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What Cold Really Looks Like

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Biology concepts – TRPA1, cold sensing, oxygen sensing, proteasome function, hypoxia, normoxia, hyperoxia, phototransduction, optogenetics, methyl anthranilate

Last week we learned that the TRPA1 ion channel causes you pain when you are too cold and helps you to avoid the cell damage that cold can produce. Even if that’s all it did, it would be pretty amazing, but there’s much more. It turns out that TRPA1 can do some amazing things - like keeping the right amount of oxygen in your cells.

Prolyl hydroxylase domain enzymes (PHD1, 2, and 3) are the primary mammalian sensors for oxygen in the blood and tissues when oxygen levels are normal (normoxia) or low (hypoxia). Oxygen binding to the PHD acts as an "on" switch for the binding of another molecule to PHD, a molecule called 2-oxoglutarate (2-OG). 2-OG can only bind to PHD if O2is already bound.


On the left is a cartoon that shows how ubiquitin and PHD proteins
help mediate the destruction of unneeded damaged proteins. On the
right is the proteasome, the structure which recognizes the proteins
targeted for destruction and carries out the cutting that
releases amino acids.
The function of 2-OG bound to a PHD is to trigger the destruction of another type of protein, called hypoxia inducible factors (HIFs). They do this by modifying some of the amino acids of the HIF so that cell thinks the HIF is old or defective. Old and defective proteins are recycled for their parts by a big complex of proteins called a proteasome.

When there is sufficient oxygen in the blood and tissues, the PHD is bound by O2 and 2-OG, so the HIFs are degraded. But when there is hypoxia– little O2 and 2-OG are bound to the PHD – and there is no destruction of HIFs.

If they aren’t targeted for the proteasome, HIFs are free to do their job. They turn on genes that work to increase oxygen in the blood and tissues, including making more red blood cells, using more iron for heme, stimulating the production of new blood vessels, and triggering cells to use glycolysis instead of the citric acid cycle because glycolysis doesn’t need O2(here’s a review).

When oxygen levels in blood and tissue return to normal, more O2 will be free to bind to the PHDs and the HIFS will then be degraded. Their effects on genes will be turned off as their concentration decreases.


Oxygen sensing in the cells is important at all stages of life. At one
time it was believed that very premature infants, with less than
mature lungs, would benefit from a high oxygen environment.
What it actually did was make them blind due to oxygen mediated
damaged to the retina.
This is all well and good for normoxic or hypoxic situations, but how would it help in times of too much oxygen (hyperoxia)? And believe me, too much oxygen is a very bad thing. Short bursts of high oxygen can be disorientating, with central nervous symptoms that affect breathing and may cause myopia.

Prolonged exposure to high levels of O2 (or short exposures to very high levels) can cause cell destruction, collapse of lung alveoli, retinal detachment, and seizures. Scuba divers, firemen, and anyone else using oxygen tanks must be aware of the dangers of either running out of oxygen or breathing in too much.

This is where TRPA1 ion channels enter the picture. A 2008 study showed that TRPA1 can be activated by O2. In hyperoxic situations, there is too much oxygen to be bound up by the available PHDs, so some is left to interact with TRPA1 channels in the membranes of the vagus and sensory neurons, as well as in tissue cells. The O2 can open the TRPA1 channel directly and lead to firing of the neuron.

The more O2 there is, there more activation of TRPA1, and this is good. In hyperoxic situations, the body constricts many blood vessels to limit the excess oxygen getting into the tissues. Hyperoxia also ramps up the cells’ protective mechanisms against reactive oxygen species damage.

 What we don’t know is which responses to hyperoxia are controlled by the TRPA1 channel activity.  A 2011 study goes onto show that the PHDs lose their inhibitory function on TRPA1 in both hyperoxia and hypoxia. This is a similar conundrum to the one we saw last week - where TRPA1 senses cold, but responds to many of the “hot” agonists of TRPV1. Here, the same sensor is stimulating different responses to too much ortoo little oxygen.


Some situations with low oxygen tension can create big problems.
On the left is pneumonia; the filling of the alveoli with edema fluid
limits the amount of oxygen that can get to the bloodstream. In the
middle is Payne Stewart; at altitude, his plane lost cabin pressure,
everyone on board basically went to sleep, and the plane flew in a
straight line until it ran out of fuel and crashed. On the right is a diver
who specializes in going as deep as possible on one breath. Many
participants drown.
The same channel that senses really cold temperatures in your skin and tells you that this bad by stimulating pain also helps you keep a normal amount of oxygen in your tissues – a system that has little or nothing to do with pain. Weird enough for you? Well it gets weirder.

It seems that your TRPA1 cold sensing channels are important for tanning in the summer! A 2013 study shows that a process called phototransduction uses G-protein coupled receptors to stimulate TRPA1 in melanocyte and keratinocyte membranes and results in an influx of calcium. This destabilizes the membranes and facilitates the transfer of melanosomes from melanocytes into the surrounding keratinocytes, as we have talked about before.

Phototransduction in general is where light energy is changed (transduced) into another form of energy. The best example is in the retina of the eye, where rods and cones turn visual light into neural signals that are then processed in the brain as images – that’s how you see. In the skin, the energy of the UV light is turned into chemical energy (flow of ions in and out of channels) to stimulate cellular activity.


The retina is the most obvious example of phototransduction. Light
energy is converted to chemical energy and information. Light
strikes the retina, and excites the rods and cones. On the level of
the membrane, the light (hv) set in motion a series of reactions that
results in the opening or closing of ion channels, including
the TRPA1 channel.
A second 2013 study from the same group says that retinol (hear the word retina in there? As in the retina of your eye?) is the photoactive chemical that starts the G-protein couple receptor cascade that then results in TRPA1 activation and melanin synthesis in melanocytes.

A new photosensitive protein called optovin has been identified in zebrafish. It mediates TRPA1 activation via a sensitive part of the TRPA1. Optovin allows for optical control of TRPA1-expressing neurons, meaning - optovin absorbs light, generates singlet oxygen radicals and these interact with the the oxygen-sensitive cysteine residues on TRPA1 and activates the receptor. Sound familiar? This is similar to the binding of oxygen that helps the body recognize and respond to hyperoxia.

In an effort to take advantage of this great system, the research field of optogenetics has been born. Let’s say you want to study what happens when a set of neurons fires. Introduce optovin and TRPA1 (or a similar system, like opsin or retinal) into the appropriate neural pathway and then you can fire them at will just by shining a light on them. Imagine, shine a laser pointer on a mouse and instantly he starts to jump, or drool, or tell a joke.

Optogenetics was the method of the year in 2010! On the left
is how it works, using phototransduction molecules to stimulate
responses in target cells. On the left is how it works in a live rat.
The light is positioned so that it can illuminate the altered
neurons so that processes can be turned on and off with light.

One last exception for the day – one that will lead to some amazing stories for next week. In mammals and many other animals, TRPA1 senses noxious cold (in addition to the amazing things we just talked about), but in some species it acts completely the opposite.

In mosquitoes, TRPA1 senses heat instead of cold. A 2013 study shows that larval A. gambiae (the mosquitoes that carry malaria) rely on TRPA1. If you decrease the amount of TRPA1, the mosquito larvae don’t exhibit thermal locomotive behaviors that would normally keep them in the preferred temperature of water. This might be important for killing mosquito larvae in water; if you can use antagonists to TRPA1 to move them away from their optimum temperature, they’ll die as babies and never become bloodsuckers.

In fruit flies, TRPA1 is also important for circadian (daily) locomotor activity patterns (2013 study). Instead of having a light/dark drive their activity, the temperature fluctuations between day and night can also serve to entrain circadian cycles. There are activity cells in fly brain for morning, daytime, and evening activity levels. TRPA1 isn’t expressed in morning neurons, so it’s activation by heat is what increases activity in day and evening.


TRPA1 gene function (painless in fruit flies) controls many
circadian behaviors. Depending on the amount of firing, it
tells the fly what time of day it is, and this time controls
which behaviors will be favored.
Another 2013 study shows that TRPA1 is used as thermoregulatory control of circadian rhythm in drosophila. Loss of TRPA1 altered behaviors and changed the expression of an important circadian rhythm protein called Per in the pacemaker cells.

In this one regard, birds are a lot like mosquitoes and flies. Chickens for example, have TRPA1 channels that induce pain due to high heat, just like their TRPV1 channels (which, you remember, don’t react to capsaicin).

A 2014 study showed that chicken TRPA1 is a heat and noxious chemical sensor – it acts opposite to the TRPA1 in humans, even though we are both homeotherms (maintain a body temperature within a small range). Chicken TRPA1 is almost always co-expressed with TRPV1, so they double up on heat but might have less cold sensing – why? - cold can still be damaging to cells so they need to know to avoid it.

The weird TRPA1 of birds lends itself to a bizarre use for us. Methyl anthranilate (MA) is a non-lethal bird repellent, and the same 2014 study shows that it works by activating bird TRPA1 pain sensors. MA doesn’t activate TRPA1 in other species, like humans; three amino acids critical for its MA activity are different in bird and mammal TRPA1.

Since MA doesn’t work on human TRPA1, it can be sprayed on crops to keep birds away – it’s a chemical scarecrow - if it only had a brain! It can also be sprayed on surfaces to keep birds from congregating. MA works as a repellent by stimulating the trigeminal nerves via TRPA1 in the bird’s beak, eyes and throat. 


Grapples (pronounced grape – ple) are apples soaked in
methyl anthranilate (MA) so they taste like grapes. MA is
sensed as hot in birds by TRPA1 but does not activate
the human TRPA1. We taste it as grape flavor and smell.
For me – if you want to taste grapes, eat grapes!
Very similar to MA is dimethyl anthranilate (diMA). It also activates bird TRPA1 and can be used as a repellent, but we use it for flavoring grape Kool Aid. Too bad Jim Jones wasn’t leading a flock of chickens – they’d all still be alive.

Both MA and diMA are naturally occurring in concord grapes, strawberries, other fruits, and are especially important for flavor of apples. Maybe that’s why they make grapples – grape-flavored apples. Actually, grapples are apples soaked in MA, not a genetic hybrid. DiMA is also released from musk glands of foxes, and is produced in rotting flesh – does spoiling meat taste like apples or grapes to you?

Next week – odd changes in TRPA1 and TRPV1 turn animals into better hunters.



Bellono, N., & Oancea, E. (2013). UV light phototransduction depolarizes human melanocytes Channels, 7 (4) DOI: 10.4161/chan.25322

Bellono NW, Kammel LG, Zimmerman AL, & Oancea E (2013). UV light phototransduction activates transient receptor potential A1 ion channels in human melanocytes. Proceedings of the National Academy of Sciences of the United States of America, 110 (6), 2383-8 PMID: 23345429

Saito S, Banzawa N, Fukuta N, Saito CT, Takahashi K, Imagawa T, Ohta T, & Tominaga M (2014). Heat and noxious chemical sensor, chicken TRPA1, as a target of bird repellents and identification of its structural determinants by multispecies functional comparison. Molecular biology and evolution, 31 (3), 708-22 PMID: 24398321




For more information or classroom activities, see:

Oxygen sensing –

Proteasome –

Phototransduction –

Optogenetics –

Methyl anthranilate –




Sneaking Up On A Snake

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Biology concepts – thermosensor, sight-hunters, snake hearing, mutation, TRPA1, pit vipers

We have been talking about taste sense for many weeks. I
remember a 1975 movie called, A Boy And His Dog, starring a
very young Don Johnson. It was a post-apocalyptic story of a
guy, his dog, and cannibalism. The best line of the movie? “Well,
she might not have had good taste, but she sure tasted good.”
Of course, this isn’t the kind of tastes we have been talking about.
We’ve come a long way since we started talking about taste sense. We have learned about how TRPV1 capsaicin receptors sense pain and heat. We have also learned that TRPV1 capsaicin receptors have cousins that sense cold - TRPM8 and TRPA1. They may generate pain, and they certainly help to warm us when we are cold.

We have even learned that in rare cases, the cold receptors can be heat sensors, like in chickens and insects where TRPA1 sense hot instead of cold. And this leads us to today’s exception. It’s time to talk about how these relatives of taste receptors help animals to become better hunters and to better sense their environment. Today let’s focus on snakes.

Snakes have a number of ways to catch prey (see this post). Some lie in wait, blending in with the jungle or background until a moving potential dinner catches their eye and moves across their path. Vision is their primary way of finding dinner. As a consequence, most sight-hunting snakes are diurnal (active in daylight).

Here is the southern black racer. You can see it has big eyes with
round pupils so lots of light can enter – it’s a sight hunter. Many
grow to be 5 ft. (1.5 m) long, so they can look intimidating. But
they are not venomous and will usually exit the seen if disturbed.
The non-venomous Southern black racer (Coluber constrictor priapus) is a sight-hunting snake of North and Central America. It’s called a racer because it is quick, reaching 4 mph (1.8 kph) in a very short time. Even though it is a constrictor, it typically doesn’t coil around the lizard, mole, or bird (I said they were quick) that it catches. It prefers to crush them into the ground to suffocate them. Sometimes nature can be a little rough around the edges.

Other snakes use the combination of scent and taste that we talked about a while back. The Jacobson organ (more scientifically called the vomeronasal organ, VNO) in their mouth can sense the molecules that the tongue pulls in from the air. Like it or not, every organism has molecules floating off of them continuously. Snakes' VNO can pick these up. See this post for more on the VNO.

Some snakes “hear” their prey coming. True, snakes don’t have an outer ear opening or the small bones that convert sound waves into mechanical waves in our middle ear (see this post for an explanation). But they do have a cochlea, the organ for sensing the vibrations and converting them to a nerve signal. Many snakes can sense the vibrations that their prey generate when they move through the environment using this cochlea and their lower jaw.

Similar to something called bone conduction hearing in animals with ears like ours, vibrations that travel through the bone can also cause movement in the hairs of the cochlea. As we discussed previously, the bending of the sensory hairs of the cochlea are transduced to chemico-electrical signals that travel to the hearing centers of the brain.

