Wednesday, May 29, 2013

Gas, Knuckles, And The Little Blue Pill

Biology concepts – dissolved gas, cavitation, arthritis, decompression sickness, ebulism, gas embolism

It is certainly true that some folks love cracking their knuckles.
The little research that has been conducted indicates that
about 25-30% of people are habitual knuckle crackers,
with the habit lasting on average 35 years. Fine for them,
but we’re the ones who have to listen to it.
You approach the piano, interlace your fingers and bend your hands backwards, trying to crack your knuckles. Not satisfied, you pop each knuckle individually, followed by making small circles with each thumb and wrist.

This symphony of cracks and clicks makes you feel as though you can reach any key and can work faster and more dexterously than you could’ve before. Will you sound better now that you have cracked your knuckles? Nope – you don’t play piano; you’re here to move it to the next room.

Question of the Day – What makes the sound when you crack your knuckles and does it help or hurt you?

 A knuckle is the joint where your carpal meets your metacarpal. A joint is any hinged meeting of two bones, made up of a sac (bursa) that keeps everything together and a small space between the bones (synovial space). Fluid in the space between the bones (synovial fluid) keeps the friction low as the bones flex in the joint.

Cracking joints can be done many at once or one at a time. Big joints can be cracked just as smaller joints. Chiropractic practices make a living out of cracking joints. There is an immediate feedback in hearing the joint crack; some treatment must have been rendered.

No matter how or why the joints are cracked, the production of the noise is the same in each case. Manipulation of the joint stretches the joint, separating the two bones, and creating a larger space than normal.

In physics, pressure is related to volume, being inversely related. The synovial joint has a certain amount of fluid, enough to fill the normal space. By increasing the joint space volume, the fluid will be filling a larger space. The same amount of fluid in a larger space means that the fluid will be under lower pressure.

This is a generalized cartoon, but it describes the anatomy
of most joints. The bursa is made up of the synovial
membrane and the synovial fluid that buffers the joint.
The bone ends are protected by the cartilage. The muscle,
tendon, ligament and capsule hold the joint together.
Picture a syringe. When the plunger is pushed in there is low volume in the syringe. As the plunger is pulled out, the volume in the syringe increases. The air pressure inside the syringe is now lower than outside the syringe so air (or liquid) rushes in to equalize the pressure.

This decreased pressure in your closed joint will affect the dissolved gases in the synovial fluid. All fluids of the body, like blood or other extracellular fluid, even saliva, contains many molecules, including dissolved gases; CO2, N2, O2. Gases in solution are under pressure just like in their gaseous state. When the pressure decreases, the amount of gas that can stay in solution decreases (it becomes less soluble). When gas becomes insoluble, it comes out of solution and begins to form small bubbles (ebulism, a gas embolism). It is the formation of the bubble(s) that you hear.

Cavitation (formation of a cavity) in small joints wouldn't seem to be a high-energy event, and it isn’t, but it is enough to make the noise you hear. There is still some question as to how such a large noise can be made this way, but x-rays can show the presence of gas bubbles in the popped joint immediately after cracking.

After cracking your joint, the joint remains a little larger for a period of time, and slowly returns to its normal volume. During the time period that the joint is returning to the normal volume, pressure slowly increases. More pressure means more gas solubility, and the bubbles disappear. It takes a while, so you can’t crack that knuckle again for 15-20 minutes.

Here is a demonstration cartoon of pressure and gas solubility.
An reduction in volume the volume from (a) to (b) causes an
increase in pressure – the same amount of stuff in a smaller
space – and this brings an increase in pressure and drives
more gas into solution in (c). When popping your knuckle, we
go the opposite direction, from (c) to (b), to (a), so less gas is
soluble and bubbles will form in the synovial fluid.
During the refractory period, the joints are a little larger and a little looser. The stretch and movement sensors in the tendons around the popped joint are stimulated, giving heightened sensory response in that joint, while the muscles around the joint under go a relaxation immediately after cracking. No wonder many people say they feel invigorated or relaxed after popping joints.

Is it bad for you to crack your joints? Does it do damage to your joints, either immediately or over time? There hasn’t been a lot of research done in this area, but what has been done shows that knuckle cracking does not lead to osteoarthritis.

A 2011 study is the most comprehensive done to date. These researchers looked at cracking and the frequency of cracking as well. No amount of cracking seemed to promoted arthritis development. A 1990 study stated that knuckle crackers were more likely to also have small amounts of hand inflammation and lower grip strength. However, this study could not conclude that knuckle cracking caused the inflammation or loss of grip strength.

Arthritis comes from the Greek originally, where artho = joint, and
itis = inflammation. So that's all arthritis is. There are two major
forms, osteoarthritis is causes by a wearing down of the cartilage
on the ends of the bone and a lass of the synovial buffer in between
the bones. In rheumatoid arthritis, there is an autoimmune reaction
where your body attacks its own joints and causes great
inflammation. Knuckle cracking could only cause osteoarthritis, and it
apparently doesn’t even do that.
However, sometimes gas can be deadly. No, I’m not talking about THAT kind of gas! In your blood there is some dissolved oxygen traveling around unescorted. Ninety-nine percent is bound to hemoglobin, but still there is a little free oxygen as well. The oxygen is on its way to your cells to provide an electron acceptor during the production of ATP via oxidative phosphorylation.

