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Mostly Dead Is Slightly Alive

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Halloweenhas morphed into a holiday where people see how much it takes to scare them. Horror movies, haunted houses, dangerous pranks; people like to be scared.

Miracle Max had his own methods for determining if someone was all dead 
or just mostly dead. They involved a bellows and Carol Kane’s 
voice.  But the point is made, for centuries, people were just guessing 
if others werereally dead. There were few experts, and they were
probably just comedians in make-up.
What scares you the most– spiders, public speaking, death? These three are high on every list of common fears, but it wasn’t so long ago that another fear was in first place – taphophobia. Never heard of it? I bet that its mere definition will be enough to send a chill up your spine.

Technically, taphophobia means “fear of graves” (taphos = tomb, and phobia = fear of), but its common use is “fear of being buried alive.” Premature burial is not an urban legend, incidents have been documented in nearly every society – and not all of them were just in the movies or books.

In the 1800’s and earlier, being dead was a lot like being a duck….. you know, if it looks like a duck, walks like a duck, and quacks like a duck….. The appearance of death was often enough to make a diagnosis and start going through their pockets.

As a good example of the wisdom of the age, George Washington had these last words, "Have me decently buried, but do not let my body be put into a vault in less than three days after I am dead…….., tis well." He wanted a sufficient amount of time to pass to ensure that he was in fact dead.

The Irish wake probably originated in the leaving of the
tomb unsealed for several days, just in case the dead
person might wake. Later, stories came about concerning
the lead in pewter tankards from which the Irish would
drink. Lead poisoning could induce a state that resembled
death. Sometimes, a wake is just another reason to raise
a glass of ale.
Manycultures built time delays into their death rites to make sure someone was truly dead. Greeks washed the dead….. and some would wake up. In more difficult cases, they would cut off fingers or dunk the bodies in warm baths. The custom of the Irish wake began with the Celts watching the body for signs of life. But mistakes were made, often in times of epidemic.

The hopes of preventing the spread of infection often lead to burying the dead before they were quite dead. I give you plague victim Eric Idle in Monty Python’s Search for the Holy Grail – “But I’m not dead yet…. I’m feeling much better.”

Even without epidemic, most people in the 18th, 19th, and early 20th centuries died at home, having never seen a doctor. If someone couldn’t hear a heartbeat or feel a pulse, then the patient was dead. But these were lay people, did they know how to feel for a pulse? Maybe they relied on another indicator of death - rigor mortis (rigor = stiffness, and mort = death).

In humans, rigor mortis begins 2-6 hours after death. Rigor is caused by a loss of ATP production. Follow me here--- no breathing, no oxygen; no oxygen, no ATP production. With no ATP, the muscle  can’t relax. This may seem strange, since it takes ATP to contract a muscle in the first place.

As described in the text, the thick filament (myosin) pulls
itself along the thin filament (actin) by grabbing and releasing
actin monomers. A single sarcomere (contractive subunit,
~100,000 in a muscle cell) has millions of myosin heads. They
grab actin fibers that run on all sides of the myosin fiber.
Thepicture at the side should help with this explanation, but I won’t give you all the gory details. Your muscle cells have systems that look like ratchets, using to proteins called myosin and actin which pull past one another to shorten (contract) the muscle fiber. The myosin is bound by ATP, which then hydrolyses to form ADP + P. When ADP + P is bound to myosin, it can reach out and bind to the actin.


The ADP + P is released from the myosin and it flexes the head of the protein, which pulls it along the actin. When a new ATP is bound, the myosin lets go from the actin, and the cycle is repeated.  Each muscle fiber in each cell has millions of myosin heads resulting in a contracted muscle.

In rigor, there is no more ATP, so the myosin doesn’t let go of the actin, therefore, no relaxation can take place. The muscles remain the length they were at death. After about 72 hours, the muscle proteins start to break down, rigor will lessens and the body will become limp again. But as we will see below, some conditions can mimic the signs of rigor, increasing the chances of premature burial.

In an effort to see how bad the situation was, the English reformer, William Tebb, in 1905 made a study of accidental premature burial. Tebb was quite the joiner; the weirder the society, the more he wanted to join or lead it. He worked with the Vegetarian Society, the anti-vivisection movement, the national Canine Defense League, and formed National Anti-Vaccination League in 1896.

William Tebb’s book on premature burial was a best seller.
You’d think he had a product to sell given the way he
described some of the incidents. In one, Madame Blunden
was buried in a crypt under a boys school. The next day, the
students heard noises from below. They opened the tomb
and coffin just in time to see her die from lack of oxygen.
In his book, Premature burial, and how it may be prevented, with special reference to trance catalepsy, and other forms of suspended animation, Tebb professed that he had found 219 cases of near premature burial and 149 live burials. He had some stunning stories of scratches on the lids of coffins and noises from newly filled graves.

In her 1996 book, The Corpse: A History, Christine Quigley documents many instances of premature burial and near-premature burial (I LOVE the title). Skeletons were outside their coffins, sitting up in the corner of their vault after being opened years later. Others were found turned over in their caskets, with tufts of their own hair in their hands.

How might this happen? What conditions might make it look so much like you were dead that even your loved ones would let them plant you in the ground? The list is long and varied, but here are some of the more common things that can make you look dead:

Asphyxiation– anything that cuts off your supply of air can make you look dead once you fall unconscious – continuation of this condition leads to actual death. You look dead enough and won’t respond to external stimuli, so people assume you are dead. Close the coffin lid, and soon you really will be dead of asphyxia.

Catalepsy– Many things can bring on this catatonic state in which the muscles are rigid (like rigor mortis after death) and no pain is enough make you respond, one example is epilepsy. Hypnotists call their trances catalepsy (Greek for to grab and take down), but true catalepsy is much more severe and can last hours to days. Severe emotional trauma can also bring it on, so you can certainly be scared enough to look like you are dead.

Catalepsy is denoted by muscle rigidity, so it can look like
rigor mortis. But there is also waxy flexibility in some cases.
The dead-looking not dead people can be posed, and they
will hold the pose indefinitely. What little girl wouldn’t love
a cataleptic doll for Christmas!
Coma– In medicine, a coma is unconsciousness that lasts more than six hours and from which a person cannot be roused and will not respond to stimuli. Injury or inflammation of the cerebral cortex and/ or the reticular activating system in the brain stem can lead to coma. The things that can injure these structures are myriad, from traumatic injury, to drug overdose, to stroke or hyperthermia, etc.

To show how medicine has changed, there is now a battery of assessments called the Glasgow coma scale (GCS) that are carried out on coma victims to assess their state and prognosis. In centuries past, you might look at them, hold a mirror under their nose, maybe lift and drop an arm….. bury them.

The GCS has traditionally been used in the hospital environment, but new evidenceshows that a prehospital GCS (assessment at scene or in route) can be just as accurate and may benefit treatment choice in pediatric traumatic brain injury patients. The study compared prehospital and emergency department GCS scores and showed that they were similar. They also compared outcomes with prehospital scores and showed a positive correlation. If assessment and treatment can be begun earlier, outcomes should improve.

Apoplexy– this not a very accurate term any longer, and has meant different things at different times. It can refer to bleeding within an organ or bleeding during a stroke. A stroke is very likely to leave survivors that look like they are dead, and are unresponsive. Nevertheless, there are stroke victims who regain consciousness.

Due to the above conditions, many people in the 1700’s and 1800’s made a hunk of change by promoting safety coffins and vaults. These might be as simple as attaching a rope to the hand of the deceased, and running this rope to the surface where it was attached to a bell.

In other coffins the alterations were more elaborate. There might be glass plates to view the face of the dead or a periscope to keep an eye on the corpse. Some thirty designs were patented just in Germany in the second half of the 19th century, including some that contained vibration sensors, and later… a telephone line.

Waiting mortuaries were built in the 1800’s, mostly in
Germany. Since the best sign of death was the beginning
of the rotting process, these mortuaries were basically
holding cells for bodies while nature took its course. If they
didn’t start to smell, they had to look for fangs or a way to
arouse them.
To be successful, those folks above ground must have been very alert. A coffin has only about 20-40 minutes of air, so a person could go from dead to live to dead without the change being noted. To counteract this small window of time, Germany also built waiting mortuaries, where dead bodies could be held for longer periods of time. It came to be accepted that the only reliable sign death was putrefaction --- waiting mortuaries did not smell like flowers or fresh baked bread.

Modern EEG and EKG have reduced the chance of premature burial or cremation, but mistakes do get made. In 2007, a Venezuelan man awoke during his own autopsy, and Quigley also writes of several modern instances of near-premature burial. Furthermore, the need for quick burial during epidemics has been replaced by the need for timely organ harvests – maybe they aren’t done with that kidney yet!

Next week we will take Halloween and death one-step further – could Halloween, or anything else for that matter, literally scare you to death?


It’s All in the Numbers - Sizes in Nature

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If all the animal species are broken up into groups, the light 
blue section includes insects, and the rest of the 
circle colors represent every other animal on Earth!
Comparisons help to make very big or very small numbers meaningful, and biology is chock full of big and small numbers. For instance, there are more insects in the world than there are humans. By more, I mean ALOT MORE, something like 1.5 x 1018 insects. But what does that number mean? Consider looking at it this way; the world population hit 7 billion last year and that's a big number, but even if we were to double our population again in the next ten minutes, there would still be 100 million insects for every human on earth. This certainly makes an impression, but it seems small when comparing the most numerous organisms, bacteria, to humans.

Bacteria outnumber us by orders of magnitude more than insects do; they live everywhere, in every environment. They have been found in 0.5 million year-old permafrost as well as 40 miles up in the atmosphere. There are approximately 100 million to 1 billion bacteria in every teaspoon of dirt, so in total there are currently 5 x1030 bacteria carrying out their daily routines. That means there are about 5 x 1019 living bacteria (that is 50,000,000,000,000,000,000) for every person who has EVER LIVED. Another way of visualizing this might be to imagine that each bacterium is a penny being stacked. The column would be a trillion light years high. That’s about five times the diameter of the observable universe.


Nanobacteria are still controversial, the 0.2 µm diameter is 
close to the smallest size that could still hold DNA. 
For comparison, the white line in panel A is 1 µm long, 
and in Panel C the line is just 0.1 µm.
While the redwoods might be slightly taller than the sequoias, 
the mass of the sequoias is much greater because the 
trunks have such a large diameter.
Even using comparisons and analogies, these numbers are almost too big to comprehend. It isn’t much easier when talking about sizes. The scale of life is amazing, from the smallest bacteria (called nanobacteria), just 0.2 µm in size (1/5,000,000 of a meter), to the biggest living thing on Earth, a Giant Sequoia called General Sherman. This behemoth of a tree is more than 83 meters (272 ft.) in height and 1,225,000 kilograms (2,701,000 lb.) in mass. This means that from smallest to largest, life spans more than eight orders of magnitude. In terms of biomass, the difference between the smallest bacterium and General Sherman is even greater, about 1 x 1023, about the same as difference in mass as one human compared to seven Earths.

On a smaller scale, the difference in size between bacteria and nucleated cells (eukaryotic cells) is still pretty stunning. A single macrophage cell of your immune system can ingest more than 100 bacteria without flinching, and macrophages are nowhere near the biggest eukaryotic cells. These different sizes demand some distinctions in how cells conduct their business; for example, how they move molecules into and within themselves.


A macrophage reaching out and ingesting bacteria.
The bacteria are the small, connected rods.
Eukaryotic cells, unlike prokaryotic cells (bacteria and Archaea), have specialized systems, like actin filaments, cytoskeleton, and microtubules. These apparatus are designed to act like conveyor belts; they carry different molecules through the cell to their needed destinations. Eukaryotes also have specific receptors for bringing in specific molecules. These are fast systems of uptake and movement, and can work against a concentration gradient.


The cytoskeleton of the eukaryotic cell stretch out like fibers.
They help it move, can convey molecules from place to place,
and holds the cells shape.




Unfortunately, bacteria only have diffusion to move molecules around their insides. This makes things doubly hard on them because bacteria have limited access to resources; most often they meet up with few molecules that are important to them (being a small cell in a big environment). Therefore, they need to get as many of these resources into their cell as possible and move throughout their entire volume quickly.

Diffusion is the movement of molecules from places where there a lot of them toward places here there are fewer of them (from high concentration to low concentration). Think of a crowd pouring out onto the football field after a big win. You start with many people in the stands and very few on the field, but end up with about an equal number of people in all parts of the stadium. Bacteria count on consuming their nutrients this way. Important molecules diffuse into the cell, and then get metabolized for energy or other building blocks. This breaking down and reassembly of molecules helps ensure that the concentration of important molecules is always lower inside the cell, so diffusion into the cell can continue. Importantly, as the width or length of a cell doubles, the volume increases by a factor of eight; therefore, prokaryotic cells remain small so that they can get molecules everywhere they need them quickly. It is the only way for diffusion to remain profitable for them.


Diffusion is the movement of from where there are 
many to where there are few. If it is water 
molecules that are moving, then call it osmosis.
Diffusion is not quite as simple as people pouring out the stands. There are several aspects of this process that are important to bacteria. The first of these is the diffusion rate, which is based on a diffusion coefficient for each different molecule, and the liquid it is moving through. For oxygen moving through water, the diffusion rate is about 1 mm/hr. This means that for an average sized bacteria it only takes 1 millisecond (1/1000th of a second) for an oxygen molecule to travel across the entire cell.

There is also the mixing rate; this refers to the time it takes for a molecule that enters the cell to have an equal probability of being found in any part of the cell. A 1µm (1/1,000,000 of a meter) bacterium has a mixing time of roughly 1 millisecond. But since the volume increases by a factor of eight as the size doubles, it would not take much growth for the mixing time to become problematic if a cell was to rely on diffusion alone.

Finally, there is the issue of traffic time. Every reaction that takes place in a cell involves two or more molecules finding one another and then interacting. In both prokaryotic and eukaryotic cells there are some systems designed to help bring molecules together, but in the end, it is basically luck – they have to run into one another. The number of molecules can affect this time; say you want molecule A to meet molecule B. If the cell contained only one of each molecule, this could take a while, but if there are 1000A’s and 1000B’s, then the traffic time will be decreased considerably. For average sized bacteria, traffic times exist in the range of 1 second, but again, if they are much bigger, the chances of molecules meeting their partners goes down dramatically.

If the bacterium grows too big, the diffusion rate, mixing time, and traffic time can become too long to permit survival. Therefore, size limitations seem to be set for bacteria. However, some bacteria just have to be rule breakers. There are two excellent examples of bacteria that have evolved ways to overcome the diffusion problems associated with increased size, and we'll start to look at them next week.



Schulz, H., & Jørgensen, B. (2001). Big Bacteria Annual Review of Microbiology, 55 (1), 105-137 DOI: 10.1146/annurev.micro.55.1.105



For more information on numbers in nature, diffusion, and cytoskeleton, as well as web-based activities and experiments, go to:

Cell size and volume:
http://staff.jccc.net/pdecell/cells/cellsize.html
faculty.massasoit.mass.edu/whanna/121_assets/15-week_2_prelab.pdf
http://www.youtube.com/watch?v=qdvKM1m0jnE
http://www.cellsalive.com/howbig.htm
www.nsa.gov/academia/_files/collected_learning/high.../surface_area.pdf
www.smccd.net/accounts/bucher/modules/DuzSizeMatter.pdf
http://www.accessexcellence.org/AE/AEC/AEF/1996/deaver_cell.php


scaling in nature:
http://www.nature.com/scitable/content/the-sizes-of-organisms-span-21-orders-15321100
http://learn.genetics.utah.edu/content/begin/cells/scale/
http://www.dnatube.com/video/596/Size-Analogies-of-Bacteria-and-Viruses
http://www.smithsonianeducation.org/educators/lesson_plans/size_shapes_animals/index.html


diffusion:
http://www.biologycorner.com/bio1/diffusion.html
http://highered.mcgraw-hill.com/sites/0072495855/student_view0/chapter2/animation__how_diffusion_works.html
http://staff.jccc.net/pdecell/cells/diffusion.html
http://hyperphysics.phy-astr.gsu.edu/hbase/kinetic/diffus.html
http://www.wisc-online.com/objects/ViewObject.aspx?ID=ap1903
http://www.biologycorner.com/2009/09/16/diffusion-lab/
http://chem.lapeer.org/Bio1Docs/Diffusion.html
http://www.biologyjunction.com/osmosis__diffusion_in_egg_lab.htm
http://phet.colorado.edu/en/contributions/view/3415


cytoskeleton:
http://www.cellsalive.com/cells/cytoskel.htm
http://www.youtube.com/watch?v=5rqbmLiSkpk
http://www.biochemweb.org/cytoskeleton.shtml
http://www.biology.arizona.edu/cell_bio/tutorials/cytoskeleton/page1.html
http://www.biology.arizona.edu/cell_bio/tutorials/cytoskeleton/main.html
http://www.youtube.com/watch?v=zlYyoi5vpE8

Breaking the Size Barrier – Giant Bacteria, part 1

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If you double the size of a cell in each direction, the volume 
increases eight fold. This makes take eight times longer 
for a molecule to diffuse through the whole cell.
Last week we talked about how the reactions that must take place inside cells often limit the maximum size of bacteria. Because important molecules can reach every part of the bacterial cell only by diffusion, the organism can’t have too large a volume. At the same time, the bacterium needs as much surface area as possible for important molecules to diffuse into the cell. This means that they need a high surface area: volume ratio. We showed last time that if you double (2x) the length of a bacterium in three directions, then the volume is increased eight fold (8x). This would result in cubing (23=8) the mixing rate and traffic time as well. If the size of a bacterium was increased from a typical size of 1 µm to a theoretical 100 µm bacteria, it could take almost a day for two molecules to find one another (traffic time). It wouldn’t seem plausible that bacteria this size could remain alive.

HOWEVER, I want to show you two bacteria that have found ways around this size limitation. Even more impressive (and a sign of how inventive nature can be), each of these organisms has found a different way to beat the system. Our two examples are the two largest prokaryotes known, and can be seen by the naked eye. This is really something considering that we can’t see our own cells without a microscope.

Our first size offender is called Thiomargarita namibiensis (T. namibiensis). The thio- part of the name means that this is a sulfur oxidizing bacterium, while the last part of its name records that it was first found on the ocean floor just off the coast of the African country, Namibia. Sulfur bacteria change elemental sulfur (S0) into sulfur oxides (SO2-4). These reactions release enough energy to make ATP (the chemical energy of the cell). In order to carry out these oxidation reactions, some sulfur bacteria use nitrate as an electron acceptor during ATP production. This works out just fine when there is a lot of nitrogen present in the immediate environment, but at the bottom of the ocean this is not always the case. Most of the nitrogen comes within reach of the bacterium only after a storm disturbs the ocean floor.

Our “sulfur pearl of Namibia” bacterium (arrow) is as big 
as the head of the fruit fly. To compare, each 
eye of the fruit fly contains over 16,000 cells!

Therefore, T. namibiensis must scavenge as much nitrogen as possible and store it within a large central vacuole (a membrane bound sac) for the lean times. It also stores sulfur in smaller granules, leading to a speckled pearl-like appearance over the clear nitrogen vacuole (which explains the middle part of name, margarita = pearl. Often, these bacteria stick together in a line and look like a string of pearls).

T. namibiensis is a spherical bacterium. Round cells are least well equipped for good mixing and traffic times; the center is far from any cell surface. But if the cell was flattened out or narrow in one dimension the traffic times could be reduced, even if the organism was larger. For this reason, many bacteria are not round, but perhaps rod-shaped or flattened rhomboids. Here we see that T. namibiensis is huge (up to 750 µm) while still spherical. That size makes it just about the size of the period at the end of this sentence; not much compared to a beach ball, but 3 million times the volume of a typical spherical bacterium.


T. namibiensis usually occurs in chains of ten or so bacteria, with pearlescent sulfur granules as shown in the left image. In cross-section on the left, you can see both the thin band of cytoplasm and the large nitrogen-containing vacuole.

The first key to Thiomargarita’s size is that large central vacuole of nitrogen. As shown in the righthand photomicrograph (courtesy Woods Hole Oceanographic Institute), there is only a thin layer of cytoplasm (the essential, viscous, water-based medium that fills the cell) between the vacuole and the cell membrane. The vacuole itself consumes almost 98% of the total cell volume. This small layer of cytoplasm means that all the important molecules are close to the surface through which they diffuse; therefore, the large size of the cell does not violate any limitations placed on its mixing rates or traffic times. While the size of the bacterium is huge, the distance any one molecule has to travel is still small. In fact, the amount of cytoplasm in T. namibiensis is just about the same as in a normal sized bacterium.

The large diameter of T. namibiensis also helps it survive in two ways that are less evident. One advantage has to do with the diffusive boundary layer. Because of the natural friction between all molecules, there is always an area next to any surface where the flow of liquid is reduced to near zero. Reduced flow means reduced numbers of important molecules can be picked and carried; therefore, the concentration of important molecules is reduced, a bad thing for bacteria trying to survive. However, because of the huge size of T. namibiensis, much of the cell sticks up above the sea floor’s diffusive boundary layer, into the area where diffusion can be more productive.

The second survival advantage is slightly more straightforward. T. namibienisis and other megabacteria are just too big to be bothered by predators. T. namibiensis doesn’t have to worry about being eaten, because no bacterial predator is big enough to “swallow” it. This is similar to the ancient sauropod species, like Brachiosuarus or Diplodicus, which had no predators once they grew to adult

Just like a T. Rex couldn’t bring down or swallow
a brachiosaur, a normal bacterium (the white dot
in the top right hand corner) can’t eat T. namibiensis.
size – a healthy sense of self-preservation would keep any T. Rex from trying to eat an adult brachiosaur.

We have seen that limitations on bacterial size imposed by diffusion can be overcome if natural selection results in some advantageous characteristic and if there is a reproductive advantage to be being big. The development of a central vacuole permitted T. namibiensis to become bigger, and being bigger provided an advantage for survival on the sea floor. It seemed designed to end up just so, but remember that evolution is not purposeful. It is merely a series of random changes and random environmental changes that render some characteristic advantageous, disadvantageous, or moot.

Next time we will look at another giant bacterium. This second rule-breaker has a completely different solution to the diffusion/size limitation. Just as we highlighted with the nylon metabolizing bacteria a few weeks ago, nature can find an infinite number of ways to overcome a single problem. It just takes random mutation (a change), environmental pressure (a need for the change) and time (for the reproductive advantage afforded by the change to have an effect on the population).


Schulz, H., & Jørgensen, B. (2001). Big Bacteria Annual Review of Microbiology, 55 (1), 105-137 DOI: 10.1146/annurev.micro.55.1.105

Girnth, A., Grünke, S., Lichtschlag, A., Felden, J., Knittel, K., Wenzhöfer, F., de Beer, D., & Boetius, A. (2011). A novel, mat-forming Thiomargarita population associated with a sulfidic fluid flow from a deep-sea mud volcano Environmental Microbiology, 13 (2), 495-505 DOI: 10.1111/j.1462-2920.2010.02353.x



For more information on surface area: volume, sulfur bacteria, and T. namibiensis, please see below:


Cell surface:volume laboratories:
http://www.oocities.org/capecanaveral/Hall/1410/lab-B-24.html
www.nnin.org/doc/SurfaceVolumeRatioB_TG.pdf
http://illuminations.nctm.org/LessonDetail.aspx?id=L609
http://www.neiljohan.com/projects/biology/sa-vol.htm


sulfur bacteria:
http://www.moldbacteria.com/bacteria_testing.html
http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/E/Eubacteria.html
http://filebox.vt.edu/users/chagedor/biol_4684/Microbes/greensul.html
http://bmb-it-services.bmb.psu.edu/bryant/lab/Project/GSB/index.html
http://m.biotecharticles.com/Biology-Article/Green-and-Purple-Sulfur-Bacteria-705.html
http://filebox.vt.edu/users/chagedor/biol_4684/Microbes/purprnb.html


Thiomargarita:
http://web.mst.edu/~microbio/BIO221_2005/T_namibiensis.htm
http://www.sciencenews.org/sn_arc99/4_17_99/fob5.htm

Fish Guts and Cancer – Giant Bacteria, part 2

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The gut of a fish is a strange place to go looking for bacteria. It’s an even stranger place to find the second largest bacterium on Earth.