This is from a scientific paper showing the bone hearing of a python.
The red is the lower jawbone. The bark blue is the quadrate bone
and the green is the equivalent to our stapes bone of the middle
ear. The light blue is the inner ear space and the purple is where
the cochlea is housed. Vibrations go from red, to blue, to green to
light blue, to purple. You can see how sound waves would find it
tough to get to the cochlea.
A 2008 study showed that many snakes rest their jaw bones against the ground. The vibrations caused by moving animals are transferred from the ground to the bone, and from the bone to the buried cochlea. The sensation in the brain is a lot like muffled knocks, not unlike the bass that is turned up too loud in peoples’ cars.

This was followed by a 2012 study that showed pythons have very sensitive vibratory hearing, but poor sound pressure hearing. Almost all their hearing input comes from the vibrations they sense in the ground or tree, or whatever they happen to be lying on. So be on tip toes, that snake may hear you coming.

But how does any of this relate to a receptor for painful cold and controls mammalian breathing rate? Well, another way some snakes find their prey is by sensing the heat they give off – even from a few meters away.

Pit vipers are a subfamily of the Viperdae family, called Crotalinae.There are two types of vipers; all of them have hinged fangs, the ones that are folded up into the upper jaw when the mouth is closed, but protrude for striking as the mouth is opened. Pit vipers differ from true vipers in that they have pits (duh!); more about these below. True vipers live exclusively in Africa and tropical Europe and Asia.

In America, where I live, there are a lot of pit vipers. Cottonmouths, rattlesnakes (all 30 species), water moccasins, copperheads – these are all pit vipers. From southern Canada to Argentina, and from Eastern Europe to parts of Asia, pit vipers are not rare. Eyelash vipers (Bothriechis schlegelii) of South America are arboreal (live in the trees). They have bright coloring, but sit still and wait for their prey to happen by. They strike from above, so they scare the heck out of jungle hikers.

On the left is the eyelash viper. You can see it doesn’t mean business
because its hinged fangs aren’t extended. In the middle is the two-striped
forest pit viper. It is protecting it’s young, so the fangs are extended. On
the right is a sidewinder rattlesnake. Sidewinders are amazing and will
get their own post soon.
The amazing thing is that there aren’t any pit vipers or true vipers in Australia. The land of a million weird and painful deaths has nothing to offer in the way of hinged fang venomous snakes. I’m sure there’s a movement to import some.

But it’s specific part of the pit viper that we are interested in today – namely the pit. The pit organ is located between the eye and the nostril, on each side of the snake’s head. It is a hollow pit, so the actual business end of the pit organ is inside the snake’s skull.

The pit is lined with epithelium, but it also has a membrane that is stretched across the base. As a consequence of the location membrane, there are air pockets on each side of the membrane. The trigeminal nerve innervates the membrane and there are thermosensors in the cells of the membrane.

So, the pit organ is a thermosensor that helps them locate prey animals (or predators). But wait you say. Sure, pit vipers may use a thermosensitive ion channel to sense the heat given off by passing prey animals. But we just said they use a COLD sensing ion channel, TRPA1. What gives?

The pit on a pit viper is located between the nostril and the eye.
It would be easy to mistake the pit for the nostril. The cartoon
shows the pit anatomy. The air chamber helps cool the air
quickly and stops the TRPA1 receptors from firing again. This
is so the snake won’t get a residual image of something warm,
when the target may have moved in the interim period.
The explanation is two fold. 1) We said a couple of weeks ago that TRPA1 might sense painful cold on its own, or may work with other TRP’s to respond to very cold temperature. But whichever way it works, it is very similar to TRPV1 for heat sensing and TRPM8 for cold sensing. 2) Remember that in birds, lizards, and many insects, TRPA1 actually senses heat, not cold.

So maybe it’s not so terribly bizarre that pit vipers use TRPA1 to sense their prey. But before they touch it??? We eat chili peppers and we react to the capsaicin in our mouths and noses. We go out on a summer day, and the heat activates our TRPV receptors in skin and other tissues. We eat something cold (or menthol) and we feel the cold sensations it touches or tissues. But snakes feel the heat of their prey before they eat, from a distance away! There must be more at work.

And there is. The TRPA1 ion channels in the pit organs of pit vipers have a mutated version of TRPA1. Here’s how things work according to a 2010 study that identified TRPA1 as the heat sensor. The pit is a hole with a membrane stretched toward the back. Consequently, there is an air chamber on both sides of the membrane.  The membrane is highly vasculature and has the sensitive nerve endings with the TRPA1 channels.

The TRPA1 receptors are always firing, but at a low rate. Neutrally warm objects don’t change the firing rate, but warmer objects (as little as 0.001 ˚C warmer than background) will increase the firing rate. The receptor is mutated according to a 2011 study, with 11 amino acids of the pit TRPA1 divergent on only pit-containing snakes. These changes make the receptor so sensitive that it can react to infrared light signals (heat) from several feet away. That would be like our mouth burning over a chili pepper that we walked past in the supermarket.

Since the sensors are spread across the entire membrane, the effect on locating the source is sort of like vision or a pinhole camera. Light passes through the pupil and diverges before it hits the retina. This provides for a larger spread of the “image” across the membrane and allows for precise two-dimensional map of the target. The difference in heat between the target and the background gives a “picture” of the object that is warm.
The Taylor’s Cantil viper will play dead and then strike, but this
brings up an important point. DON’T get near a pit viper, even if
you are sure it’s dead. The pit is wired directly to the brain and
muscles. A dead snake, even one with a severed head, can still
strike as long as there is any residual neural electrical flow. People
die every year from snake bites from dead snakes.

The picture generated is also a little like hearing, since the heat will reach one pit earlier or more strongly. By comparing the timing and the strength of the signals from each pit, the distance and direction to the target can be detected by the brain (see this post for localization of sound waves).

Because the heat “picture” pit vipers pick up is based on the difference between the temperature of target and background, most pit vipers hunt when coolest, so temperature gradient between environment and prey is greatest. Prey will stick out the most.

Snakes can also use the pit more conventionally, as a thermosensor for its whole body. The basal rate of firing will tell the snake when to move to shade if it’s too warm or move to sun if it’s too cold. This is how it regulates its body temperature.

Pythons and boas can also have heat-sensing pits, but they are
5-10 times less sensitive because of their differing anatomy.
The amazing thing is that they evolved the same special power
independently from pit vipers, although they both use mutated
versions of TRPA1. The nostril has a black arrow and the pits
have red arrows.
The exception to today’s exception: some non-pit vipers have pits. In terms of evolution, pits evolved once in pit vipers, but they have sprung up several times in boas and pythons. These pits are less sophisticated (no membrane or air chambers), are less sensitive, and are located in different places.

Boas and pythons with pits have 3-4 simple pits in their upper lips. They don’t have the suspended membrane for sensing temperature, the TRPA1 sensors are housed within the epidermal cells at the back of the pit.

Next week – vampire bats and mosquitoes get into the mutated thermosensor act as well.



Christensen CB, Christensen-Dalsgaard J, Brandt C, & Madsen PT (2012). Hearing with an atympanic ear: good vibration and poor sound-pressure detection in the royal python, Python regius. The Journal of experimental biology, 215 (Pt 2), 331-42 PMID: 22189777

Gracheva EO, Ingolia NT, Kelly YM, Cordero-Morales JF, Hollopeter G, Chesler AT, Sánchez EE, Perez JC, Weissman JS, & Julius D (2010). Molecular basis of infrared detection by snakes. Nature, 464 (7291), 1006-11 PMID: 20228791

Geng J, Liang D, Jiang K, & Zhang P (2011). Molecular evolution of the infrared sensory gene TRPA1 in snakes and implications for functional studies. PloS one, 6 (12) PMID: 22163322



For more information or classroom activities, see:
Pit vipers –

Bone conduction hearing –

VNO (Jacobson organ) -

They Can See The Blood Running Through You

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Biology concepts- thermosensors, TRPV1, hematophagy, taste sense, alternate splicing, echolocation


All three species of vampire bat live in Central to South
America, the common vampire bat (Desmodus rotundus),
the hairy-legged vampire bat (Diphylla ecaudata), and
the white-winged vampire bat (Diaemus youngi).
Any idea what the picture to the left shows? A hint – this may be the most sophisticated piece of machinery ever devised by nature. Together with the organism to which it’s attached, this piece of evolutionary engineering is capable of almost everything a billion dollar jet can do.

It’s the nose of the common vampire bat (Desmodus rotundus). These bats belong to the family Phyllostomidae, one of three families of leaf-nosed bats (Rhinolophidae and Megadermatidae being the other two families). One of the exceptional skills mediated by this nose makes use of the same receptor that makes our mouths burn when we eat chili peppers. Vampire bats can detect the hot blood in your veins from far away!

It’s the noseleaves of the vampire bat that are so amazing, but maybe we should include the rest of the bat head as well. The ears, teeth, mouth, and eyes all work with the nose to give this bat some jet fighter skills.

Leaf nosed bats come in some very odd varieties. The picture on the below and right will give you some idea of the shapes and sizes possible. The question is – what’s the reason for these bizarre growths and why isn’t one odd shape enough? The answer will best be found if we know what their function is, because in biology – form follows function (except for proteins, see this post).

Here are some different leaf nosed bats. Top middle is the Ridley’s leaf
nose bat; bottom left is the Honduran white bat. Top right is the
Commerson’s leaf nose bat and the middle bottom is the greater
spear-nosed bat. The bottom right image is of the cleaf nosed bat of
Vietnam, a more newly discovered variety. It was first described in
2008, but it took 4 years to determine if it was a new species or just
a variant of another species.

Two basic needs of the bat are to find food and find its way. Whether it's a fruit bat, an insectivorous bat, or a vampire bat, a bat must be able to negotiate obstacles within its environment and find a source of nutrition.

To accomplish these tasks, especially given that most bats are nocturnal, they use echolocation. They send out a high-pitched sound, and it bounces off objects and returns to their ears. This is very much like the radar used in airplanes. But this isn’t all they use. Bats can see just about as well as humans; the phrase “blind as a bat” might as well be “blind as a Bob.”


We said most bats are nocturnal. This is Livingstone’s fruit bat
or Comoro flying fox. It is a fruit eating bat of the Comoros
Islands in the western Indian Ocean (just northwest of Madagascar)
and is at least partially diurnal. Other bats may be seen during
the day, but it almost always because they have been disturbed
in their hiding place or they were disturbed in their
feeding the night before.
Bats can also smell their way to food, especially fruit bats. But to answer the question about the noseleaves we have to return to echolocation. Vampire bat sounds emitted for echolocation come through their nose, not their mouth! According to a 2010 study, the leaves aren’t used to gather the returning sound, but to focus the outgoing sound so that the “pictures” formed by the returning echos will be most accurate.

Different shapes help to increase the difference in the reflectivity of objects in the area of focus as opposed to those in the periphery. This allows the various species to hone in what they need to discern and dismiss those things that are uninteresting. Different backgrounds and different needs require different nose leaf shapes.

This answers the question about the wild shapes of noses, but it brings up another question. If vampire bats find their food by echolocation, sight, and smell, then why do they have heat sensors?

To answer this new question, consider the sizes of the vampire bat and its intended prey. The bat weighs about 2.5 oz (71 g), but it needs blood for food (mammalian blood for common vampire bats, bird blood for hairy legged and white-winged species). In fact, vampire bats are the only mammals that completely depend on hematophagy (blood meals). Because of this, they often feed on animals that are over 1000x their size.


Pigs are a favorite source of blood for vampire bats. Here, a
sleeping pig has been bitten on the snout. Why the snout – read
on. Notice the bat can hold its weight with its wings, and that
there seems to be more blood than you would expect from
such a small bite. Again, read on to know why.
To get to the blood of say a cow or horse, vampire bats would have to have teeth so large that they couldn’t lift themselves for flight. No, they have to be very careful about where they bite a victim; somewhere that will bring enough blood to feed on, but won’t cause the huge animal to kill them. Vampire bat teeth are so sharp that prey animals rarely feel the bite, and since the bats are nocturnal, the victims are most often asleep at the time and stay asleep during the feed.

The bats need to locate a place on the sleeping animals where blood vessels are near the surface. This is where the heat sensing comes into play. Vessels close to the surface will give off the most heat to the environment, and vampire bats can “see” these vessels from up to 20 cm away!

The vessels in question need to be covered with less hair, so the bat almost always goes for the lower leg or snout. They will land on the ground, and walk or run up to the prey from behind the animal to make the bite. Vampire bats wings are much stronger than most other bats, so they have an easier time moving along the ground, supporting some of their weight on their wings.

On the left you can see the incisors of the vampire bat. The cheek
teeth and canines are used to shave off any hair from the site, but
the incisors do the cutting. The lack enamel, so they are always
razor sharp. On the right, the tongue is being used to take in the
blood. The tongue is deeply grooved, so the anticoagulant saliva
runs down into the wound and more blood can easily be lapped up.
Their teeth then cut a 5 mm x 5 mm gouge in the victim and they lap up the blood that comes out. It isn’t too common, but vampire bats do feed on humans. This leads us to another amazing skill.

Instinct tells the vampire that a good feeding once will probably mean a good feeding again – if they can find the same animal. So how do they find the same animal several night is a row? They hear them.

A 2006 study showed that vampire bats do tend to feed on the same individual (be it human or cow) for several nights in a row. They can distinguish their previous victim by the sounds of their breathing! Every animal has a unique breathing pattern and sound profile, and the vampire bat can distinguish between individuals to find the one that matched a previous good meal. Imagine if we could find our favorite meal again by listening for the clinking of the right pans!

Returning to a good feeding spot each night, the vampire bat searches for a surface vessel to drink about 1-2 teaspoons of blood (4-5 ml). This isn’t enough to harm the animals, and is what allows them to go back several nights in a row.