Oxygen’s counterpart, carbon dioxide, is also present in the blood, on its way back to the lungs to be exhaled. Most of the CO2 is locked up as part of carbonic acid (H2CO3) or its conjugate base, bicarbonate (HCO3), and this helps to maintain the pH balance of your blood. Yet there is a little free CO2 dissolved in your blood as well.

The major dissolved gas in your blood is N2, nitrogen gas. Remember that air 80% nitrogen. This also happens to be the most soluble gas in your blood, so more of your body’s allotment of nitrogen is carried this way; less need for carrier molecules like hemoglobin or bicarbonate.

This is all well and good until the pressure on your body changes, like when you go scuba diving. Water weighs much more than air, so for every 10 m (33 ft) you descend in the water, the pressure on your body doubles. With more pressure, more gas will be soluble in the blood. This is the opposite reaction from when you stretch your joints while popping your knuckles.

The increased gas volume dissolved in your blood is no problem as long as you allow it to dissipate slowly. But if you have been at depth for some time, and then you ascend too quickly, your body doesn’t have time to adjust to the change in pressure.

The return to normal pressure means less gas will be soluble in your blood. Where is all the gas you added to your blood by diving deep going to go? It’s going to come out of solution and form bubbles. This is decompression sickness, sometimes called the bends.

If you’re lucky, decompression sickness will only be as bad as the
burst blood vessels in the skin shown on the left. Gas bubbles
coming out of solution do damage to the endothelial cells that line
the blood vessels, causing them to become leaky. Blood then spills
into the tissues. On the right is what might happen when more gas
comes out and starts to coalesce in the joint. The darker portion in
the left joint is a gas bubble. The big red arrow should help you
find the bubble.
Decompression sickness is a macro version of your knuckle joints, occurring all over your body. The bubbles have a tendency to form in, or move to, your joints, and this is painful. Remember that after you crack your knuckle, the volume goes back down and the gas is under greater pressure again and goes back into solution. No such luck in decompression sickness, the pressure remains lower than when you were diving and the bubbles take much, much longer to be resorbed by the body.

In the meantime, you are doubled over in pain (“the bends”). Pain is one thing, but if a bubble in your blood happens to get stuck somewhere, that’s called a gas embolus. Nothing downstream of the bubble is going to be getting oxygenated blood, and that means it will die.  If it is in heart vessel, that causes a heart attack, if it’s in your lungs capillary beds, that’s a pulmonary embolism, if it is in your brain, that’s a stroke. Any of these can kill you.

The best way to treat the bends is to prevent them. You must ascend in stages, allowing time to adjust to the lower pressure at each depth. Your body will take the excess gas out of the blood if given time. When you learn to dive, much time is spent on the math involved in preventing decompression sickness; if you have been at such a depth for so long, you will need to ascend in X number of stages, with Y minutes at each stage depth.

If you don’t follow this, you’re in for a great deal of pain and a trip to a decompression chamber. In the chamber, they will pump in extra air to increase the pressure on your body, just like being at depth again. This will put the gas back into solution. Then they will release the pressure, a little at a time, allowing your body to take the excess gas out of your blood; the equivalent of a staged ascension for depth.

Here are your two choices to deal with recompression (reducing
pressure as you ascend) when diving. On the left is a dive table, giving
you the stages of your ascension needed to avoid the bends, according
to your dive number, time, and depth. OR, you can ascend as fast as you
like, and then spend 24 hours in the decompression chamber on the
right. This is, of course, assuming you don’t die before they get you
to the nearest chamber.
Every once in a while you hear about someone on a plane having a stroke or a heart attack. This might be someone returning from Hawaii or some other tropical paradise. If they had scuba dived in the morning (greatly increased pressure), and then to plane altitude (lower pressure) they could induce bubble formation even if they ascended correctly.

Even pressurized airliners have lower than normal air pressure (your ears pop), so no one is advised to fly after diving at depth for at least 24 hours. Dives that don’t require a staged ascent should still be completed at least 12 hours before flying. If you go diving in the morning, get on a flight immediately afterward, and then start popping your knuckles – could your hand explode?

It gets worse for some guys. Certain drugs can affect the amount and solubility of gases in your blood, like nitric oxide (NO)-generating or -manipulating drugs. NO vasodilators increase the nitrogen gas in your blood. Name a nitric oxide-based vasodilator -–- yep, Viagra. A 2013 study has shown that pretreatment of rats with Viagra promotes decompression sickness when the pressure on their bodies is increased and then rapidly returned to normal. The question is, was it louder when the rats cracked their knuckles?

Next week, another question in biology - can bacteria change the earth - the whole earth?

Blatteau, J., Brubakk, A., Gempp, E., Castagna, O., Risso, J., & Vallée, N. (2013). Sidenafil Pre-Treatment Promotes Decompression Sickness in Rats PLoS ONE, 8 (4) DOI: 10.1371/journal.pone.0060639

deWeber, K., Olszewski, M., & Ortolano, R. (2011). Knuckle Cracking and Hand Osteoarthritis The Journal of the American Board of Family Medicine, 24 (2), 169-174 DOI: 10.3122/jabfm.2011.02.100156


Wednesday, May 22, 2013

I Know Why She Swallowed The Fly

Biology concepts – carnivorous plants, minerals in biology, symbiosis, cryptids,

The Thing From Another Planet was a 1951 B-horror movie.
Arctic researchers find a space ship in the ice and thaw out
the pilot. He turns out to be a walking plant that needs
blood to feed his little seedlings. Never minds that the plant
is growling, feels just fine at -60 degrees, and is wearing
clothes. They finally kill him with electricity.
The man-eating tree is a cryptid (hidden) organism. Cryptid means there is no scientific proof for its existence, but for some reason there are people that say it exists. In this case, a German explorer named Carl Liche trekked through the Madagascar jungle and described the natives forcing a girl to climb the trunk of a tree. The branches (arms) grabbed her and lifted her to the top where she was crushed and absorbed. There was no explorer Carl Liche and the story was an utter fiction.