Epulopisciumfishelsoni (E. fishelsoni) hangs out in the intestinal tract of the brown surgeonfish, commonly called the lavender tang. While it seems logical that E. fishelsoni would be named for the site where it was found – inside a fish – it was actually named for its discoverer, Lev Fishelson of Tel Aviv University.  

Epulopisciumfishelsoni is shown in the left image. The white line is approximately 100 µm. On the right is the Lavender Tang.  E. fishelsoni lives in this fish’s gut, and only in this fish’s gut.

Before T. namibiensis (last week’s post) was discovered, E. fishelsoni was the biggest kid on the block, having been first seen in 1985. It can be seen with the naked eye, reaching a maximum length of 0.7 mm, but it also has large size variations. In fact, this is one of the keys to its success.

E. fishelsoni’s changing size is a daily routine. In the early morning, E. fishelsoni is only about 10 µm long, only 2-5 times bigger than typical bacteria. As the surgeonfish starts to feed, more food is available to the bacteria in its gut. With this signal, E. fishelsoni starts to grow. By late afternoon into evening, the maximum size has been reached and they can be seen with the unaided eye (if you happened to be in the fish’s gut to see it – I wouldn’t recommend it as a holiday destination).

However, after the night passes, you would find just the small cells again in the morning. You would also see that the number of bacteria has increased.  The large cells have divided into daughter cells, splitting their cellular contents between their two or three new partners. Then, as a new day passes and food becomes available in the gut, these cells grow large and divide overnight. 


Could you imagine having your baby grow 75x bigger in one day?
Think of it this way: you bring home your 22-inch long newborn baby in the morning and place it in its crib.  That night, you find that you have a baby that is 140 ft. tall. You start to build the world’s largest crib, but by morning, the giant is gone and you find two 22-inch babies in the crib. It would continue like this everyday. Parenting is difficult.

E. fishelsoni’s shape is also different than that of T. namibiensis. E. fishelsoni is shaped like a long grain of rice, as opposed to the spherical T. namibinesis. This can help meet diffusion needs (see this post), since the distance to travel is much shorter for molecules brought in on its long sides. The elongated shape is enough to make the new daughter cells viable. But as the cells grow during the day, merely being longer than they are wide isn’t enough to overcome diffusion rate, mixing rate, and traffic time limits. E. fishelsoni must know another trick in order to survive at is maximum size.

In the majority of molecular interactions, it is a cellular protein that partners with a molecule that has diffused into the cell. What might E. fishelsoni do to increase the chance that an enzyme will find its substrate (the molecule an enzyme acts on and changes in some way) quickly?

Remember in the “It’s all in the Numbers” post, we saw that one way to reduce traffic time was to increase the number of one or the other interacting molecule. It is impossible for the bacterium to raise the concentration of nutrients, but it can raise the number of proteins made by the bacterium.


The central dogma of molecular
biology.
We need a bit of background to help explain E. fishelsoni’s trick to producing more copies of its proteins. There is a central dogma (core belief) to cell molecular biology: DNA goes to RNA goes to protein. This means that DNA is transcribed to a message (mRNA), which is then translated into a protein. However, if you want to make more protein, you can’t just transcribe more RNA from the DNA in the cell. This process is highly regulated and can only be manipulated to a certain degree. The other problem with this solution is that the proteins would be produced near the site of the DNA, so these extra proteins would have to travel a long distance to mix through the entire cell – this wouldn’t solve the mixing time (diffusion) problem.

What if the cell made more copies of its DNA and spread them out through the cell? Then the cell could produce much more RNA and hence much more protein. Having the DNA spread throughout the entire bacterium would solve the mixing time problem.


Fold number of chromosomes is a cell’s ploidy. 
N= haploid number of chromosomes, N in humans = 23, 
but we are diploid, so the total number of 
chromosomes is 2 x 23 = 46.
How would a bacterium make more copies of its entire DNA (its genome)? Isn’t the number of copies of DNA determined and unchangeable? In general, bacteria are haploid, meaning that they have one copy of each (usually just one) chromosome. Human cells (except for sex cells) are diploid, meaning they have two copies of each chromosome (one from Ma and one from Pa). Some plants exhibit triploidy, especially the seedless varieties of fruit, like bananas and watermelons. Finally, while polyploid cells (poly = many and ploid = fold) can occur naturally in lower animals and some plants, in humans it is often associated with cancer cells. The more copies of the genome there are in a cancer cell, the worse the prognosis (predictable outcome) for the patient.

E. fishelsoni has found a way to make being polyploid work for it. The early morning version of the bacterium (the small cell) is haploid, but as the cell volume increases hour by hour, the amount of bacterial DNA also increases through the circadian cycle (the daily sequence of physiological events).


Green color in inset shows the huge amount of DNA dispersed throughout  
E. fishelsoni. Courtesy of: Ward, R.J., Clements, K.D., Choat, J,.H. 
and Angert, E.R..  2009.  Cytology of terminally differentiated  
Epulopiscium mother cells.  DNA and Cell Biology 28:  57-64.
By evening, the mega-E. fishelsoni has 85,000 copies of its genome! Scientists don’t have a -ploidy name for a number that big; just plain polyploid. This is a huge amount of DNA for a prokaryotic cell, and is 25% more DNA than contained in a human cell.  The new DNA copies are spread throughout the cytoplasm to provide thousands of local protein factories. Wherever there is a diffused nutrient, the proper protein it needs to interact with won’t be too far away. Therefore, E. fishelsoni can disregard the usual size limitations placed on it by diffusion.

This bacterium still has much to teach us; for instance, I wondered about all that extra DNA. If there are 85,000 copies in the parent cell, but the two or three daughters that result from it are haploid (1 copy/daughter cell), what happened to the other 84,997 or 84,998 copies of the genome? I asked Dr. Fishelson about this, and he said, “there are several questions concerning this enigmatic bacterium, one of which is what you are asking about - what is the fate of the ‘surplus DNA’ as the daughter cells are produced?” If we figure out how E. fishelsoni gets rid of its extra DNA, we could take advantage of the process. Wouldn’t it be something if we learned how to beat cancer by studying a bacterium in the gut of a fish?




Bresler V, Montgomery WL, Fishelson L, Pollak PE. (1998). Gigantism in a bacterium, Epulopiscium fishelsoni, correlates with complex patterns in arrangement, quantity, and segregation of DNA J Bacteriol., 180 (21), 5061-5611 : 9791108


  For more information and activities on ploidy, central dogma, see below:

Ploidy –

Central dogma –

Give Thanks For The Cranberry

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Biology concepts – epigynous berries, seed dispersion, scarification, drupe, endocarp


Ocean Spray alone sells 86.4 million cans of jellied cranberry
sauce each year. No matter which sauce you prefer, I bet it
has a lot of added sugar. Cranberries alone are tart enough
to shrink your head.
Cranberry sauce is a Thanksgiving staple, but it’s a lot like fruitcake at Christmas – you either love it or hate it. Let me give you some reasons to love it.

Cranberry (Vaccinium macrocarpon) is one of very few commercially grown fruits native to North America. The vine needs cool temperatures and acidic, sandy soil conditions, so New England, Southern Canada and the Pacific Northwest are prime growing locations. Similar latitudes in Europe also support growth of cranberries (Vaccinium oxycoccus) in their bogs. We have previously talked about bogs where the acid conditions preserve human remains and produce bog mummies.

But there is an exception in the Southern Hemisphere – Chile in South America. In the northern part of Southern Chile, volcanic ash soils mimic the sandy soils of peat bogs, both in consistency and acidity. Runoff from the Andes Mountains allows for water, and the temperatures are similar to those in Washington and Oregon - perfect for cranberry growing.

The Ocean Spray Company harvests berries in North America in autumn, but it needs berries in the summer too. In January of 2013, Ocean Spray bought the cranberry processing interests in Chile. The harvesting period in Chile is March to May, just in time to supplement Ocean Spray’s dwindling supplies.

Cranberries are tart compared to other fruits; they have five times as much acid as their close cousins, the blueberries. Why? It may be the acidic soils they grow in. In terms of evolution, growing in peat bogs was a good choice. Not many things can grow in a bog, so competition is low. Competition for what is the question – there is very little nitrogen in the soil of a bog, and the water is acidic too.

Plants need fresh water and nitrogen to survive, so the cranberry evolved better nitrogen tapping mechanisms, as well as leaves and stems that can retain their fresh water very well. Not many other organisms have adapted to these conditions, but the cranberry thrives, transferring the acids to its leaves, stems and fruits.

This is the bog copper butterfly (Lycaena epixanthe) that
lives its entire life on a cranberry vine. It not only survives
the acidic condition of the plant – it eats it up. It lays its eggs
on the under side of the leaf, and the pupa and the larva can
survive a flood that covers the plant for months.

This acidity is also a help when it comes to pests. Several acidic compounds have been isolated from V. macrocarpon that stop insects from eating the leaves and stems. I’m guessing insects don’t like Sour Patch Kids. The exception is the butterfly Lycaena epixanthe; it spends its entire life feeding on the cranberry plant.

The second reason for the high acid content of the cranberry is that it doesn’t need to be sweet. The blueberry is much sweeter, but it  has to be. Blueberry bushes spread their seeds by having birds, rodents, or humans eat them one place and excrete them in their feces somewhere else; sweetness promotes consumption.

Seed dispersal is the most basic reason for any plant producing a fruit. If a seed falls directly beneath the parent plant, no one wins. Both patent and child will require the same nutrients, and they will end up competing for everything. Things would also get very crowded.

Several mechanisms of seed dispersal have evolved. Wind is a popular way to disperse seeds. You’ve seen those helicopter seeds from Maple trees – they catch the air and twirl down vertically, but also move horizontally. Sycamore trees have tufts on their seeds to catch the wind as well.

Fruiting is also a way to disperse seeds. Animals need carbohydrates, and fruits are an important source for many animals. When they eat the fruit, they also eat the seeds. Later on, the animal grabs a copy of Sports Illustrated, locks the door, and deposit the seeds somewhere else.


These are some of the types of fruits. The peach is a drupe. It
has an edible mesocarp. The coconut is also a drupe, but its
mesocarp is more fibrous (flake coconut). The tomato is a true
berry. It’s pericarp and locules or all edible. The raspberry is an
aggregate fruit, many ovules and mesocarps held together. The
raspberry is also a drupe, which you know when you get those
seeds stuck in your teeth. Each little fruit is a druplet.
In fact, some seeds must pass through the digestive tract of an animal in order to germinate. Some seeds, like those of drupes (drupa = overripe olive), have a hard endocarp (seed coat), derived from the ovary wall. In fact, that’s what makes a drupe a drupe. Fruits like peaches, almonds, coconuts, olives, are considered drupes and each little part of a blackberry or raspberry is a druplet.

The germinating embryonic plant isn’t strong enough to break through the drupe endocarp on its own. Something must be done to weaken the endocarp. The weakening (scarification) may come from scratching the surface, freeze/thaw, fire (for the Ponderosa Pine), or perhaps from the digestive enzymes of an animal. Many berries, like blackberries, currants, and raspberries requiredigestive scarification in order to germinate. But the cranberry isn’t one of these berries.

Why don’t cranberries need to be eaten for seed dispersal? Because they float! When the bog (or similar sandy wetland) floods, the berries are carried away from the parent plant, away to some far off place that may or may not be suitable for cranberry vine growth. That’s the problem with floating; you gotta go with the flow.

Cranberries float because they have air pockets trapped within them. Floating fruit isn’t that exceptional, apples float too. It’s a good thing; think how may lives this has saved during bobbing for apples season!

On top we see the coconut – it’s a drupe with a tough exocarp.
You can see the germinating plant coming through one of the
eyes. Seed dispersal for the coconut is shown on top right. We
don’t know where palms come from originally, because they
could spread around the world in just one generation. The
cranberry also floats, because of the air pockets shown on the
bottom right. The frog is just a bonus – cute, huh?

Given their bouyancy, it amazes me that it wasn’t until the 1960’s that someone thought of flooding the bogs in order to harvest the cranberries. They have machines that shake the vines and release the ripe berries.

Cranberry plants grow very low to the ground, they have long runners (rhizomes), that can extend six or more feet from the parent vines, and these can sink roots to become new plants. Because of their short stature, it only takes about 18 inches of water to flood a cranberry bog for the wet harvest. So those commercials with the two goobers standing waist high in water in their waders are a bit of a stretch.

The cranberry was probably at the first Thanksgiving; they are hearty and ready to be harvested just about the time we are sitting down to our turkey and stuffing.  But, the pilgrims misled us – the cranberry isn’t a real berry! And don’t say it was because the pilgrims were from across the ocean. The cranberry is closely related to the European lingonberry, so the mistake had already been made.

The cranberry is a false berry, also called an epigynous berry (epi = in addition to, and gynous = ovary). A berry is a fleshy fruit derived from a single ovary. False berries develop from an inferior ovule and contain tissues from parts of the flower other than the ovary, while true berries develop from superior ovary tissue only (see picture). Other examples of epigynous berry-producing plants are bananas, coffee and cucumbers.


Here is one difference between real and false berries. All true
berries are hypogynous, where the ovary (in red) is above
where the petals and pistil come out. False berries have an
inferior ovary. Another difference is that the true berry is
made from only the ovary, while the false berry incorporates
other parts of the flower. Below on the left is the red currant,
and on the right is the cranberry. As a berry, the currant is true
and the cranberry is false. But really, can you tell the difference?
The V. macrocarponfalse berry fruit is indispensible as a Thanksgiving sauce, but medicine has found other uses for cranberry compounds. In the first 10 months of 2013 alone there were 86 papers published on the merits of cranberry compounds.

Most people who know about medicinal cranberries have had a urinary tract infection (UTI). For a hundred years or so, old wives (and young wives) have espoused the virtues of cranberry juice in preventing or treating UTIs.

Recent years have seen many studies try to validate the home remedy. As for if cranberries work, there is evidence on both sides. Hundreds of published reports say it’s the best thing since sliced bread, and hundreds say it doesn’t do a darn thing. Such is science – and that’s a good thing. Argue away so we know we get it right in the end.

One 2013 study found that sweetened dried cranberries added to the diet made a real difference in women who were susceptible to UTIs. Half the women in the study didn’t have even one UTI while on the study, and they all had reduced numbers of incidents.

As for why caranberries may work, scientists first thought it was the acid that killed the UTI-causing bacteria. Then it was believed that cranberry compounds prevented the attachment of the bacteria to the wall of the urogenitial epithelium via the bacterial fimbriae (appendages for attachment). This may actually be true, but other actions are also possible.

Another 2013 study showed that for the UTI causative agent Proteus mirabilis, eating powdered cranberry was very effective for preventing UTI. In this experiment, the researchers found that the organisms did not swim well or swarm when exposed to cranberry compounds. In fact, the gene that expresses proteins for their flagella (for motility) were inhibited by cranberry powder.

In addition, their urease virulence factor was also suppressed. A virulence factor is any molecule that helps an infectious organism to colonize and/or obtain nutrition from a host, or helps it to evade or suppress the host immune system.

This is a dividing bacterium showing the fimbriae that help it
attach to surfaces. You can see the difference between these
and the flagella that help in the motility of the organism. It
may be that cranberry compounds mess with both to
prevent UTIs.

Not to be a downer, but a different group carried out a meta-analysis (an organized compilation of many studies involving a lot of statistical math) of many cranberry/UTI studies in 2013 and determined that cranberry compounds have no effect on the prevention or treatment of UTIs. So, all that talk about just how cranberry molecules suppress UTIs (fimbriae, acid, down regulation of host molecules) can be ignored if you don't believe they work.

The news is better on other fronts. In obese men, cranberry juice was able to inhibit the stiffening of blood vessels, an important factor in development of cardiovascular disease (CVD). The effect was greatest in men with metabolic syndrome– a combination of high blood pressure, blood glucose, and cholesterol, as well as obesity.

A second study confirmed this by showing that 1 cup of cranberry juice each day reduces blood glucose levels and CVD risk in men with type II diabetes. And this is just the beginning; 2013 studies also show how cranberry compounds may help you age well– this makes sense, some vines have been producing cranberries since before the American Civil War. Other studies show that cranberry is a potent anti-viral agent as well as preventing bacterial UTIs. Respect the berry – uh, false berry!

Next week, let’s talk about another symbol of Thanksgiving, the indian corn that you think is just decorative is actually a fascinating story of discovery.



Burleigh AE, Benck SM, McAchran SE, Reed JD, Krueger CG, & Hopkins WJ (2013). Consumption of sweetened, dried cranberries may reduce urinary tract infection incidence in susceptible women -- a modified observational study. Nutrition journal, 12 (1) PMID: 24139545

McCall J, Hidalgo G, Asadishad B, & Tufenkji N (2013). Cranberry impairs selected behaviors essential for virulence in Proteus mirabilis HI4320. Canadian journal of microbiology, 59 (6), 430-6 PMID: 23750959

Lorenzo AJ, & Braga LH (2013). Use of cranberry products does not appear to be associated with a significant reduction in incidence of recurrent urinary tract infections. Evidence-based medicine, 18 (5), 181-2 PMID: 23416416

Ruel G, Lapointe A, Pomerleau S, Couture P, Lemieux S, Lamarche B, & Couillard C (2013). Evidence that cranberry juice may improve augmentation index in overweight men. Nutrition research (New York, N.Y.), 33 (1), 41-9 PMID: 23351409

Shidfar F, Heydari I, Hajimiresmaiel SJ, Hosseini S, Shidfar S, & Amiri F (2012). The effects of cranberry juice on serum glucose, apoB, apoA-I, Lp(a), and Paraoxonase-1 activity in type 2 diabetic male patients. Journal of research in medical sciences : the official journal of Isfahan University of Medical Sciences, 17 (4), 355-60 PMID: 23267397


For more information or classroom activities, see:

Seed dispersal mechanisms –

Scarification –

Different types of fruits –

Fimbriae and flagellae –



Corn Color Concepts

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Biology concepts – maize, transposon, antigenic variation, cereal grain, food grain, caryopsis



The Corn Palace in Mitchell, South Dakota, uses corncobs
to make murals on the sides of the building - yes, the mural
on the right is made of corncobs. Each year’s murals have a
different theme, and they use 13 different shades of corn in
their artwork, but after the drought of 2012 they only had 8
shades to work with for 2013. This is a picture of the palace
as it appeared in 1907. Notice the questionable decoration
on the center minaret – of course this was 25 years before
the rise of the Nazi party.
Thanksgiving decorations typically include some colorful earns of dried corn, commonly referred to as “Indian corn.” However, this corn has a history much more involved than mere decoration. People might be less inclined to hang it around their house if they knew how much it has in common with the organisms that cause gonorrhea, Lyme disease, and Pneumocystis pneumonia.

One of the first misconceptions we have to get out of the way is that corn is actually corn. The word corn doesn’t literally refer to the stuff on the cob we eat in the summer and the stuff we pop on a cold afternoon. What we call corn is much more accurately called maize.

The word "corn" comes from an old german/french word. In most uses before the 1600’s, corn meant the major crop for one particular area or region. In England, corn meant wheat; in Scotland or Ireland, it most likely means oats. There is even mention of corn in the King James Bible. This was translated several times and hundreds of years before maize arrived in Europe. The “corn” of the Bible most likely means the wheat and barley that were grown in the Middle East at the time.

When Columbus took maize (Zea mays) across the Atlantic to Europe, he might have referred to it as the chief crop of the Indians; therefore, it was Indian corn. After a while, domesticated maize became so ubiquitous that the word “Indian” was dropped, and all maize became corn – like all facial tissue becoming Kleenex.

The history of maize is, well, a-maizing. The corn we know today is the most domesticated of all crops. It can’t survive on its own; it has to be managed by man. Rice and wheat have naturally wild versions of themselves that still grow in nature, but there is no wild corn, it is purely man-made.


Today’s “corn” is actually a selective breeding result from a
grass called teosinte and a grass called gamagrass. Genetic
experiments have confirmed that each of these grasses was
involved in the evolution of maize. There was also some back
crossing of early maize with the grasses again. You can see
how the kernels and plants have changed over time.
The earliest corn-like plant was called teosinte. It's a grain plant with very small, vertical kernels. This plant was bred with something else, maybe gamagrass, and over time became early maize. Early maize was then bred back to teosinte, and the cob emerged. A recent article from Florida State shows that corn was being bred and harvested as early as 5300 BCE.

The early plants were quite variable, growing from 2 to 20 feet tall. The ears, when they developed, were small and had only eight rows of kernels. More breeding took place, especially when the plants were brought north. At that time, ears grew near the top of the plant, and the growing season in the north was too short to allow full development.

Maize is a grass, so it has the nodes and internodal growth as we discussed a few months ago. Corn grows about 1 node unit for each full moon; the Indians needed a corn that would mature in just three moon cycles. So they planted kernels from stalks that had the lowest ears, thereby selecting for plants they could harvest before it got too cold. Their selection was for size and production, but colors came along for the ride.

There are many color genes possible in maize. A new version, called glass gem corn, shows just how many colors are possible (see picture). Indian corn, as we define it now, can be found in most of these colors; sometimes ears are all one color, sometimes they are combinations of colors. It all depends on who is growing nearby, but we need to know a little more about corn in general to explain this.

This Carl’s glass gem corn. The photographer swears there
was no manipulation of this image. The corn is just this
pretty! I’d hate to eat it. This strain was the result of many
years of selective breeding, and the seeds were passed
down through a couple growers before they got this result.

Maize is a food grain, meaning that has small fruits with hard seeds, with or without the hulls or fruit layers attached. More specifically, maize is a cereal grain, because it comes from a grass. Wheat is a grass, so is barley, rice, and oats. Basically, these are the grains your morning cereal is made from, so which came first, the breakfast “cereal” or the “cereal” grain? The answer is out there.

And by the way - yes, grains are types of fruits. The fruit is more precisely called a caryopsis (karyon means seed); a small fruit and seed from a single ovary, which doesn’t split open when mature (indehiscent). One of the characteristics of most grains is that the pericarp (the fruit) is fused to the seed coat, so it is difficult to talk of the fruit without including the seed.


The point of this cartoon is to show you that there are
many layers to the kernel. The whole thing is not the
embryonic plant, just the germ. Some people say wheat
germ is healthy to eat. It would take a lot of kernels to get
much germ. You can see the hull is made up of several
layers as well, this is here the color is expressed. The
endosperm is what tastes food. It is many cells, all
storing the sugars.
The hull is a little more vague. Corn has a husk(the leaves that surround the ear), which is often considered the same thing as a hull. But each kernel on the ear also has a hull, the epidermis that is more brittle when dried. In other plants, husk and hull mean the same thing.

It's the hull that shows the color of a kernel of maize. You can pop blue, red, or purple corn, but the popcorn will still be whitish yellow.The color genes are present in all the cells of a kernel, but they are only expressed in the epidermis or hull; this will be important in a minute or two.

