agree fully. Look at the pictures published just below.

The major terrestrial biomes of the world include desert, tundra, taiga, deciduous forest, grassland, and tropical rainforest. But these lists are often incomplete or vague. Chaparral is often left off the list; it has climate very similar to desert, plants able to deal with desert-like heat, and plants that come from grassland biomes. What is even weirder, it is the only biome where the wet season is the same as the winter season. Overall, it’s an in between biome and muddies the waters, so it often falls through the cracks.

Biomes may be classified by climate (Holdridge scheme), which generally equates to latitude, but we have already seen exceptions to that. Another scheme, Whittaker’s biome-typing, works to classify regions based on temperature and precipitation. Other systems are based on some combination of these factors, but if they are using the same factors, why don’t they agree better?

This is a busy picture, but the different colors represent different biomes,
and vary from map to map. The thing to notice is the pattern is different
in each map; no one can agree on what biomes are where.
For these schemes, the discriminating factors are abiotic (non-living influences), so they do not take in the periodic movements of animals or the invasiveness of some species in defining their boundaries. But some abiotic factors are changing quickly; like temperature, while others take much more time to change (geography). Therefore, as conditions change, these biome designations will either diverge, or will come to represent a different flora and fauna. No naming system has got these sets of problems licked.

Another problem is in the naming itself. Who decides on the name, and what does it mean in different areas of the world? The World Wide Fund For Nature (WWF) has a naming system that tries to be specific and generic at the same time. What is often called rainforest is designated by WWF as either “tropical and subtropical moist broadleaf forest” or “tropical and subtropical dry broadleaf forest” depending on the amount of precipitation. Don’t really roll off the tongue, do they?

Locality plays a role in the naming problem. Mediterranean scrub biome - is it by the sea, not always. Is it only scrub brush, not always. So that name isn’t so good. But even around the Med it’s called different things – maquis in Italy, garrigue in France, phyrygana in Greece and batha in Spain. In America, it’s the high chaparral – like the TV show. But in Chile, it’s called matorral (mata = shrub in Spanish). In South Africa, it’s the renosterveld or fynbos, but Australians know it as mallee scrub or Kwongan heath.

Carolus Linnaeus (1707-1778) developed a binomial system for naming in botany and zoology, specifically to alleviate the locality and organizational naming problems. But a system such of this was never developed for ecology. Why not?

All of this imprecise naming and description, and we’ve only touched on the terrestrial biomes. There's a whole set of problems attached to the aquatic biomes as well. Some definitions list only one biome in water, with different freshwater regions (ponds, lakes and such), and marine regions (oceans, reefs, estuaries).

The Tollund Man was found in a sphagnum peat bog in Denmark. The highly 
acidic peat tans the skin and the low oxygen condition preserves 
the clothes and hair. Only the phosphate in the bones is lost, so bones remain
in place, but not rigidly. You can see the rope around his neck. Autopsies in 
1950 and 2002 confirmed that he was hung rather than strangled. Tollund Man 
was most likely a sacrifice to the bog gods.
Other systems define each of the regions as a biome. This can also cause problems. One freshwater biome is a wetland – but what kind of wetland? There are bogs, swamps, marshes, fens (as in Fenway Park in Boston) and carrs (fens overgrown with trees). Each has a different type of feeder system, different majority floral and fauna, and even a different acidity. How could those all be the same biome?

Most bogs are found in boreal forests (taiga) in Great Britain and Scandinavia. They were thought of as sacred places where the gods lived, and where human sacrifices were often made. This is why you may find bog bodies, mummies of people who lived thousands of years ago. The acidic conditions and low oxygen preserved the tissues (but dissolved the bones usually).

So - are the bogs considered part of the taiga, or just habitats within a biome? Or are they their own biome within a biome? Not easy to decide. Biomes are essential for organizing the life on Earth, but the learning would be easier if we could find a Linnaeus for ecology.

Next week, can you have mold without mildew? Just what are they anyway?

Nevo, E. (2012). "Evolution Canyon," a potential microscale monitor of global warming across life Proceedings of the National Academy of Sciences, 109 (8), 2960-2965 DOI: 10.1073/pnas.1120633109
Guo, Y., Zheng, Z., La Clair, J., Chory, J., & Noel, J. (2013). Smoke-derived karrikin perception by the / -hydrolase KAI2 from Arabidopsis Proceedings of the National Academy of Sciences, 110 (20), 8284-8289 DOI: 10.1073/pnas.1306265110  

Wednesday, July 10, 2013

Grin and Water Bear It

Biology concepts – tardigrade, cryptobiosis, anhydrobiosis, eutely, hyperplasia, hypertrophy, dry vaccine, dormancy

The original toughman contests were supposed to show us the
toughest of the general population. I’m not so sure how tough
it is to have a nickname like “Butterbean,” but maybe that
proves his toughness. On the other hand, do you get a cereal
box cover and a mohawk because your tough, or do you get
tough because you have a mohawk.
In the early 1980’s, a forerunner to the mixed martial arts craze was temporarily popular in the United States. Called the “ToughMan” contests, non-boxers would enter the ring for fights against other nonprofessional fighters. The rules were supposedly the same as in boxing, although many contests were run without proper supervision, and the tournaments sometimes required a participant to fight several times in one evening. Think legalized bar fights.