Myths, hoaxes, misidentifications, misunderstandings, they all have accounted for various cryptids, but every once in a while a cryptid turns out to be real. Gorillas? Once thought to be fictitious monsters. But a man-eating plant? Would you settle for small animal-eating plants? Those we have. The question is why?

Question of the Day – Why do some plants eat bugs?

Venus flytraps are active trap plants. They have a movement that requires energy, and the movement of the trap is one stage - the prey is digested by the part that moves. Much research has been devoted to the mechanism of its fast trap closure, and many hypotheses are still floating about.

We do know that it takes about 1.5 milliseconds to transmit the signal from the trigger hairs in the trap to the motor cells that close it. The signal is electrochemical, very similar to an action potential in an animal neuron. Channels pump ions across membranes, and the difference in the charges of each type of ion (sodium and potassium) cause an electrical impulse.

It seems that the electrical impulse causes water channels to open across various cells near the base of the trap. Water pressure is quickly changed from high to low and low to high in different layers of cells and this cause shape changes. Different shapes cause different stresses, and this closes the trap.

A relatively new hypothesis is that the open configuration is full of elastic stress, so that when water pressures are changed between layers of cells, there is an elastic snap to the closed state. The closing only takes a 0.2 seconds. After that there is a slower portion that brings more complete closing and the start of digestive enzyme secretion.

This is a visual representation of the electrical signal produced
 by triggering the venus fly trap. The red line is the first touch
to a trigger hair. It is not enough to reach threshold and close
the trap. If a second touch occurs before the first has dissipated
to much (green line) the threshold is crossed and the trap
closes. If the second signal is too late (blue line), the
threshold won’t be reached.
To reduce false or unproductive closures, the each trigger hair in the trap produces a sub-threshold action potential. One trigger hair being touched won’t close the trap. As the first signal dissipates, if a second signal is generated by a second hair being touched, the sum of the dying first signal and the second signal can raise the charge above the threshold level and the trap will close (see picture at left). However, in very warm weather (above 36˚C/97˚F) it only takes one trigger hair signal to close the trap – it has something to do with the molecules moving faster in higher temperature environments so that one signal can reach the threshold level.

Other carnivorous plants have semi-active, two-stage traps. The aquatic bladderwort is an interesting example. It is one of the smallest carnivorous plants, with a trap that is just 10 mm wide at its opening. In order to eat, bladderworts create a negative pressure inside the trap by pumping out the water. A trap door maintains the negative pressure inside, but if the trigger hairs outside the trap are touched, the door collapses and water + prey are sucked inside. The trap door then assumes its original shape and the prey is caught inside the trap (see video here).

Sundews are two-stage trap plants as well, having sticky liquid drops perched atop small pedestals. The prey, maybe a fly, gets stuck in the gummy drops. Only then does the tentacle slowly curl around the fly, becoming an “outer stomach” as termed by Charles Darwin (see picture). The digestive enzymes are secreted and the fly is no more.

A different species of sundew, Drosera glanduligera, has a different kind of trap. A new study from Germany shows that it has brittle hairs (called snap tentacles) at the edge of the trap that when triggered, catapult the prey into the resin glue. The catapult is quicker than the venus flytrap, occurring in less than 75 milliseconds. Only then will the prey be slowly pull down toward the portion of the plant that secretes enzymes.

On the left is a typical sundew, D. capensis. When a fly is stuck, a
slow curl of the tentacle will finally do him in and trigger digestion.
On the right is a rarer sundew, D. glanduligera. The number steps
show the catapulting of prey from the trigger hair into the glue in
the middle of the plant. It all occurs in just milliseconds.
There are also passively carnivorous plants, those that allow the prey to do the work. Pitcher plants are slippery on their edges; prey fall into the pitcher and can’t escape. Amazingly, the seeds of the Shepherd’s Purse are carnivorous, but the plants themselves are not. The seeds lie on the ground and exude toxins that attract and poison insects that pass by. The seeds also secrete enzymes that then digest the insects. This leaves a circular ring of very rich soil, giving the germinating plant an advantage.

In many of the plants, the digestive enzymes have started to be identified. A 2012 paper from Germany has looked the protein portions of the venus flytrap digestive fluid. It contains nucleases (digest DNA and RNA), phosphatases (remove phosphate groups), phospholipases (break down fats), chitinases (to digest the insect exoskeleton), and proteolytic enzymes (to break down proteins). Most of these are derived from pathogenesis proteins, so it is believed that digestion evolved from several self-defense processes.

There are 600 known species of terrestrial carnivorous plants and 50 in the water, but scientists are now realizing that many more plants use a mechanism similar to the Shepherd’s purse and can be considered at least semi-carnivorous. Would you believe that tomato and potato plants have sticky hairs that may trap aphids and other insects. They die and drop to the ground around the stem. This enriches the soil and the plant absorbs the nutrients.
Tomato vines have sticky hairs on their stems. It turns
out that they can trap bugs, hold them until they die,
drop them to the ground, and let their carcasses
fertilize the soil around the plant. Now that’s
miracle grow!