So how can Indian corn have kernels of different colors? The same way that you and your siblings look different. Each kernel is a different seed, so each is a different potential plant. The male flowers of the corn tassel send out grains of pollen to pollinate the female flowers. Each pollen grain has a sperm cell, and each has undergone the same process of mitosis and meiosis as human sperm – there is genetic variation there.

The female flowers are the silks on the ear of corn. Each silk is connected to a different ovary (potential kernel). Again, each egg is a different version of the maternal plant’s genome. Different silks could be pollinated by different male plant pollens floating around in the air – nothing says that all the kernels must have the same dad.

What we call Indian corn is just corn that has not been bred
so much as to have only color gene, and can be pollinated by
different dads. You can see that Indian corn can have several
colors or one major color. The interesting parts are those
spots and streaks. Read on for more about them.

So, it isn’t to difficult to see that different kernels could be different colors, either from random assortment and mendelian genetics, or from different pollens meeting different eggs. The reason we eat yellow corn or white corn or yellow/white corn is because the color genes have been selected for by breeding, and the pollination process is highly controlled. This is not the case with Indian corn.

So that’s the story for corn color – or is there more? Look closely at Indian corn above; some kernels have streaks or spots of color. How does that happen?! This is completely different from having kernels of different color, and relates to one of the great exceptions in DNA biology.

Barbara McClintock found that by observing the chromosomes of maize very carefully, specifically chromosome nine, and by looking at the resulting kernels from selective breedings, she could match changes in the chromosome to changes in color streaks and spotting.

She noticed changes in the length of the arm in some cells, and related this to the movement of genes along the chromosome. To this point, all scientists believed that genes stayed in the same place on a chromosome forever. McClintock saw genes jumping from one place to another. She called them transposons.


The mechanism of transposon control in corn is a bit
complicated. The C gene codes for pigment, but can be
disrupted by the Ds transposon. (top). If Ds never moves
out, then the kernel will be white in this example. If the Ds
gene never moves in, the kernel will be completely purple.
If it jumps out and in or in and out, then you get spots. The
bottom image shows that the early the change, the larger the
spot, because more daughter cells will have the functional
or dysfunctional gene.
But this jumping is not haphazard. It was under the control of another gene. When one gene (Ds) was activated to jump by another gene (Ac), its new position disrupted a third gene’s (C) sequence (Ds = disrupter, Ac = activator, and C = color).

When Ds was located inside C, no color was produced, but when it was not, the daughter cells could produce color. A kernel has many cells that divide and divide, so some progeny could switch back and forth and produce cells on the hull that may or may not be able to produce the color protein (see picture). If the move to disrupt C occurred early, more daughters would be produced and more of the surface would lack color. If it was late, the spot would be smaller (see bottom image to left).

This idea of jumping genes was revolutionary …. and not well accepted at first. Even though Barbara’s science was impeccable, others just weren’t as good at spying the small changes in the chromosome. It took a while for the laboratory techniques to catch up to Barb’s eyes – then they gave her the Nobel Prize.

From our new knowledge of transposons have come many discoveries – some not so savory. Some infectious agents, both bacterial and eukaryotic, use jumping genes to escape our immune system. Neisseria gonorrhea was one of the first shown to do this. Our immune system, given time, will find bacteria that have taken up residence inside us; in gonorrhea's case, through sexual transmission.

N. gonorrhea has found that if it can change its costume, our immune system must start over looking for it. The proteins it has on its surface are what our immune cells recognize, we call them antigens. Gonorrhea organisms can go through antigen variation; they have many surface antigen genes, and can switch them out if they are detected.


Variable surface glycoproteins are like selecting for antibiotic resistant
bacteria. One organism may switch its VSG for antigenic variation,
just like one bacterium might pick up a resistance gene.
When the immune system finds and mounts a response to the
organisms with the “blue” VSG, they are killed, but now the “green”
VSG organisms can proliferate. This is like when the antibiotics kill
off the susceptible bacteria, the resistant ones (green) then
have more room and food to overgrow.
They do this by moving different surface antigen genes in and out of an expression site. Only the surface antigen gene in the expression site is transcribed and translated to protein, but they can jump in and jump out when needed. Antigenic variation also occurs with Borrelia burgdorferi, the causative agent of Lyme disease, the Plasmodium falciparum of malaria, and Pneymocystis jirovecii, a eukaryote that causes the pneumonia most AIDS patients contract.

In the case of Pneumocystis, a 2009 study showed that there are over 73 major surface glycoprotein (MSG) genes that can be switched in and out. They differ by an average of 19%, so the protein sequence of each is markedly different. Even though we don’t know the function of the MSG, it would appear that it is designed to increase the variation of the organism, probably to avoid an immune response.

Still have that warm and fuzzy feeling about Indian corn as a representative of Thanksgiving?

Next week, we start to look at the last of the four biomolecules - lipids. Can you believe some people can't carry any fat on their body, no matter how much they eat?


It just so happens that Barbara McClintock and her corn made up a portion of a recent exhibition at the Grolier Club in NYC, entitled, "Extraordinary Women of Science and Medicine: Four Centuries of Achievement." The exhibit included one of Barbara's ears of corn and some of her breeding materials. The catalogue is available from Oak Knoll Books. Thanks to Karen Reeds, independent curator and museum consultant for the heads up.


Pohl ME, Piperno DR, Pope KO, Jones JG. (2007). Microfossil evidence for pre-Columbian maize dispersals in the neotropics from San Andres, Tabasco, Mexico. Proc Natl Acad Sci U S A. , 104 (16), 6870-6875 DOI: 10.1073/pnas.0701425104

Keely SP, & Stringer JR (2009). Complexity of the MSG gene family of Pneumocystis carinii. BMC genomics, 10 PMID: 19664205



For more information or classroom activities, see:

History of maize –

Transposons –

Antigenic variation -



The Best Cure for Insomnia Is To Get A Lot Of Sleep

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Biology concepts – theories of sleep, REM sleep, circadian rhythms, neural plasticity

You open the door to your house and find your roommate sprawled out on the couch. Is he sleeping, unconscious, or dead? Knowing your roommate, you figure it could be any of them – you stop yourself short of naming a preference.


You find your roommate passed out in his underwear,
and can’t decide if he is sleeping, unconscious or dead.
If you have chosen Homer as a roommate, you have
already clued us in to your decision-making abilities.
The live/dead question is easy; hold a mirror under his nose and see if it fogs up. If he’s not breathing, there’s only one thing to do – go through his pockets and look for loose change (with a nod to “The Princess Bride”). But if you do see condensation, how do you decide if he is passed out or just sleeping - or are you considered unconscious when sleeping?

Sleep is voluntary, at least most of the time. I try to stay awake at the ballet, but I don’t always succeed. But besides drinking yourself into a stupor, going unconscious is usually not voluntary. Unfortunately (or fortunately), you weren’t there to see what preceded the crease marks on your roommate’s face or his drooling on the couch pillow, so how can you identify his state?

Sleeping implies that one has a diminished ability to respond to external stimuli with reduced sensory perception. However, unconsciousness appears much the same. The difference lies in the degree of diminished capacity; you can be roused more easily from sleep and perhaps not at all from deeper unconsciousness. Some people I know must pass out every night, because they are tough to wake up. You might parse the difference and just say that sleep is more easily rousable unconsciousness.

Sleep has stages and these stages have cycles. If deprived
of a particular stage the night before, your body will
change your cycles so that you make up the lost time in
that stage on the next night. Source for image: http://xavier 
appsychology.wikispaces.com/Chapter+5,+ Period+6
A more profound difference between the two exists, but you won’t be able to detect it in your roommate without monitoring his brain waves. In sleep, you go through different phases, each with characteristic brain wave patterns. In 2007, a revised set of sleep stages was published, identifying 4 distinct phases, although stages 2 and 4 are repeated more than twice. Stage 4 is REM sleep, in which many many animals dream.

In general, the safer an animal is, the more it dreams. Predators dream more than prey and big species dream more than small species, though there are several exceptions to this rule. For example, ruminants (cows, deer, goats, and buffalo) dream very little (about 5 minutes/night), and cetaceans(whales, dolphins, porpoises) may not dream at all.

In contrast, animals that are born immature (not able to live on their own) tend to experience lots of REM sleep. These altricial (meaning “requiring nourishment") animals, including marsupials, cats, dogs, and most rodents, may have 6-8 hours of REM sleep a night. What is more, as adults they continue to dream heavily – about what, I have no idea.


Do you know the differences between dolphins and porpoises? Dolphins have longer bodies and snouts, and porpoises have a straight front edge on their dorsal fin. But, they are both cetaceans and have the same sleep patterns. Opposums, the only marsupials in North America, have immature young, and for some reason they dream much more. They are probably dreaming about the day their kids will get off their back.
 But even this exception has an exception. Many birds are born very immature. They have no feathers, they can’t fly, they usually have their huge eyes closed, so they are definitely altricial species. But, birds have extremely short cycles of non-REM and REM sleep. Avian REM cycles might total only 5 minutes in a night, and each episode might be only 9 seconds long. What can you get done in a 9 second dream?


Brain waves recorded on an electroencephalogram
(EEG) show that dolphins and birds have normal
activity in one hemisphere while the other is at rest.
The heartbeat is constant showing that there is
normal body rhythm. This is unihemispheric sleep.
Image is taken from: Ridgeway, S. et. al. J. Exp. Med.
209:2902-2910, 2006.
REM sleep is deeper and harder to be roused from compared to non-REM sleep, the short cycles might be related to birds’ sleep pattern, which is unihemispheric (one half of the brain) in non-REM sleep, and is probably related to their need to keep watch for predators. Birds don’t lose muscle tone when they sleep; often they have to remain on a perch while they sleep. How embarrassing it would be for a bird to fall asleep and then fall off their branch- they would deserve to be eaten.

Other species of bird can sleep while flying, the arctic tern for example, whose migration can be as long as 22,000 miles one way. During flight, the eye connected the active half of the brain will remain open to navigate, but the bird will not dream, since both hemispheres are required in all animals for REM sleep.

Dreaming less doesn’t necessarily correlate with sleeping less. Animals that dream little may still sleep a considerable amount. For prey animals, sleep may represent a dicey time when they must be on the lookout. But it might also represent a way to stay motionless, blend in, and avoid predators. Either theory is practical, since predators seem to take the old, young, and diseased, whether sleeping or not.

Indisputably, every animal needs to sleep to survive, but why? It is interesting that science hasn’t quite figured this out yet. It is known that many beneficial events occur during sleep, but just being good for you doesn’t make them vital. But it must be vital, since even hibernating animals will cycle from hibernation to sleep in order to reap the benefits. Several theories exist for the necessity of sleep:

Energy conservation theory of sleep. Smaller animals carry less fat than large animals, which means they have a smaller margin of error in energy usage – they must conserve energy or feed more often. By sleeping longer, smaller animals keep their metabolic rate low and conserve more energy for when they need it, like for finding more food.

Related to this, animals with fewer predators seem to sleep longer than animals who may be hunted by many other species (as discussed above). However, since resting saves 90% as much energy as sleeping and that animals could watch for predators while resting, there clearly must be additional reasons to sleep instead of just rest.

Repair theory of sleep. This theory contends that non-REM sleep is important for repairing the physical body. Indeed, cell division and protein synthesis increase during non-REM sleep. On the other hand, REM sleep is necessary for restoring mental function, but we will leave the reasons for why we dream for another discussion.

Information packaging theory of sleep. You may sleep in order to provide the brain with time to process all that occurred the previous day, and be ready to take in more the next day. This relates to something called neural plasticity (new connections, ie. learning) and memory consolidation. Recent evidence shows that sleep deprivation harms recall, so sleep may help move information from short-term to long-term memory.


One theory of sleep is that your brain returns to a set
point so you can learn things the next day. Learning
means making new connections between neurons;
these connections are reinforced by neurotransmitters
being released to stimulate the next neuron in series. If
the neuron isn’t fired, it will not release neurotransmitters
to stimulate the next neuron in the path. If they are not
repeatedly fired, the pathway will no longer exist, and
new connections can be made.
In terms of plasticity, a 2007 study indicated that the slow brain waves in non-REM sleep are linked to our ability to learn new information. Dr. Guioli Tononi stated that neural connections become progressively weaker during slow wave sleep, so that by morning, the connections are ready to record new information, but still strong enough to hold the old memories. 


An extension of this study, published in 2011 by the same group showed that in some groups of neurons, synapse size and number was affected by the amount of sleep that fly and the amount of experience that the fly had. More experience required more sleep in order to prune the connections and strengthen those that were used repeatedly. After a few hours of wake, synapse size and number increased, and sleep was required to reduce those that are weak and strengthen the remaining circuits.

If sleep provides all these benefits, and higher animals can’t survive without it (even insects and worms have periods of inactivity that look a lot like sleep), then how is it that the giraffe sleeps only 2-4 hours per day? As prey, nature may have deemed it more important to stay alert; or maybe they just can’t find a long enough blanket.

Cetaceans, like birds, only let half their brain sleep at a time, so they probably don’t dream either. Being mammals, they still have to be able to surface to inhale and exhale while sleeping, called conscious breathing. This might require that some part of their brain be active at all times.

I say might because most cetacean sleep studies have been done in captive animals (the smaller species). But in 2008, the boat of a cetacean research team accidentally floated into the middle of a pod of inactive sperm whales. The whales were unresponsive to the researchers and had both eyes closed. This agreed with another observation that electronically tagged sperm whales spent about 7% (1.68 hr/day) of their drifting with the tide. If this is true sleep (not unihemispheric), it would be a new finding in cetaceans and would indicate that that sperm whales sleep less than any other mammal.


The American bullfrog is fully alert when inactive, so is it
asleep? Scientists think that the bullfrog is so territorial and
is such a good parent that it will not let its guard down until
it dies.
An even more amazing exception to the sleep rule is the American bullfrog (Rana catesbeiana). Brain wave studies (electroencephalography) of the nocturnally active bullfrog did show signs of rest during the day, but bullfrogs had no loss of sensory perception. They could react to stimuli just as if awake. Other frogs show similar brain waves, but are much harder to arouse. The bullfrog might be the only animal to pull a lifetime all-nighter. He should really be ready for that math test.

Nobody yet knows exactly how sleep restores the brain or why bullfrogs and giraffes need so little, but we do know that people who are deprived of sleep suffer physically, emotionally, and intellectually – or worse. How would you like to be condemned to death for not taking a nap? We’ll talk about this in a few weeks. But we've got winter and Christmas things to discuss first.

Daniel Bushey, Giulio Tononi, Chiara Cirelli (2011). Sleep and Synaptic Homeostasis: Structural Evidence in Drosophila Science DOI: 10.1126/science.1202839

For more information, classroom activities, and laboratories on theories of sleep, and sleep in animals, see:
sleep –


stages of sleep and REM sleep –

sleep in animals –
http://thebrain.mcgill.ca/flash/capsules/outil_jaune07.html

Snow Saves Lives

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Biology concepts – subnivean zone, chionophiles, antifreeze proteins, UV vision, snow blindness, photokeratitis


Rudolph the red nosed reindeer didn’t start as a song or
even a Rankin and Bass stop motion special. It was a story
published by the Montgomery Ward Stores.  The author’s
brother-in-law was Johnny Marks, the king of Christmas
songs. He adapted the story into a song that was recorded
by Gene Autry in 1949. Then it went viral. The TV
special didn’t appear until 1964.
Rudolph with his nose so bright – only he could lead Santa’s sleigh through the snowstorm. What a great mutation, a beaming red nose – although that might be quite the draw for predators. In real life, reindeer have indeed evolved to overcome the snow, but also to rely on it. You could even speculate that Rudolph would die without the snow.

This leads a biologist to ask, "Just who and what is depending on the snow; how does snow affect the living world?" Many animals have snow in their name, but that isn’t always a good clue. The snowy egret and the snow crab are examples.

The snowy egret is called that only because of its white plumes, while the snow crab is so named because its hunting season is when the snow is the deepest. Mike Rowe, the hardest working man in show business since James Brown, taught watchers of The Deadliest Catch that the snow crab is better called the opilio crab (Chionoecetes opilio). Fisherman that go to sea to put them on your table are a breed unto themselves.

Egrets and crabs don’t help us to investigate the question of the effects of snow on life. The easy observation is that snowy winters are something that organisms have evolved to overcome or even use to their advantage. They have developed ways to survive the harsh conditions of the snowy season or to exploit the white stuff.


The snow leopard is unique amongst cats. It has blue-green or
gray eyes, while most other cats have yellow or black eyes. It
also can’t roar. It has a partially ossified (turned to bone)
hyoid cartilage, which was thought to be the key to cat roars,
but it just can’t manage more than a screech. Maybe it just
doesn’t feel like roaring – or maybe it fears an avalanche.
The snow leopard (Panthera uncia) is an animal that overcomes snow. It has evolved large paws to act as snowshoes. The snow leopard can easily stalk prey and run in snow as deep as 36 in (1 m). Their paws also have fur on all surfaces, to insulate their footpads from the cold and wet snow.

On the other hand, their markings are better suited for their preferred living and hunting grounds. They aren’t nearly as white as you would expect. They like to live on rocky ledges and they descend into the forests to hunt prey when the weather gets really cold (because that’s where the prey are), so their brown tints and spots help them blend in to both habitats.

The lemming is an example of a small mammal that exploits the snow for cover, others being mice, voles, and shrews. The Norway lemming (Lemmus lemmus) moves from the low mountainsides up to higher elevations (opposite of the snow leopard for obvious reasons) as the snow falls. They don’t live underground, although they may nest there, but they don’t live on top of the snow either.

The lemmings dig vast networks of tunnels in the snow where it meets the ground. This is called the subniveanenvironment (sub = below, and niveus is Latin for snow), and they race around looking for vegetation to eat and other lemmings with which to mate. The many openings in the snow may seem to be doors to the subnivean environment, but the lemmings rarely come out of the snow. They are more likely vents to release carbon dioxide from lemming breath and plant decomposition.

Lemmings don’t jump off cliffs in large numbers when they
get older. That is a myth. However, they may be a little
challenged when they run for new feeding grounds in great
numbers – some seem to find their way to cliffs and accidently
go over head first. They are solitary except for mating times,
as is seen here. He’s taking flowers to his girl.

Some animals, like some big cats and large owls have evolved a hearing sense that allows them to pinpoint lemmings under the snow, but the subnivean tunnels work well enough that lemming populations usually skyrocket every 3-4 years, and then plummet as resources become scarce. Their success is in some ways their downfall.

And speaking of falling, the lemmings are also responsible for some human tragedies. When the temperatures fluctuate and the tunnels remodel with ice and snow, the layers of snow can become unstable. The dense snow above the tunnel system will crush and slide off the subnivean layer and …. look out below, here comes the avalanche. And I thought skiers that flock to resorts in order to fall off the mountain repeatedly were the lemmings!

You wouldn’t expect it, but some small arthropods (insects and such) have found ways to live in the snow. When a warmer winter day pops up, so do the snow fleas (Hypogastrura nivicola). You will see them as black specks on the snow – appearing in the thousands at the bases of trees. They aren’t really fleas at all, but a species of springtail (see picture). The reason they come out is not known exactly, but I think that any snow melt due to warmth might drown them in their below ground hiding places.

On the left is a convention of snow fleas discussing the merits
of elm leaves as decaying foliage – or maybe that’s the buffet.
On the right is a single snow flea, called a springtail. The back
legs can apply a load and then are released. They spring from
place to place, but they aren’t “fleaing.”

Snow fleas have an antifreeze protein that keeps them alive over the winter. This isn’t an exception, many animals have chemical mechanisms to prevent freezing, but the protein in snow fleas is unlike any other. The snow flea anti-freeze protein (sfAFP) may serve humans as well. See the post here for more on anti-freezing mechanisms, and here to show that snow midges are the largest animals in many parts of cold Antarctica.

A 2008 project produced the protein in a laboratory and showed that it may be possible to use it to preserve organs for transplant a longer time. Storage at cooler temperatures would allow for longer shelf lives for organs, but they can become damaged by ice crystal formation. The researchers also made a version of the protein using D-amino acids. We have talked about these before – but here they work to our advantage, by making the protein less susceptible to enzymatic degradation, while still providing antifreeze function.           

Snow melt mosquitoes, on the other hand, are winged. Living from northern California up to the arctic tundra, snowpool Aedes mosquitoes (many species) lay their eggs and their larvae develop in the pools of melted snow as the weather warms. This gives them a head start on the rest of the mosquito world. It would seem many forms of life have found ways to exploit snow.

Watermelon snow is caused by an alga that grows in the
snow. Chlamydomonas nivalis is a green algae, but it also
produces a lot of anthocyanins (red) pigments. They
absorb the sunlight and generate heat. This melts some
of the snow and gives the algae the water it needs to grow.
The algae serves as a food source for other animals
during the winter, including the snow fleas.

Then there are the chionophiles(chioni is Greek for snow, and phile = lover). We have talked about the psychrophiles, organisms that prefer cold temperatures, but chionophiles need the snow to survive.

It may seem counterintuitive, but many organisms need the snow to keep them warm. It’s the wind that blows heat away from around the skin, so a layer of snow actually helps trap heat and protect form the wind. Lemmings give snow a big thumbs up (if they have thumbs) for snow as an insulator.

It isn’t just animals that need a “blanket” of snow to retain heat and protect from the wind. Winter wheat needs the snow, but for several reasons. Sure, the snow provides insulation for the young shoots that were planted in the late fall and go dormant until the spring. Nothing worse than frozen wheat.

But the snow also provides a source of water when it melts. This loosens the ground to give the wheat plants strength to push through the earth, and for early water for growth. Snow also gives stability to the young plants out on the plains. Lots of wind out there, enough to knock down and break the fragile plants when they are young. A cast of snow surrounding the stem helps keep them upright. The wise man says, “ Rain versus snow, the wheat doesn’t know the difference, but the farmer wants snow in the winter.”


Winter wheat is susceptible to grey snow mold, even though
it can produce antifungal compounds. This can decimate
entire crops of wheat, especially if the snow fall lasts deep
into the spring. The bottom image shows a close up of pink
snow mold on grass. This is a particular problem on golf
courses – I’m not going to cry over that.
Growing in the snow has also created a problem for wheat, a problem caused by another snow grower. Snow molds (gray or pink) remains dormant in the summer, and only start growing when covered by a layer of snow. As the snow melts in the spring, the damage is down, causing circular patches of gray or brown grass, including wheat, which is a grass.

Snow mold doesn’t attack plants on exposed soil – but they may be killed by the more extreme temperature. They do attack where there is snow, and there is more damage in the deeper snow banks – it seems they do their damage under cover of snow only – more snow, longer time for complete melt, more damage.

The snow mold excretes its antifreeze proteins, not to prevent itself from freezing, but to keep ice crystals from forming or altering around the fungus. Perhaps they are protecting their food to keep it growing and a good source of nutrients; often that food is wheat. But wheat also has tricks. A 2002 study shows that winter wheat produces several proteins that inhibit the growth of the mold.

Now back to Rudolph. To understand his exception with snow, we first need to talk about photokeratitis(photo = light, keratin = the protein found in cornea, and it is = inflammation), better known as snow blindness. For Eskimos and other humans, the 90% of the sunlight’s UV waves bouncing off the snow is enough to burn the cornea and lead to fuzzy vision or even blindness. The cornea is a protective structure, keeping the UV rays from injuring the retina.


This is part of the study that discovered UV vision in
reindeer. I get the part where they examine the retina,
but what I need to know is how they get them to read
the lines of letters on the eye chart.
Other animals are prone to snow blindness as well. Polar bears have a nictating membrane to protect the eye, but the reindeer have gone much further. Of all the mammals, only the reindeer actually sees in the UV range.