Famous participants in the toughman contests included “Butterbean” Esch – a 350 lb. boxer with one punch and an iron jaw, and of course, who can forget Mr. T. The contests are still held in many states, but MMA now has the majority of the fan base, even more than traditional boxing between trained fighters.

These guys were tough, but were they the toughest? Humans as a rule are weak for their size, scared of more things than they should be, and less inclined to fight to the death for a morsel of food or potential mate – well most are. So…..

Questions of the Day: What is the world’s toughest animal?

Ask a hundred people and you may get a hundred different answers. The bull elephant can fight off an entire pride of lions and can lift five tons. But can you really give the prize to an animals that is scared of a mouse?! Maybe they aren’t afraid of mice, but they will avoid them if possible, according to one of the more scientifically consistent episodes of Mythbusters.

A good second choice might be the honey badger. It supposedly knows no fear, and proves it by depriving lions of the prey they just killed. In one case, three honey badgers stole a entire carcass from seven lions! The South Africa National defense calls their armored personnel vehicles ratels, the afrikaans word for honey badger.

This is the toughest animal on Earth, although it may not
look it. The water bear looks more like a teddy bear,
although the claws might do some damage if you are a
bacterium or a protist. The mouth has stylets to puncture
plant cells and suck out the liquid nutrition.
But I will try to convince you that a type of bear is the toughest animal on the face of the Earth, a water bear to be specific. This animal has long claws on each foot and a mouth that takes up a good portion of its head. On the other hand, it's less than 1 mm long!

The water bear is more scientifically known as a tardigrade (latin for slow walker), a phylum that falls somewhere near arthropods and nematode worms. There are two classes (eutardigradia and heterotardigradia) and more than 900 species, but there may be some overlap in those descriptions.

The adult tardigrade will have 40,000 cells, and will never have more. What is more, every species of tardigrade is matures with a specific number. This is called eutely (eu = good, and telos = end). Many lower organisms may be eutelic; their cells have a limited number of divisions, so they grow to that number and then stop.

It isn’t just whole organisms that might be eutelic, organs can be as well. For example, the nematode Ascaris ALWAYS has 162 neurons. The research model nematode C. elegans has exactly 959 somatic cells, although a 2011 study has shown that C. elegans can lose critical cell nuclei as they age – tell me about it. Other nematodes, rotifers, and gastrotrichs have also been shown to have cell constancy at the body and/or organ level.

Tardigrades do grow after they reach adulthood, just not by adding cells. Growth by additional cells is called hyperplasia (excess formation), while growth by existing cells becoming larger is called hypertrophy (excess nourishment). 

The gingiva around the teeth can overgrow in response
to some developmental disorders, but more often it is a
result of drugs given for epilepsy or other diseases. The
point here is that whether it is from hypertrophy
(increased cell size) or hyperplasia (increased cell
number), it looks the same. These are histologic
determinations and don’t really matter for clinical evaluation.
Prostate enlargement is often due to an increase in cells, hence the name benign prostatic hyperplasia, but hyperplastic growth doesn’t have to be pathologic. When you lose part of your liver, some can grow back by through hyperplasia. Likewise, hypertrophy is great when it is your muscles getting bigger, but not necessarily so good when your heart’s ventricles overgrow (ventricular hypertrophy).

Different tardigrade species are adapted to nearly every environment on Earth. They live in the Arctic and the Antarctic, in the mountains and the oceans, in the deserts and the jungles. All are found near water, some marine and some limnal (freshwater), some in the water and some just next to the water held in mosses or lichens.

But wherever you find them, you’ll find them in great numbers. The density of tardigrades can approach two million per square meter. Yellow crazy ants (Anoplolepis gracilipes) form supercolonies of incredible density, yet they can only muster about 2000 individuals per square meter. Haven’t heard of crazy ants? You will – look them up.

Tardigrade toughness doesn’t come from their pursuit of prey or their ability to fend off predators, but their willingness to live in conditions that would kill anything else, and I mean anything, else.

Cold, not a problem. Tardigrades can have liquid nitrogen (-346˚F/-210˚C) poured on them and they’re just fine. Heat – boil them for a couple of hours and then watch them lay eggs and go back to eating. Radiation isn’t a problem either; they can take 5700 grays of ionizing radiation without blinking.... well, they could if they had eyes. Humans curl up in a ball and die when exposed to 5 gray.

It is important to know how much radiation is absorbed
by the body, not just how much is in the air. The Gray,
named for Harold Louis Gray, is equal to 1 joule of energy
absorbed per kilogram of matter. Harold Gray is considered
the Father of Radiobiology. The old dose name was the
rad, and 1 Gray is equal to 100 rads. A chest X-ray is
typically about 0.0006 Grays.
Some tardigrades live in black smokers at the bottom of the ocean, yet most of them can take 6000x normal pressure in stride. To sum it all up, in 2007 the Russians fired tardigrades into space for 12 days (near absolute zero, total vacuum, cosmic radiation). They came back and starting having babies. Now that’s tough.