No matter the method of the trapping, the reason is the same; the plants need nutrients. Not glucose, proteins or lipids – they're photosynthetic for gosh sakes. They can make their own proteins, nucleic acids and fats from the carbohydrates they produce during photosynthesis. That is, they can if they have the correct additional materials.

Proteins are made of amino acids, and amino acids contain a lot of nitrogen. Nucleic acids (DNA, RNA) are made from nucleotides, and these include a lot of phosphorous. Many biomolecules and physiologic processes use minerals like nitrogen, potassium, and phosphorous. These are the amin constituents of the fertilizers humans add to the soil to help crops, flowers, and in my case - weeds, grow.

Carnivorous plants often live in nutrient poor soil. Sandy soil (flytraps), tropical jungle soils (sundews), and Andean mountain tops (bromeliad described below) are all mineral poor. In jungles, for instance, most of the minerals are tied up in the huge trees, and such little sunlight penetrates to the ground that few plants can live there; therefore, there is little recycling of nitrogen and phosphorous in the topsoil. Eating insects is just an adaptation to allow them to live where other plants can’t.

Many minerals are made available by digestion of insects.  Carnivorous plants get 5-100 % of their seasonal nitrogen and/or phosphorous gain, but only 1-16% of their potassium uptake. If there is one nutrient these plants covet more than the others, it's the nitrogen.

Many plants acquire nitrogen from symbiotic bacteria around their roots that fix nitrogen gas in the soil. Fixing means converting from gas to a solid. Carnivorous plants do not have these advantages so they had to come up with another strategy. However, help doesn’t always come from digestion of insect prey.

High in the Andes Mountains grows the world’s largest
bromeliad. It can be alive for 140 years before it flowers
the first time. The tall stalk is what holds the flowers.
The business is lower, rounder, and full of sharp spines.
Birds live there, but can also be skewered there. They
say most fatal accidents do occur close to home.
The Roridula genus of South African plants acquire minerals from prey with a little help. It has sticky leaves but no digestive enzymes. Its sticky fluid is resin, not mucus; therefore, enzymes can’t be included because they are not soluble in resin. 

When prey insects get stuck in the resin, they are consumed by another animal. This consumer defecates either before or after its meal. The feces are nitrogen rich remnants from a previous bug meal, so this is an indirect mechanism for profiting from killing for a meal.

Another example of this is Puya raimondii, the world’s largest bromeliad. This plant is about 2-3 m tall, but when it flowers, the stalk may rise as much as 12 m! Birds can live in its foliage and when they defecate, they provide nitrogen to the plant. But P. raimondii has huge sharp spines that can actually kill some of the birds. As the birds rot, they also release minerals to be used by the tree; therefore, P. raimondii is semi-carnivorous.

It isn’t all death and destruction. Take the nepenthes pitcher plants for example. These are the largest of the pitchers, holding more than 2.5 liters of digestive fluids. Their pitchers are little ecosystems. Some larvae, particularly a couple of species of mosquito, can survive ONLY inside the pitcher liquid.

I don’t think I can do this picture justice. The only
things this tree shrew lacks are a magazine and a
can of air freshener.
On the other hand, a 2013 paper shows that the nepenthes pitchers also secrete antimicrobial agents, making them very sterile environments… except for all the digesting corpses. The pitchers also house assassin insects, such as swimming ants that can live in the pitchers without being harmed. Their leftovers and feces help to feed the pitcher plant.

One last exceptional case of acquiring nitrogen. Borneo tree shrews trade their own feces for nectar from three species of nepenthes pitcher plants. The shrews sit on the edge of the pitcher facing the outside of the plant, like on a little toilet (see picture on left). They lick the nectar from the edges of the trap and then make a deposit of feces into the pitcher. The nitrogen rich feces will sustain the plant in times of low insect number. Is it really worth it? 

Poppinga, S., Hartmeyer, S., Seidel, R., Masselter, T., Hartmeyer, I., & Speck, T. (2012). Catapulting Tentacles in a Sticky Carnivorous Plant PLoS ONE, 7 (9) DOI: 10.1371/journal.pone.0045735  

Buch, F., Rott, M., Rottloff, S., Paetz, C., Hilke, I., Raessler, M., & Mithofer, A. (2012). Secreted pitfall-trap fluid of carnivorous Nepenthes plants is unsuitable for microbial growth Annals of Botany, 111 (3), 375-383 DOI: 10.1093/aob/mcs287  

Schulze, W., Sanggaard, K., Kreuzer, I., Knudsen, A., Bemm, F., Thogersen, I., Brautigam, A., Thomsen, L., Schliesky, S., Dyrlund, T., Escalante-Perez, M., Becker, D., Schultz, J., Karring, H., Weber, A., Hojrup, P., Hedrich, R., & Enghild, J. (2012). The Protein Composition of the Digestive Fluid from the Venus Flytrap Sheds Light on Prey Digestion Mechanisms Molecular & Cellular Proteomics, 11 (11), 1306-1319 DOI: 10.1074/mcp.M112.021006

Wednesday, May 15, 2013

Biodiversity Counts!