Their cornea doesn’t stop UV rays from entering the eye, yet they don’t suffer damage. The pigments of their retina absorb the energy and convert it into images, just like our eye does with visible light only. A good study would determine how they are protected – you work on that. It might be related to a new study that shows that reindeer eyes change color with the seasons, becoming blue in winter.

Being able to see in the UV range is what saves the reindeer. Predators that blend in with the snow still show up easily in UV, and well as urine stains in the snow that mark the territories of predators or other reindeer. Using his UV vision, the reindeer is better protected from predation. And it only works because of the snow – no snow, no reflected UV light. And thus we learn…. snow saved Christmas.

Next week, the biology of one of the original Christmas gifts.



Hogg C, Neveu M, Stokkan KA, Folkow L, Cottrill P, Douglas R, Hunt DM, & Jeffery G (2011). Arctic reindeer extend their visual range into the ultraviolet. The Journal of experimental biology, 214 (Pt 12), 2014-9 PMID: 21613517

Kondo H, Hanada Y, Sugimoto H, Hoshino T, Garnham CP, Davies PL, & Tsuda S (2012). Ice-binding site of snow mold fungus antifreeze protein deviates from structural regularity and high conservation. Proceedings of the National Academy of Sciences of the United States of America, 109 (24), 9360-5 PMID: 22645341

Pentelute BL, Gates ZP, Dashnau JL, Vanderkooi JM, & Kent SB (2008). Mirror image forms of snow flea antifreeze protein prepared by total chemical synthesis have identical antifreeze activities. Journal of the American Chemical Society, 130 (30), 9702-7 PMID: 18598026

Kuwabara C, Takezawa D, Shimada T, Hamada T, Fujikawa S, & Arakawa K (2002). Abscisic acid- and cold-induced thaumatin-like protein in winter wheat has an antifungal activity against snow mould, Microdochium nivale. Physiologia plantarum, 115 (1), 101-110 PMID: 12010473



For more information or classroom activities, see:

A great book on the mechanisms of survival in the winter and how cold and snow affect life is entitled
           Winter World, The Ingenuity of Animal Survival
           Bernd Heinrich
           2003
           ecco publishing, an imprint of Harper-Collins
           ISBN 0-06-019744-7

Snow blindness –

Reindeer –

Subnivean layer –

Winter wheat –

Snow mold –

Watermelon snow -




A Gift Worth Its Weight In Gold

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Biology concepts – toxicity, trace elements

Say hello to the Holterman nugget of New South
Wales, Australia, supposedly the largest gold
nugget ever found. Strictly speaking, it isn’t a nugget,
but rather a huge vein of gold in a piece of quartz.
And Bernhardt didn’t find by himself, but he was a
shameless media hound and built himself a legend.
In 2ndcentury Rome, practitioners of Mithraism, a popular pagan religion of the time, had a feast on December 25 to celebrate the god Mithras, the “Invincible Sun.” This also coincided with other feasts for Saturn and the winter solstice. People gave gifts to one another during these holiday celebrations. This practice of gift giving was adopted by Christians when the pagan and Christian traditions were merged, as they often were.

Today, Christmas presents are most often associated with the gifts of the three kings who came to see the baby wrapped in swaddling clothes (although by the time they arrived, Jesus was already a toddler – camels will never be confused with jet planes). Their gifts were gold – a gift for a king, frankincense – a gift for a priest, and myrrh – a gift for one who was to die (used in burial rights).

These three gifts are not exempt from our search for biologic exceptions and amazement. In terms of biology, they are indeed gifts.  This week we will talk about gold, with the others to follow on successive posts, like the ghosts of Christmas past, present, and future.

At December 2012 prices, a 150 lb (69 kg) person has about 37 cents worth of gold in his/her body, excluding any dental work. Hardly worth trying to harvest, but nice to know you’re worth more than you thought. How did the gold get there and is it doing anything?

Living organisms rely on small amounts of some metals and other elements in order to carry out their metabolic reactions. As such, these elements that are needed in small amounts are called trace elements. Examples of important trace elements include selenium, iron, copper, iodine, and zinc. Zinc is probably the king of the trace elements, as it is used in over 200 different reactions in mammalian physiology.

Copper is used in many biochemical pathways,
and it is showing promise as an anti-inflammatory
agent. But NO! people - you can’t get the anti-
inflammatory effects by wearing the copper
bracelets or copper-impregnated compression
wear! On the other hand, copper impregnated
clothes are antimicrobial.
Zincworks to control what genes are activated to make proteins (zinc finger transcription factors), as well as DNA and RNA production and destruction. It is stored in the brain to control just how active some neurons become when stimulated, and plays an important role in neural plasticity – the reordering of neuron connections after experiences and sleep, you may know it as learning and memory. Make sure you take your zinc before studying for that big test!

Because you need only a “trace” of these substances to maintain growth, development and health, they are also called micronutrients. Their functions can be quite diverse. Iron is the oxygen carrier in hemoglobin, but you only need a trace in your diet because you are so good at preserving what you already have. Selenium is contained in a non-traditional amino acid called selenocysteine, which is important for antioxidant proteins (selenium replaces sulphur in the traditional cysteine).

The biologic rule is that gold is not a trace element! Supposedly, no living organism uses gold in its physiology, but you know there has to be an exception. In 2002, Russian scientists investigating a membrane bound enzyme of the aurophilic (au = gold, and philic = loving) bacteria, Micrococcus luteus, showed that the enzyme contained gold in its active site (the area that binds the molecule to be chemical reacted). The gold was important for converting methane to methanol, giving the bacteria a way to produce energy when traditional food sources were scarce.

But we, and presumably ever other organism don’t have this system, so why is there gold in our body? It turns out that we have many things in our body that we don’t use, they just accumulate, things like lead, mercury, cobalt, arsenic. Some are toxic at low levels and some are useful unless we get too much of them. We have discussed the problems associated with having too much iron, and copper excess can be toxic as well. We said zinc is important for many reactions, but too much zinc can hinder copper absorption and you can end up with a copper deficiency. This is just as dangerous as copper excess.

The liver is the site of much detoxification in the body.
Two systems are at work, one to break down or modify
fat soluble toxins, and the other to prepare them and
water soluble toxins for elimination in the bile or urine.
Toxic heavy metals often just get stored in the liver and
cause damage later.
If the element itself or amount of the element is toxic, then we have to get rid of some; this is the job of the liver. In some cases even gold can be toxic; as we accumulate more and more gold in the liver and kidney, it can disrupt their functions. Poor liver and/or kidney function – you die. The classic form of toxic gold found in nature is called gold chloride or “liquid gold,” which causes organ damage in humans and severe toxic effects in other organisms, but there is an exception.

A microbiologist and a professor of electronic art at Michigan State Universityhave worked with a bacterium that can withstand gold chloride levels that would kill every other known organism. They found that Cupriavidus metallidurans was hundreds of time more resistant to gold chloride than any other organism.

C. metalliduranstakes in the gold chloride and processes it to pure 24 karat gold, and then deposits it in a thin layer as part of the community of proteins and insoluble products that the bacteria builds around its colony. These organized layer of proteins, lipids and carbohydrates are called biofilms, and are being recognized as very important in bacteria ecology and pathology. In the case of C. metallidurans, the biofilm is intrinsically valuable to Wall Street.

Other organisms accumulate gold as well – bacteria, fungi, algae, fish, etc., but as does everything else in biology, it starts with the bacteria. It turns out that some bacteria excrete high levels of acidic amino acids – aspartate and glutamate (atemeans acid). Yes, amino acids that are used to build proteins are organic acids, hence the name.

To dissolve gold out of powdered and broken rock,
many mines like this one in Brazil spray the ore with
sodium cyanide in water. They collect the runoff and
precipitate out the purer gold. I guess they don’t worry
about all the living things contaminated with the
cyanide.
Thebacterium Chromobacteriumviolaceumactually makes and excretes cyanide. Cyanide binds stably to gold and silver, so it is used in gold mining to bind and concentrate very fine gold particles in rocks. Then the gold can be collected and precipitated. These examples show that if gold is in the immediate environment of these various organisms, it can be dissolved by the organic molecules and taken up by the bacteria when they feed.

Once gold is consumed and stored by the bacteria, it enters the food chain; millions of organisms feed on bacteria, and millions of organisms feed on the feeders, and so on. Eventually, we end up eating a little gold as well. This is similar to how fish that ingest food and swim in water contaminated by mercury runoff can end up increasing the human levels of mercury – the difference is that mercury is much more toxic than gold.

The accumulation of gold in sedentary organisms may provide someone with a gold rush. A 2010 study showed that the saprobicfungi (those that feed on decaying material) around an existing gold mine contain much higher levels of gold than ectomycorrhizalfungi (those that are parasitic)in the same area.  The accumulation of gold in soil bacteria and fungi may be able to provide scientifically astute miner with clues as to where they should dig the next mine!

The blue toadstool  (Entoloma hochstetteri) is an
example of a saprobic fungus. It gains all the
nutrients it needs from the soil and from decaying
organic material. Therefore, it picks up and
accumulates other things in the soil – like gold maybe.

 Bacteria may prove even more important to miners. December 2012 evidence indicates bacteria that dissolve and ingest gold in the rocks and soil purify it to some degree. When they form biofilms, the gold becomes insoluble again, and nuggets or flakes are formed. Veins of gold may be due to bacterial byproducts and corpses flowing into cracks in the rocks. Makes you look at your gold ring differently, doesn’t it.

We might be able to thank gold-loving bacteria for more than our jewelry – gold is finding its way into medical treatments and tests these days.  Because gold was rare, pure, inert, and costly, early physicians thought it just had to be good for you. Many remedies had gold incorporated into them, including a popular cure for alcoholism called the Keely cure.

The cure was so widely accepted (and patented by Dr. Keely) that even Theodore Roosevelt himself sent his brother, Elliott, to Dr Keely’s clinic in Dwight, IL to be cured of his addiction. It didn’t work, Elliott drank to the point of depression, and died from injuries that resulted from his jumping from a window.

More recent uses of gold include as an anti-inflammatory agent rheumatoid arthritis, including a compound called aurothiomalate. Just how this works remains a mystery, but a 2010 study in chondrocytes (the cells that make cartilage and are present in joints) showed that this drug down-regulates a signaling enzyme (MAP kinase phosphatase 1) that is important for expression of several inflammatory proteins, including cyclooxygenase, p38 MAP kinase, matrix metalloproteinase-3 and interleukin-6.

The aquatic or semi-aquatic plant Bacopa caroliniania can
be loaded with gold nanoparticles and made to give off
light.  Depending on the energy of the UV light shone on
it, it can glow from green to gold to red. Someday, maybe
our tree lined streets will have natural streetlights.
Gold isfinding a home as a treatment in other conditions as well including in cancer, viral infections, and parasitic diseases. But gold is being used most often as a carrier. Because gold is practically inert, nanoparticles of gold can be used to carry drugs to specific targets or to be used as imaging agents to illuminate very small structures.

Most spectacularly, gold may help light a dark world. Plants can now be grown with gold nanoparticles that are small enough to be taken up into the leaf cells. When exposed to UV light, the gold releases energy at a wavelength that stimulates chlorophyll to bioluminesce. The plants actually give off light like natural street lights.

That’s a lot of biology for a hunk of metal used for wedding rings and retirement watches – a way cool gift for any biologist. Next week, the biology of frankincense.

 Nieminen, R., Korhonen, R., Moilanen, T., Clark, A., & Moilanen, E. (2010). Aurothiomalate inhibits cyclooxygenase 2, matrix metalloproteinase 3, and interleukin-6 expression in chondrocytes by increasing MAPK phosphatase 1 expression and decreasing p38 phosphorylation: MAPK phosphatase 1 as a novel target for antirheumatic drugs Arthritis & Rheumatism, 62 (6), 1650-1659 DOI: 10.1002/art.27409

 Levchenko, L., Sadkov, A., Lariontseva, N., Koldasheva, E., Shilova, A., & Shilov, A. (2002). Gold helps bacteria to oxidize methane Journal of Inorganic Biochemistry, 88 (3-4), 251-253 DOI: 10.1016/S0162-0134(01)00385-3
 

The Resin For The Season

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Biology concepts – sap, resin, latex, mucilage

Frankincense is a solid material than starts out as a 
liquid that oozes from a tree. In the presence of air, 
the resin turns hard. When burned, many 
fragrant and brain altering compounds are released.
We saw last week that gold doesn't just look good, it has a significant place in biology. This week we take a look at frankincense, a natural tree product prized for its use in sacred rituals. The Catholic Church is the number one purchaser of frankincense, but that may be about to change, especially for medicine. The wise men must have done some heavy thinking before they made their gift choices for Jesus – gift cards are so impersonal.

A 2008 study may have defined just why frankincense is used in religious rituals. Burning the resin releases incensole acetate (IA), one of the resin’s key components, which activates transient receptor potential vanilloid (TRPV3) ion channels in the skin and brain. This ion channel is responsible for mediating a warm feeling in the skin, but TRPV3 channels also mediate brain activity.

The researchers in Israel found that IA activates the cFos transcription factor in the brain, leading to anxiolytic (anxio = anxiety, and lytic = destroying) and anti-depressive feelings. Mice without TRPV3 channels did not show cFos activation or behavior changes when exposed to IA. It appears that burning frankincense makes one feel happier and more in tune with whatever activity is going on at the time, including religious rituals.

The fact that there is a psychoactive agent in frankincense is amazing enough, but there’s more biology to this second gift. Recent evidence indicates that the oils and other compounds in frankincense may save lives– if the trees that produce frankincense don’t disappear in the next 50 years. Unfortunately, their extinction is a distinct possibility – we must save this precious sap, or resin, or whatever it is.

Trees can produce various oozings and liquids. Pancake syrup most often comes from the sap of a maple tree, while your stick of Wrigley’s spearmint uses the latex that exude from many different kinds of plants. Gum drippings may also be used in chewing gum (Chiclets used chicle gum), but gums are now more commonly found in paints and erasers. The aloe vera you use on burns is a type of mucilage, rich in glycoproteins. But many plants, especially coniferous trees, exude resins when they are under attack or are damaged.

Amber is fossilized resin. Scientists learn much from organisms caught 
in it and thus preserved. Recent evidence also shows that amber can 
help us track bug attacks on plants from the days of dinosaurs. 
Gum is semi-solid, and rubbery. The gum shown is chicle, used 
for many years in Chiclets gum. Mucilage is produced by 
many pants, including as a treat and trap for insects in carnivorous
plants like this sundew. Maple sap is clear and dilute when tapped from
a tree. It must be boiled for hours to reduce it to syrup. Latex rubber is 
naturally white. The first car and bicycle tires were all white, not
just white-walled.
Gums can also be used for defense, but are made directly from disintegrating internal plant material. They harden to a certain degree after being exuded from the plant tissue, but are more known for their ability to increase the viscosity of a liquid, due to their long polysaccharide molecules. Bacterial agar plates use a gum from seaweed to grow microorganisms.

Sap is the sugary fluid that travels up and down in the xylem of vascular plants, providing the different structures with carbohydrate to produce ATP at the cellular level. Therefore, sap is a nutritive liquid and all trees produce it – but not all taste good.

Mucilage is similar to sap. It also contains glycoproteins and other carbohydrate-containing molecules, and is important for food and water storage in almost all plants, especially cacti. However, mucilage can be used for other purposes, like luring insects into carnivorous plant traps, such as the flypaper plant.

People used to lick mucilage everyday, but technology has reduced its role in our lives. When mixed with water, mucilage is an adhesive, like on the backs of stamps. You don’t have to lick your computer screen to send an e-mail, so mucilage is less important to us in these modern times.

Resins become definite solids when exposed to air. They are not nutritive, and contain primarily the byproducts and secondary metabolites of other cellular processes. While gums and saps are soluble (will dissolve) in water or fat, resins are stable in water but will dissolve in alcohol.

The reason for resin production is not fully understood. They may play a role in defense or tissue injury, but may instead serve to rid the plant of unneeded or unwanted waste products. Indeed, when trees are cut to harvest frankincense, the first resin produced is discarded, because it contains many toxins and foul smelling chemicals.

The Boswellia sacra tree grows in a harsh
environment. The roots can grip onto stones and
they grow out of the ground as buttresses to keep
the tree stable on the cliff sides.
Resinsare produced mostly by coniferous trees (like pine trees). This makes frankincense an exception, since it comes from the Boswellia sacratree, a deciduous tree (trees that lose their leaves in the winter). Frankincense is different from other resins in another aspect as well, it is technically a gum resin, since it has many compounds that are of the gum variety within its resin. The gum-like essential oils in frankincense are one of the reasons it is sought after as an incense.

B. sacra grows only in the middle eastern countries of Yemen and Oman, and possibly in Somalia. The tree is only 2-7 meters (6-23 ft.) when fully grown, and starts producing resin at a fairly young age of 8-10 years. Its small stature may be due in part to the arid climate that it lives in; there is so little water to be had that B. sacra survives only on the moisture it absorbs from fog.

However uninviting its environment might seem, B. sacra is well adapted to this area and is very finicky in growing anywhere else. In fact, a recent study indicates that they are more finicky than even previously believed. Though living in two different areas (Oman/Yemen vs. Somalia), it had been accepted that these plants were the same species. But based on chemical evaluation of the essential oils of the resins from trees in these two regions, the Oman/Yemen trees of B. sacra are truly different than the B. carterii trees of Somalia.

Initial gas chromatography-mass spectrum analysis did not show significant differences in the kinds of volatile molecules present, but there were large differences in the amounts of the individual compounds in the resin from each species of tree. Later experiments also showed chemical differences in the same compounds from each species.

Yemen and Oman are side by side and Somalia is
just across the Gulf of Aden. But recent studies show
that the frankincense trees that grow in Yemen and
Oman are distinctly different from those in Somalia.
This speciation difference shows that B. sacra REALLY likes to stay close to home. There’s nothing wrong with that, except that the small area that it grows in happens to be one of the most unstable parts of the world. The trees have been over harvested for resin, and this affects the rate at which the trees reproduce. Heavily tapped trees have seeds that germinate only 8-16% of the time, while trees that have not been tapped for resin germinate seeds at a rate of over 80%.

Add goats grazing on the existing trees, global warming, fires, and low genetic diversity in individual stands of trees to the low rate of propagation and this spells trouble for the B. sacra species. Estimates are as dire as a 50% decrease in frankincense production in the next 15 years, to a 90% loss of trees in the next 50 years – but there is hope.

A recent DNA study shows that trees from different parts of the Dhofar region are genetically distinct, and that there is a low level of heterozygosity in the trees of a single area. This low level of genetic diversity results in trees less able to survive changes in environment or biology (genetic diversity is key to natural selection). But some stands show more genetic diversity and arguments are now being made to initiate conservation efforts for the diverse stands, while increasing cross-pollination of the least genetically diverse trees. It is hoped that these efforts, as well as attempts to grow B. sacra in the Sonora Desert of North America, could stave off extinction of B. sacra.
 
The hippocampus is important in your sense of well-
being. Studies have shown that in people with
depression, the hippocampus is smaller, perhaps from
poor neurogenesisor from increased cell death. Why
the seahorse? In Greek, hippocampus means, “horse sea
monster.” I can see the resemblance.
Whyis it important that we save the frankincense trees? Because it is becoming evident that the resinous compounds in frankincense could have great medical benefits to humans – and unhappy mice.

We mentioned above that IA (incensole acetate) of frankincense acts on the brain to increase feelings of well-being. Mice bred to be submissive and to give up (quit) earlier in a test of depressive activity show a much stronger will to live and more positive behaviors when given IA. Recent research in Israel shows that IA influences brain molecular biology, especially in the hippocampus, altering depressive behaviors as much as other chemical interventions. It is hoped that IA may be a viable anti-depressant drug in the future.

This same group showed in 2008 that IA was a significant anti-inflammatory agent, through its inhibitor action on an important transcription factor (called NF-kB) that stimulates expression of inflammatory proteins. In mice with traumatic brain injuries, IA administration resulted in reduced inflammation and pressure on the brain, reduced neuron degeneration, and prevented loss of cognitive function. Their more recent study also indicates that IA is protective in stroke and in the damage that can come after strokes by reintroducing oxygen into the damage part of the brain (when blood flow resumes).

Boswellic acid is also of use in myeloid leukemia, a type
of cancer of the white blood cells. It seems that BA can
induce the cancer cells to commit suicide, and die after a
period of time like most cells do. BA trigger apoptosis by
stimulating the release of important compounds from the
mitochondria, suggesting to the cell that its energy making
organelles are irreparably damaged.
Anothercompound in frankincense is showing promise as an anti-cancer drug. An essential oil molecule called Boswellic Acid (BA) has been shown to slow the rate of cancer cell growth. A recent study has delineated at least part of the mechanism of BA-mediated inhibition of colorectal tumor growth.

Cancer is the result of mutations in genes that code for the production of proteins that keep cells living, growing, and dividing forever. BA stops the synthesis of some of these proteins. It turns out that BA stimulates production of a micro RNA (miRNA, a short RNA molecule of about 22 nucleotides) that can bind to the messages transcribed from DNA that would be translated into pro-cancer proteins and stop the proteins from being made. Do you think the three kings had any idea that they were giving a gift that can stop inflammation, depression, and cancer – or they did they just think it smelled nice?

Next week – The third of the original gifts, myrrh. There's a biologic reason frankincense and myrrh were given together as gifts, but science didn't figure it out until just a couple of years ago.

Takahashi, M., Sung, B., Shen, Y., Hur, K., Link, A., Boland, C., Aggarwal, B., & Goel, A. (2012). Boswellic acid exerts antitumor effects in colorectal cancer cells by modulating expression of the let-7 and miR-200 microRNA family Carcinogenesis, 33 (12), 2441-2449 DOI: 10.1093/carcin/bgs286

Moussaieff, A., Gross, M., Nesher, E., Tikhonov, T., Yadid, G., & Pinhasov, A. (2012). Incensole acetate reduces depressive-like behavior and modulates hippocampal BDNF and CRF expression of submissive animals Journal of Psychopharmacology, 26 (12), 1584-1593 DOI: 10.1177/0269881112458729

Coppi, A., Cecchi, L., Selvi, F., & Raffaelli, M. (2010). The Frankincense tree (Boswellia sacra, Burseraceae) from Oman: ITS and ISSR analyses of genetic diversity and implications for conservation Genetic Resources and Crop Evolution, 57 (7), 1041-1052 DOI: 10.1007/s10722-010-9546-8
 
For more information, see:

Resin –

Sap –

Gum –

Latex –

Mucilage –

Boswellia sacra –
http://www.iucnredlist.org/details/34533/0
 

One Myrrh-aculous Christmas Gift

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Biology concepts – synergism, multidrug resistant cancers

The Commiphora myrrha is the classic source for myrrh
resin. It is a short tree that grows in low moisture and
poor soil areas. Its branches are very thorny; some
propose that the crown of thorns Jesus is said to have
worn was made of myrrh twigs.
The three original Christmas gifts are usually listed as gold, frankincense, and myrrh, but why that order? Some say it is because you give gold to a king, frankincense was used by priests, and myrrh was used to anoint the newly dead.

The order goes along with representations of how he was born (as a king), how he lived (as a preacher), and how he died. But I think that sells myrrh short. True, it was used in consecrating and embalming dead bodies, but it is so much more. As with gold and frankincense, there is “myrrh” here than meets the eye.

Likefrankincense, myrrh is a resin from a tree that grows in the Middle East, in this case Yemen, Somalia, Eritrea, and Ethiopia. Frankincense and myrrh trees even come from the same family, the Bursceraceae. Being deciduous trees, both frankincense and myrrh are exceptions to the rule that coniferous trees are more likely to be resin producers.