Rabies can be spread by bats, and they don’t have to bite you.
When a bat bites an infected animal, it takes in the virus. The
virus grows in the animal and gets distributed to the saliva as
well. Startled bats sometimes spit, and if this gets into your
eyes, mouth, nose, or an open wound, you could contract the
infection. It’s rare overall, but rabies kills about 60,000
people a year.
This doesn’t mean that feeding by vampire bats is without negative consequences. One, the idea of being fed on gives me the heebie jeebies. Two, the vampire bat is a common vector for rabies virus. And three, in the cattle of Latin America, repeated feeding by vampire bats is associated with reduced milk production in dairy cattle and reduced mass gain in beef cattle. So if you wake to find a vampire bat licking your ankle, best to shoo him away and try to breathe differently tomorrow night.

How do vampire bats locate that ankle vessel they need to feed on? Back we go to that amazing nose. The heat sensors of bats are called pit organs, just like in the pit vipers we talked about last week. There are three to four of these organs in the noseleaves of the bat, and a couple across the upper lip as well.

As opposed to the pit vipers, vampire bats have adapted a heat sensor, not a cold sensor to use as their infrared detector for blood vessels. TRPV1, the same receptor that is used for the capsaicin burn and heat regulation in mammals, is present in very high numbers in the neurons of the pit organs.

But this is no ordinary TRPV1. Mammals can’t detect heat from 20 cm away with a regular TRPV1 – this is a modified TRPV1.  A 2011 study found that this version of the protein is missing the last three amino acids on the carboxy terminus (the end produced last). This small change increases the sensitivity of the receptor from 43˚C all the way down to 30˚C, so that small differences in heat can be noted from almost a foot away.

One more amazing fact - the bats have regular TRPV1 too. The two version of the protein come from the same gene and the normal one is used throughout the bat’s body for all the things we use TRPV1 for: heat regulation, reproduction, cancer inhibition, etc. Only in the neurons of the pit organs is the mRNA altered after it is transcribed from the gene (alternately spliced) to make the slightly shorter, more sensitive protein.


Here is a cartoon of how blood clots. On the bottom flow chart,
the first anti-co line is where desmolaris and draculin work.
The third line is where desmoteplase acts.
Now our bat friend has located a victim, found a surface vessel and taken a bite to let the blood flow. There’s yet another problem. Mammalian blood clots to prevent loss. The bats must either keep biting, which might wake their prey, or have a way to keep the blood flowing.

Their mouths have specialized salivary glands that make anticoagulants so no clot is formed. There is one anticoagulant that someone with a sense of humor named draculin. It acts to prevent blood clot formation. We have mentioned a second anticoagulant before, called desmoteplase. One of our Halloween posts talked about how it may be good for people that have had strokes. It dissolves any clots that may form.

A 2014 clinical trial is showing that desmoteplase is better than the tissue plasminogen activator clot busters now being used (rtPA), since they have a half-life of four hours (as opposed to 5 minutes for rtPA) and it’s breakdown products aren’t as toxic to nerves and the blood brain barrier as compared to rtPA.

A newer anticoagulant is called desmolaris. A 2013 study showed that it works on yet another part of the clotting system to prevent clot formation. And this isn’t all of them. A 2014 protein survey suggests that there may be dozens more anticoagulant proteins in vampire bat saliva.
Which flying machine is more complex and cool?

Lets add up the vampire bat’s technologies and compare them to an F16. The bat can fly and turn better. The bat has radar and infrared heat detection. It has high powered listening devices that can discriminate between two individuals. Finally, it has biological weapons that allow it to do its work without alarming the target.

All that in a “machine” that can fit into the palm of your hand. Defense aeronautical engineers must feel so embarrassed.

Next week, let’s take it just a bit further. Female mosquitoes aren’t just looking for you, they’re tasting and feeling for you. They use CO2 gradients as well as my prodigious heat to find me on a warm picnicking evening.



Vanderelst D, De Mey F, Peremans H, Geipel I, Kalko E, & Firzlaff U (2010). What noseleaves do for FM bats depends on their degree of sensorial specialization. PloS one, 5 (8) PMID: 20808438

Patel R, Ispoglou S, & Apostolakis S (2014). Desmoteplase as a potential treatment for cerebral ischaemia. Expert opinion on investigational drugs, 23 (6), 865-73 PMID: 24766516

Ma D, Mizurini DM, Assumpção TC, Li Y, Qi Y, Kotsyfakis M, Ribeiro JM, Monteiro RQ, & Francischetti IM (2013). Desmolaris, a novel factor XIa anticoagulant from the salivary gland of the vampire bat (Desmodus rotundus) inhibits inflammation and thrombosis in vivo. Blood, 122 (25), 4094-106 PMID: 24159172

Gröger U, & Wiegrebe L (2006). Classification of human breathing sounds by the common vampire bat, Desmodus rotundus. BMC biology, 4 PMID: 16780579

Gracheva EO, Cordero-Morales JF, González-Carcacía JA, Ingolia NT, Manno C, Aranguren CI, Weissman JS, & Julius D (2011). Ganglion-specific splicing of TRPV1 underlies infrared sensation in vampire bats. Nature, 476 (7358), 88-91 PMID: 21814281




For more information or classroom activities, see:

Leaf-nosed bats –

Echolocation –

Alternate splicing –

Anticoagulants -

How Do Mosquitoes Find You?

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Biology concepts – semiochemicals, hematophagy, proboscis, thermosensing, TRPA1


Sure, mosquitoes suck blood and pass along malaria
that kill more humans than any other infectious disease.
But would it be good to get rid of them. They provide
food for birds – one scientist suggests that elimination
of Arctic mosquitoes could reduce northern bird
populations by 50%. And mosquitoes pollinate flowers
too, like blueberries and cranberries. See, they’re
not all bad.
We can start our summer series of biology questions by continuing our discussion of taste and thermosensing. It seems that some people are bitten by mosquitoes if they peak out the front door, while other people can sit outside next to tall grass or ponds for hours with suffering a single bite. Unfortunately, I happen to be in the former category.

How do mosquitoes find some people and not others? Are some people just tastier than others?

First let’s get some common misconceptions and basic information out of the way. Do mosquitoes bite you (or any other animal)? No, they have no teeth, so they don’t bite in the traditional sense. What they do have is an elongated set of mouthparts called a proboscis. The sheath on the outside retracts as the longer parts inside pierce the skin like a hypodermic needle. Only this is a flexible hypodermic needle, small enough to go around individual cells and look for a small vein or venule.


On the left is a drawing of the mosquito proboscis parts. Most sit
in a groove of the labium, which retracts as the rest is injected
into the skin. The maxillae and mandibles are like our upper and
lower jaws. They are the sharp parts. The hypopharynx is what
delivers the anticoagulant saliva. On the right is the parts put
together. The fuzzy part is the labium and the sharp tips are
from the maxillae.
Take a look at these videos taken from a 2012 PLoS One study of a mosquito biting a mouse. The squarish objects are skin cells, and the red streaks are blood vessels. The second video in the sequence shows what happens when the proboscis finds a vessel and starts to suck out the blood. Makes you respect the mosquito a bit more – these are some determined females.

Of course it’s only the females that feed on blood. This suggests that feeding on blood is related to having babies. And it is – just not in a “gotta get the baby some food” sort of way. Most mosquito species require a blood meal in order to develop viable eggs. Females get energy from drinking nectar (full of carbohydrates), but they need protein to produce yolk for the eggs. They get the protein from feeding on blood. If the female doesn’t feed on blood, the eggs will be produced, but they won’t be able to hatch and become larva.

But here is one of our exceptions – some mosquitoes have gotten around the need for blood meals. All 92 species of mosquito in the genus Toxorhynchites (elephant mosquito) don’t need to feed on blood. Instead, their larvae feed on the larva of other mosquitoes, and the gather the proteins they need to lay viable eggs from their larval meals. They store the amino acids in their larval and pupal bodies, until they become adults and need them to lay eggs of their own.

Compare the sizes of the elephant mosquito (left) and
A. aegypti.  I’m very glad that the females of the
Toxorhynchites genus don’t suck blood. They could drain
people dry! Even though their size is small, species like the
one on the right can consume 300 ml a day from every
caribou in a herd when they are swarming.

 

This suggests that the elephant mosquitoes could be used to combat disease spreading mosquitoes, like the Aedes aegypti mosquitoes that spread dengue fever, yellow fever and the current disease of interest, chikungunya fever. And the elephant mosquito has been used as a natural biocontrol agent. What's weird is that A. aegypti females actually help the situation.

 

A. aegypti, and many other mosquitoes that lay eggs in water, have larvae that eat bacteria. So they want to lay eggs where there are a lot of bacteria. Well, the eating of larvae by Toxorhynchitesspecies leaves lots of little pieces of mosquito larva in the water, and this provides bacteria with a lot of food. A June 2014 study showed that A. aegypti females actually prefer to lay eggs in water that contain predators for their larva, because it increases the bacterial numbers so much. Thos that survive have lots of bacteria to feed on. It’s a calculated behavior – risk being eaten or risk starving.


So some mosquitoes will go a long way and risk death in order to get a good meal for their potential offspring. They’re looking for mammals usually, but even here there are exceptions. Some mosquito species, like Culiseta melanura, feed almost exclusively on bird blood – they say it tastes like chicken.


The picture represents the transmission cycle for
eastern equine encephalitis virus (EEEV). It can’t be
transmitted from mammals to other animals, so they are
called dead-end hosts. But it can produce disease in
them. Humans most often will present with a limiting or
subclinical disease, but horses have a hard time with it.
The major source is in birds, and the transmission from
bird to bird is by mosquitoes that rarely bite humans. The
way into dead-end hosts is by a mosquito that normally
bites mammals occasionally biting a bird, or the rare
occasion that a bird specific mosquito will bit a mammal.
But just because they feed mostly from birds doesn’t mean they aren’t important disease transmission. They are – for horses. Eastern equine encephalitis virus is passed from bird to bird by C. melanura, so the birds, especially cardinals, are a reservoir of virus. Then, when another species of mosquito that is less particular about its host species bite a bird then bites a horse or person, the disease can be spread. There are even cases where a C. melanura will occasionally feed on a human and spread the disease directly.

With this background, we still need to answer our question of the day – how do mosquitoes find a blood meal. Believe it or not, your socks help answer the question. For many years it was assumed that mosquitoes followed the heat of warm-blooded animals in order to find a meal, but this was an assumption that was not tested rigorously.

Then it was discovered that carbon dioxide (CO2) is a strong cue for mosquitoes seeking sustenance. CO2 means respiration, and respiration possibly means mammals. The mosquitoes have taste receptors in their antennae and mouths that will sense changes in CO2 and they will follow the path of more carbon dioxide right to your nose and mouth (see this post).

Large people and pregnant women tend to exhale more CO2, so they will be more attractive to mosquitoes. But there are large individuals who never get bothered by mosquitoes. Maybe there’s more to it.

Semiochemicals are part of the answer. Semio- comes from the Greek meaning signal, like in semaphore flags. So semiochemicals are molecules emitted by organisms for communication. Pheromones are the most famous of the semiochemicals – and we know that these are used in many animals, from helping to guide ants to follow the path of their predecessors, to influencing mate choices in many animals.

Semiochemicals might be attractants or repellants. In some cases, they can be both. Take human body odor – it contains dozens of semiochemicals, people find body odor repulsive, but mosquitoes enjoy it like the smell of fresh apple pie. Of course, body odor is only offensive nowadays; before the advent of deodorant, daily or three times daily baths and showers, perfume, aftershave, and of course Axe products – everybody smelled like that guy that lives under the bridge.


On the top of this image is a general idea of semiochemicals.
If they work on members of the same species (like mating
signals), then they are called pheromones. If they work on
other species, they are called alleochemicals. Each can be
either attractive or repellant. On the bottom is a homemade
mosquito trap. You might be able to see that it has been
baited with old shoes and grimy socks.
Bacteria feed on the sweat, sugars and proteins that mammals exude, and they give even more semiochemicals. This can make you more or less attractive to mosquitoes. In general, people with many types of bacteria on their skin are less attractive, while those with mostly a few attractive species will get bitten more often. Having a high number of bacteria is a turn off too, probably because that would expose the mosquitoes to more possible pathogens as well. Is it possible to be so disgustingly colonized that even mosquitoes won’t land on you?

Mosquitoes are attracted to several different semiochemicals, including octenol, CO2, and nonanal. On mosquito antennae, especially the female antennae, there are receptors in the sensilla (see this post) for at least 27 different chemicals in human sweat.

Studies have shown that old socks are a good experimental attractant for mosquitoes. Instead of using an arm or other body part, scientists will compare the attractive ability of someone’s old sweat socks to individual chemicals or mixtures of chemicals. Of course, whose socks you use matters as well. Some people are classified as high attractors (HA) and some as low attractors (LA), so studies often include comparisons of chemicals or mixtures to both HA and LA socks.

But there are other considerations as well. People with blood type O secrete different semiochemicals and are more attractive to many species of mosquitoes. Go ahead, try to change your blood type so you’re less attractive to mosquitoes.

Different species may aim for different body parts. Some seem to prefer feet and ankles, but this may be because they are closer to the ground. If convection currents created by the body heat rising suck the mosquitoes in from below, then it is really the fact that they are following their noses and not going after feet particularly. A small 1998 study showed that mosquitoes that went after feet and ankles preferentially did not do so when the volunteers lied on their backs and raised their feet high in to the air. But, what we have stumbled across in this discussion is body heat.


This is part of a complex figure from a 2011 scientific paper.
In addition to the pretty colors used, the message is that these
researchers identified TRPA1 ion channels on the proboscis
of a species of mosquito. They don’t just sense heat with
their antennae, but also their sucking parts. I wonder if the
interior parts also have TRPA1 to help them find a vessel
when the proboscis is inserted into the tissue.
But what was old is new again…. Scientists are again looking at heat as an attractant for mosquitoes. As compared to HA or LA socks, heat isn’t a strong attractor, but warm socks attract more mosquitoes than cold socks. On the other hand, a 2010 study says that heat and moisture is a greater attractor than heat alone, so it would seem that people working outside in the heat would be the perfect attractors for mosquitoes.