Biology concepts – biodiversity, kingdoms of life, animalia, plantae, fungi, protist, archaea, bacteria, extant, extinct

It seems that contests counting things in jars
always involve food. M&Ms, jellybeans, candies,
and gumballs are common things to estimate. I like
another estimate game – how many grains of sand
can be held in one human hand?
Amazingly, only about 10,000.
At some point in our lives, we have all tried to win the prize by guessing how many jellybeans are in the jar. Number estimation is a skill few people possess, just try ordering mulch by the square yard – you end up with either half as much as you need or buried in pine bark!

There is a large group of scientists playing the jellybean game for a living, but their jar is the entire earth. The jellybeans are species of organisms. The prize? Well, you don’t get to keep the jellybeans; and just how will we know who wins?

The Question of the Day – How many species of life are there on Earth?

It seems like a straight forward question, but let’s look at it in a bit more detail before we try to answer it.  What is it we're counting, animals? Animals and plants? Let’s include everything – everything that is considered alive. So what is considered alive? You can have a great discussion as to what should be considered alive, but for these purposes, let’s stick to the kingdoms of life as taught in every biology class – Archaea, Bacteria, Protists, Fungi, Plants, and Animals.

So now that we know the biodiversity we are assessing, we need to define our unit. We said above that we would count species, but it isn’t that simple. We have discussed before what constitutes a species in general – those animals that can breed and produce fertile offspring. So we don’t count ligers and tigons (crosses between tigers and lions), but should we count all the hybridizations of orchids? More than 24,000 species are named already, with about 800 added each year. For our purposes, and for most people estimating species, we will stick with those found in nature, unaided by man.

In 2012, Japanese botanists crossed two orchids and
created a new orchid. No big deal right, orchids are
crossed all the time. But this was the first time that a
photosynthesizing orchid was crossed with a purely
parasitic orchid that doesn’t perform photosynthesis.
They think the plants are doing some photosynthesis –
they’re pretty anyway. Is this a species we should
count in our estimate?
We are counting species, but is it live (extant) species or all species including those that are extinct? The World Wildlife Federation estimates that between 0.01% and 0.1% of all species go extinct each year. However many species we end up with as an estimate for all life on Earth, this is a huge number of species to lose EVERY YEAR. It is scary to think how many undiscovered species will go extinct this year. There must be thousands and thousands of species that we will never get to describe using a live specimen or discover how they might add to the diversity of the planet.

Scientists refer to “catalogued” species, but does that refer to those alive at the time the were described, or any species that has ever been described and named? Scientists estimate that extant species account for only 3% of everything that has lived on Earth, so including all species would greatly increased the overall number. However, in most estimates of species on Earth, the species being talked about are alive now, except for the one went extinct just this second, and the one that will go extinct two minutes from now, and the one….

The opposite action is also occurring; we discover new species every year. Most people think that perhaps a few new species are found each year, but it’s really in the thousands. The International Institute for Species Exploration (IISE) at Arizona State University publishes a list each year of the newly discovered species. For 2011 the list was more than 18,000 species long! You can see from the picture (below, right) that many discoveries were made in every kingdom of life in the decade of the 2000’s, more than 170,000 discoveries in all.

This graph shows the relative number of new species in many groups of
organisms. The scales are variable for each group and can’t be compared
amongst the groups. The trends show that in some groups, more and
more species are being discovered each year, while in others, fewer and
fewer are being found. In still others, some years a bunch are found and
some years provide few or no new species.
If 170,000 were discovered in ten years, the total number of species on Earth must be huge. Let’s break down the numbers of catalogued species and the estimates by kingdom.

Animalia – These are what most people think of when asked to name a species. Most animals are relatively big and can be seen in everyday life. The number of catalogued species includes the dinosaurs and humans, birds and sponges.  The numbers in each group vary greatly.

People love to study birds – so we have probably found a greater percentage of the total number of birds than we have worms. We have named about 10,000 species of birds, and more than 22,000 species of annelids (segmented worms). But there are probably many more annelids that we have not found as compared to birds. Therefore the estimate for annelids will be harder to make and perhaps less accurate.

For all animals, the total number of catalogued species by 2010 was 1.2 million. A recent paper (2011, Mora et al.) has predicted the number of species in most kingdoms based on several mathematical models. The authors predict that there are more than 9.9 million animal species on the Earth and in the oceans. According to this estimate, we have found only 12% of all the animals on Earth!

Meet the Giant Gippsland Earthworm 
(Megascolides australis). It can reach 3meters 
(10 feet) in length. First described in 1878, this 
worm lives in the deep clay soil in a small 
area in Australia. Similar worms live in North
America, but they are rarely observed.
Plantae – Plants include the non-vascular mosses, the vascular, spore-forming ferns and horsetails, the seed bearing gymnosperms (conifers and such) and the fruiting and flowering angiosperms. So many of these organisms are crucial for human life (medicine, food, oxygen!) we have done a good job of cataloguing them. The 2011 Mora paper surmises that we have already described nearly 50% of the total number of species.

Their methodology uses a lot of math to relate the number of higher taxa (phylums, orders, families) that are known in well-described kingdoms to the possible number in lesser studied groups. They found that there was a consistent pattern in which the more families there are now can be used to predict how many total genera there might be, and each level then can be used to predict the number in kingdoms for which the number of higher taxa are known. They also use methods to predict unknown higher taxa, so they can be included in the species estimate.