Myrrh resin is an oleo-gum-resin, since it is has essential oils (oleo) and long polysaccharides (gums), as well as resins. It is more complex than frankincense, containing over 300 individual secondary metabolites and other compounds. Being a more complex substance, it might follow that myrrh would have more uses than frankincense, both in ancient times and now. And here is an instance in biology when the logical answer is the correct answer. In addition to being used as incense in rituals and perfumes, it had other mystical properties. It was so prized that it was often worth more than gold.

Greek soldiers always carried myrrh in their travel kits because it was a potent antibacterial and anti-inflammatory agent. Being soldiers, they were likely to be wounded, and those wounds would get infected and swell. If they died, it's good that they had myrrh, because it was also used as an embalming agent and to consecrate the dead bodies.

In Greek mythology, Myrrha was a young lady who committed an awful 
no-no, and was chased across the desert by her father. The gods took pity on 
her and turned her into a tree so she wouldn’t have to run anymore. 
The myrrh resin that drips from the tree is said to be her tears. But I don’t get 
the part where she gives birth to Adonis while she is still a
 tree – family trees aren’t supposed to be literal.
In fact, the Egyptians were some of the first to use myrrh in this way. Combined with natron, a form of salt from the desert, they would stuff the bodies of the dead to pull out the water. This was a big part of the mummification process. The myrrh was there to prevent rotting and to help with the smell.

Myrrh smells good, but tastes horrible. In fact, the name myrrh originally came from the Aramaic word for bitter. To this day, the bitter taste of myrrh oil or powdered myrrh has limited it use in medicines. A recent study fiddled with making emulsions of myrrh in water in order to cover the taste, or adding fat-soluble compounds and using it as a suppository (there is usually good uptake of drugs from the south end of the gastrointestinal tract).

But the ancients still consumed myrrh despite the taste. It is said that someone gave Jesus myrrh dissolved in wine as a painkiller while he was on the cross. Others mixed it with red raspberry leaves to soothe a sore throat. Pliny the Elder wrote of using myrrh to kill bugs in wine and wine bottles before bottling the drink for transport and sale.

Though myrrh has been used for centuries, we have just now started to explain how myrrh functions in these capacities. For example, it is now known that compounds in myrrh called terpenes can interact with opioid receptors in the brain. This is how they act as painkillers.

Myrrh and frankincense components are also being tested in combination as antimicrobial agents. Oils of myrrh alone can kill or slow down some microorganisms; so can oils of frankincense. But adding them together has been shown to be a case of 1+1=3.

This is a demonstration of the concept of synergism. Let’s say that one antimicrobial drug can kill or stop X number of organisms when given at a certain dose. It is often the case that as you increase the dose, you will kill or stop more organisms – up to a point. Almost any drug becomes toxic when you ingest a lot of it. The lowest amount you can give to do the job is the miminal effective dose, and the most you can give is the maximum recommended safe dose.

To get a bigger bang for your buck, sometimes you can add a second drug to the regimen. Drug 1 inhibits or kills X number of organisms and drug 2 affects Y number of organisms. Often, giving drug 1 and 2 together will then inhibit or kill X+Y organisms. This is an additive effect. Drugs with additive effects often work on different targets; they are like eating a foot-long hotdog from both ends. The hotdog goes away twice as fast because the two mouths aren’t competing for the same part of the hotdog.

The white dots are paper soaked in two different antibiotics.
They are put on a plate of bacteria (the hazy diagonal lines).
As the drugs diffuse out, they kill the bacteria (darker, clear
areas, but their concentrations go down the farther they
travel. But look between them, the area where they both are
low concentrations is a bigger cleared area (between red
lines). This is synergistic action.
Everyonce in a while, using drug 1 and drug 2 together gives you a bigger effect, greater than X+Y; this shows synergy. Synergistic effects are the exception, they don’t come around often and a researcher is lucky to find them. Synergism in drug activity can mediated by different mechanisms, but it may be caused by the second drug turning off the fall-back pathway a cell may use when the primary pathway is affected by the first drug - there are many redundant pathways in cells.

Synergism and additive effects are examples of pharmacodynamic effects; basically, how the drugs work on cells. We will later see how some drugs have pharmacokinetic effects on each other.

When a groupin South Africa tested two myrrh oils in combinations with three frankincense oils, they found that a combination of B. papyrifera and C. myrrha oils were synergistic in controlling both Cryptococcus neoformans, a fungus, and Pseudomonas aeruginosa, a gram negative bacterium.

The anti-inflammatory mechanisms of myrrh are just being worked out as well. Recent studies from South Korea indicate that myrrh stops the inflammatory process by inhibiting the production of molecules that promote inflammation. Their 2011 studyindicates that myrrh turns off the enzymes that produce nitric oxide, prostaglandins, and some inflammatory cytokines (messengers that have many effects) when inflammation was stimulated by LPS, a cell wall component of many bacteria called lipopolysaccarhide, also called endotoxin. LPS is responsible for things like septic shock and necrotizing enterocolitis.

Rheumatoid arthritis (arthus = joint, and itis =
inflammation of) is mediated by an autoimmune
process that brings much inflammation. Myrrh
has been used for hundreds of years as an anti-
inflammatory drug, but we are just now figuring
out why it works.
They added work in 2012 that shows that myrrh is very good at controlling inflammation after a rupture of the large bowel (which usually causes peritonitis and is very dangerous). This is probably due to its ability to stop inflammation induced by the LPS of the gut bacteria and its ability to kill the organisms as well. Those wise men were really quite wise – they didn’t know why myrrh worked, but they knew it worked, and that was enough.

But even they did not suspect all the wonders of myrrh. It is with cancer that one myrrh component is turning out to be a gift. There are several species of myrrh trees, and a couple, C. mukul and C. molmol, contain a compound called guggulsterone (I love saying that name out loud – go ahead, it’s fun). Guggulsterone is not necessarily toxic to cancer cells by itself, but it may solve a big problem that currently affects many cancer treatments.

We talked a while ago about how bacteria have pumps to kick antibiotics out of their cell, and thereby prevent their action. Cancer cells also have a pump to do this to many cancer chemotherapeutic drugs. The most common of these drug pumps is a membrane channel protein called P-glycoprotein (P-gp). This protein is present in some normal types of cells, working to pump out toxic compounds, like in liver cells and skin cells. This means that cancer drugs on these types of cancers have a hard time staying in the cells.

P-gp pumps cancer drugs back out of cells with
the help of changing ATP to ADP. This can lead to
drug resistant cancers. We are looking for inhibitors
that might block the action of P-gp by taking away
its ATP or by competing with the drug for the pump,
so less drug is pumped out.
Other cells can up-regulate the production of P-gp once they start to receive the cancer drugs. Either way, it leads to multidrug resistant (MDR) cancers – a serious problem. Many attempts have been made to develop P-gp inhibitors, but most have been either ineffective or toxic.

Enter guggulsterone (let’s call it GGS for short) – new research shows that this compound from myrrh can reverse MDR in several types of cancer. The mechanism is just now being uncovered; GGS can act as a competitive inhibitor of P-gp, meaning that it is pumped out just like the cancer drugs. But the more time P-gp spends pumping out GGS, the less time it is pumping out cancer drug, so it becomes more effective. It does not appear that GGS stops production of P-gp or other actors in this play, it just keeps them busy – but it does it without being toxic. This is a pharmacokinetic effect, one drug (GSS) has an effect on how another drug (cancer drug) is acted on by the cells, in this case by keep the drug in the cancer cell much longer.

In the cases of pancreatic cancer and gall bladder cancer, very new studies show that GGS in combination with the cancer drug gemcitabine, works much better than the drug alone. The combination causes higher levels of apoptosis in these cancers, perhaps through the action of keeping more drug in the cancer cells, but GGS may have other cytotoxic effects as well.

Osteoporosis leads to less dense bones, which can alter posture 
and lead to bone breaks. It looks like the guggulsterone in 
myrrh can prevent bone resorption after menopause. It may 
even increase density and be a treatment for bone breaks.
And this is the most amazing part, even though it may be inducing damage in some cells, a new use for GGS is to prevent damage to heart muscle cells (cardiomyocytes). The cancer drug doxorubicin (DOX) is a very good cancer killer, but its use is limited because it damages the cardiomyocytes. GGS has recently been found to protect cardiomyocytes from DOX damage by preventing the up-regulation of many pro-apoptotic proteins. But GGS helps kill cancer cells by promoting apoptosis – what gives? Become a biologist and find out, it can be your gift to the rest of us.

Next week – the biology of New Years’ exercise resolutions!


Xu, H., Xu, L., Li, L., Fu, J., & Mao, X. (2012). Reversion of P-glycoprotein-mediated multidrug resistance by guggulsterone in multidrug-resistant human cancer cell lines European Journal of Pharmacology, 694 (1-3), 39-44 DOI: 10.1016/j.ejphar.2012.06.046

Wang, W., Uen, Y., Chang, M., Cheah, K., Li, J., Yu, W., Lee, K., Choy, C., & Hu, C. (2012). Protective effect of guggulsterone against cardiomyocyte injury induced by doxorubicin in vitro BMC Complementary and Alternative Medicine, 12 (1) DOI: 10.1186/1472-6882-12-138

de Rapper, S., Van Vuuren, S., Kamatou, G., Viljoen, A., & Dagne, E. (2012). The additive and synergistic antimicrobial effects of select frankincense and myrrh oils - a combination from the pharaonic pharmacopoeia Letters in Applied Microbiology, 54 (4), 352-358 DOI: 10.1111/j.1472-765X.2012.03216.x


For more information or classroom activities, see:

Myrrh –

Additive and synergistic effects in pharmacology –

Multidrug resistance in cancer –
http://mayoresearch.mayo.edu/mayo/research/chang_lab/

It’s An Exercise Resolution

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Biology concepts – exercise, stress, aging, mood, neurotransmitters, monoamines, endocannabinoids, endorphins, blood brain barrier


Exercise is a common New Year’s resolution. You want to
test yourself and gain in body and soul what comes from
accomplishing physical tasks. However, there is such a
thing as biting off more than you can chew. Make small
goals and add length and intensity slowly, so you can
always feel you are improving.
It’s New Year’s resolution time! Last year we talked about how difficult your brain makes it to change a habit and we gave you some strategies to help you succeed. But succeed at what? It’s time to decide on a resolution.

Two of the most popular resolutions are to lose weight and to exercise more. These two can be linked, although they don’t have to be – you could just starve yourself. I don’t think anyone should make a resolution to starve this year, so let’s look in more depth at exercise as a good habit.

There are two major questions to be answered as to a “getting fit” resolution. The first is obvious – why would more exercise be good for me? We all know about how expending more energy than you take in will help you control your weight. So that’s an easy one.

Exercise also helps your health by building muscle, improving flexibility, increasing bone density, and improving both cardiac and pulmonary function. All these changes result in reduced susceptibility to diseases, especially diseases of life style, like diabetes, cardiovascular disease, cancer, and metabolic syndrome.

Those benefits were obvious, but you probably know so more. Exercise may hurt – but it also makes you feel good. Intense physical activity is a powerful mood enhancer, while at the same time reducing the effects of stress on your body. We all know folks who go for a run or go lift when they are stressed. It really does work.

Linked to de-stressing you in the short term is exercise’s effect on reducing the results of stress long term. This kind of stress means time, oxidation, wear and tear, as well as mental stress – basically, aging. Even at a cellular level, exercise may work to impede the signs of aging.

A 2010 study divided stressed women into two groups, those that began exercising and those that did not. After just a three-day exercise period, the population that began exercising showed fewer signs of aging in sample cells taken. Maybe wearing yourself out will let you wear yourself out for many more years.

People, well most people, are happier after they exercise.
Stress relief is a major contributor, I recommend that
anytime things are getting on your nerves, go out for a
brisk walk or get on your bike. The sense of
accomplishment also contributes to making you happier,
but there is so much more.

Unrelated to simply wearing you out, physical activity improves your sleep. This is so true that doctors now prescribe exercise to those suffering from insomnia. We’ll talk more about this in a couple of weeks.

The benefit you may not think of is …….thinking. Exercise actually improves cognitive (from Latin = to know or recognize) function and memory. Your brain may not be a muscle, but it definitely benefits from increasing your physical activity. This will be our subject for next week, just in time for the all the kids to have a new weapon in their arsenal for good grades.

Now for the second question about exercise, and it’s a doozie. How does exercise accomplish all these wonderful things? The effects of exercise on your physical body comes mostly from your innate ability to react to stressors. More work required from muscles results in muscles growing bigger and stronger to meet the demand. This includes your heart –it’s a muscle. No, for these biology stories, let’s focus on the mechanisms at work that affords exercise the ability to affect your brain. It’ll blow your mind.

Today let’s talk about how exercise actually makes your brain – and the rest of you, happier.


The monoamines dopamine and serotonin are intimately
involved in several mental disorders. You can see that
decreases in one lead to different problems than losses of
the other, but when they are both down, you get
depression and a will to eat more. Eating is another, not
so healthy, way of feeling happier.
The major players are neurotransmitters (NTs) and other molecules that can alter brain activity. Things like dopamine, serotonin, and norepinephrine are NTs; endocannabinoids and endorphins work to block negative inputs.

Levels of dopamine, serotonin and sometimes norepinephrine neurotransmitter are reduced in many patients with clinical depression. Each of these NTs is produced from single aromatic (meaning they have a ring structure) amino acids. Serotonin is produced from tryptophan, dopamine is produced from tyrosine, and norepinephrine is made from dopamine.

As such, they are called monoamines (mono = one and amine = amino group from an amino acid). They react with millions of brain cells to induce feelings of happiness and well-being. Having too little leads to depression or other psychiatric problems.

Depression is often treated with drugs called monoamine oxidase inhibitors, since the enzyme monoamine oxidase is responsible for degrading the monoamine NTs once they have been released from neuron to stimulate the next neuron. Less degradation means more activity, so using these drugs is like increasing the serotonin, dopamine, and norepinephrine levels in the brain.

Exercise increases serotonin in the brain, so you feel better about the world and your place in it. The increased brain serotonin may come from blood, a single study showed a decrease in blood serotonin after exercise. On the other hand, maybe exercise increases production of serotonin in the brain. Maybe it’s both.

Dopamine isn’t left out when it comes to exercise. Physical activity increases calcium (Ca2+) flow to brain, which is necessary for dopamine production. But just as serotonin can be increased in more than one way, so can dopamine activity. Published results show that moderate exercise increases the number of dopamine receptors on neurons, so more good feeling is possible.

So dopamine and serotonin are increased by exercise and make you happy. How about just decreasing any signals that make you less happy? This is the second major effect of exercise; it decreases pain and stress. This occurs through release of two other types of compounds – endocannabinoids and endorphins.


Cancer and AIDS lead to a wasting syndrome call cachexia.
Here is Robin Gibb after he was diagnosed with advanced
liver cancer. There is loss of fat and muscle as the body
tries to burn anything for fuel. These diseases destroy
appetite and mood, so cannabinoids (marijuana) can be
prescribed to elevate both. Exercise would also help by
stimulating endocannabinoids.
Endocannabionoids such as anandamide (AEA) and 2-arachidonoylglycerol (2-GT) are made from arachidonic acid; they are eicosanoid lipids, and are still another function of the lipids. Endocannabinoids are very similar to phytocannabionoids in cannabis (marijuana); they both act on the same receptors to increase appetite, elevate mood, increase immune activity, and decrease memory. This is why cannabis is used for MS and cancer patients.

A study from 2011 shows that blood endocannabinoids, especially AEA, go up after intense exercise. This increase stimulates production of brain derived neutrophic factor (BDNF) in the brain. BDNF and serotonin have a reciprocal effect; each raises the level of the other (see picture below). BDNF also stimulates neurogenesis (more on this in 2 weeks) which can be important in mood, since 50% of female depressives are seen to have a smaller than normal hypothalamus. The effect of AEA after exercise on long term mood and outlook takes just long enough for neurogenesis to begin.

Endocannabinoids also reduce nociceptive (noci = unpleasant) inputs, so your pain tolerance goes up with exercise. A 2013 study showed that exercise-induced increases in endocannabinoids increased rats tolerance for nociceptive stimuli, either by mechanical means or through heat. This is similar to how endorphins mimic opioids (like morphine) to create analgesia.


Brain derived neurotropic factor (BDNF) plays a central role
in depression. With increased stress you get more cortisol (a
glucocrticoid) which drives down BDNF and this increases
neuron die back and loss. This is why some people have a
reduced hypothalamus during depression. On the right, you
can see the loop by which increased BDNF drives serotonin
production and serotonin then drives BDNF production. Your
brain wants you to be happy.

Endorphins (endo = internal, and orphine is from morphine) are produced in the pituitary and released into the bloodstream. They interact with opioid receptors on neurons to induce analgesia (an = no, and gesia = feeling), just like morphine. Endorphins are released in times of stress or pain in body – you know, like when you try running a few miles.

Together, endocannabinoids and endorphins reduce pain and this improves mood. Runner’s high, that feeling of euphoria that is supposed to come from long intense exercise, is reported to come from endorphin release after glycogen stores have been depleted (out of immediate energy). However, the high, if you ever feel it, might actually come from reducing the stress and pain inputs. In this environment, the increased serotonin and dopamine can have bigger "be happy" effects.

This is all a great theory, but there’s one problem. The blood brain barrier (BBB) doesn’t let much of what’s in the blood into the brain. In most of the body, the junctions between the cells that make of the blood vessels are a little leaky. Many large and electrically charged molecules can get through them into the tissue. This would be bad for the brain, since many bad molecules can be in the blood as well, toxins and such. The BBB is an evolution-produced guard for our big brain.


The blood brain barrier keeps potentially damaging
molecules out of the brain tissue. On the left you see a
typical vessel, with loose junctions between the
endothelial cells that line the vessel. On the right is a
vessel in the brain. It has tight junctions to greatly reduce
the passage of molecules, and is surrounded by the ends
of astrocytes (helper cells in the brain) which also
provide another layer of protection. The only way
anything of size is getting through is to have a
dedicated transporter.
The BBB comes from the physical connections between blood vessel cells being very tight (hence the name tight junctions). Basically, unless you are small and can simply diffuse through the endothelial cells or you have a specific transporter – you ain’t gettin’ in.

How could serotonin endocannabinoids or endorphins in the blood, or calcium for dopamine production have effects on your brain if they can’t get in?

There are two answers. 1) Endocannabinoids and endorphins have some of their effects outside the brain. There are receptors for them in the peripheral system, where the painful stimuli might occur. This would work well for preventing pain and noxious stimulus inputs from getting to the brains.


Bikram hot yoga takes you through many poses for
stretching and stress relief. The sessions take place in a
105˚F room that is also humidified. You sweat like a
dog, if dogs sweat a lot. This increased heat may help
loosen the blood brain barrier so mood altering
molecules can enter, but the vast majority of mood
enhancement takes intense cardiovascular activity,
something not provided by the average yoga class.
2) It seems that exercise temporarily increases the permeability of the BBB, so serotonin from blood, Ca, endocannabinoids, endorphins, even blood levels of BDNF can get to the brain and help you be happy. As proof, a brain protein was found in the blood after exercise in a 2013 study, indicating the BBB was disrupted.

The increased permeability may come from exercise-stimulates angiogenesis (angio = blood vessel, and genesis = birth). New blood vessels are built, but new vessels are leakier. It may also be that exercise produces heat, and studies have shown that heat in the brain makes the BBB leakier. This may be why hot yoga participants seem so happy afterward – ask them ‘cause I’m not trying it.

Next week, how exercise helps you to sleep better. And it isn’t from just wearing you out. Believe it or not, your immune system is involved!



For a good resource on the structures of the brain, see Open College's Interactive Brain map.


Galdino G, Romero TR, Silva JF, Aguiar DC, de Paula AM, Cruz JS, Parrella C, Piscitelli F, Duarte ID, Di Marzo V, & Perez AC (2013). The endocannabinoid system mediates aerobic exercise-induced antinociception in rats. Neuropharmacology, 77C, 313-324 PMID: 24148812

Koh SX, & Lee JK (2013). S100B as a Marker for Brain Damage and Blood-Brain Barrier Disruption Following Exercise. Sports medicine (Auckland, N.Z.) PMID: 24194479

Heyman E, Gamelin FX, Goekint M, Piscitelli F, Roelands B, Leclair E, Di Marzo V, & Meeusen R (2012). Intense exercise increases circulating endocannabinoid and BDNF levels in humans--possible implications for reward and depression. Psychoneuroendocrinology, 37 (6), 844-51 PMID: 22029953

Vučković MG, Li Q, Fisher B, Nacca A, Leahy RM, Walsh JP, Mukherjee J, Williams C, Jakowec MW, Petzinger GM. (2010). Exercise elevates dopamine D2 receptor in a mouse model of Parkinson's disease: in vivo imaging with [¹⁸F]fallypride. Movement Disorders, 25 (16), 2777-2784 DOI: 10.1002/mds.23407

Puterman E, Lin J, Blackburn E, O'Donovan A, Adler N, & Epel E (2010). The power of exercise: buffering the effect of chronic stress on telomere length. PloS one, 5 (5) PMID: 20520771


 
For more information or classroom activities, see:

Monoamine neurotransmitters –

Exercise and mood –

Blood brain barrier –

Endocannabinoids –

Endorphins -


Exercise Puts Me To Sleep – You Too

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Biology concepts – sleep induction, circadian cycle, narcolepsy, insomnia, anterior hypothalamus, neurotransmitters, cytokines, inflammation


Harriet Tubman gained the respect of all after the Civil
War, including that of William Seward, Secretary of State
of the United States (he’s the guy that bought Alaska).
Despite this respect, she ended up penniless. Seward
provided her with a two story brick house in Auburn,
New York where she could live out her days in
relative comfort.
Harriet Tubman was a narcoleptic. No, she didn’t steal things from the Woolworth, that’s kleptomania. She led hundreds of slave to freedom in the years before the American Civil War despite fighting off the urge to go to sleep at any given moment.

Narcolepsy is a sleep disorder that affects 1 in 2000 Americans, and causes them to have episodes of extreme fatigue. They fall asleep at odd times, and are very hard to awaken. In addition, they may also suffer from wakeful dreams, and cataplexy, a condition similar to temporary paralysis. This can’t have instilled confidence in Harriet’s passengers, but she got the job done.

Narcolepsy is basically too much sleep induction, while insomnia is too little. Many people suffer from insomnia, and it can be brought on by many different conditions. Could your New Year’s resolution to start exercising end up helping both narcolepsy and insomnia. Let’s find out.

You wake up in the morning determined to wear yourself out on the treadmill sometime today. You’re going to run to exhaustion in the hopes that you will get a good night’s sleep as a result. Your doctor did say that working out would help you sleep – but is this what he meant? You run until you’re out of energy and then you sleep to refill the gas tank?

Exhaustion from exercise may play a role in inducing sleep, but there’s much more. Exercise helps in insomnia in the elderly according to some reports. Exercise also helps with narcolepsy in children and adults. But how does it help?

There are two competing hypotheses for exercise’s effects on sleep via your brain. They use two different sensors, but they both run through the brain. But first we need to know a little bit more about the sleep center of the brain to explain how exercise is affecting us.

Sleep was the subject of a series of posts a couple of years ago, starting with this post. But we didn’t talk much about the induction of sleep. Sleep used to be considered a passive process; you slept when the stimulatory inputs to the brain were diminished.