Since heat does seem to be an attractor, it would follow that female mosquitoes would have a receptor for heat. Voila, a new study shows that mosquitoes have sensilla on their antennae and palps that house TRPA1 ion channels. A 2011 study even showed that one malaria-carrying mosquito has TRPA1 receptors on its proboscis. We have talked before about how many mammals use this receptor to sense noxious cold as well as chemicals that cause irritation or pain.


On the left is a species of tick. You wouldn’t believe how big they
can get when feeding on blood. Look it up – I dare you. On the
right is a bedbug. The bedbug is not that closely related to the
tick, since the tick is an arachnid. Count the legs on each – spiders
(arachnids) have eight legs, insects have six. Both these animals
feed on blood, but no one has identified a heat sensor in them.
But in birds, reptiles and insects, TRPA1 is a heat sensor. The 2009 studyshowed that the TRPA1 were expressed on the female antennae only. But that isn’t to say that only female mosquitoes have TRPA1. A 2013 study indicates that A. gambiae mosquito larvae have functioning TRPA1 so that they can sense water temperature and stay in the most comfortable water.

So mosquitoes (most female mosquitoes) are finding suitable hosts for blood meals by using their senses of taste, smell, sight, and infrared detection. There are other vampire insects as well, ticks, bedbugs, etc. I wonder if they are using heat sensing too. These have yet to be reported on.

Next week, a related question – just how and why do mosquito repellants work?



Maekawa E, Aonuma H, Nelson B, Yoshimura A, Tokunaga F, Fukumoto S, & Kanuka H (2011). The role of proboscis of the malaria vector mosquito Anopheles stephensi in host-seeking behavior. Parasites & vectors, 4 PMID: 21272298

Albeny-Simões D, Murrell EG, Elliot SL, Andrade MR, Lima E, Juliano SA, & Vilela EF (2014). Attracted to the enemy: Aedes aegypti prefers oviposition sites with predator-killed conspecifics. Oecologia, 175 (2), 481-92 PMID: 24590205

Olanga EA, Okal MN, Mbadi PA, Kokwaro ED, & Mukabana WR (2010). Attraction of Anopheles gambiae to odour baits augmented with heat and moisture. Malaria journal, 9 PMID: 20051143

Liu C, & Zwiebel LJ (2013). Molecular characterization of larval peripheral thermosensory responses of the malaria vector mosquito Anopheles gambiae. PloS one, 8 (8) PMID: 23940815

Everybody Wants To Be Cool

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Biology concepts – TRPM8 cold sensor, menthol, evolution, cold pleasure

The old ads for menthol cigarettes are fascinating, from a biology
point of view. The “cool” and the “refreshing” aspects were reflected
by using spring and summer outdoor pictures, most often with lots of
cool water. At the end of today’s post, we see why this was so. We
also see an African American, since menthol cigarettes were targeted
much more strongly urban African Americans. They were newer
smokers and in typically hotter environments, so the coldness and
soothing abilities of the menthol were great selling points.
In 1924, Lloyd “Spud” Hughes patented the menthol cigarette. Not a big deal in the beginning, Hughes sold his patent to a cigarette manufacturer who marketed them as Spud cigarettes in 1927. They became the fifth largest seller, although there still wasn’t much in the way of profit. Kool cigarettes came along in 1933 and advertised the menthol casket nails as “soothing to the throat” and claimed they were actually medicinal.

The menthol cooled the feel of the smoke in the mouth and throat (much more next week on hos menthol feels cool). Menthol made it feel as though you weren’t sucking hot smoke into your lungs. And menthol deadened the discomfort that cigarettes could generate by irritating the lining of the throat and lungs.

These days, almost 90% of cigarettes contain some menthol, even if they don’t advertise themselves as menthol cigarettes. Why? The “cool” factor lends itself to novice smokers, while the throat analgesia appeals to the seasoned addict. But that may not be the main reason. A study from 2004 showed that menthol slows the metabolism of nicotine.

Slowing the metabolism of nicotine, menthol results in nicotine staying in the system longer and at greater concentrations - just perfect for developing a physical addiction. This, combined with the ability to comfortably smoke more cigarettes because of the slight throat numbing and apparent cooling of hot smoke would encourage more consumption, more addiction, and therefore more profit.

There is now (2013-2014) a push by the US Food and Drug Administration to ban or regulate menthol cigarettes. Did you know that menthol addition to shampoo is federally regulated but its addition to cigarettes is not? Let’s look at some of the reasons a change is being considered.

The tobacco plant has supplied cells that are used to show the
danger of menthol cigarettes. I just love that. But tobacco has been
involved in science in other ways as well. New efforts are
underway to have genetically modified tobacco produce medicines
or biodisel. And the tobacco mosaic disease actually led to the
discovery of viruses and the coining of the word “virus.” This same
virus was instrumental in establishing the fields of
virology, plant virology and all of molecular biology.
A 2013 series of experiments showed that menthol-containing cigarette smoke is more toxic to cells than non-mentholated cigarette smoke. Menthol alone had no toxic effect on the cells, so it is the combination of menthol and cigarette smoke that kills cells at a higher rate. In the most delicious irony imaginable, the two cell types that the researchers used to monitor cell death after smoke exposure were human lung cells and tobacco plant cells!!!

Additional recent evidence suggests that menthol interacts with the nicotine receptor in the brain. Brody and his co-workers showed that menthol cigarette smoke up regulates the number of nicotine receptors in the brain more than regular cigarette smoke. This might explain why it is harder for menthol cigarette smokers to quit smoking and why more of them fail in their efforts to quit.

Another 2013 study showed that menthol decreased the activity of the nicotine receptor, so that more nicotine was necessary to reach the same level of activation. Once again, this would contribute to a physical addiction.  Just a bit of information if you are considering taking up the habit - the “cool” factor and refreshing cold of mentholated smoke just may contribute to your death.

So sensing cool or cold has its place in biology and in society. Chili peppers are sensed as burning hot because they just happen to bind to and activate the TRPV1 heat sensing ion channel– it’s the biological joke being played on us that we have talked about before. TRPV1 a receptor that reacts to both environmental (temperature, pH) conditions and food substances.

On the other end of the scale is the sense of cold. Do organisms sense cold like they sense heat? Isn’t cold just a lack of heat, so that a feeling of cold is just a lack of activation of TRPV receptors? Nope. There are receptors specifically designed to sense cool or cold. Are there exceptions in cold sensing like there were for heat? You should know that answer by now.

Melastatin was the first TRPM protein discovered. The name
comes from melanin (the pigment in skin and hair cells) and
statin, which means to stop. It was important because it could stop
the invasion of tumors of melanin producing cells. We call this
maliganant melanoma, one of the deadliest cancers. Tumors with
more melastatin were less aggressive and invasive, while those with
little melastatin killed patients much sooner.
We learned recently that there are six different TRPV cation channels, and at least four of them are important for sensing different ranges of temperatures. In some cases, like with TRPV1, noxious heat (or capsaicin) results in a sensation of pain and burning, and the body’s mechanisms for cooling are turned on.

Another TRP family member, TRPM8, turns out to be the receptor channel that senses cool temperatures, from about 28˚C (82 ˚F) down to about 10˚C (50 ˚F) or even lower. The M stands for melastatin, a name for the first TRPM, before they knew it was a family of proteins. Now there are eight known members of the TRPM subfamily of TRP ion channels.

TRPM5 is particularly interesting for our recent discussion of taste, since it works to change the mechanical energy of taste particles + taste receptors into an electrical signal that is sent to the brain. Once again, we see the close relationship between the ion channels, like TRPV1 for capsaicin, and the taste sense. Maybe cold and TRPM8 also influence taste. We shall see.
Less is known about TRPM8 as compared to TRPV1 although they were discovered about the same time (early 2000’s). The pain associated with capsaicin and noxious heat aspects of TRPV1 made it sexier to study. I think we will see that TRPM8 and TRPA1 can be quite interesting in their own right.

Here’s a quick overview of the thermosensing by TRPs.
We will talk about it more next week. The TRPVs are
generally for warm temperatures, while TRPM8 is for
cool temp.s. TRPA1 will be our focus in a few weeks; it
senses painful cold. But notice, the garlic and wasabi
pictured with TYRPA1 also activate TRPV1, and the camphor
shown for TRPV1 also activates TRPM8 (next week). These are
related and complex systems.
First of all, TRPM8 is involved in thermoregulation, just as is TRPV1. In humans and other mammals (the naked mole rat excepted), when TRPV1 is activated, the body automatically thinks it is too hot and initiates cooling mechanisms. With TRPM8, the effect is the opposite. Stimulation of this ion channel tells the body that it is too cold, and mechanisms are initiated to increase the core temperature. We will talk about how TRPM8 helps to regulate body temperature next week.

The big question is why it’s important to sense cold as well as heat. For some reason, we sense cool/cold with some distinct proteins and heat with different proteins. Remember, evolution doesn’t follow a plan to make things complex, functional and efficient. Sometimes the functions occur at separate times and come from different pathways; there is no evolutionary goal or roadmap to a destination. It’s all chance.

A 2013 review has an interesting hypothesis as to why sensing cold/cold is so important, aside from just alerting us to the chance we might freeze to death. Based on mouse study results from as early as the 1970’s, and on the answers that human subjects give, it seems that coolness is an evolutionary plus. No- I don’t mean that The Fonz from Happy Days was an evolutionary leap into the future, I mean that cool sensations somehow help us survive and propagate.

We typically heat food because it increases aroma, increases taste, and reduces the work in digestion. These are all important for getting us the nutrients and the calories we need. Taste, as we said several weeks ago, is nature’s way of getting us to eat those things we need and avoid those foods that might harm us.

So why would cool foods or sensations be helpful? Cooling would decrease aroma and taste, so it must be something other than taste. The obvious reason for drinking something cold would be that it cools off our body – but it doesn’t work that way. As soon as you drink a cold drink, your body reacts to the cold by constricting the blood vessels near the cold surface so that heat is not lost. TRPM8 also invokes heating mechanisms after it is activated by the cold water or soda. So in truth, cold drinks don’t cool you off.

On the left is a mint julep, famous in Kentucky and the Deep
South during the hot summers. It contains Kentucky bourbon,
which is why it is brownish. On the right is the mojito, also
good on hot days, but uses rum, so it is popular in the Caribbean
and Florida, where the rum is. The connection? They both use
mint (menthol) to increase the coolness and refreshing
characteristics of the drinks. TRPM8 hard at work to make
your Saturday evening a success. 
Yet they still feel refreshing on a hot day – what gives? Refreshing may be the key word here. People use many words that together make up “refreshing.” They say that cold drinks revive them, restore their energy, arouse them, reduce stress. All these feelings would promote survival behaviors in a hot environment. But we might also drink a cold drink on a cold day and deem it pleasant. In this case, pleasant can be equated to useful – and useful means promoting survival.

The 1970’s experiments showed that mice would lick a cold piece of metal when they were thirsty, showing that cold helps satisfy thirst. The more amazing thing was that the mice would lick the cold metal even if they could drink all they wanted. This meant that cold drinks were a reward; they activate a pleasure center in the brain. Many studies and experiments have shown these results to be true for humans as well.

So a cold drink on a cold day might be seen as unpleasant, while a cold drink on a hot day is very pleasant (useful). But more important, a cold drink on a cold day when you are thirsty is seen as pleasant and satisfying. It’s our brain helping us to garner the things we need; if cold water is all that’s available to a cold caveman, he better want to drink it. It works the same on skin, cold applied to the skin on a hot day – such as jumping into the pool on a warm day is seen as pleasant, even if it doesn’t cool the body all that much (see above). But the same cannonball on New Years day with the Polar Bear Club, is completely unpleasant.

Comedian and late night talk show host Jimmy Fallon took
the Polar Bear Plunge in Chicago this past New Years. Basically,
3000 people jump into a 34˚F (1˚C) Lake Michigan to support
Special Olympics. Some do it for the charity, some for the thrill,
some because they are unbalanced. For those with a heart
condition, it can kill you.


The brain is an amazing organ, it works with our body to get us what we need, and tricks us into doing it – that’s basically what pleasurable things are, evolutionary tricks. But remember – too much of a good thing can be bad in an environment where we can manipulate nature.

Unfortunately, evolution doesn’t look into the future, it only worries about what keeps us alive at this moment. This explains the danger of menthol in cigarettes – we find it pleasant even if it is bad for us in the long run.

We will talk more about the TRPM8 next week, about how menthol seems to cool you down, how TRPM8 is a lot like TRPV1, and how it may save your life.



Eccles R, Du-Plessis L, Dommels Y, & Wilkinson JE (2013). Cold pleasure. Why we like ice drinks, ice-lollies and ice cream. Appetite, 71, 357-60 PMID: 24060271

Noriyasu A, Konishi T, Mochizuki S, Sakurai K, Tanaike Y, Matsuyama K, Uezu K, & Kawano T (2013). Menthol-enhanced cytotoxicity of cigarette smoke demonstrated in two bioassay models. Tobacco induced diseases, 11 (1) PMID: 24001273

Brody AL, Mukhin AG, La Charite J, Ta K, Farahi J, Sugar CA, Mamoun MS, Vellios E, Archie M, Kozman M, Phuong J, Arlorio F, & Mandelkern MA (2013). Up-regulation of nicotinic acetylcholine receptors in menthol cigarette smokers. The international journal of neuropsychopharmacology / official scientific journal of the Collegium Internationale Neuropsychopharmacologicum (CINP), 16 (5), 957-66 PMID: 23171716

Ashoor A, Nordman JC, Veltri D, Yang KH, Al Kury L, Shuba Y, Mahgoub M, Howarth FC, Sadek B, Shehu A, Kabbani N, & Oz M (2013). Menthol binding and inhibition of α7-nicotinic acetylcholine receptors. PloS one, 8 (7) PMID: 23935840


http://www.dw.de/european-parliament-approves-stricter-tobacco-regulations/a-17458107    

In lieu of additional web sources, I suggest investigating the National Center for Biotechnology Information site (http://www.ncbi.nlm.nih.gov/) from the National library of Medicine. This site has many resources, from looking at the amino acid or nucleotide sequences from any protein or gene you can imagine (GenBank, http://www.ncbi.nlm.nih.gov/genbank/) to scientific journal articles that may or may not be available to you. Look at PubMed Central (PMC,  http://www.ncbi.nlm.nih.gov/pmc/) where all articles are available free to the public. 