How do they manage these amazing feats? Basically – they die and then come back to life. Technically, it’s called cryptobiosis (hidden life), but death and self-resurrection is not a bad description. During cryptobiosis, metabolism is reduced by 1000x fold or even more, down to the level where there is NO detectable chemical activity.

There are five recognized types of cryptobiosis, based on the noxious environmental condition that triggers it – anhydrobiosis (without water), chemobiosis (chemicals), cryobiosis (cold), anoxybiosis (lack of oxygen), and osmobiosis (change in osmotic potential).

The primary form for tardigrades is anhydrobiosis. They drop their claws, retract their legs and roll up into a ball called a tun. 99% loss of water, roll up into “tun” this is important because it regulates the rate of evaporative water loss. At this level, they don't hold enough water for damaging reactions to take place or even enough water to form ice crystals. The water is replaced by a sugar called trehalose.

Trehalose production is similar to the way many organisms can protect their structures and biochemistry from environmental damage, but apparently scientists have just touched the surface of how tardigrades react to uncomfortable environments. A 2013 study indicates that there are many unidentified organic molecules present in the tuns of tardigrades that are not present in the organisms under normal physiologic situations.

The tun of a tardigrade is a very regulated structure.
When the claws are dropped and the legs retracted, the
tardigrade coils into almost a ball. In this situation, the
loss of water can be carefully controlled. The plates on
the back also form a protective armor for non-
environmental assaults – the spikes look imposing.
Amazingly, tardigrades are the only animal that can undergo all five types of cryptobiosis.  It's really like dying and coming back to life. Reviving from cryptobiosis can take a little while, usually the longer they have been in anhydrosis, the longer it takes to recover. They can’t survive this way forever either.

Earlier reports had professed that 120 year old tardigrades were revived from dried lichen and moss samples in the British Museum, and that decades old samples were just fine. But Dr. James Garey of the University of South Florida tells me that many of these reports have been called into question and cannot be repeated.

Dr. Garey’s estimate is that tardigrades can survive 1-5 years as a tun, with decreasing viability upon hydration after that. Still, could any other animal you know of be dead for five years, with no air, no water, high radiation, liquid nitrogen, and taunts about their size and lineage – and then come right back to life when the opportunity is right?

Cryptobiosis is quite different than dormancy. Dormancy doesn’t bring a huge change in physiology – like 99% dessication. Also, dormancy is preemptive while cryptobiosis is reactive. However, a very good 2011 review of tardigrade reactions shows that they can undergo both dormancy and crytobiosis – sometime simultaneously!

The question is – how do they survive the bad conditions WHILE they are forming the tun? It takes about 20 minutes for tun formation to occur, so it appears that many of the conditions they can endure require them to already be in the cryptobiologic state. They can survive the radiation when they are dessicated, they can survive boiling when they are dessicated. I don’t think it makes them any less amazing.

In early 2013, researchers from King’s College in England
developed a silicon mold with dissolvable sugar micro-
needles that can deliver a dry vaccine powder.  The system
would induce immunity through activation of skin immune
cells, would require almost no training to deliver, and no
refrigeration. The anhydrobiotic live vaccine is based on
tardigrade cryptobiotic features.
Tardigrades aren’t even considered extremophiles, since they are not designed to live in extreme environments. But this is precisely why I think they are so tough, because few of them are adapted to extreme conditions, but they can survive deadly situations anyway.

Can the exploits of this microanimal help humanity? You betcha. Tardigrades' ability to undergo anhydrobiosis has begun to influence the design of medicines. In third world countries, a lack of reliable refrigeration requires vaccines and medicines don’t need refrigeration, and can be reactivated upon ingestion.

Dry vaccines are a current goal, so the National Institutes of Health recently put out a call for proposals for research into more thermostable and reactivateable preparations. A late 2012 paper has identified a tablet form for deliver of some protein drugs, with reactivation of the molecules with saliva. This would be much better than the current reliance on hypodermics and refrigeration. So tardigrades are tough for themselves, and may fight for us as well.

Next week, just how do you describe the climate of your hometown? Biomes are scientific entities, but it seems we can't agree on what each looks like or is called.

Borde, A., Ekman, A., Holmgren, J., & Larsson, A. (2012). Effect of protein release rates from tablet formulations on the immune response after sublingual immunization European Journal of Pharmaceutical Sciences, 47 (4), 695-700 DOI: 10.1016/j.ejps.2012.08.014
McGee, M., Weber, D., Day, N., Vitelli, C., Crippen, D., Herndon, L., Hall, D., & Melov, S. (2011). Loss of intestinal nuclei and intestinal integrity in aging C. elegans Aging Cell, 10 (4), 699-710 DOI: 10.1111/j.1474-9726.2011.00713.x  

Guidetti, R., Altiero, T., & Rebecchi, L. (2011). On dormancy strategies in tardigrades Journal of Insect Physiology, 57 (5), 567-576 DOI: 10.1016/j.jinsphys.2011.03.003