Here is the hypothalamus, home of the sleep centers of the
brain. One the left you can see where the hypothalamus is
relative to the rest of the brain structures. On the right is a
cartoon showing the hypothalamus closer, including the
VLPO, the SCN, the LHA for wakefulness, and the MPO
for heat regulation.
Sleep is now known to be an active process, controlled by the anterior hypothalamusand preoptic nucleus. See the picture to help you locate this area of the brain. In the anterior hypothalamus and the preoptic nucleus, stimulation of GABAergic neurons promote sleep induction and maintenance. GABA is a neurotransmitter that is inhibitory, it stops some of neurons from firing. In this case, the neurons it inhibits are the ones that produce orexin/hypocretin. This is another neurotransmitter, but this one stimulates wakefulness.

Orexin is one neurotransmitter with two names. It was discovered by two different groups at just about the same time, and each group named it something different. Scientists haven’t decided yet which name to go with, so they use both.

There are only 10,000-20,000 neurons which produce orexin/hypocretin, so damage to any part of this area of the brain could induce narcolepsy. This may have been what happened to Harriet Tubman after her master hit her in the head when she was 12 years old. On the other hand, the brain trauma may have resulted in too much VLPO and AH sleep promotion. Either way, she was a professional napper.

So stimulating the POAH and the VLPO lead to sleep at least in part by inhibiting the production of orexin/hypocretin. But what stimulates the POAH and VLPO? Knowing nature as you do, you can bet there are several pathways. One way is certainly routed through the circadian clock. We have talked before about the sleep cycle controlled by the clock.


Yet another picture of the brain, this time highlighting the
pineal gland, where melatonin is made. The left side suggests
that light affects the pineal, but it ain’t the way the yellow
arrow shows. The right figure shows the true pathway much
more realistically. The pineolocyte is the cell type found in the
pineal gland. The melatonin is made from tryptophan and
serotonin is an intermediate structure, so you can make it
from serotonin itself.
Different hormones (like melatonin) and neural inputs/outputs stimulate the sleep and wake centers of the brain to create a semi-regular day/night cycle. Many things can mess with the cycle of melatonin and other day/night rhythms, including exercise. Now we can talk about different ways this may occur.

Temperature hypothesis:
The temperature hypothesis for sleep induction states that a one-degree decrease in your core temperature is enough to trigger sleep induction pathways on the brain. How could these two factors be linked? Well, the temperature sensing and regulating centers of your brain are located in the anterior hypothalamus, right next to the sleep centers (POAH and VLPO).

Reducing temperature is a way of saving energy by the body; this is probably an evolutionary holdover from when calories were hard to come by. Decreasing temperature signaled the brain that less activity was going on, so the body induced sleep to further reduce temperature and save energy for the next day.

It so happens that activity also decreases when the sun goes down, or at least it did before Thomas Edison and the electric light. This strengthened the link between temperature and the circadian sleep/wake cycle. To illustrate this point, a 2013 study measured the effects of drugs on both the circadian patterns and temperature. Drugs that altered the light responses in the SCN, including caffeine, also altered core temperature.


GABA (Gamma-aminobutyric acid) is a neurotransmitter
release at the synaptic cleft of some neurons. It is inhibitory
for some wakefulness neurons, so it promotes sleep. On the
other hand, noradrenaline is stimulatory for the orexin
producing neurons so it promotes being awake. In the middle
is adenosine, you know the player in DNA, RNA, and ATP. It
also happens to be a neuromodulatory and can inhibit the
GABA, NA, and orexin neurons.
In the same study, the same responses that reinforced circadian cycle (spontaneous sleep about 16 hours after light stimulation) also reduced the core temperature at the same time. Drugs that inhibited one, stopped the other as well. It would appear that temperature and day/night cycles are very much linked for sleep.

That then brings up the question of how exercise helps you go to sleep just by messing with your temperature. You exercise - you get hot - the blood vessels in your skin dilate and you sweat to dissipate some of the heat. But sweating isn’t 100% effective, your core temperature does go up. After you finish exercising, your temperature goes down slowly over time.

This decrease in temperature is the cue for your body to begin sleep. Your anterior hypothalamic temperature-regulating center can’t tell the difference between this decrease and the decrease brought about by circadian rhythms. So you may get sleepy a few hours after exercising, as your temperature comes down.

So, is right before bed the best time to exercise? Nope. Exercising stimulates your brain and cardiovascular system as well as raises your temperature. Trying to sleep right after exercise will probably be harder than normal, just because you are firing on all cylinders in your brain and heart.

The best time to exercise to help you get to sleep is about five hours or so before you plan on retiring for the evening. Your temperature goes up while exercising, and then will start to drop just about the same time you are ready for bed. This will reinforce the circadian cycles and give you the best shot at good sleep.


Insomnia is found in a number of conditions. It is
becoming a serious problem in the elderly, with people
living longer and unfortunately becoming more sedentary.
Complications are shown in the cartoon. You see that the
effects are varied, including the ability to fight off
disease. Who knew that not sleeping could lead
to diabetes!
The above plan applies to most of us, but perhaps not all of us. Very well-trained athletes might be less affected by the changes in body temperature for sleep induction. One 2013 study looked at exercise time, temperature manipulation and sleep patterns in professional and highly trained amateur cyclists. The results showed that evening exercise had no affect on sleep patterns, even if combined with a cold water dunk after the cycling routine (brrr!). Neither exercise nor exercise + decreasing temperature brought on a decreased time to spontaneous sleep. So – they sleep well because they wear themselves out each day.

Cytokine hypothesis:
The other system that may be important for inducing sleep after exercise is the immune system. Cytokinesare chemical messages that influence many different parts of the immune system. They come into play when you have an infection, or cancer, or allergy; basically any insult to your system.

There are many different cytokines, and they perform many different jobs. Certain cytokines can even mediate opposing pathways, depending on the stimulus that starts their production and release. Some promote inflammation (pro-inflammatory) when one specific injury is sense, but inhibit inflammation (anti-inflammatory) if a different insult occurs.

Exercise can be seen as a stress to the body. It can injure muscles; in fact, that's how you build muscle. You tear them down a bit through work, and they grow back bigger and stronger. This is an insult that results in cytokine production and release into the bloodstream. But the more you train, the less of an insult your body registers.

IL-1beta, TNF-alpha and IL-10 are cytokines that have been associated with sleep induction. Plasma levels of IL-1beta are highest just as sleep is induced; this is one of the things controlled by the circadian system. But prolonged IL-1beta or TNF-alpha results in short sleep, and it is easy to wake you up.


Cytokines have big roles in the brain, even if they
act indirectly. Second messengers trigger pro-
inflammatory cytokines through the brainstem
which control fever and other symptoms,
including sleepiness. You think it’s a coincidence
that you sleep more when you’re sick?
On the other hand, IL-10 is anti-inflammatory and is higher with physical training over time. A 2012 study showed that in the elderly with insomnia, moderate training over months resulted in lower IL-1beta, lower TNF-a, and higher IL-10. These were also associated with better sleep patterns.

The neurons of the sleep center are sensitive to pro-inflammatory cytokines; inflammation signals disrupt the restful sleep patterns we are looking for. This involves the pro-inflammatory stimulation of cortisol, the stress hormone, so exercise’s help in sleep may be again related to a reduction of stress effects. This is a complicated system, but the take home message is, more exercise results in less pro-inflammatory cytokine action on the brain.

Chronic fatigue is also linked to high levels of pro-inflammatory cytokines in the brain that are unhooked from the decrease induced by training for some time. In the opposite direction, narcolepsy is aided by exercise, perhaps by reducing the cytokines that would inhibit orexin/hypocretin domination (wakefulness) in the anterior hypothalamus.

A 2007 study showed that in mice that don’t make orexin/hypocretin (have narcoplepsy), running on the wheel helped them stay awake more during the day. Of course, it also led to more episodes of cataplexy, so the story is not complete.

Next week, another brain effect of exercise – it can actually build your brain and make you smarter. Start running before that next AP quiz.


For a good resource on the structures of the brain, see Open College's Interactive Brain map.



Vivanco P, Studholme KM, & Morin LP (2013). Drugs that prevent mouse sleep also block light-induced locomotor suppression, circadian rhythm phase shifts and the drop in core temperature. Neuroscience, 254, 98-109 PMID: 24056197

Robey E, Dawson B, Halson S, Gregson W, King S, Goodman C, & Eastwood P (2013). Effect of evening postexercise cold water immersion on subsequent sleep. Medicine and science in sports and exercise, 45 (7), 1394-402 PMID: 23377833

Santos RV, Viana VA, Boscolo RA, Marques VG, Santana MG, Lira FS, Tufik S, & de Mello MT (2012). Moderate exercise training modulates cytokine profile and sleep in elderly people. Cytokine, 60 (3), 731-5 PMID: 22917967

España RA, McCormack SL, Mochizuki T, & Scammell TE (2007). Running promotes wakefulness and increases cataplexy in orexin knockout mice. Sleep, 30 (11), 1417-25 PMID: 18041476
For more information or classroom activities, see:



Exercise and sleep –

Narcolepsy –

Orexin/hypocretin –

VLPO and sleep –


Pump Up Your Brain

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Biology concepts – learning, memory, attention, concentration, hippocampus, neurotransmitters, neurotrophins, executive function, processing speed, exercise


Many people exercise because of how it makes them feel,
or just because they think it helps them think more
clearly - maybe by reducing stress. They will be happy to
know that exercise actually increases the power of your
brain, everything from learning, to memory, to attention,
to decision making speed.
Many years ago, my father told me the story of how he studied while in college. He would hit the books in a solitary, silent room and just cram until he couldn’t concentrate anymore. Then he would get up, go outside, and run laps around his dorm for a while. Then he would come back and start again. Study, run, repeat. Turns out, the running makes a true difference. Exercise can actually make you smarter!

In a study from 2011, researchers took overweight kids and had them start exercising. Those that had at least 30 minutes of physical activity each day showed increased hippocampus size, and significant improvement on a CAS planning test, an alternative to the standard IQ test.

Planning basically means that their executive function (planning, reasoning, and decision making skills) had improved markedly. They also performed much higher on a math test, even though no additional math instruction had been given.

Exercise has impacts on memory, learning, attention, concentration, and processing speed. So now we know what we are talking about when we say exercise helps learning. Oh – you won’t just take my word that exercising helps? Good, always ask for evidence.

Let’s look at studies just from 2013, although there are many older studies. One study found that a single bout of moderate exercise allowed participants to more accurately complete a test on memory, reason, and planning - and it took them less time. Another study indicated that exercise reduced the loss of cognitive function in middle-aged women. Yet another publication talked about how master athletes (over 50), have a larger brain volume and better cognitive function as compared to their sedentary counterparts.

We can go on. Exercise has been shown to support the cellular structure of the white matter (myelinated) neurons of the cerebral cortex in patients with vascular disease, important for higher thinking functions. And another study shows that processing speed is increased after starting a regular regimen of cardiovascular activity.


The upper image shows where the hippocampus is located
within the brain. There are two, one in each hemisphere.
They are connected as well. The lower image shows the
regions of the hippocampus, including the dentate gyrus
(DG) the area where much of the neurogenesis after
exercise is found.
Finally, we will mention just one of the many 2010 studies. Nine-ten year old kids that exercised regularly had 12% larger hippocampi (plural of hippocampus, part of brain for learning and memory). They were faster on recall tests and they learned new information faster.

So now that you are convinced that exercise does help cognitive functions, the question still remains as to how exercise carries out this miracle. The first thing to get clear is the difference between memory and learning. It might seem that they are the same thing; you have some experience, either verbal, aural, visual, etc. and if you remember it, then you have learned it. But there are subtle differences.

Specialists define learning as a process that will modify a subsequent behavior. Memory, on the other hand, is the ability to remember past experiences. Memory is the record left by a learning process, so you need to have memory to learn. You learn to play piano by studying the notes and the instrument, but you then play it by using your memory to retrieve the notes and fingering that you have learned.

Back to the mechanisms of how exercise help memory and learning. The easy explanation is that exercise helps you sleep, improves your mood, and drives more oxygen to the brain. These undoubtedly help you study better or even notice more that can be used to build knowledge. These are the factors my dad counted on when he went running. But there’s much more.

The hippocampus is important for learning and memory. Many studies of exercise and cognitive function have shown increases in the size of this part of the brain in exercise participants. Those kids that increased their “IQ,” they had an increased hippocampus. So did mice from studies in the 1990’s.


Neurogenesis is the production of new neural cells from
stem cells. There are stem cells located in the brain. They
can become any type of brain cell, depending on stimuli in
the local area. Normally, only a small percentage of
stimulated stem cells will become neurons, but after
exercise the number that survive goes up dramatically.
Exercise upregulates neurogenesis, oxygenation, synaptic plasticity, neurotransmitter populations, myelination, processing speed, and long-term potentiation (LTP). O.K., that’s a lot of big words, so let’s take them one at a time. Remember that all these things are linked together. Plasticity, neurogenesis, and LTP apply to memory. Neurogenesis and processing speed apply to new learning and executive function. Neurotransmitters, plasticity and oxygenation combine to affect attention.

Neurogenesis
A lot of the benefits from cardiovascular exercise come through the making of new neurons (neurogenesis). Yep, this is a huge exception to the rule that central nervous system neurons last your entire life and can’t be recovered or new ones produced. Neurogenesis is how the hippocampi of all those exercisers got bigger.

Regular exercise induces neurogenesis through action of brain chemicals, trophins and NTs. We talked about brain-derived neurotrophic factor (BDNF) 2 weeks ago with respect to mood and we said we revisit this factor. This neurotrophin actually stimulates your brain to make new neurons! More neurons means more connections, and more potential learning.

For most all of the cognitive functions, the lynchpin seems to be BDNF. How does exercise increase BDNF? We aren’t sure yet. It may be that exercise is a stress, this increases the calcium flowing into the brain. The calcium activates many transcription factors, and BDNF is known to require calcium for transcription.

But nothing is ever simple. It is probable that serotonin, IGF-1, and BDNF are all needed to increase neurogenesis in the hippocampus. Inhibitors of any one of these drastically reduce the amount of exercise-induced neurogenesis.

Plasticity
Think of plasticity as a general process, the altering of neurons and their connections. It involves making more neurons (neurogenesis) and the number (developmental plasticityor synaptogenesis) and orientation of the dendritic connections with other neurons (synaptic plasticity).


The images show the increase in the number of dendrites and
possible synaptic junctions over time. The increase in dendrites
is called arborization (arbor = tree) for obvious reasons. The
increase in synapses is called synaptogenesis. Exercise increases
both of these. This image isn’t a result of exercise, but it would
be is similar.
BDNF doesn’t just induce new neuron formation, it can increase the number and size of the connections (synapses) between neurons. IGF-1 is probably involved in this as well, as its main function is to support the growth of fragile, newly formed neurons and connections.

Plasticity is crucial to learning and to memory, since all learning and memory is just a map of connected circuits that work together to access certain information. It is the number and pattern of the connections that determine the amount retained. More connections must help this process.

Long term potentiation
LTP is for memory and learning – the reinforcing of neural connections to make them stronger. Exercise increases LTP, probably through synaptic plasticity, more connections between two neurons would help reinforce each other when they fire. We talked about LTP last year, so read that post and know that exercise increases it.

Unfortunately, for best increases in memory the exercise must be long term. In a 2013 study, neurogenesis was apparent only 14 days after initiation of exercise, and these were immature neurons. LTP wasn’t increased appreciably until 56 days.

Processing speed
Increased speed probably comes through increased IGF-1 and oxygenation, and their effects on the support cells in the brain. Oligodendrocytes and astrocytes help the neurons do their job at peak efficiency. In particular, oligodendrocytes make the myelin sheath that increases transmission speed.


Meet the glial cells. Astrocytes mediate the travel of fluids
and nutrients from the capillaries to the neurons and
between the neurons and the cerebrospinal fluid.
Oligodendrocytes make the myelin sheath around some
axons. Microglial cells are the immune system of the brain,
they phagocytose intruders. Finally, the ependymal cells
line the ventricles in the brain, the spaces that hold the
cerebrospinal fluid.
Astrocytes, on the other hand, are important for blood flow to neurons, and cerebral spinal fluid movement. These two functions would be particularly important for moving neurotrophic factors toward the neurons.

Attention and concentration
Exercise also helps your attention and concentration. And no, these two aren’t exactly the same. They’re more closely related than memory is to learning, but there are still some differences. Both are important for making you smarter, because only by focusing do we take information in – you have to notice something to learn it.

When you are in a room full of people talking, you can still follow the conversation between yourself and one other person. This is one of several different forms of attention. In general, attention is a thinking process for directing and maintaining awareness of stimuli in one’s environment.

Concentration is the ability to control attention for a sustained period. Attention shifts as we wander from thought to thought about different things in our mind or environment, but concentration requires attention to one thing without wandering. In more clinical terms, concentration is a combination of two types of attention; sustained attention and selective attention.

Sustained attentionis staying on task, keeping your mind on a single task over time. Selective attention is more about how you pick what you pay attention to. If there are many activities going on within range of your sense, but you focus on one thing and pay no attention to the others, that is selective attention.


Attention span is not equal to sustained attention. It is
focused attention; how long until your brain diverts to
some other stimulus. In 2000, Americans had a 12 second
attention span on average. In 2010, it was down to 8
seconds. Heck, a goldfish has a 9 second attention span,
and we make fun of them!
Attention is centered in the reticular activating system (RAS), near the brain stem. But it connects to other centers that work in attention as well, like the prefrontal cortex and the parietal cortex. The RAS accounts for shifts in levels of awareness to different things. Exercise activates the RAS, which increases alertness, and therefore attention and concentration – my dad was ahead of his time.

It turns out that increased dopamine, serotonin, and norepinephrine in the brain, and particularly the RAS is crucial for attention and concentration. And we talked two weeks ago about how exercise increases all these. In ADHD, they give drugs (methylphenidate) that increase the apparent levels of dopamine. This helps us make sense of studies that show regular exercise alleviates the symptoms of ADD/ADHD.

One last point that I find interesting. The type of exercise seems to make a difference for the increase in neurotrophins. A 2012 studyshowed that rats that ran on exercise wheels had increased BDNF in the hippocampus, but rats that lifted weights (climbed ladders with weights on their tails) increased only IGF-1. The two proteins work in different pathways, so rat studies show us that it is best to include both aerobic and resistance training in your exercise program. And a rat shall lead them.

Next week, can you die from not getting enough sleep. Yep, and that's not the weirdest part of fatal familial insomnia.


For a good resource on brain structure and function, see the Open College’s interactive brain.



Patten AR, Sickmann H, Hryciw BN, Kucharsky T, Parton R, Kernick A, & Christie BR (2013). Long-term exercise is needed to enhance synaptic plasticity in the hippocampus. Learning & memory (Cold Spring Harbor, N.Y.), 20 (11), 642-7 PMID: 24131795

Cassilhas RC, Lee KS, Fernandes J, Oliveira MG, Tufik S, Meeusen R, & de Mello MT (2012). Spatial memory is improved by aerobic and resistance exercise through divergent molecular mechanisms. Neuroscience, 202, 309-17 PMID: 22155655

Davis CL, Tomporowski PD, McDowell JE, Austin BP, Miller PH, Yanasak NE, Allison JD, & Naglieri JA (2011). Exercise improves executive function and achievement and alters brain activation in overweight children: a randomized, controlled trial. Health psychology : official journal of the Division of Health Psychology, American Psychological Association, 30 (1), 91-8 PMID: 21299297

Tam ND (2013). Improvement of Processing Speed in Executive Function Immediately following an Increase in Cardiovascular Activity. Cardiovascular psychiatry and neurology, 2013 PMID: 24187613

For more information or classroom activities, see:

Most of the information for this post comes from recent scientific journals, here is more general information from the internet.

Memory classroom activities –

Hippocampus –

BDNF –

Neuroglia –

An Infectious, Genetic Disease? Better Sleep On It.

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Biology concepts – thermoregulation, sleep, genetic disease, infectious disease, central dogma of molecular biology, form follows function


Even rats have to get some sleep. It was nice to have the sleeping cap,
but unnecessary for a sleep deprivation study. Not a good use of
research dollars.
“I’m dying for a good night’s sleep.” Is this just hyperbole, or an impending warning of death? For laboratory rats, sleep deprivation does kill. During their insomniac downward spiral, the rats tend to get hot and can’t cool down – you know, they can't thermoregulate (see Can’t We Just Go With The Flow). This doesn’t mean that a loss of the ability to thermoregulate is what kills the rats, but it does suggest a connection between sleep deprivation and the hypothalamus.

We looked at the hypothalamus in our story of endothermy. This evolutionarily old brain structure implements a set point temperature for the body and receives information about the temperature of different parts of the body. When the body temperature deviates from the set point, the hypothalamus initiates bodily mechanisms to normalize the temperature.


Apparently one of the effects of sleep deprivation is that you
become semi-transparent.
People with severe insomnia tend to sweat more and have higher core temperatures even though they say they are cold. They also have extreme high blood pressure, pulse, and appetite. These symptoms suggest that sleep deprivation messes with the hypothalamus, since functions of the hypothalamus include themoregulation, sleep, hunger, thirst, reproductive readiness in females, and stress responses. What scientists don’t know yet is just how sleep deprivation actually kills the rats or harms people.

Dying from a lack of sleep is not just a rat problem, a few very unlucky humans die from it as well. Fatal familial insomnia (FFI) is a very rare genetic disorder; it has been reported in only 40 families worldwide. Before describing the truly horrible way these patients die, let’s look at what causes the disease.

FFI is caused by a point mutation in the gene for the prion protein PrPc. A point mutation means that one nucleotide on the DNA is changed, which leads to a change in the protein coded for by the DNA. Three unit (nucleotides) segments of the RNA (made from the DNA template) work together (called a codon) to code for one protein building block (amino acid). In the case of FFI, the amino acid called aspartic acid is changed to one called asparagine, and this changes the protein’s shape. 


The left image shows mRNA bases recognized in sets of three
(codons) by tRNAs with amino acids attached (Ser = serine, tyr =
tyrosine). The amino acids are linked to because proteins. The
lower section is the genetic code, showing which amino acids are
coded for by which codons. The right image shows how proteins
fold. The primary structure is the amino acid sequence. The
secondary structure comes from interactions of adjacent amino acids,
including spirals called helices or sheets. The tertiary structure comes
from the folding up of the entire protein, while the quaternary
structure comes from the interaction of different proteins into a
larger complex.
PrPc is made up of 250 amino acids linked together in a chain. Each different amino acid carries a different shape and charge and will interact with every other amino acid differently. The sequence of amino acids in a protein cause it to fold into a specific shape. It is the protein’s conformation (shape) that determines its function. This is the opposite of what we determined for evolved organism characteristics, where form follows function (see Do You Have To Be Ugly To Hear Well?). With proteins – function follows form!

Mutation of that single amino acid at position 178 (aspartic acid is negatively charged, while asparagine is positive) causes the folding, and therefore the function, of the protein to change. Aspartic acid is sometimes abbreviated "D", while asparagine is called "N"; therefore, the mutation is often indicated as D178N (D at position 178 is changed to N).

Many genetic mutations result in no change in amino acid, or a change that bring a large enough change the shape to cause a change in function. But when it does, good or bad things can happen. On one hand, the altered protein might confer an advantage to the organism, one that promotes survival in the environment or after an environmental change.This positive selection through reproductive advantage become the new normal – and this is evolution

On the other hand, the change in amino acid sequence, form, and function could be destructive. Disease might be the result, or perhaps a change in the organism that reduces reproductive success. One of these two results is what occurs with the FFI mutation of the prion protein.