 

What’s So Repelling About Repellents?

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Biology concepts – thermosensing, repellent, odor receptors, gustatory receptors, semiochemcials


Science explains our world, and then technology and engineering
build a model of that for our use. The better we know how our
universe works, the better we can make use of it. In the 1985
film Real Genius, this difference is stated when the scientist
students ask what a 6 megawatt laser might be for, one student
says, “Let the engineers figure out a use for it.” In this case, they
used it to fill a house with popcorn.
Science exists to describe our universe in terms of rules and mechanisms; what is and how it comes to be. Knowing that something exists is only half the equation. Science seeks to explain how something exists in terms of the rules of the universe. Observation is good, but it only shows us the question – mechanisms of action and interactions show us the answers.

As an example – we know that certain naturally occurring oils and well as some man made chemicals keep mosquitoes from feeding on us. This is the observation. But the question is –how do mosquito repellents work? The answer is more interesting and more complicated than you would initially think. Repellents rarely repel.

Investigating how chemicals keep us from getting bitten will teach us about how the living systems work, will give us a better understanding of our universe, and then give us better insect repellents. Don’t think that’s important? Consider the hundreds of millions of people who are infected every year (several million die) with mosquito-borne diseases (malaria, encephalitis, dengue fever, yellow fever, filiariasis). So yes, we need more repellents.


Mosquito borne diseases can be unpleasant at best. Top left is
filariasis, a worm is transmitted via mosquito and it clogs up
your lymphatic vessels, so that body parts swell from excess
fluid. Top right – malaria can result in so much red blood cell
lysis that your spleen (the guy who cleans them up) can
rupture. Bottom left – Dengue fever is often called breakbone
fever, the pain is not something an image can express. But the
hemorrhagic form of the disease can produce some bleeding
in weird places. Oh, and it can kill you too. Bottom right –
yellow fever is caused by a virus transmitted by mosquito. Your
liver breaks down and causes your whole body to turn yellow
and you bleed into your skin.
We should start with the repellents for which we have good ideas of their mechanism of action. But there aren’t any. We have some hypotheses and working ideas of the modes of action of mosquito repellents, but nothing is definitive yet. Let’s look at two of them and see if we can find some common pathways.

Citronella oil
Citronella is a combination of many different natural oils produced in lemongrass plants (Cymbopogon nardus and Cymbopogon winteratu). As a natural oil and a flavoring in Asian cooking, one would think that citronella oil would be considered just about the safest insect repellent this side of a slap with an open palm.

But no, Canada says that one small component of citronella oil called methyleugenol, can increase the likelihood of tumor formation in rats. Of course this was when methyleugenol was distilled from the oil, given by itself in large doses, and introduced directly into the stomach. But Canada is still in the process of banning citronella oil as an insect repellent. Of course, you can still eat thai food in Canada, which is often flavored with lemongrass.

The EU, on the other hand, said that the repelling function of citronella oil hadn’t been proven and it was deemed illegal to use in the EU in 2006. Oh, you could eat it, and use it soap or perfumes, you just couldn’t use it to keep mosquitoes away. They reconsidered in 2014 and some restricted uses of citronella oil as a repellent are now allowed.


Citronella oil comes from the lemongrass plant (Cymbopogon
nardus or Cymbopogon winteratu). There are two major species
for acquiring the oil, and the oil from each is a little different in
the percentage of each chemical. Lemon grass is also used in
cooking, the woody stalks are used with extra long cook times.
The torches that burn citronella oil work pretty well, but you
have to stay in the volatilized cloud of oil for them to be efficient.
Despite these issues, the U.S. Environmental Protection Agency (EPA) says citronella is safe and effective as an insect repellent. One weird side issue – you can take all the lemongrass you want from the US to Canada, where its oil is under attack, but you can’t bring any lemongrass from Canada to the US, where it is considered safe. Hmmmm.

Citronella oil probably works in a couple of ways. It's strong and sweet smelling, so it covers up and dilutes the odors that mosquitoes use to find you. If they’re detecting all the citronella in the air, then they aren’t smelling you. But research also shows that citronella oil activates TRPA1 ion channels. In us, they detect cold and noxious chemicals and are interpreted as pain. It is very possible that the detected signals in mosquitoes just come through as something unpleasant and to be avoided.

In this way, citronella would be an actual repellent. It repels on contact as well, as the taste is thought to activate bitter taste receptors and contact greatly reduces feeding time.

But citronella only seems to work when you are in the cloud produced by burning the candles or torches, or within the area of the spray. And if you’re using an oil or cream with citronella, it should really be reapplied every 30-45 minutes- not the most user-friendly method for discouraging pests.

DEET
World War II in the Pacific was an insect nightmare for the US Army. In response to the plethora of insect-borne disease that ran through the allied forces, defense scientists starting looking for better insect repellents. In 1946, their efforts produced N,N-Diethyl-meta-toluamide, or DEET.

Just how they came up with DEET is a mystery to me, it must have been a massive exercise in trial and error. Why? Because we know less about how DEET works than we do about citronella oil. And that’s with the benefit of 40 years of research. They didn’t have a clue how it worked or even what systems it was targeting when developed in the 40’s.


Guess which hand has been treated with DEET. The
mosquitoes come very close to the hand that was treated,
but don’t land on it. This argues that DEET is less repelling,
than it is disguising. On the right, the structure of DEET is
similar to several human semiochemicals, it fits into the lock
and key system of several odor receptors and activates or
inhibits them.
Originally it was believed that DEET disrupted the mosquito’s ability to detect semiochemicals(octenol) produced by mammals, especially humans, so mosquitoes couldn’t find a mammalian host to feed on. Then they played around with the idea that it blocked detection of CO2.

More recent studies have been more rigorous, but haven’t helped solve the puzzle. A 2008 study suggested that DEET was actually repellent; the mosquitoes didn’t like the smell and would avoid it. But other studies have shown different mechanisms of action.

A study in the journal Nature in 2011 found that mosquito odor receptors could be confused by DEET. The receptors for octenol were less responsive in the presence of DEET, but other receptors more more responsive.  The conclusion of the study was that odorants from humans could be detected, but their pattern was confused, so the mosquito didn’t recognize the target as a target. It’s as if we disappear from the mosquitoes radar when we wear DEET.

A 2010 study showed similar results. DEET activated certain odor receptors but not others when given alone, but the opposite effects were seen when DEET was given in the presence of things from human sweat that would normally attract a mosquito. Once again, the signals were confused. This is really more of a chemical disguise for us, not a repellent. Next time your kids go outside, you should insist that they apply their mosquito confusant.

However, a 2013 study in the Journal of Vector Ecology found that heat and moisture were critical elements for recognition of targets by female mosquitoes, and that DEET messed not with odor, but with detection of heat and/or moisture. Different from the other studies, but still more of a masking than a repellent.


Something a little disturbing. Mosquitoes can learn to ignore
DEET. Most mosquitoes will be confused by DEET and never
find you. But if they do and then are repelled by the taste, they
learn from that and the second taste is not repellent. Hopefully
they just don’t find you a second time.
There was an interesting study from 2013that showed that if you mutate or knock out Orco, one of the co-receptors (a protein that works with many different odor receptors so that they can function properly), then two things happened. One, DEET didn’t have any effect on the mosquitoes, and two, mosquitoes that normally preferred humans greatly would then settle for any mammal.

Weird - Orco is needed for both DEET to work and for mosquitoes to find humans more attractive. I haven’t figured that one out yet. The researchers showed that DEET only maintained an effect on the Orco mutant mosquitoes when they landed on a DEET covered surface, and then they didn’t like it at all.

This suggested that DEET might have more than one mechanism, confusion in the air and repellent taste on contact. Older studies supported this idea, as a couple of studies in 2005 and 2006 showed that contact with DEET would reduce feeding behavior in mosquitoes and one in 2010 showed that fruit fly bitter taste receptors are activated by DEET.

So, we have studies that say DEET is a confusant rather than a repellent, others that say it is a true obnoxious smell that they can’t stand, and yet others that say DEET is confusing to the smell and repellent to the taste. But there are more. Other studies suggest that DEET actually inhibits the smelling of anything, while others say that it inhibits an important protein called cytochrome p450.

Used commercially since the 1950’s, DEET has been the gold standard for efficiency for many years. Although it has to be used at fairly high concentrations, it can keep mosquitoes away for 4-6 hours at concentrations where citronella oil might work for less than an hour. At 100% concentration, DEET is active for more than 12 hours. What’s more, if you combine DEET with 5% vanillin, it works two hours longer!


A lime with cloves stuck in it as a mosquito repellent – really?
Well, lime is kind of like citronella oil, and clove has eugenol,
which acts on TRPV1 ion channels. But how many would you
have to have, or do you wear them like earrings? Penny royal
contains menthol and mosquitoes stay away from it. But it
also has toxins that will kill you.
As good as DEET is, people still question whether it’s safe. The EPA in a 2014 review said that DEET is safe for human use and poses no identifiable risks for human health, even in children. But this doesn’t keep people from suspecting chemical usage of carrying negative effects.

On the other hand, DEET dissolves plastic, foam rubber, spandex, gore-tex, and nylon. I can see where this might make people leery about slathering it on their skin for hours at a time. And a few people are allergic to DEET, so the best current repellent isn’t without some negatives.

One last point – a newer repellent called picaridinis almost as effective as DEET and doesn’t eat your back packing equipment and clothes. The interesting point is that picaridin is a synthetic version of piperine, the spicy chemical in black peppercorns. Add to this that menthol is also a fairly decent mosquito repellent, and we have some good arguments that TRP receptors might be involved in repelling activity – as with citronella oil. Piperine is a TRPV1 agonist, and menthol activates TRPM8 and TRPV1. All our talk about spicy food and heat/cold receptors has an impact even in the spread of malaria and other deadly diseases!

Next week, another question to answer - do sunflowers really turn with the sun?



DeGennaro M, McBride CS, Seeholzer L, Nakagawa T, Dennis EJ, Goldman C, Jasinskiene N, James AA, & Vosshall LB (2013). orco mutant mosquitoes lose strong preference for humans and are not repelled by volatile DEET. Nature, 498 (7455), 487-91 PMID: 23719379

Stanczyk NM, Brookfield JF, Field LM, & Logan JG (2013). Aedes aegypti mosquitoes exhibit decreased repellency by DEET following previous exposure. PloS one, 8 (2) PMID: 23437043

Klun JA, Kramer M, & Debboun M (2013). Four simple stimuli that induce host-seeking and blood-feeding behaviors in two mosquito species, with a clue to DEET's mode of action. Journal of vector ecology : journal of the Society for Vector Ecology, 38 (1), 143-53 PMID: 23701619


East To West And Back Again

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Biological concepts – carbohydrates, heliotropism, monoecious, dioecious


I’m trying to think of a situation where quantity is better than
quality. Perhaps some could argue that since quality is subjective,
one person’s quality would be another person’s attempt for
quantity. In friends and experiences, I go with quality. You can
travel to every place on Earth, but if you don’t come back
changed, there was no quality. You can have many
acquaintances, but you really need only one true friend.
When it comes to the number of economically important plants, the Americas have not got many to show off. But what the two continents lack in number they make up for in quality. We have talked before about the biology of corn from North America and how it has been important for the development of molecular medicine.

Potatoes, cocoa beans, peanuts, and vanilla are also from the New World and deserve posts of their own. We’ll hear about vanilla later this summer. But one plant from the Americas has been important for food, oil, and decoration – the sunflower.

If we are going to talk about sunflowers, one question immediately comes to mind. Do sunflowers really turn to follow the sun?  The answer is more complicated than it would first seem, and the answer is just part of the amazing biology of this plant.

First things first – the sunflower (genus Helianthus, about 50 species), as named in Carolus Linnaeus in 1752, does not refer to their tendency to follow the sun. Instead, he called them sunflowers because, ”Who could see this plant….without admiring the handsome flower modeled after the sun’s shape.”

Analysis of nearly fossilized human waste from the caves of Arizona (4000 BCE) show that sunflowers were an important part of the Native American diet. Sunflowers were tough, so they could grow in the Great Plains and other environments that got little rain and lots of sun. They could also grow in temperate environments. Basically, all of North America was there home.

The buffalo would trample huge swathes of land in their migrations, and the torn up ground was perfect for germination of the sunflower seeds. Slowly, this rapacious weed became a cultivated crop. Hybrids were grown, crossing prairie species with forest species and such. In modern science, the sunflower has been used extensively to study genetics of hybrids, much of this work being done at Indiana University in Bloomington, IN – my alma mater, thank you very much.

Number two - the sunflower isn’t a flower, it’s an inflorescence. This is a scientific word for a group of flowers bunched together on the same stem. We talked long ago about the Philodendron selloum inflorescence that controls it’s own temperature and gets hot to attract pollinating beetles.