For plants, the Mora group predicts that there are 314,000 species extant on Earth. Other estimates also come out at about 300,000 species, but they include algae, which are actually protists, not plants.

FungiThese organisms range from the invisible to the visible. In fact, in the paleoworld, fungi represented the largest organisms on Earth. Even today, the largest single organism is a fungus in the Malheur National Forest in Oregon, where a single 8,000 year old honey mushroom covers 2,200 acres (8,900 square meters) of land.

On the top is a fossilized prototaxite fungus in Saudi Arabia 
that once reached 20 ft (6 m) in height and was the tallest 
organism on the early Earth (this one is on its side). On the 
bottom is the national forest where a single honey mushroom mat 
has killed 2200 acres of trees. Each mushroom is a clone,
connected by a rhizoid mat just under the ground.
If you compare plant diversity to fungi, fungi win hands down. Described species of fungus lag behind; only 43,000 species have been named, but there is much more room to add new species. Estimates are that by the time we are done, whenever that is, we will have nearly 700,000 different mushrooms and other fungi.

Protista – Protists are a bit of a catch-all kingdom. Some have aspects that make them look like plants; they perform photosynthesis or they have central vacuoles. Others are much more animal-like. Overall, they are free-living organisms that are usually single celled or made up of many cells not forming tissues. Two examples show you the diversity in this group. Giant sea kelp (Macrocystis pyrifera) is a type of brown algae that can grow at a rate of 2 ft/day and can reach a length of 300 ft (91.5 m), while picoplankton are 0.2 microns (0.00000002 m) in diameter, are single celled, and may or may not perform photosynthesis.

The estimates for the number of protists vary greatly. A 1998 study indicated that they had no reason to believe the total number of protist species would be greater than 3000. However, a 2005 report puts the estimate number anywhere from 140,000 to 1.6 million. The Mora group’s paper estimates that about 73,000 will be found; that’s 57,000 more than have been described as of 2010.

Archaea and Bacteria – These are the prokaryotes. They live in tar pits and arm pits; they own the planet and probably outer space as well. There are more bacteria in a scoop full of dirt then people who have ever lived on Earth. But for the purposes of our discussion today, the important part is that same scoop of dirt has thousands of undiscovered bacteria.

The J. Craig Venter Institute is leading the Global Ocean Sampling Expeditions to discover new marine microorganisms. A pilot expedition in 2003 identifed 1800 new species in just a couple of months. This was followed by global expeditions in 2005-2009 and an expedition to the European waterways in 2009-2010. They will analyzing the data and naming species for decades to come.

This map represents the expeditions of the Global Ocean Sampling Projects
of the Venter Institute. As they traveled, they would acquire 200-400 gallon
samples of water from different depths every 200 miles and put them
through a series of filters to catch smaller and smaller organisms. The filters
would be dried and used for DNA analysis. In just a couple of months, 1.2
million genes were identified using this methodology.
Most bacteria and archaea can’t be grown in the lab because we don’t know what they require to live. This makes them hard to describe and classify.  Therefore, the Venter Institute uses DNA techniques from dried whole organisms to identify new “species.”

But perhaps classification is not the proper term for these organisms. I talked to Dr. Mora about why prokaryotes were not analyzed to the same degree as other kingdoms in their paper.  He rightfully pointed out that species definitions don’t really apply to prokaryotes as neatly as they do other types of organisms.

Certainly they don’t conform to the mating and fertile offspring definition of species since they don’t mate. Also, since they swap DNA as usual business (lateral gene transfer), who is to say where one species stops and another begins.

Other sources are little more daring in projecting possible numbers of prokaryotes. It is possible that there are a billion distinct bacteria and archaea, but it more likely that the number is in the 10-20 million range.

What are our final numbers when add up all the estimates? Predicted species numbers for life on Earth range from 11.3 million in the Mora paper, to perhaps more than 1 billion if you include prokaryotes. If we leave the bacteria out of the equation, there could still be as many as 30,000,000 forms of life on the planet. We have described about 2 million (according to IISE), so only 28,000,000 left to find!

Mora, C., Tittensor, D., Adl, S., Simpson, A., & Worm, B. (2011). How Many Species Are There on Earth and in the Ocean? PLoS Biology, 9 (8) DOI: 10.1371/journal.pbio.1001127
ADL, S., SIMPSON, A., FARMER, M., ANDERSEN, R., ANDERSON, O., BARTA, J., BOWSER, S., BRUGEROLLE, G., FENSOME, R., FREDERICQ, S., JAMES, T., KARPOV, S., KUGRENS, P., KRUG, J., LANE, C., LEWIS, L., LODGE, J., LYNN, D., MANN, D., MCCOURT, R., MENDOZA, L., MOESTRUP, O., MOZLEY-STANDRIDGE, S., NERAD, T., SHEARER, C., SMIRNOV, A., SPIEGEL, F., & TAYLOR, M. (2005). The New Higher Level Classification of Eukaryotes with Emphasis on the Taxonomy of Protists The Journal of Eukaryotic Microbiology, 52 (5), 399-451 DOI: 10.1111/j.1550-7408.2005.00053.x

Wednesday, May 8, 2013

It’s An Airtight Case

Biology concepts – respiration, aerobe, anaerobe, CAM plants, plastron respiration, cutaneous respiration

Question of the Day – what living thing can hold its breath the longest?