When the mutated prion folds differently, it forgets its day job and moonlights as a sinister evil force. Every other prion protein it contacts, WHETHER MUTATED OR NOT, is coaxed into changing its shape. The new prions turn to the dark side, then change other prion proteins they contact, multiplying the effect. The poorly folded prion proteins will stick together, come out of solution, and form solids (plaques) where they settle out. In different prion protein diseases, this settling out occurs in different parts of the brain. In FFI, it is the hypothalamus.


In the top image, the PrPc on the left is properly folded. The green
represents alpha helices and the blue arrows represent beta-pleated
sheets. The right image shows the malfolded version of PrPsc. It is a
tighter structure, which partially explains why protein-degrading
enzymes don’t work on it. . The lower cartoon shows that the PrPsc
can force the PrPc to assume the improper form, and these then
aggregate into plaques.
The prion plaques are longer lived then the regular prion protein; normal cellular enzymes whose job it is to degrade proteins won’t work on prion plaques. And worse, if some of the malfolded protein is transferred to another animal, the recipient will develop plaques and disease as well. That makes this an infectious disease that isn’t caused by a bacteria, fungus, parasite, or virus. The prion is an infectious protein! What a terrible exception to the rules of infectious diseases.

We see here a protein that can replicate itself (not by building more of themselves, but by changing the form of normal proteins), and that makes it a repository of biologic information. This is an exception to the central dogma of molecular biology, which says that DNA is the sole information storing material.

FFI moves from person to person through heredity, but if a non-affected person comes into contact with some brain material from an FFI patient and that material entered their bloodstream, it can be transmitted this way as well. A prion protein disease called Kuru is famous for being transmitted from person to person.

The Fore tribe in Papua New Guinea once observed a ritual wherein they honored a dead tribe member by eating part of their brain (called ritualistic mortuary cannibalism - gasp!). Because of this, there was an epidemic of Kuru in this tribe in the early 1900’s. Over a period of 3-6 months victims would become unsteady, irrational with bouts of laughter, and then degrade mentally and physically to the point of death. There are more than twenty known prion diseases (mad cow disease, Creutzfeldt-Jakob, scrapie, etc.), and Kuru suggests that some might have no genetic component, only person to person transmission.


A member of the Fore tribe is shown on the left. This tribe used
to celebrate the lives of departed members by eating their brains.
This spread a prion protein disease called Kuru, a protein disease
that is infectious! The Fore tribe still lives in Papua New Guinea,
although there are fewer of them than before Kuru.
The differences between the various prion diseases are based on the specific prion protein mutation, what part of the brain is attacked, and how potent the prion is at refolding normal prion proteins. For instance, the D178N mutation in FFI also occurs in Creutzfeldt-Jakob Disease (CJD), but a normal polymorphism (an amino acid change that doesn’t change form or function) at position 129 determines the fate. If amino acid 129 is methionine, the the person gets FFI, if it is valine, then they get CJD. 

The families that suffer from FFI have the D178N mutation, and also pass on the polymorphism for methionine (M) at position 129. Even more gruesome, some cases of prion protein diseases can be sporadic, not associated with either an inherited mutation or transmission. The malfolded prion can very rarely arise out of nowhere in isolated individuals.

The mutated PrPc is passed on via inheritance. You get one copy of each chromosome from each of your parents, so for an individual gene, you might get two normal copies, 1 mutant copy and 1 normal copy, or 2 mutant copies. Some diseases require that you must inherit two mutant copies for symptoms to show (recessive), but other require only one mutant copy (dominant, it dominates the trait from the other parent).

FFI is autosomaldominant(not associated with the X or Y sex chromosomes), so the chance of getting a mutant copy and the disease if one parent has it is 1 in 2; these are bad odds. But, if everyone with FFI dies, then why is the disease still showing up in families. Remember that we said above that some genetic diseases can, but don't have to, affect reproductive success. Unfortunately for those with FFI, the symptoms appear in the victims’ fifties, after they have had children. Natural selection doesn’t eliminate FFI from the population because FFI doesn’t appear affect reproduction.

The first symptoms of FFI include sweating while feeling cold. Later, the ability to get a good night’s sleep is lost, followed closely by the inability to nap. As the disease progresses, there are panic attacks, phobias, and no sleep whatsoever. After 4-6 months, mental abilities start to degrade. In its final stages unresponsiveness precedes death. 

This is especially sad way to die, because during the majority of the disease course the patient is aware of everything going on. At least with middle to late Alzheimer’s disease the patient is blissfully unaware of their dementia.


For both the gross and microscopic images, the left example is from prion protein disease victim, while the right example is from a normal brain. The brains on the left show how great the loss of tissue can be in Creutzfeldt-Jakob disease. The microscopic image from the diseased brain shows the plaques and the resulting holes in the brain structure. The small gaps in the normal brain on the right are a result of shrinking of tissue after it was on the slide.
On autopsy, the hypothalmus of an FFI sufferer looks like it has been hit with a shotgun blast. Holes are present in the tissue, representing areas where neurons have been lost due to inflammation and triggered cell death. The affected area of the brain takes on a spongy appearance, so prion protein diseases are lumped together and called transmissable spongiform encephalopathies (encephalon = brain and pathy = disease). Unfortunately, there are no cure, treatments, or vaccines for any of these prion diseases.

It is the hypothalamus' control of sleep cycles and circadian rhythms that promotes survival in animals. But what about plants? They don’t have a hypothalamus. Can they suffer from loss of circadian activity? In a word – yes!  And this will be our starting point next time.


For more information or classroom activities on prion proteins, central dogma, infectious or genetic disease, the genetic code or protein structure, see:

Prion protein and diseases –

central dogma of molecular biology –

infectious disease –

genetic disease –

genetic code –

protein structure –
nwabr.org/sites/default/files/learn/bioinformatics/AdvL5.pdf
 

Plants That Don’t Sleep Will Take The Dirt Nap

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Biology concepts – nastic movements, turgor pressure, evolutionary pressure, tropism, osmosis

If you don’t let a Mimosa pudica (sensitive plant) plant rest at night, it will wilt away to nothing. A plant that needs a good night’s sleep? Really? We have talked about how sleep revitalizes different brain functions, especially within the hypothalamus (The Best Cure For Insomnia Is To Get A Lot Of Sleep), but plants don’t have a hypothalamus or any brain for that matter. So why does it die if it can't rest; is it out of its mind?


The prayer plant on the left is how it looks during the day, but
on the right, the leaves have folded or curled up. They also stand
straight up, as if at attention. A tough way to spend the night, but
it must serve some purpose.
The prayer plant (Maranta leukoneura) folds up its leaves at night and tilts them upward. When morning comes, the leaves tilt back into their day position and unfold to catch as much sunlight as possible. The folded leaves might look like they are praying (hence the name), and it may appear that they are sleeping, but this is just anthropomorphism.

Humans have a need to feel connected to the rest of Earth’s life, and in the process, we tend to see the behaviors of other organisms in human terms, trying to assign some human motivation to them. So, is the plant sleeping? Does it need to rest? No. Sleep in animals implies inactivity and neural rearrangement, and these don’t occur in plants.


Charles Darwin performed crucial experiments
in plant movement in his later life, including the
identification that chemical signals moving in the
plant are responsible for growth toward the light
(heliotropism). Notice that his son got pretty good
billing as an assistant.
However, the fact that the plant carries out this activity every night suggests that it has evolved in response to some pressure, some need. Surprisingly little is known about why plants move their leaves at night, but there are a few hypotheses. Some scientists believe that changing the angle of the leaves helps funnel dewdrops and overnight rain down the trunk or stem to the roots. Charles Darwin published two books on these plant movements, his theory being that the behavior reduced the chance of chill or freezing.

Another hypothesis suggests that leaves fold up to keep the rain from pooling on them and promoting bacterial or fungal growth. Or perhaps, apposing one leaf closely to the opposite leaf reduces the amount of water lost overnight. However, aquatic plants don’t have to worry about loss of water, but some immersed plants, like Myriophyllum Mattogrossense, still fold up at night. It may be a holdover from their terrestrial days, as most of today’s aquatic plants evolved from terrestrial plants.

My personal favorite proposes that by folding up their leaves, the plants give nocturnal predators a better shot at seeing, hearing, and smelling nocturnal prey. By helping the predators, plants are indirectly protecting themselves from animals that would eat them- plants are sly little devils (more anthropomorphism). It is probable that different plants move for different reasons, so one hypothesis almost certainly won’t cut it for all organisms.

Plants have night moves other than folding leaves. Morning glories (Ipomoea violacea) close their flowers overnight. The reasons for this movement may be a little plainer. Dry pollen sticks to pollinators better than wet pollen, so closing off the stigma to rain or dew keeps the pollen dry. It also takes energy to maintain an open flower; this energy would be best spent when pollinators are around. If the plant’s pollinators are diurnal, they why leave the buffet open all night?


Just as animals have an internal clock, plants gauge
their movements according to the circadian period.
Often plants match their rhythms to pollinator animals
they depend on or to avoid the active periods of
predators. Anyway, I like the picture.
There are also flowers that have the exact opposite behavior, opening their flowers as the sun sets. Philodendron selloum (Is It Hot In Here Or Is It Just My Philodendron) is a classic example, with its spathe closing down in the early morning hours.

Moonflowers (Ipomoea alba) are another example.  At about 8:00 pm, the moonflower opens. A single flower can go from completely closed to fully open in less than a minute (http://www.moonlightsys.com/themoon/flower.html). The morning glories and the moonflowers are both of genus Ipomoea, but they have opposite behaviors – different pressures lead to different adaptations, even in closely related species.

These movements of plant structures are independent of the direction of the stimulus, ie. they are not following the sun or being blown by a particularly wind, so they are called nastic movements. Nyctinasty (nyc = night or darkness, nastic = firm or pressed close) is the specific movement of leaves or flowers in a daily pattern, open during the day and closed at night. If directed by the position of a stimulus, the movements are called tropisms (heliotropism, thigmotropism, gravitropism).


The left picture shows that changes in the pulvinus shape could affect the direction of the entire petiole and all the leaves, or individual leaves (like on the sensitive plant). The middle cartoon indicates that filling the central vacuole with water can change the shape of the cell, pushing in one or more directions. The right image shows just how the extensor cells on the bottom must be inflated to lift the petiole, while turgidity in the flexor cells makes the leaf drop.
Nyctinastic movements are accomplished by the flow of water in and out of specific cells in the pulvini (swellings, singular is pulvinus) at the base of the petioles (the stalk that attaches the leaf blade to the stem). It is not unlike our muscle movements in that there is an extensor and a flexor pair. When K+ and Cl- are pumped into the extensor cells on the bottom of the pulvini, they become hypertonic and water follows the ions through osmosis. This causes the extensor cells to swell due to increased turgor pressure.

Turgor pressure refers to the pressure of the cell contents against the cell wall. This increased turgor pressure at the bottom of the petiole pushes the leaf up. In an opposite fashion, night causes a movement of ions to the flexor cells on the top of the petiole. Water flows out of the extensors and into the flexors by osmosis, causing the stem to droop. Flowers and leaves open and close by the same movements, with the extensor and flexor cells located at their bases.

Turgor pressure is the same mechanism which causes the venus flytrap (Dionaea muscipula) to snap closed its jaws of death when an insect disturbs its trigger hairs. These hairs are located on the nectar laden, red lobes of the trap. Touching just one trigger hair doesn’t spring the trap, two must be displaced within 20 seconds of each other. This saves energy and unnecessary trap closings; each trap snaps shut only four or five times, then dies. If you thought the moonflower moved fast, check out the venus flytrap (http://www.youtube.com/watch?v=ymnLpQNyI6g). I’m just surprised we can’t hear the water shooting into the flexor cells!


The venus flytrap supplements its diet of water and carbon
dioxide with proteins from the insects it catches and digests.
The bright surface with nectar draws them in, where they trigger the
mechanosensor hairs. The magnified image on the right shows a
trigger hair with its hinge that transmits a signal to the pulvini to
swell quickly and snap the trap shut.
The trigger hairs are mechanosensors. The stimulus that trips the trigger and causes the flow of ions and water in the extensor and flexor cells of the hinge region is directionally irrelevant; therefore, the snapping shut of the trap can be considered a nastic movement. In this case, as with the sensitive plant (Mimosa pudica), the movement is called haptonasty (hapto = touch).

A small percentage of plants have nyctinastic movements, so they are an exception to the rule that plants don’t move actively, but even a small percentage means that thousands of species do have these movements. This many exceptions underscores the point that nyctinasty must perform an important function.

Just as humans with fatal familial insomnia die from a lack of sleep (An Infectious, Genetic Disease), the sensitive plant has a much shorter lifespan when nyctinasty is prevented. A plant hormone that stimulates leaf opening was identified in 2006. When given to plants continuously, it caused the leaves to remain open. When nyctinasty was prevented in this way, the leaves were noticeably damaged within a few days, and the plant was dead in less than two weeks. It may not be sleep, but whatever it is, it is just as important.

Some plants are open during the day and some are open at night, just as some animals are active during the day and some during the night. And just as plants adapt to a time schedule to promote survival, animal adaptations are crucial to life in the light or the dark. But that doesn’t mean that some organisms won’t throw us a curve, as we will discover next time.


Ueda, M., & Nakamura, Y. (2006). Metabolites involved in plant movement and ?memory?: nyctinasty of legumes and trap movement in the Venus flytrap Natural Product Reports, 23 (4) DOI: 10.1039/b515708k





For more information, classroom activities or laboratories on nastic movements or turgor pressure, see:

nastic movements –

turgor pressure –

Form Follows Function - It’s About Time

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Biology concepts – circadian rhythm, vision sense, adaptation, parasitism,form follows function


The sun and the moon are symbols of different
activity cycles. As with everything else, we have to give
them human characteristics (anthropomorphism).
Many animals are active in the day or the night, but not both. So what are humans, diurnal (active in the daytime), nocturnal (active in the nighttime), or something else?

Maybe humans are two species, because I know folks who can’t accomplish anything before noon, and do their best work after 11:00 pm, whereas I get up around 5:00 am and am pretty much useless after 8:00 pm.

Whether diurnal or nocturnal, organisms are physically and behaviorally adapted to their activity pattern. This includes the way they sense their environments. Diurnal animals are more likely to have color vision, while nocturnal animals may only see in black and white. The upside for nocturnal animals is greater visual sensitivity, so they can see better than diurnal animals in low light conditions.

The reasons for these different visual talents lies in the types of light receptors on the retina. Rods sense light, but only its presence or absence (white/black). Different receptors, called cones, detect various wavelengths of light (colors). Diurnal animals have about 5-10 times more cones than nocturnal animals (3 types, one for yellow, one for green to violet, and one for red to orange), but they only function in higher levels of light. Therefore, the greater number of rods in nocturnal animals allow for more sensitive night vision, a good thing to have if you are active after sundown.


Rods (yellowish) and cones (blue) are different light receptors located on the retina. Rods are more numerous and detect low levels of light. Cones are less numerous and sense colors of light, but require more light. As shown in the middle image, the tapetum is located beneath the retina in some animals, and can bounce light back to the retina. This bouncing around is responsible for animals glowing eyes at night.
Many nocturnal species have an additional adaptation to improve their night vision. Their retina has an iridescent layer called the tapetum lucidum that bounces the available light around so it may hit more rods. This improves sensitivity, but at a cost to acuity (the image gets a little fuzzier). When you shine a flashlight in the woods at night, the little pairs of reflections you see are the tapetum lucida of the animals looking back at you. The light bounces around inside the eye and some escapes back out through their pupils and that is what you see. Some look at your flashlight to see if you are a predator, others look to see if you are worth eating.

But not every animal with a tapetum lucidem is necessarily nocturnal. An interesting new study has looked at the visual system of the Peter’s elephant nose fish (Gnathonemus petersii). This weakly electric fish has a long nose-like appendage that was thought to mediate location and communication through electrical pulses. But scientists at the University of Cambridge have found that this fish has surprisingly good vision to go along with electrical impulse usage.

The elephant nose fish lives in the dark, murky waters of Central Africa. For this low light environment, it has evolved a unique retinal arrangement for its rods and cones. The cones are arranged in discrete packets, each housed in a cup lined with a tapetum lucidem. Behind these cones are the rods that work in lower level light. In this way, the visual field can respond with cones and rods at the same time. It is believed that this gives the elephant nose fish the ability to pick out predators moving quickly through its visual field.
 
Humans don’t have a tapetum lucidum, so when reflected light bounces off our retinas and back out the pupils, they appear red like the retinal blood vessels and tissues. This is the eerie red eye effect on some flash photography. I always thought it was a sign of vampirism!

Other nocturnal animals, like many owls, rely on hearing and smell more than vision. They are adapted to maximize these senses. We have discussed previously the changes in owl anatomy (Do You Have To Be Ugly To Hear Well) as examples of form following function to improve hearing. Other animals, like raccoons, have a heightened sense of touch. Their paws have elongated sensor pads, and thousands of touch receptors. With these, raccoons can differentiate textures well enough to tell if a fruit is ripe or not, even in the darkest night.


Raccoons have a strong sense of touch for moving around in the dark.
Their elongated paws have thousands of touch receptors to increase the
sensitivity of this sense. On the dorsal (back) side of the raccoon’s paw,
whiskers (vibrissae) on the ends of their digits heighten the sense of touch.
Raccoons don’t even have to touch something to sense it; they have vibrissae (whiskers) on the ends of their digits, above their claws. Whiskers in general are a potent aid to nocturnal animals, whether located on faces, paws, or bodies (remember the naked mole rat’s whiskers on its torso in Take Off Your Coat And Stay A While).

Even plants can be adapted for nocturnal activity. Moonflowers, night-blooming philodendrons, and other flowers that rely on nocturnal pollinators tend to be white (since their pollinators most likely can’t sense color), and strong smelling. Indeed, the increased temperature of the P. selloum spadix (Is It Hot In Here Or Is It Just My Philodendron) is an adaptation to nocturnality.

So why be nocturnal? Anyone who has tried to negotiate an unfamiliar room in the dark knows that being active in the dark brings certain obstacles that must be overcome. There must be distinct advantages to it or needs for it, or else nature wouldn’t go to the trouble of adapting. Some scientists believe that nocturnality arose from originally diurnal organisms taking advantage of an underused ecological niche. Being active at night can be a form of crypsis (hiding), either to make them better hunters, or to avoid being hunted.

Nocturnality can also reduce the amount of water lost to the environment, and can lower the thermal stress on certain species of animals. For example, many frogs lose water through their skin, so daylight and higher temperatures can dehydrate them quickly.

That doesn’t mean that certain species won’t be exceptions. Moths are all nocturnal, except for the polka-dotted wasp moth, that is. There are four species of wasp moths, all diurnal, but the polka-dot is the prettiest, so we will fall into that old trap and give the pretty one all the attention. Diurnally active, this moth has abandoned many of the nocturnal adaptations of its brethren.


The polka dot moth has color and patterns that might be useful
for mating or for warding off other animals, but they would
be wasted if the animal was nocturnal.
For instance, it is beautifully colorful - usually a no-no for nocturnal moths. Since color doesn’t show up at night, moths are generally white, tan, or grey. Second, the coloration, especially the bright rump, mimics a wasp (hence the name) and warns of a toxic mouthful if consumed. This defense is called aposematism (apo = away from, and soma = body, basically, keep away from me). Many brightly colored insects will make predators sick, purely a diurnal method of survival, as the warning colors would be of no use at night.

Just as this moth species is diurnal when its close relatives are nocturnal, there is a single genus of primate that has chosen to be nocturnal when all others, including humans, are diurnal. Owl monkeys (8 species) live in Central and South America, and leave their sleeping sites about 15 minutes after sunset each day. They forage for fruits and the odd flower or insect until just before sunrise, then retreat to a hollow tree or within dense foliage to sleep away the day.

Owl monkeys adopted a nocturnal pattern after millions of years being diurnal, so it must have afforded them some advantage or was an answer to some overwhelming stressor. They have adapted by developing larger eyes, with more rods and fewer cones. They still see color, but less so than other monkeys.


The owl monkey is nocturnal, so it needs to have more sensitive vision.
For this reason, it eyes (and eye sockets) are huge! Compare the eye
size and skull morphology in the diurnal capuchian monkey. Form of
the skull follows the functional capacity of the eye.
Owl monkeys are interesting to science for being the source of another exception, as they are the only primates susceptible to the human form of malaria. In The Perils of Plant Monogamy, we used malaria in chimps and humans as an example of divergent evolution; malaria developed into species-specific forms. But the owl monkey is susceptible to both the primate and human species, so they can substitute for humans in malaria research.

Malaria is caused by a parasite, and as such, depends on its host organism for nutrition. The rule is that parasites are active when their host is active (feeding). A good example is the intestinal parasite of the surgeonfish, E. fishelsoni (Of Fish Guts And Cancer).

As I am sure you have committed to memory and made a part of your life, E. fishelsoni grows to an amazing size and replicates its DNA thousands of times before it divides into two or three progeny organisms. It takes tremendous energy for a bacterium to grow 80 fold and produce 85,000 copies of its DNA in one day, so it must occur when nutrients and carbohydrates are plentiful - during the day when the fish is feeding. Although it is a stretch, I guess you could call E. fishelsoni a diurnal parasite.

The malaria parasite, Plasmodium falciparum, has chosen a different path. P. falciparum’s host is man, and man is diurnal (teenagers and third shift workers excepted), but the parasite works to produce many progeny (gametophytes) and have them mature in the nighttime. The reason is simple; malaria has two hosts.


Plasmodium falciparum needs two hosts to complete its life
cycle. One immature form (sporozoite from oocyst) grows
only in the mosquito, while another (gametocyte) forms only
from mature sporozoites in the human red blood cells.
While one stage of the organism grows in the human, another needs to be inside a mosquito in order to complete its life cycle. After finishing its development, it is ready to be injected into another human when the mosquito feeds again. The key is that the mosquito is nocturnal and the gametophyte is short-lived. The gametophyte must be produced and mature just in time to be sucked and deposited into the mosquito gut. P. falciparum has been pressured to conform to the activity of one host while it is inside a host with the opposite activity pattern.

It is common that most species within a group will have similar activity patterns, since they are derived from common ancestors and therefore many characteristics are similar, including those that determine fitness for day life or nightlife. But there are exceptions. For instance, most rodents are nocturnal, but we see squirrels all day long - they are diurnal. Also, we mentioned above that most primates are diurnal, but the owl monkeys are nocturnal.

But there are bigger exceptions, organisms that aren’t diurnal or nocturnal. Ants, primates, and cats have species that are all over the place; some are nocturnal, some are diurnal and some are neither. It is the in-betweeners and the neithers that we will talk about next time.


Kreysing, M., Pusch, R., Haverkate, D., Landsberger, M., Engelmann, J., Ruiter, J., Mora-Ferrer, C., Ulbricht, E., Grosche, J., Franze, K., Streif, S., Schumacher, S., Makarov, F., Kacza, J., Guck, J., Wolburg, H., Bowmaker, J., von der Emde, G., Schuster, S., Wagner, H., Reichenbach, A., & Francke, M. (2012). Photonic Crystal Light Collectors in Fish Retina Improve Vision in Turbid Water Science, 336 (6089), 1700-1703 DOI: 10.1126/science.1218072


For more information or classroom activities on activity cycles, night vision or adaptation, see:

diurnal/nocturnal –

night vision –

adaptation –
http://www.nationalgeographic.com/xpeditions/lessons/17/g35/smcreatecreature.html

Sunrise, Sunset – Life In the Twilight

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Biology concepts – activity patterns, crepuscular, co-evolution, active pollination

Nocturnal and diurnal activity patterns are like vanilla and chocolate cupcakes. But what if you like rose hip or green tea flavors – are there cupcakes out there for you?