Sunflowers actually have two types of flowers, the rays and the
discs. The ray florets have a longer petal, they are yellow because
bees see yellow best. The rays are fertile, and have very small
stamens and pistils that provide pollen and ovules. The disc florets,
when male, may have a sterility gene, and this makes sunflowers
very good for studying hybridizations. They also have a naturally
occurring restorer gene, so that they can again make
functional pollen.
In the sunflower, there are two types of flowers, the ray florets around the edge that every one thinks are the only flower petals, and the disc florets, which everyone assumes are the seeds. The ray florets are sterile and therefore for show only; they attract the pollinators.

The ray florets are usually bright yellow, but the disc florets are different colors in different species. They can be yellow, maroon, or even red. The red varieties all stem from a single mutation, but that isn’t the weird part. The disc florets start out male, and produce stamens and pollen, but then turn female as they mature, with the stigma pushing its way up through the middle.

This makes the flowers “perfect” and the sunflower monecious, meaning that have both male and female structures on one plant, but it also makes them smart, as the different timing reduces the chances of self-pollination (pollen and stigma aren’t around at the same time).  For more discussion of monoecious(meaning “one house – male and female flowers on same plant, maybe even as the same flower as with the sunflower) and dioeciousplants (male and female flowers on separate plants), see this post.

But even in this, the sunflower can be an exception. The florets mature from the outside discs to the inside discs over time. So while the inner ones may still be male, the outer ones may have become female. In times when pollinators are more rare, if a disc floret remains unpollinated, its stigma may bend down enough to touch the pollen of the still male florets more towards the center of the inflorescence! This is rare, but does occur in species that are annuals.


An achene is a type of fruit that has a hard shell and the seed is
inside. Strawberries are accessory fruits, where the accessory
organs from many achenes join together. The achenes are the
little pieces on the outside. The papery husk (exocarp) of the
sunflower achene is  made from the ovary wall and protects
the seed until it is ready to germinate, like being stuck in dry,
hard, cold ground, or in the belly of a bird.
And third, the disc florets each produce a single fruit (achene), which we call (incorrectly by the way) a sunflower seed. Inside the achene shell is the sunflower seed that we eat. A single sunflower inflorescence can have as many as two thousand disc florets, so that’s a lot of fruit. In species that have more than one inflorescence, each inflorescence will have many fewer than two thousand. Flowers are energetically very costly to produce. Incidentally, almost all the wild varieties have more than one inflorescence, the domesticated versions are bred to have one.

Now for the answer to today’s question – do sunflowers follow the sun? Well, yes and no. Young sunflower plants, including the very small, juvenile flowers, have the capacity to grow very quickly. This means lots of cell growth, and the need for lots of sunlight (to produce ATP and carbohydrates by photosynthesis).

The ability to follow the source of sunlight, called heliotropism (helio = sun, and tropic = loving) requires lots of cell growth. The flower stalks don’t turn so much as they grow in a different direction. As long as the cell growth is rapid enough and the stalk is small enough to respond to changes in cell size, the plant can appear to turn.


Heliotropism is seen in many plants; they need the sun for their
very lives, so it isn’t surprising that their biology would evolve to
maximize sun exposure. The reason the cartoon uses grass – that’s
the plant in which heliotropism was first studied. What scientist
discovered this marvel of nature? Charles Darwin.
The sunlight causes destruction of a plant hormone group called auxins, so they build up in the cells of the shady side. Auxins like indole acetic acid (IAA) promote cell growth and division, so there is much more growth (longer cells and more cells) on the shady side. The uneven growth pattern makes one side longer than the other and forces the stalk to turn (see picture).

So, immature flowers will face east in the morning and west in the afternoon. But that is only part of the answer. By morning, they’re facing east again. How does thathappen? A current review (2014) suggests that there may be a diurnal rhythm of several plant hormones, or a natural easterly face that is altered by light signaling. The actual mechanism for the daily turning waits to be identified.

But even this is only half the story. As the stalk gets larger and the heavy inflorescence matures, there can’t be enough cell division or hormone action for the plant to move this massive flower. The mature flowers face east all the time. But why east? Maybe they just can’t bring themselves to move one morning, and since they start out facing east, they stay that way when they give up.

Maybe, but I would imagine there’s a more biologically reason than surrender. The 2014 review cites a study that hypothesizes that facing east protects pollen from the mature florets from sun damage. Final answer, sunflowers follow the sun until it’s time to make little sunflowers, then they settle down and face the rising sun.

So young sunflowers turn with the sun, but how about another question – Why? It’s an inflorescence, not the most efficient photosynthesizer (more about this soon), so why would that structure turn to keep facing the sun? It seems like it would keep the flower in one place and turn the leaves to the sun. Hmmmm.

Now that we’ve answered the question of the day and raised another, let’s talk about the sunflower and world history. But for some unfortunate biology, you might eat sunflower roots like French fries.


The Jerusalem artichoke tuber (top) looks a little like ginger root,
but it is sweeter and not so fibrous. See the text for why you almost
grew up eating McDonald’s sunchoke fries instead of potato fries.
One species of sunflower, Helioanthus tuberosus, has an edible tuber root that is often called a Jerusalem artichoke. Since the sunflower is from North America, you know that the Jerusalem part of the name is wrong. And it’s not an artichoke either.             How it got its name

Around 1600, the Jerusalem artichoke became a popular foodstuff. Easily grown and propagated, the sunflower tuber was a great source of carbohydrates and protein. It was easy to prepare, lasted a long time in storage, and didn’t taste like dirt or wood. Cultivation of the Jerusalem artichoke took off, and it became the primary food for many poor people and a delicacy for the rich.

The South American potato filled the same role, so who would win out as the food of the day? The Jerusalem artichoke (also called a sunchoke) had one big drawback, and it lost the battle. The potato won out, and 250 years later the great potato famine changed the immigration/emigration and ethnic patterns of the world.

What was this thing that cost H. tuberosus the war? It gives you gas. Among the many carbohydrate molecules produced by the Jerusalem artichoke is inulin. This polymer of six carbon sugars is one of those sugars that humans can’t digest, like cellulose. But our gut bacteria can.


Inulin is a branched chain of six carbon sugars. They come in several
varieties and together are called fructans. The “n” means there can be
any number of these units in the chain. They are a good source of
natural fructose, and chicory (right) is the most commercial source of f
ructans. Chicory has been used as a coffee substitute, a salad green
(endive and radicchio are types of chicory) and even in brewing beer.
In breaking down inulin, bacteria produce fructose monomers. They use these monomers as an energy source, and in doing so, produce carbon dioxide. In Central Europe, where the potato vs. Jerusalem artichoke battle was taking place, about 30-40% of the population have a genetic predilection for poor fructose absorption. This means more fructose stays in the gut….more bacteria food. This means much more carbon dioxide and …. flatulence. 

In U.S. finer restaurants and gastropubs, the sunchoke is making a comeback, mostly because Americans can usually absorb fructose just fine. And the fructose helps diabetics too. Many diabetics use the high fructose:glucose ration to even out their glycemic indices.

What’s more, a 2014 study found that mice fed a high fructose diet over time do develop type II diabetes and/or fatty liver. Preceding the disease development, many specific genes change their expression patterns. If their diet was supplemented with extract from Jerusalem artichoke, many of the genes showed normal expression, and the diseases did not develop. Not bad for a sun chasing flower.

Next week, another question to investigate - what/who makes the loudest noise in life?




Vandenbrink JP, Brown EA, Harmer SL, & Blackman BK (2014). Turning heads: The biology of solar tracking in sunflower. Plant science : an international journal of experimental plant biology, 224C, 20-26 PMID: 24908502

Chang WC, Jia H, Aw W, Saito K, Hasegawa S, & Kato H (2014). Beneficial effects of soluble dietary Jerusalem artichoke (Helianthus tuberosus) in the prevention of the onset of type 2 diabetes and non-alcoholic fatty liver disease in high-fructose diet-fed rats. The British journal of nutrition, 1-9 PMID: 24968200




 

Let's Get Loud

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Biology concepts – vocalizations, mechanical sounds, sonar, decibels, stridulation


Today it seems that truth is more complex than ever.
van Goethe was a German statesman and a very successful
writer. He wrote novels, scientific treatises, lyric poems, as
well as dramas. Born in 1749, one might say that his quote
was true for his day; it was a simpler time. But think how
simple our time will seem to those who live a hundred
years from now – unless we’ve found our way back
to the Stone Age.
I have worked for years in science, and I’m supposed to be a big boy and realize that things are complicated. But I still get frustrated when I can’t get a simple answer. It seems nothing's simple, every answer has a caveat – heck, I make a blog of the exceptions to answers!

This week’s question is no exception – What living thing makes the loudest sound? Notice I said living thing, because I didn’t want to exclude anyone from the contest. Who knows, maybe some bacterium living in Wyoming makes a heck of a racket, it’s just that nobody is around to hear it. Or maybe a redwood falling down is the loudest. See, nothing’s ever simple.

This leads us to a second question – one which we have to answer first. What’s a sound? We are surrounded by air, and air has mass and density – it’s stuff. You can push stuff around. When you push the air, it moves away, which creates a wave, because the air you move then moves the air next to it, and so on.

A sound wave is generated when a force creates a vibration, and that vibration moves air, and that vibration is then propagated through the air. The air moves in the same direction the vibration was moving, and this makes it a longitudinal wave (see animation below).


A sound wave is a longitudinal wave, where the source moves
in the same direction as the wave. There is a compression of
the medium (air or water) and then a rarefaction with fewer
molecules as the compression moves on. The wavelength is
the distance between compressions and the frequency (how
high or low the sound is) is 1/wavelength.
So now we have a sound wave, but do we have a sound? It’s like the old question, if a tree falls and nobody’s there to hear it, does it make a sound? If you define a sound as a sound wave, then yes it does. Does that mean that every sound wave is a sound? There are sounds waves that dogs hear and we don’t because the frequency is too high – are they sound? There are waves that are too low or too soft for anything to hear, are they still sounds?

If you define sound as something your brain recognizes, then a sound doesn’t occur until the sound wave is transduced (changed in form) by a your ear to an electrical chemical impulse and that impulse is interpreted by the auditory cortex of your brain. See, nothing has a simple answer.

So, does a lonely falling tree make a sound? Scott McFarland of the University of Oregon installed microphones all over Crater Lake National Park 100 miles southeast of Eugene. In the remotest parts of the preservation land, he has heard everything from buzzing mosquito wings to, yes, falling trees. Unfortunately, he has also heard human intrusion.

Even from the most isolated areas, about 20% of every recording included airplane noise. He also heard cars, people, and detonations. It seems that no place is really naturally quiet anymore. But there were those falling trees -does that mean they do make a sound? Nope, it was a sound wave captured by recording equipment, transduced to digital information, stored, changed back to a sound wave by a speaker, and then to a neural impulse by our inner ear. It still isn’t interpreted as a sound until it reaches a brain, any brain. If a rabbit or bull moose is nearby, their ears would transduce the sound wave and they would “hear” something, even if they don’t think to themselves, “Hey, a tree just fell.” So again, it’s not so simple, maybe something with a functioning ear is in range.


The old tree falls in a forest question started out as a philosophical
question. It was meant as a thought experiment to students to
discuss the nature of what is real versus what is observable. However,
when it existed as a philosophical question, no mention of sound was
made, but was concerned with whether the tree existed at all if no one
was there to perceive it. It wasn’t until 1883 that the sound reference
was made, and then it was posed as more of a scientific question,
as we approach it in today’s post.
The human hearing sense is pretty sensitive. The pressure needed to generate a sound wave that a human could hear is about one billionth the value of atmospheric pressure. But this sound wave would be just barely audible (depending on the frequency), so it would be soft.

This brings us to a very short discussion of what it means to be loud or soft. We often measure loudness in decibels (db). A decibel is one tenth (deci) of a bel (named for Alexander Graham Bell), which is a unit of power or intensity.

Every 10 db increase represents a 10 fold change in intensity, so the scale is logarithmic. In acoustics(from Greek akoustos = hearing, and ic= pertaining to) this means that decibel is a measure of sound pressure, compared to a reference pressure (20 micropascals – we’ll get back to this).


Howler monkeys are the largest of the New World monkeys. But in
one way they are like old world primates. Howlers are the only new
world monkeys with color vision in both males and females. They all
see like we see, so they can discriminate different shades of green, red,
and blue. In most new world monkeys, the color receptor gene is on
the X chromosome, so females may get two types and be color vision
function, but all males get only one, and see only black and white.
A fairly recent gene duplication in howlers have given it color
vision again.
Examples of things that are loud (high sound pressure) would be a jet taking off 25 meters away (150 db), a clap of very nearby thunder (120 db), or a Harley Davidson 25 feet away (70 db). Note the distances; sound waves dissipate in power as they travel, the transference of energy along the wave goes in all directions and is not 100% efficient. This is why you can’t hear your brother playing with your Rock’em Sock’em Robots when you’re down the hall.

So who’s the loudest? The howler monkey (genus Alouatta, 15 species) has a great claim to being the loudest living thing. Used for communication over tremendous distances, the howl of this primate reaches 128 db from several feet away (hear it here). Howlers have an enlarged hyoid bone that is U-shaped. This creates an air sac on their throat that they can use to make their howl resonate.

The howl is really more of a growl for males but is higher pitched for females, and they can be heard more than 3.5 miles away. The question is why do they do it. A 2014 study concluded that the black howler monkey (Alouatta pigra) use their calls for several reasons, but most relate to defense.


The lesser water boatman (Micronecta scholtzi) is only 2 mm
long, but packs a big auditory punch. It’s a freshwater (aquatic
rather than marine) insect. Many marine animals have loud
calls, but here is an example of one that lives in slow moving
streams and ponds. You can hear it when standing on the bank.
This means the sound is so loud it can traverse the water/air
boundary, which usually stops most sounds.
They howl most often in defense of feeding areas. The volume of the howl makes the monkey seem bigger than he/she is. They also use it to defend infants or mates from males that are not part of the group. It calls attention and help comes a runnin’.

If we look at smaller land animals, some of them are loud too. Cicadas can produce stridulations (see this post) that reach 100 db from a foot away. But the king of the small animals would be the lesser water boatman.