It may seem like an exaggeration, but people whose
tissues are low on oxygen (hypoxic) can have a bluish
hue (cyanosis). Blood that is oxygenated is redder
than blood that is deoxygenated. In animals with more
hemoglobin than humans, like whales, the blood can
actually turn almost purple. Blue Man Group will turn
you blue - from laughter, not disease.
The world’s record for holding one’s breath (voluntarily) was set in May, 2012 by Denmark’s Stig Severinsen. Even though it wasn’t technically cheating, he did hyperventilate with almost pure oxygen for 19 minutes before he then held his breath for an amazing 22 minutes and 0 seconds!

Hyperventilation works by reducing the CO2:O2 ratio in your blood. CO2 concentration is measured by sensors in your large blood vessels. Signals are sent to the brain to increase the breathing rate if there is too much CO2 in the blood or to reduce the breathing rate if the pCO2 is too low. By breathing fast and breathing pure O2, there will be less CO2 in the blood and your brain will tell you to stop breathing until the pCO2 increases to normal levels.

Stig said he used two mental tricks to increase the time he can hold his breath. One is scientifically valid; biofeedback allows Stig to slow his own body activity. By concentrating on his heartbeat, Stig has learned to stimulate neural pathways to reduce his cardiac output and his overall metabolism rate -lower metabolism and heart rate - less need for oxygen. His second technique? He thinks about dolphins.

Twenty-two minutes seems like a long time; indeed, this feat required arduous training by Stig. In truth, 22 minutes isn’t very long at all. In fact, humans are weenies when it comes to going without oxygen. Lots of animals can hold their breath longer than we can.

Sperm whales and elephant seals are the banner carriers for the marine mammals in our contest. Sperm whales can submerge for more than two hours, while elephant seals may stay under water for an hour or more. Being mammals, they have physiology very similar to humans in some respects, but they do have modifications that allow for the long submersions.

Elephant seals have a large proboscis; hence the
elephant name. There are two species, Northern and
Southern, with the Southern species being slightly
larger. Males can weigh over 5 tons and they fight for
females. The females are more like 1500-2000 pounds,
making this the largest relative difference in weights
of two sexes for any mammal.
Whales and seals have more blood than humans do – duh! Even compared pound for pound, they have 3x as much blood. More blood means more oxygen carrying capability. They also have increased oxygen carrying proteins in their blood and tissues. In addition, they can reduce their metabolism in all but the most necessary organs, and they can divert their blood to just these organs.

New research shows that marine mammals also have oxygen carrying proteins in their brains, called neuroglobin and cytoglobin. So, while blood levels of oxygen may plummet when diving, the brain remains oxygenated.

Sea turtles and crocodilians are examples of reptiles that can hold their breath for amazing lengths of time. Aligators and crocodiles can stay submerged for a couple of hours, while a Galapagos sea turtle can easily stay underwater for 4-7 hours, depending on its level of activity. Maybe they think about Stig in order to stay submerged longer.

Sea turtle hibernation is controversial, but some freshwater turtles do just that. They can stay submerged for weeks or perhaps months at a time! But many turtles cheat at our contest, they have a bimodal respiratory system, through their lungs and through their skin. Cutaneous gas exchange is apparent in all freshwater turtles to some degree, but it is much more efficient in some soft shell turtles, according to a 2001 study.

Let’s look at a different type of reptile. The Belcher’s sea snake (Hydrophis belcheri) is the most venomous snake on the face of the Earth, or under it, as the case may be. It is a sea snake that can remain submerged for 7-8 hours. Sea snakes like H. belcheri have a single lung that runs almost the entire length of their body, and their trachea can also transfer oxygen to the blood. This reduces the “dead space” in their respiratory system and allows them to absorb more of the oxygen they inhale.

This diagram gives you an idea of how little respiratory
space humans use for gas exchange. The only places
that move oxygen in to the blood are the pinkish
alveoli at the ends of each airway. Sea snakes use
their available respiratory space to exchange gasses.
Humans, as a comparison, only absorb about 15% of the oxygen in each breath, partly because the gas exchange takes place only in the alveoli (terminal air sacs). Oxygen in the nose, pharynx, trachea, bronchi, and bronchioles is just exhaled without any chance to be used by the body.

However, sea snakes are cheaters as well. Their bodies have been streamlined to help them move through the water. One adaptation in this direction is the complete loss of scales. As a result, these snakes have evolved the ability to exchange some oxygen and carbon dioxide with the water through their skin. So they aren’t really holding their breath when submerged.

Almost all amphibians are cutaneous (skin surface) breathers as well. In air, most amphibians can survive exclusively by exchanging gasses through their skin, and in water, adult gills or rudimentary lungs are supplemented by exchange of gas from the water. Cold water and turbulent water contains more oxygen, so in these environments amphibians can survive indefinitely by garnering oxygen from water.

Indeed, the largest family of salamanders (the plethodontidae), don’t have any lungs at all. They exchange gasses only through their skin and the mucosa surfaces of their mouths. And many of these salamanders are primarily aquatic, they don’t take a breath in their entire lives – but they aren’t holding their breath either.

But none of these animals are the champion breath holders. There are organisms that laugh at holding their breath for a couple of hours. But let’s limit our discussion to those organisms that require oxygen. It’s no fun watching an anaerobic bacterium hold its breath; it doesn’t need oxygen! In many cases, air kills them!