Who knew lizards like cupcakes. I bet they just lick
off the icing.
In a word – yes. In fact, there are so many organisms that are neither nocturnal nor diurnal that I hesitate to call them exceptions – like how everyone has mocha cupcakes now. And I bet you know some of animals with extraordinary activity…… ever heard of sweat bees or deer or infants?

Diurnal animals have developed color vision and ways to deal with the heat and the sun. Nocturnal animals have sensitive vision and other adaptations to make use of the dark. But there are some animals that are active on the edges of both situations; dawn and dusk. What adaptations would help an animal succeed in this niche?

In general, crepuscular (latin for twilight) animals have vision most like nocturnal animals. A tapetum lucidum (Form Follows Function) is present behind the retinas of many crepuscular mammals. Your cat is crepuscular, although she will adapt to a diurnal pattern as a pet…..if she feels like it, you know how cats are.


Those great light shows put on by nature in the evenings
have a name – crepuscular rays. Impressive trivia
for your next party. Photo by van049.
There are advantages to crepuscularness (I just now invented that word). By curtailing activity during the heat of the day, less energy is spent conserving water. Not surprisingly, many desert species are crepuscular. Heat, on the other hand, doesn’t seem to be as much of an issue, since there are endothermic as well as ectothermic species that are active in these time frames, for instance desert lizards like the gila monster.

The dim light available at dawn and dusk is also an advantage for crepuscular animals. There may be enough light to see, but not enough to make these animals stick out like a sore thumb. This works for deer; along with their coloring, the dim light helps them blend into the background. Deer caught out during the day become very stressed and confused. They may end up playing in traffic; just a case of clouded judgment due to sunshine.

The aim of the crepuscular pattern is often to reduce the chance of being eaten. Most terrestrial predators are diurnal or nocturnal (except for several cat species), so crepuscular animals are active after diurnal predators have had their warm milk, and before nocturnal animals drink their coffee.


Chimney swifts perch on vertical surfaces and
have saliva that dries like glue and is practically
insoluble. They use it to build nests on chimney
walls. They have weak claws and can’t perch on
branches, they can perch on vertical surfaces
using their stiff tail feathers, but mostly they just
fly 16-18 hours each day.
Slightly more common are the crepuscular birds, including the American woodcock, which is a ground bird that eats worms and nests in brushy young forests. The chimney swift is also crepuscular, but it nests in chimneys and other vertical surfaces, eats insects out of the air, and can maintain flight for an entire year. These are birds with very different behaviors, diets, and ranges, but are both crepuscular. As is the rule in nature - maybe the only rule without an exception - it is impossible to predict the behavior of one species based on characteristics similar to other species.

In the plant/pollinator part of the community, some crepuscular pollinators have developed special relationships with plants that flower in the evening only. This represents a special form of crepuscularness (there’s that new word again, I think it will catch on) called vespertinal (vesper = evening in latin)activity. These plants and insects are active only in the evening, and often co-evolve mutualistic relationships.

In the desert where the Joshua tree lives, water is at a premium, and the heat doesn’t help the water situation.  Remember in our discussion of nastic movements (Plants that Don’t Sleep) we saw that turgor pressure of water is responsible for the opening of the flowers. But open flowers promote water evaporation! Therefore, the best strategy for the Joshua tree is to have its flowers open outside the heat of the day. Et voila - it is vespertinal.


Joshua trees are native to the Mojave desert. They
were named by the Mormon settlers who were
reminded of Joshua raising his arms in prayer.
Predictions are that 90% of the trees could be wiped
out by global warming by the year 2100.
The price of water also has also driven the Joshua tree to produce no nectar – it must have some other way to attract the yucca moth. It is the yucca moth who really taken this upon its (her) shoulders. She has found a way to make pollinating the Joshua tree flowers pay off for her species. But only the yucca moth has made this connection, and this makes their relationship an exception to a biological rule.

Since they are available to one another in the same part of the day (evening) it is more likely that vespertine plants might have a single pollinator, which we learned a few weeks ago (The Perils Of Plant Monogamy) is the exception to the rule of multiple pollinators.

The female yucca moth is not drawn to the flowers by nectar, but by the need to propagate her species. At one flower, the female moth gathers pollen and balls it up into a large mass. Palps (appendages like arms but located near the mouth) hold the pollen ball as she travels to another Joshua tree; almost always to another tree. We know that cross-pollination is better than self-pollination (Is It Hot In Here), but the question remains, how does the moth know that?

At a second tree, the yucca moth lays an egg inside the carpal (which houses the ovule and is where the seeds will form once the flower is pollinated), but only in one or two of the many caprals. Then the moth swipes the pollen ball over the stigma (the top of the carpals), ensuring that the seeds will develop.

Most pollinators are passive, they transfer pollen as a result being drawn by some attractor (nectar, odor, color, etc.). Pollen transfer is not the reason for their visits. But yucca moths are an exception to this rule; they are active pollinators. They visit the flowers with the express intent of collecting and transferring pollen. But why spend energy to purposefully pollinate?


In the left image, you can see the palps that the yucca moth uses to gather up a pollen ball. These are modified mouth parts, and mouth parts are modified ancient legs. The middle image shows the yucca moth actively pollinating the flower after it laid its egg inside the carpal. The right image shows the larvae growing inside one ovule tube (the top-left cavity), eating the seeds as food.
The seeds are the payoff. The moth larva eats the seeds of that one carpal while developing. This is symbiotic mutualism, both species benefit from their relationship – food for the moth larva, and sure pollination for the Joshua tree.

But certain precautions must be taken. Production of seeds (and fruit) takes energy. If the flower won’t produce enough seeds to make it worth the energy expenditure, the tree will abort the flower.  So, if moths deposit eggs in too many carpals of the same flower, the larvae will eat too many seeds, and the flower will commit suicide. This will kill the larvae as well. To prevent this, the moths emit a chemical scent to indicate that a flower has been visited and pollinated; other moths will move on to flowers that have not been marked as occupied.

The yucca plants and yucca moth are an example of the vespertine lifestyle, but are there organisms that live exclusively on the other edge of the night? Yep.

Several types of bees are active only in the early morning hours, just after sunrise. This type of activity pattern is called matutinal (Matuta, the Roman goddess of dawn). Some flowers open up very early in the morning, and these are the targets of matutinal bees. The morning glory is a good example, although the flowers remain open long after the early bird bees have gone to bed.


This is the false dandelion. Sweat bees and
schinia moths appreciate for giving them
food and helping in reproduction. I appreciate
it for not being a true dandelion– the lawn
care expert’s mortal enemy!
Other matutinal flowers include the plants of the pyrrhopappus family. These are perennial herbs of the American southwest, south central, and southeast grass lands, and include the carolinus species that is called a false dandelion. They flower for two-four days a year, opening at sunrise and closing by 10:00 am on a hot, sunny day.

The matutinal flower moth (schinia mitis) and the sweat bee (Hemihalictus lustrans) have relationships with the pyrrhopappus plants. The bees use them as their exclusive source of pollen, although they must visit other flowers, like the morning glory, for nectar.

The Schinia mitis moth is more dependent on pyrrhopappus than are the sweat bees. Food, shelter, mating, and a place to lay eggs are all supplied by these specific herbs, as well as shelter and a food source for the larvae. The moths mate on the open flowers between 7:00 am and 9:45 am (rain or shine), and the female then lays the eggs deep within flower.


The mitis moth egg is laid deep within
the false dandelion flower for protection.
Its going to cramped quarters for the larva.
The reason for flowers developing a matutinal lifestyle might be similar to those for vespertine or fully crepuscular species, ie, water and energy savings. But the pollinators, especially the bees, seem to have followed suit for other reasons. True sweat bees (many people misidentify them) take advantage of the early morning hours to avoid the lines at the flowers; it is a simple matter of reduced competition. On the other hand, the mitis moth has co-evolved with the flower and become completely dependent upon it. If the flower is open only in the morning, the moth better be ready on time.

Who knew that so many plants and animals had thrown off the yoke that tethered them to either day or night activity, and now work at the edges of both? Next time we will take it even further; some organisms have stopped working on any schedule at all.





Chen Y, & Seybold SJ (2014). Crepuscular flight activity of an invasive insect governed by interacting abiotic factors. PloS one, 9 (8) PMID: 25157977

Rockhill, A., DePerno, C., & Powell, R. (2013). The Effect of Illumination and Time of Day on Movements of Bobcats (Lynx rufus) PLoS ONE, 8 (7) DOI: 10.1371/journal.pone.0069213



For more information, classroom activities, or laboratories on crepuscular activity, yucca moth reproduction, or Schinia mitis moth reproduction, see:

Crepuscular activity –

Yucca and yucca moths –

False dandelions and moths –
http://www.jstor.org/pss/25084173

When The Early Bird Is Also The Night Owl

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Biology concepts – cathemerality, circadian rhythm, adaptation, predator/prey relations


One carnivorous and three vegetarian friends
stranded on a island – what could go wrong?
The 2005 movie ”Madagascar” had some animals that we recognize from zoos; a lion, a zebra, a hippopotamus, a giraffe. But who were the bad guys? They were called the “Foosa” but what kind of animal was the foosa?  And who were those little primates they were trying to eat?

Being an island, Madagascar has developed ecosystems all its own. There are plants and animals that live there and nowhere else on Earth. This can lead to some interesting and exceptional behaviors and activities.


Tenrecs are a weird group. Different species can
be a few grams to over a kilogram, may have between
30 and 45 teeth, are related to elephants, and a have
a common anal and urogenital opening like birds. With
all that going on, being blue and yellow doesn’t seem
that weird.
Madagascar has its share of diurnal activity (daytime) and even more activity under the cover of dark (nocturnal). The streaked tenrec (Hemicentetes semispinosus, one of about 30 species) is crepuscular (active at dusk and dawn), so that activity pattern is covered as well. This black and yellow-striped cross between a hedgehog and a shrew (just by the looks of it, not by parentage) feeds on worms and other invertebrates. A study from early 2011 described a unique behavior from the tenrec, one that may cause us to include the cricket in the tenrec’s ancestry.

The quills on the tenrec come in two sizes, the long ones are for protection, but the shorter ones can be rubbed together to make high pitched (ultrasonic in many cases) sounds that can be used for communication or navigation. In the low light conditions of sunrise and sunset, scientists are considering the idea that tenrecs use stridulation (making sound by rubbing body parts against each other) to echolocate in their surroundings, similar to bats. They can also keep tabs on one another, communicating constantly with other tenrecs, even with a mouthful of worm.


The short spines on tenrecs are controlled by individual
muscles, so that one spine can be rubbed against another
to make noise.
Crickets, beetles, and some vipers stridulate, but the tenrec is a stridulating exception in two regards. One, it is the only mammal known to do so; and two, it is the only animal of any kind known to communicate both vocally and by stridulation. Madagascar would be a cool place to visit – weirdness like this is around every corner.

Even though the tenrec is a Madagascar native, I didn’t see him anywhere in the movie. Some animals are too weird even to be believable in a cartoon about talking animals.

The movie did feature a primate group from Madagascar, one that had a penchant for dance. Lemurs (from Roman mythology, lemurs = ghosts) are playful and energetic, and some are even said to dance, but I don’t think they crave house music like in the movie. The Sifaka verreauxi is called the dancing lemur, as it is the exception to four legged motility among the lemurs. S. verreauxi walks on two legs, but the outward turn of their hips make them sway back and forth, like they are dancing.


Lemurs of the genus Sifaka bounce around on two
legs to cover ground quickly. This looks like dancing, and
probably gave the movie makers the idea to turn the
lemurs into a group of party animals.
In the movie, I saw no less than seven different types of lemurs, but in truth there are about 100 lemur species and subspecies live on Madagascar and the nearby Comoro Islands (and nowhere else). Together, they are a microcosm of Madagascar activity patterns. Some lemurs species, like the large Sifaka verreauxi, are diurnal, while the smaller species, like the aye-aye, are generally nocturnal. Some are even crepuscular, active at both dusk and dawn (so they are not vespertinal or matutidnal).  But the weirdest types of lemurs are those that don’t show any of these patterns; in fact, they show no pattern at all! If that isn’t an exception, I don’t know what is.

The lack of an activity pattern does have a name, cathemerality (from the Greek, cat = complete and hemera = day). Cathemeral animals are active for periods of the day and/or periods of the night. In some cases, the periods of activity are driven by competition, when competitors are resting or prey is active. In other cases, periods of activity might be influenced by the seasonal temperatures or even the phase of the moon.

Whatever the stimulus, cathemeral (sometimes called metaturnal) animals can sleep day or night and hunt day or night, with no period of adjustment needed. African lions are cathemeral, driven by hunger and the success rates of their hunts, or by a need to conserve water.

In Madagascar, the red-fronted lemur (Eulemur fulvus rufus) is cathemeral in activity, as is the blue-eyed black lemur (Eulemur macaco flavifrons). Among primates, only humans and this species of lemur have blue eyes. However, the males have black hair while the females are reddish, so there is no chance of little blonde-haired, blue-eyed lemurs.


It is called the blue-eyed black lemur, so why is it
reddish-brown? This species is sexual dichromatic;
picture above is of a female, only the males are black.
The blue-eyed black lemur sees in color and is generally adapted to diurnal living; this is witnessed by the increase of its nocturnal activity when there is a full moon and with the nocturnal light level in general. However, the blue-eyed lemur has at least some activity spread across the 24-hour day all year round. This is one of three cathemeral patterns of lemurs in Madagascar lemurs.

A second cathemeral pattern is seasonally driven. In summer, when the daylight hours are greatest, it is enough for some cathemeral animals to limit themselves to daylight activity, but expand their active hours a bit during winter, so they are active in both day and night. This is driven by a need to find sufficient food.

The third cathemeral pattern is one in which there is mostly diurnal activity in one season and mostly nocturnal activity in another season. This may be driven by changes in temperature or perhaps resource availability. In Madagascar, the tropical climate ensures that food is always available, and the lack of a winter means that the temperature ranges between 60˚F and 80˚F all year round.

Many scientists believe that cathemerality may be an transient evolutionary middle ground, that all the species that display cathemeral activity are merely moving from diurnal to nocturnal, or the opposite direction. This is also known as an evolutionary disequilibrium hypothesis, as opposed to the idea that cathemerality is a stable evolutionary strategy.  A recent study using genetic markers across time (phylogenetics) indicate that there was a common ancestor lemur that was cathemeral as far back as 9-13 million years. This would indicate that cathemerality is VERY stable. These results therefore suggest that the three cathemeral patterns are related to stable patterns predation risk or food gathering.

However, the diets of the red-fronted lemurs and the blue-eyed black lemurs are very different considering that they are closely related species, called true lemurs (eulemurs, eu = true). Red-fronted lemurs eat only leaves, while blue-eyed black lemurs eat fruits. But they are both herbivores, and are both potential meals for a predator. This would be a good reason for being cathemeral; the lemurs can just choose to be active when the predator isn’t. Great idea, huh? Well, Madagascar’s biggest predator apparently read the lemurs’ playbook.


The fossa is not a cat, it is not a mongoose, it is not a monkey.
It is a predator and it is found only in Madagascar. It has
retractable claws, the same as all cats except the cheetah.
The fossa (pronounced foosa - get the connection to the movie?) is really Madagascar’s only big predator. It looks like a cat as it walks, and has retractable claws like most cat species, but its tail is as long as its body, like a monkey or a lemur. The fossa’s snout is more mongoose-like, as is the length of its body compared to the length of its legs. The film version of Madagascar didn’t do justice to the physical nature of the fossa; the bad guys in the movie pass for large cats.

The fossa spends much of its time up in the trees (it is arboreal) and chases the lemurs from tree to tree. Its long tail and sleek body design help it to move and maintain its balance as it moves through the branches. Most interesting, and an exception to mammal body design, the fossa’s outside digits on its rear paws are its biggest, this helps it to grasp the surfaces of the trees.


The long tail of the fossa helps it chase down
lemurs in the trees by improving its balance.
It also helps that the fossa hunts lemurs in
groups, using cooperative strategies.
Up in the trees we have the lemurs; some diurnal, some nocturnal, some crepuscular, and some cathemeral. What a buffet for the fossa! No matter what time he (or she) wishes to dine, there could be lemur on the menu, so the fossa has adopted cathemerality as well.

The movie was accurate in showing the fossas and lemurs active in both day and night now, but did the lemurs become cathemeral to get away from fossas? Maybe. The lemurs evolved before the fossa; were they cathemeral because they didn’t have to worry about predation, and a few species have stayed that way? Could be. Did the fossa become cathemeral to take advantage of the lemur smorgasbord? Nobody knows –yet. You can be sure that there are scientists who support each possibility.

Whichever way it happened, it points out a wrinkle that few people consider. Some animals can actually change their activity pattern. The shift is often in response to some ecological or physiologic pressure. Skunks are crepuscular - except for males in the mating season - they become diurnal.

Another example is the short-eared owl of the Galapagos Islands. The owls are crepuscular on islands that have a predatory buzzard species, but on islands without buzzards, the owls are diurnal. Finally, some anole species change their activity pattern from diurnal to nocturnal as the temperature rises. Even their color can change from green to brown as the temperature changes.

These shifts in activity patterns occur often enough that they can’t be called exceptions, but the majority of animals do hold a single pattern throughout the year. As such, nocturnal animals interact with other nocturnal animals and the same with diurnal animals. This isn’t a tough concept to grasp, even the movie got it right. Unfortunately, some folks in 1880’s Hawaii just didn’t seem to understand, and they are still dealing with the problems it caused.


Griffin, R., Matthews, L., & Nunn, C. (2012). Evolutionary disequilibrium and activity period in primates: A bayesian phylogenetic approach American Journal of Physical Anthropology, 147 (3), 409-416 DOI: 10.1002/ajpa.22008

For more information and classroom activities on cathemerality, lemurs, or fossa, see:

Cathemerality –

Lemurs –

fossa –
http://www.pbs.org/wgbh/nova/madagascar/classroom/l2_intro.html

Big Bugs, Little Bugs

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The titan beetle (Titanus giganteus), is not necessarily
a gentle giant. Its jaws can snap pencils and easily cut
into human flesh…. and they fly. Calm down, the adults
don’t feed, they just look for mates, so you won’t wake
to one nibbling your toes away.
Today, the biggest insects are goliath beetles, atlas moths, and giant stick insects. But during the carboniferous period (360 -300 million years ago), there were millipedes that were 2 m (6 ft) long and dragonflies (order Protodonata) the size of eagles!

Today’s question is:
How did insects get so big in the carboniferous period, and if they were big once, why are they so much smaller now?

It wasn’t just the insects that grew large way back then, the first large plants flourished in this same time period. Some ferns grew to be 20 m (65 ft) or more in height, and the diameters of trunks were increased. While not as big as today’s largest plants, the change was significant, as plants before this period did not exceed 3 to 5 ft in height.There was plentiful carbon dioxide in the atmosphere and the environment was warm all year round. This allowed lots of photosynthesis and lots of growth.

Nice picture to give scale, but humans and the
Arthropleura never co-existed. Even though the
species alive today aren’t as big, you still have
to beware. Many centipedes are venomous and
some millipedes can emit hydrogen cyanide gas.
Plants were evolving lignan in this carboniferous period (carbonis = coal, and ferrous = producing). Lignan is the stiffest of the plant molecules and is what allows them to grow tall.  This is also what gives the carboniferous period its name, as the lignan of plants is the major component of the coal that formed from their remains.

Horsetails, another type of plant of the carboniferous age and which are still around today, also grew much bigger. Horsetails today do not get any taller than about 1 m (3 ft), but in the carboniferous period, they were often 10-15 m (33-48 ft) tall.

Butit was the arthropods that get all the publicity. Scorpions almost a meter in length deserve to have a lot of attention paid to them! And consider the yuck factor of a 7 inch cockroach scurrying around at your feet.

The plants got big during the Carboniferous period.
Some lycophyte trees were 30 m (98 ft) tall and had
trunks of 2 m (6.5 ft) diameter. Their closest
relatives today are the club mosses, which are about
20 cm or less in height. Talk about deflating your ego.

What allowed these animals to grow so large? Scientists think it was related to the lignan. With lignan, the plants could grow larger and support more photosynthetic material. The carboniferous period is when the first forests appeared.

With more and bigger plants, more carbon dioxide was converted to carbohydrate, and more oxygen was produced as a result. The oxygen content of the air in the carboniferous period reached levels of 35% or more (today it is about 21%).

More oxygen in the air meant that more oxygen could be transferred into the blood of animals.  They could carry out more oxidative phosphorylation and produce more cellular energy (ATP), especially since there was all this plant material around to eat to gain carbohydrates (or plant-eaters to hunt down and eat). This growth spurt especially applied to animals without traditional circulatory systems. Insects, for instance.

Insectsuse spiracles on the sides of their bodies to take in air. The oxygen and other gases are moved through a system of smaller and smaller tubes (called trachea) to bring the oxygen to all the cells of the body. The carbon dioxide produced during cellular respiration is removed in the same way.

The spiracles of a flea are on the side of its abdomen
and the air travels through the tracheae to bring
oxygen to every cell. It seems like he would drown if
he took a dip in the hot tub.
This is not a particularly efficient way to move gases in and out of cells. A slightly bigger bug must have a much more voluminous system of trachea, and at some point, the respiratory system would have to be bigger than the entire volume of the insect! There would be no room for all the other organs. But with a high concentration of oxygen, the spiracle/tracheae system is efficient enough, and the insects can grow very large.

Highoxygen in the air also meant high oxygen in the water. Carboniferous era fish and amphibians grew large as well. Some toothed fishes of this time were impressive predators, and were more than 7 meters (23 ft) in length. Isopods in the oceans were also huge. Even today some of these crustaceans can be pretty impressive. Bathynomus giganteus can grow to more than over 16 inches in length. 

So big plants brought big oxygen levels, which brought big animals. But why are the arthropods so much smaller today as compared to then? Well, the oxygen levels are lower now, so according to a 2006 study the inefficient spiracles system could not support the large body. Insects had to get smaller.

Here is an isopod that grabbed a ride when a deep sea remotely operated 
vehicle was recovered. They look even creepier from the front with 
silver eyes. Isopods are related to shrimp and crabs; I think we’re going 
to need much more butter and lemon.
But there is an additional hypothesis that may also contribute to the small size of many insects, especially flying insects. According to a 2012 study, the size of flying insects is related to another aspect of oxygen. When the explosion of plants in the carboniferous period raised the oxygen levels, the air became more dense (oxygen is a heavier gas). The insects were able to become better fliers, since their wings could move more air.

The data says that one reason flying insect
got smaller was to avoid being easy catches for the birds
that were becoming better fliers and hunters. Really?
Name me a couple birds that would go after this guy if
he was flying today.

Millionsof years later, birds evolved. As they became better fliers (their ability was also based on their ability to move air over their wings), they became better hunters. Better hunting birds could catch flying insects (and terrestrial insects for that matter) better. So it became a disadvantage to be big. The smaller insects now had a reproductive advantage; they were the only ones surviving to have offspring. Over a period of time, the insects grew smaller on the whole.

So today we have fairly small arthropods and insects, although my wife has personally never seen a small insect. According to her they are all large enough to carry off small children and have evil looks in their eyes.

Matthew E. Clapham1 and Jered A. Karr (2012). Environmental and biotic controls on the evolutionary history of insect body size Proc. Natl. Acad. Sci. USA DOI: 10.1073/pnas.1204026109

Next week – ideas for long studies on the nature of science.
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