This small freshwater insect (Micronecta scholtzi) can put out a stridulation of 105 db, even though it’s entire body is only 2 mm (0.078 in) long! A 2011 paper in PLoS One broke down the song of the male into three different parts, each with its own peak intensity. The loudest part could be heard from a riverside, even though the insect is underwater. By comparing peak db to size, the male outcalls every other organism we will discuss. 

But it’s only the male that calls so loud. Why? Because he’s looking for a mate, and it’s his penis rubbing against his abdomen that makes the stridulation. This sort of eliminates the females from participating in the contest.

But back to the bigger animals. Bats are extremely loud, but their calls are of such high frequency that we can't hear them. Parrots can call to each other in the range of 100 db, but we can go bigger. In fact, the biggest animal may have the biggest voice as well.


The blue whale is the heaviest animal to yet live on Earth.
Being this large, it still has two natural enemies – man, who
hunted it to near extinction, and the orca. Orcas coordinate
their attacks on the blue behemoths, often trying to separate
babies from their mothers. Nearly 25% of sighted blue whales
have scars from either orcas or monumentally stupid octopus.
The blue whale(Balaenoptera musculus) is the largest living animal and the heaviest animal ever to live on Earth (yet). The whale’s song can reach 188 db! Some of the frequencies are too low for us to hear, but the higher pitched (higher energy) sounds can be detected 800 km (497 miles) way (hear it here).

Interestingly, a 2009 study shows that blue whale songs are getting lower in frequency. Since the whaling ban of 1966, male blue whale songs have been using lower and lower tones. The authors suggest several reasons for this. Males may not need to call out so loudly to find females because the ban has resulted in higher numbers of whales. But it is also possible that more man made noise in the ocean is forcing them to use lower frequencies.

The sperm whale is right there too. It doesn’t really vocalize, but it makes clicks to echolocate each other and prey. The clicks are made by forcing air through two lips (folds of tissue) in front of their blowhole. These clicks come in several varieties, but the “usual” click can reach 230 db. This makes them the kings of sound, if you don’t limit your choices to sounds made with the mouth.

Sounds in water are louder than in air, because the density is higher and the transmission is more efficient. So decibels in water are relative to 1 millipascal instead of the 20 micropascals in air. If you want to compare directly, you need to subtract 61.5 db from the water sounds. This still makes the sperm whale clicks 170 db and the blue whale song about 127 db, just about the howler monkey level. So the sperm whale wins our contest.


The different pistol or mantis shrimp are not very large, but
they have second largest sound to size ratio in the natural
world. Only one claw is the pistol. The right image is an
enlargement of the claw. S= socket, pl = plunger, D= dactyl,
p = propus. The muscles of the dactyl close it so fast, that the
water displaced in the socket by the plunger shoots out at
100 km/hr. This produces the cavitation bubble.
But for interesting and functional loud noise, I like to go with the pistol shrimp (family Alpheidae, hundreds of species). A special engineering twist allows them to cock one pincher like a gun. When they release it, the sound wave travels so forcefully and fast that the water around it turns to vapor and a cavitation bubble is produced (see video). The temperature in the immediate vicinity reaches 4000˚C and prey within 1.8 meters is stunned or killed! The sound, from several inches away, is 218 db (before subtracting the 61.5 db to match air measurements) when the bubble collapses.  

A 2006 study describes that the hoods of the carapace (shell) that partially cover the eyes of the pistol shrimp are to protect themselves from their own explosive snap. The study suggests the hoods evolved first, and that allowed for the development of stronger and stronger snaps. If this continues, the pistol shrimp may start taking humans out!

Next week, another question about the extremes of life.



Van Belle S, Estrada A, & Garber PA (2014). The function of loud calls in black howler monkeys (Alouatta pigra): Food, mate, or infant defense? American journal of primatology PMID: 24865565

Sueur J, Mackie D, & Windmill JF (2011). So small, so loud: extremely high sound pressure level from a pygmy aquatic insect (Corixidae, Micronectinae). PloS one, 6 (6) PMID: 21698252

McDonald, M., Hildebrand, J., & Mesnick, S. (2009). Worldwide decline in tonal frequencies of blue whale songs Endangered Species Research, 9, 13-21 DOI: 10.3354/esr00217

Anker A, Ahyong ST, Noël PY, & Palmer AR (2006). Morphological phylogeny of alpheid shrimps: parallel preadaptation and the origin of a key morphological innovation, the snapping claw. Evolution; international journal of organic evolution, 60 (12), 2507-28 PMID: 17263113


Does Life Come In XXXS?

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Biology concepts – characteristics of life, archaea, bacteria, mycoplasma, synthetic biology, symbiosis, parasitism, nanobacteria, genome

As part of this blog, we have talked about some pretty small life. Wolffia globosa is the smallest flowering plant, only 0.6 mm long. We also talked about archaea, a different kingdom than bacteria, but still on the smallish side of life. The tardigrade is the toughest animal, but is also one of the smallest, at 100 µm (0.00394 inch).


The organism on the top is T. dieteri, and arthropod, just
as is any crab or spider. The size is deceiving. The pictures
on the bottom are to scale and are copepods, also
arthropods. The organism on the top is a parasite of the
organisms on the bottom. The small blue line? That would
be the scaled size of T. dieteri. So…. it’s SMALL.
The question for today is – is there a minimum size for life? Candidates might include bacteria or archaea; heck there’s an arthropod, Tantulacus dieteri, that's only 85 µm long! As long as we can keep finding smaller and smaller cells, we know that the minimum size for life is that small or smaller. So we keep looking – you’d be surprised how important it is to keep looking for smaller life.

Here’s one thing we should be able to agree on, viruses don’t get to play in our game. Viruses are very small, but they're not life! We’ve talked about this before - the seven characteristics of life (see this post). Viruses need a host in order to replicate, they don’t manage homeostasis, and they aren’t cells, so they aren’t life.

So how small has actual life become? Let’s assume that since tardigrades and T. dieteri are over 50 µm, huge when compared to some bacteria, our current minimum for life is probably a bacterium or archaea.

Let’s go straight to the genus of smallest bacteria we know about – the mycoplasma (from mykes = fungus, and plasma = formed). They were first described in 1898, but the observer didn’t have a clue what he was looking at; hence the fungal part of the name.

Mycoplasma don’t have the traditional cell wall of many bacteria, so they look different and this might be why they were mistaken for fungi. Whatever the scientists thought of them, they were confusing enough to be roundly ignored for 50 years. Rediscovered in the 1950’s-1960’s, this time they were thought to be L-forms of bacteria. L-forms are organisms that for some reason have lost their cell wall.

There are stable forms of L-bacteria; they can live divide and live on without their cell wall. There are also unstable L-forms as well; those that may revert to walled bacteria at any moment. Are mycoplasma simply bacteria that have lost a cell wall? Nope. They didn’t have a cell wall to lose. They have no cell wall genes, so if they had a cell wall, it was millions of years ago, before they became their own genus.


The difference between some free living cells. You can
probably see the E. coli in bright green, but you may have
to squint to see the mycoplasma above it. It’s pink. Really,
it’s there. Compare these sizes to those of the arthropods
above. 1 mm is equal to 1000 µm.
Mycoplasma is really, really, SMALLLLLLL.
Mycoplasma are generally described in the range of 0.2-0.8 µm in diameter. But this is a little misleading, because they are often not spherical. Even without a cell wall, they can take interesting three-dimensional forms and maintain them. Mycoplasmapneumoniae, which causes a form of …..….. anyone?…….. right, pneumonia, is pear shaped, so its 0.25 µm diameter is actually the measurement on its short side.

So mycoplasma are small, but they still have to play by the rules. They contain DNA and salts and proteins and ribosomes and other things that take up room. A single ribosome is about 50 nm in diameter (0.05 µm or 0.00000005 m), so there must be a certain volume required for the cell to function – a minimum size for life.

Which of the mycoplasma species is the smallest? Mycoplasma genitalium is considered to be the smallest mycoplasma known, and the smallest form of free-living organism - my gosh – you can fit about 400 M. pneumoniae inside one E. coli! As such, it is the current minimum size for life that we have. M. genitalium is 200 nm (0.2 µm) x 600 nm (0.6 µm), so they’re pretty dawg on small. Let’s put it this way, there are 25,400,000 nm in one inch – mucho small.

It is important to note that M. genitalium is free living, but does need some help. It uses cholesterol in its membrane but doesn’t make it itself. It picks it up from the cells that it lives near……wait for it….. your genital epithelium.


One of the human diseases that is becoming more
convincingly associated with M. genitalium is pelvic
inflammatory disease (PID). Resulting when many
different sexually transmitted diseases go untreated,
PID can cause permanent damage to the reproductive
organs of women. It is important to get treatment early.
The inflammation of PID may be associated with the
fallopian tubes or ovary, and will cause a chronic pain
in the lower abdomen, bleeding and pain on urination.
M. genitalium is a cause of non-gonococcal urethritis (inflammation of the urethra). A late 2013 review states that 1-3% of the general population is infected with M. genitalium, more than with gonorrhea. It is linked to pelvic inflammatory disease, and the review cites studies showing that people infected with this mycoplasma are more at risk for HIV and have more dual infections. It’s a sexually transmitted organism, just another reason for proper restraint. But even though it's helped out by your genital epithelium, it can live on its own and divide outside a host, so it's considered a free-living organism.

The idea of free-living is important because M. genitalium also has a very small genome (amount of DNA in one cell, including the list of all its genes). M. genitalium has about 580 kbp of DNA where kbp = kilobase pairs. Remember that DNA is doubled stranded (usually) so each base is paired with another. Knowing this, we count them as a unit. In all, M. genitalium has just 520 or so genes; it can make about that many proteins.

Genome size could be another way of determining the minimum size of life - what's the minimum number of genes or number of base pairs of DNA for an organism to still meet all seven characteristics of life? As of summer 2014, no organism smaller in size than M. genitalium has been described, but there have been some other organisms discovered with smaller genomes.

Nanoarchaeum equitanswas thought to have the smallest gene for a while, with only 491 kbp of DNA. It is an archaea that lives on the edge of hydrothermal vents at the bottom of the ocean. But it is an obligate symbiont with another archaea; it can’t survive without its partner, so can you say it has the minimal genome? It relies on another organism’s DNA.


On the left is the leafhopper in which N. deltocepahlinicola makes
his home. Well inside its cells that is. The leafhopper survives on
phloem and xylem; high in carbs but little protein. The bacterium
makes the amino acids the leafhopper can’t in exchange for energy
in the form of ATP. On the right is a colored photomicrograph of
the abdomen. The red is one type of endosymbiont bacteria,
the green is N. deltocephalinicola.
This is also true of Carsonella ruddii (159 kbp, 182 genes) and Nasuia deltocephalinicola. They are bacteria that must live inside insect cells, like those of grasshoppers. N. deltocephalinicola has the smallest known genome (112 kbp, 137 genes), but it doesn’t even make ATP, it steals it from the arthropod cells. This could hardly be considered free living, and so it can’t be considered the minimal genome for life. And even at that, their cell sizes are still bigger than M. genitalium.

So why is it important to find the minimal size and minimal genome for life? So we can use the information. J. Craig Venter (of the human genome project) wanted to develop a synthetic form of life (synthetic biology); a bacterium that could be developed to provide hydrogen for energy or eat waste to reduce pollution. Others say we need to know so that we can better recognize life on other planets, or life that may have come here from other planets (astrobiology).

Being J. Craig Venter, develop a synthetic form of life is exactly what he and his research institute did. It’s interesting that Venter was one of the scientists that first sequenced the entire M. genitalium genome in 1995. Some 15 years later, Venter’s JCVI-syn1.0 (2010) was the first synthetic life, housing 1000 kbp and 500 or so genes. The genome was based on that of another mycoplasma, M. mycoides. They modified the genome, and introduced it into a cell membrane that had been evacuated of all its constituents. The resulting cell was capable of growing, dividing, you know…. living.

If M. genitalium represents our current estimate for the minimum size of life, it’s only because we’re thinking of life as we know it. Perhaps we have already found life that is smaller, and the minimum size is actually much smaller than M. genitalium.


This is a photomicrograph of a meteorite from Mars. The
small spheres (like the ones the arrows point to, are
supposedly nanobacteria. Proof of life on Mars,
contamination from Earth nanobacteria, or just mineral
spheres that look a little like incredibly tiny bacteria?
The answer is C.
Something termed a nanobe and something else called a nanobacterium were described 20-30 years ago. Nanobes were first found in the rocks that came up during oil drilling in Australia, while nanobacteria were also found in surface rocks.  The size of both (about 1/20 size of M. genitalium) negates their use of ribosomes and DNA. They stain for DNA, but this may be artifact, the artificial result of other things picking up the stain.

But nanobes/nanobacteria have their proponents. Some scientists say that since no DNA has been exhibited, they are a completely different form of life, so size restriction (big enough to hold ribosomes) doesn’t apply. Nanobacteria are also claimed to be important in human disease, as these structures are found in many calcifications of diseased tissues.

On the other hand, nanobacteria are probably just mineral formations. A 2013 study showed that they form spontaneously from many different biological fluid samples, and their appearance in diseased tissues is more a sign of disease than a cause of it. We’ll just have to keep looking for something smaller.

Next week, another question tackled and dissected - think pink.