Cockroaches, ticks, and ants do last a long time underwater, just try flushing one. But they can’t win our contest either. They seem to trap a bubble of air as they submerge. They have long hairs on their abdomens that trap air via the surface the surface tension and cohesion of water.
A plastron is the bottom portion of the turtle or tortoise shell,
made up of flat pieces. On the right is the plastron of a tick.
In some ticks there can be gas exchange from water to bug
through the plastron. This is called plastron respiration.

Surrounded by the bubble, they can oygenate their tissues via the breathing holes on the sides of their bodies (spiracles). This allows them to be underwater for nearly an hour and still be breathing. New research in ticks shows that the plastron (flat portion under the abdomen) is capable of some gas exchange itself via the air trapped by the hydrophobic hairs on the abdomen.

We make a big deal about how plants take in carbon dioxide and give off oxygen, and they do during photosynthesis in their chloroplasts. But that’s only half the story. They also have mitochondria that produce ATP from photosynthesis products via oxidative phosphorylation, just like we do.

For plants that grow in hot, dry environments, loss of water is a serious threat. To minimize water loss, some can close the pores in their leaves (stomata), but this also prevents gas exchange, including taking up carbon dioxide and oxygen. The stomata will open only at night, when the temperatures are cooler and water loss would be lost. This is the only time they exchange CO2 and O2 with the environment as well.

CAM (crassulacean acid metabolism) plants can store the carbon dioxide they take in at night in the form of malate. They then can perform photosynthesis even though their stomata are closed. CAM physiology also reduces the amount of O2 bound by RuBisCo enzyme instead of CO2. RuBisCo + O2 leads to inefficient carbon fixation, so waiting until night time when CO2 is relatively more abundant and more soluble will increase photosynthesis productivity. As a result, CAM plants hold their breath for 8-15 hours every day!

CAM plants close their stomata during the hot day, but
exchange gasses during the cooler night. They convert
carbon dioxide to malate as a temporary fixation, which
they store in the central vacuole. During the day, they
convert the malate to carbon dioxide and then to
carbohydrate in the chloroplast using normal
photosynthesis pathways. CAM plants include the
prickly pear, as shown on the extreme right and left.
But the winners of our lack of oxygen survival contest – bacteria, of course! Bacteria come in many flavors, including those that don’t need oxygen for respiration (chemosynthesizers and anaerobes), those that can take or leave oxygen (facultative bacteria), and those that must have oxygen in order to make ATP (obligate aerobes).

Mycobacterium tuberculosis is an example of an obligate aerobe. I talked to Martin Gengenbacher at the Max Planck Institute in Berlin about M. tuberculosis and its survival time without oxygen. He has recently published a great review of M.tuberculosis biology. In a series of experiments that resulted in the development of something called the Wayne model, M. tuberculosis was sealed in a vessel in which they consumed all the available oxygen over time.

However, even after the oxygen was gone, the organisms remained viable for 25 days! They do seem to go dormant, but this dormancy is not the same as ceasing activity completely. It seems that some metabolism and respiration is maintained in the complete absence of oxygen – even though we know that M. tuberculosis absolutely requires oxygen to survive.

These 25 days make M. tuberculosis better than any of our other example organisms at living without gas exchange, though there may be other obligate aerobes that can perform similar feats. But there’s more to the skills of the tuberculin bacterium. In tuberculosis, the body has a difficult time killing off the organism, so it does the next best thing – it walls off the bacteria and traps them in a prison cell of immune cells. These whirls of cells are called granulomas and are very complex structures.

On the left shows a tuberculin granuloma forming and breaking
down. You can see in the middle a formed granuloma, with
macrophages surrounded by a fibrous cuff and lymphocytes.
When immunosuppression sets in, the granuloma breaks down
and the organisms is released to cause disease. On the right is a
photomicrograph of granulomas. In the right corner is a
tuberculosis bacterium before granuloma formation.
Granulomas are extremely hypoxic (oxygen poor), and M. tuberculosis does undergo dormancy in these structures. But again, Dr. Gengenbacher states that this is a metabolically active dormancy, which would by definition require ATP, and therefore require cellular respiration.

The patient still has TB, but no symptomology. This remains the case until the patient undergoes some form of immunosuppression, some disease or condition that prevents the immune cells from keeping the organism in prison. There have been cases where TB has reactivated some 50 years after the original infection. So – M. tuberculosis can hold its breath for half a century! We have a winner.

Next week, another question to ponder. Just how many species call Earth home? 

Gengenbacher, M., & Kaufmann, S. (2012). Mycobacterium tuberculosis: success through dormancy FEMS Microbiology Reviews, 36 (3), 514-532 DOI: 10.1111/j.1574-6976.2012.00331.x  

Fielden, L., Knolhoff, L., Villarreal, S., & Ryan, P. (2011). Underwater survival in the dog tick Dermacentor variabilis (Acari:Ixodidae) Journal of Insect Physiology, 57 (1), 21-26 DOI: 10.1016/j.jinsphys.2010.08.009  

Williams, T., Zavanelli, M., Miller, M., Goldbeck, R., Morledge, M., Casper, D., Pabst, D., McLellan, W., Cantin, L., & Kliger, D. (2008). Running, swimming and diving modifies neuroprotecting globins in the mammalian brain Proceedings of the Royal Society B: Biological Sciences, 275 (1636), 751-758 DOI: 10.1098/rspb.2007.1484