Manhart LE (2013). Mycoplasma genitalium: An emergent sexually transmitted disease? Infectious disease clinics of North America, 27 (4), 779-92 PMID: 24275270

Wu CY, Young L, Young D, Martel J, & Young JD (2013). Bions: a family of biomimetic mineralo-organic complexes derived from biological fluids. PloS one, 8 (9) PMID: 24086546

Gibson DG, Glass JI, Lartigue C, Noskov VN, Chuang RY, Algire MA, Benders GA, Montague MG, Ma L, Moodie MM, Merryman C, Vashee S, Krishnakumar R, Assad-Garcia N, Andrews-Pfannkoch C, Denisova EA, Young L, Qi ZQ, Segall-Shapiro TH, Calvey CH, Parmar PP, Hutchison CA 3rd, Smith HO, & Venter JC (2010). Creation of a bacterial cell controlled by a chemically synthesized genome. Science (New York, N.Y.), 329 (5987), 52-6 PMID: 20488990


Fall Leaves And Orange Flamingos

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Biology concepts – pigment, carotenoids, flamingos, cyanobacteria, bacteriophage, trophic cascade effect, spirulina, alga


These are the two species of Old World flamingos, the greater
(upper left) and the lesser (bottom right). Their ranges are
included, pointed out by the convenient arrows. Even though
the pictures don’t show it because I couldn’t get them to stand
next to one another, the greater is twice the height of the lesser,
hence the names. Notice the color variation as well. However,
color isn’t based on species.
There are two species of flamingos in Asia and Africa, the greater and lesser flamingos. There are also four New World flamingo species, but let’s focus on the two Old World species for today – the answer to our question holds for the New Worlders as well. Why are flamingos pink? Well, they aren’t always pink. And the reason they can be pink isn’t simple, but it’s something to which we can all relate.

The greater flamingo(Phoenicopterus roseus) is much larger than the lesser flamingo (Phoenicopterus minor) –- that makes sense. Greater flamingos average about 140 cm (55 in) tall, but they only weigh about 3 kg (6.6 lb). They're mostly legs, and there isn’t a lot of meat on those legs. If given a choice at the next flamingo fry, choose a breast over a drumstick.

The lesser flamingo weighs in at only 2 kg (4.4 lb) on average and are half as tall as the greater flamingo. But they make up for this in numbers. There are over 1.5-2.5 million lesser flamingos in East Africa, maybe twice as many as the greater flamingos, even though the larger species has a much broader range.

Flamingos are freaky birds. Their knees seem to bend backwards, but it's just an illusion since those backward bending joints are really their ankles. They tend to stand on one leg, and the reasons for this are not completely known. Some birds do it for camouflage, since on one leg they look more like branches. This probably doesn’t work for flamingos – since they’re pink!

A 2010 study showed that flamingos stand on one leg much more often when they are in water, so they hypothesized that they do it to reduce the amount of body heat that is lost to the water. Also, the scientists saw that the flamingos stood on one leg in the water for less total time as the temperature increased. This was definitive proof for leg position as a method of thermoregulation.

Other theories state that flamingos might stand on one leg because it takes a lot of energy to pump blood down and then back up those long legs Birds live on the edge of starvation everyday; by pulling up one leg at a time, they can reduce the distance and therefore the energy needed for moving blood. Or, they may do it to reduce the fungal and parasite loads on each leg – that last explanation is weak, I think.

All species of flamingos feed by turning their heads upside down.
In this way, they can scoop in some water and filter out their
food. Evolution is funny, they could have just evolved scooping
lower jaws, but for some reason they have scooping upper jaws
and therefore turn their heads over. Remember that evolution is
a point to point exercise in mutation and possiblebenefit; it
doesn’t move toward simple or toward logical.

Flamingos also have those funky looking beaks, but they’re functional because they eat with their heads turned upside down. As a result, it’s their lower jaw that is fixed and their upper jaw swings free. They don’t use their jaw to chew their food; they don’t really have teeth.

Instead, flamingos are filter feeders. This isn’t unheard of, there are other birds that filter their food to keep only things within a certain size range and then swallow them whole, but they are the biggest of the filter feeding birds. When their two jaws come together, they form a sort of comb assembly on the sides, the wider the distance between the comb’s “teeth,” the bigger the objects that can fit through.

Old studies shows that they use the “teeth” (actually called lamellae) to exclude things that are too big, and then to filter out things that are too small, like excess water. The tongue sits in a deep groove and pulls in and pushes out water and those things it doesn’t eat. This pumping occurs up to 20 times per second in lesser flamingos and 6-8 times/second in greater flamingos (see this video and watch for water squirting out). Different bill shapes and different spaces and lamellae sizes are specific to each species, and each eats according to its filter.

The popular answer for why flamingos are pink is because of their diet. All that stuff we talked about above is related to that answer, but you can now sense that it’s a little more complicated. The greater and lesser flamingos have different filters because they eat different things. Yet they both end up pink.


Here are the major source of nutrition for the Old World flamingos.
On the top left are the brine shrimp that make up the majority of
the diet of greater flamingos. On the bottom is A. fusiformis, the
major calorie provider for the lesser species. On the top right are
spirulina tablets from a health food market, made from dried
Arthospira organisms. Notice that none are pink, yet the flamingos
are pink. Just how do they pick up color from their food?
In the picture to the left you see the foods of the greater and lesser flamingos. Greater flamingos have a tongue/jaw filter that excludes all but the tiny brine shrimp and those things smaller (larvae of aquatic beetles and flies), so this is what they eat. The filter assembly of the lesser flamingo is much narrower, it only lets tiny cyanobacteria (lower image) into their gullet.

Cyanobacteria are sometimes called, perhaps incorrectly, blue-green or red algae. Alga has no clear-cut definition; some consider anything with chlorophyll and no protective cells over their gametes to be an alga, but others exclude all prokaryotes from the classification. I think the term cyanobacteria (Cyanophyta) is much more accurate.

The cyanobacteria that lesser flamingos eat used to be called Spirulina, but are now classified as species of Arthospira. A. fusiformis is the main dietary source of nutrition for lesser flamingos (of course greater flamingos eat them too; their filters let them in and keep them in), but there is also A. maximus. Together, they make up the spirulina that is popular in health food markets today.

We said above that the answer to today’s questions was that flamingos are pink or orangish based on the food they eat. But their food isn’t pink or orangish!! Look at the picture, spirulina is green. The explanation is related to something you see every year, and is something we have talked about before. It’s just like how the leaves turn colors in Autumn.

The green leaves in summer have red and other pigments, but they’re masked by so much chlorophyll (see this post). In fall, the leaves stop making chlorophyll, so the other colors shine through. The spirulina and brine shrimp have red and yellow pigments, but again there is so much green that the other colors are masked.


Here are two lobsters. Actually, it’s one lobster and one dinner.
The only difference is boiling water. The carotenoids in the shell
of the live version are bound to proteins and this changes their
light absorbing and reflecting properties (color). The hot water
denatures the proteins and frees up the carotenoids to be the
color they always dreamed of being.
When digested, the chlorophyll breaks down or is eliminated. But some other pigments, especially the carotenoids, stick around and get deposited in the tissues and feathers, now you can see them because the chlorophyll isn’t there to mask them. Why do the brine shrimp that the greater flamingos eat turn them pink? Because they feed on cyanobacteria that contain carotenoids. Their carotenoids are released when the flamingos digest the shrimp.

There's another reason for the different colors of food and flamingo. The pigments are sometimes complexed to proteins, and this can make them look brownish, bluish, gray, or green – like the many species of brine shrimp, aquatic beetles, and larval flies. This is very similar to lobsters and shrimp. They're bluish or grey when scooting around in the water, but turn red/pink when they are cooked.

Carotenoids come in many varieties; their chemistries run the gamut from alcohols to esters to plain hydrocarbons. We see them in carrots (alpha and beta carotenes - orange) and tomatoes (lycopene - red) for example. Spirulina has many carotenoids, but the one there in highest concentration is called astaxanthin (pink, as in salmon meat). The percentage of different carotenoids and the total amount of them in the diet  determines the color of the feathers and skin. This is why some flamingos can be bright orange, while others are very light pink.


These are just a few of the dozens of carotenoids found in nature.
The longer the carbon chain, the lighter the color, from red to
yellow. This is just a basic generality, different side chains and
rings can alter the color well. And just to let you know, carotene
was named for carrots, not the other way around.
On the other hand, if there is little carotenoid in their diet, the feathers will be white. The pigment is lost over time, so the pigment trapped there when they were produced will fade. But flamingos molt, so that new, pink feathers replace old whitening ones. That is, if they eat their carotenoids. In zoos, their diet is often supplemented with canthaxanthin that keeps them a presentable pink. The exception – babies always start out grey.

For lesser flamingos, their food is sometimes their doom. A 2006 study found that blooms of toxic cyanobacteria produce two different toxins (microcystin and anatoxin) and have been responsible for several die offs in lesser flamingo population over the last 20 years. They have also found that in some instances, the spirulina they eat will also produce toxin, but they don’t know if it is enough to kill them. Microcystin from an algae bloom is the same toxin that shut down the Toledo water system earlier this week.

What may be worse, a bacteriophage(a virus that infects bacteria, see this post) has been increasing in the alkaline lakes where the spirulina grows according to a 2014 study. It infects and kills the A. fusiformis. The kill off of the cyanobacteria leads to a trophic cascade effect; the average adult needs 70 grams of A. fusiformis a day to survive, and that is dry weight, not saturated with water. Lose the base of the food chain and everything else loses too.


Lake Natron is VERY salty, and it contains lots of other minerals.
Natron is a combination of salt and minerals that the Egyptians
used to mummify the bodies of those who could afford it. Not
everyone got to be mummified; if that were the case, we would
have many undead walking around, placing curses on
successful tomb hunters. The minerals are so concentrated that
dead animals that fall in end up mummified and calcified. They
look like gargoyles on a French cathedral.
One last interesting point. While the lesser flamingos can live and eat in several alkaline lakes of eastern Africa, they all fly to one particular lake when it’s time to mate – like a Club Med for pink birds. Lake Natron in Tanzania is their destination. This lake is highly alkaline, hot (nearly 130 ˚F), and just chock full of minerals. The flamingos handle it just fine, but many other birds die from crashing into the highly reflective waters. The carcasses then calcify (basically, turn to stone), and wash up as little gargoyles. Even with all this deadly water, there are two species of fish that live in those waters – I wonder if the stonefish is one of them.

Next week, another question to investigate - can living anything short of an astronaut make it to space?



Anderson MJ, & Williams SA (2010). Why do flamingos stand on one leg? Zoo biology, 29 (3), 365-74 PMID: 19637281

Peduzzi P, Gruber M, Gruber M, Schagerl M. (2014). The virus's tooth: cyanophages affect an African flamingo population in a bottom-up cascade. ISME J. , 8 (6), 1346-1351

Kotut K, Ballot A, & Krienitz L (2006). Toxic cyanobacteria and their toxins in standing waters of Kenya: implications for water resource use. Journal of water and health, 4 (2), 233-45 PMID: 16813016

 

Biology Position available

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I was asked by the Adella Ramirez, the chairperson fo the science department at Waller High School to post the following:

Waller High School in Waller ISD, Waller Texas is in need of an AP and duel credit Biology teacher due to a late resignation (our teacher left to go to a private school). The schedule is quite favorable.

Contact info:
Brian Merrell (Principal)
Waller High School 
20950 Field Store Road
Waller, TX 77484
ph 936-372-3654


Sometimes, Cold Hurts

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Biology concepts – nature of science, TRPA1, thermoregulation, noxious sensor, chemical sensor, mutation, protein domains

"As we acquire more knowledge, things do not become more comprehensible, but more mysterious."


Albert Schweitser was an organist without compare. He toured
the world playing different organs for concerts. Some of these
organs were huge, this one has five keyboards and dozens of
different knobs and buttons. The money from his concerts
went directly to building his hospital complex in Africa
(bottom). At its height, there were over 70 different buildings.
All care was, and is, free.
These are the words of Albert Schweitzer, physician, theologian, philanthropist, and organist. Yep – he played a mean organ. Albert was born in the Alsace part of France in 1875, and was raised in a household of ministers and musicians. He turned out to be both - but so much more.

Schweitzer became a minister, but toured the world's great churches giving organ concerts for big bucks. He used the money to put himself through medical school and establish a hospital in French Equatorial Africa in the 1910’s. He expanded his hospital to over 70 buildings and treated up to 500 patients at a time, always funding his efforts with his organ concert money and the money he made from writing books.

He was awarded the Nobel Peace Prize in 1952. His quote above is true, whether he was speaking of the secrets of life in the spiritual or scientific sense. I personally phrase Schweitzer’s sentiment a little differently. The more we know, the less we know we know. Scientific knowledge is meant to do two opposite things – one, answer questions, and two, create questions. Every decent answer we think we find should bring to mind many more questions.

This naturally occurs when science works at its best, but the hardest part is knowing if we have an answer. If we aren’t sure about the answer, we have to keep looking. Of course we always keep looking, but some answers come to be so well supported that it is not the answer we question but the details of the answer – like evolution or fundamental forces.

But if the answers are tentative or not well supported, then how good are the questions that spring from them? Can our questions only be as good as our previous answers? This I where we're lucky, because bad questions can lead to good answers, if we keep our minds open to what we see and don’t find just we are expecting to find.

How does this apply to our discussion of thermoregulation and heat/cool sensing? Well, what happens when you find a thermosensor that you can’t get a good answer as to what it does? Makes it hard to design new questions doesn’t it?


The left image is of Thomas Hunt Morgan, an American researcher
who set out to disprove Darwin’s theory of evolution using fruit
flies. He chose them because they were cheap and bred quickly –
a new generation came along every 10 days. He started
inspecting them for mutations, and then bred the mutants to
normal flies. The proportion of mutant offspring was EXACTLY
as Darwin predicted. On the right are two images of different
mutants, often these are induced using radioactivity. On the
bottom, you can see a leg growing where an antenna ought to be.
The sensor ion channel that I speak of is the TRPA1. Studies assign it a role in pain sensation – just like TRPV1 for heat. But what stimulates it to generate a pain signal?

TRPA1 was first described in drosophila melongaster (fruit flies). Historically, fruit flies have made great models because they eat cheap and reproduce quickly. You can read about the history of their use in genetics in a great book called The Violinist’s Thumbby Same Keene. 

The scientists would induce mutations in flies (and their subsequent offspring) by giving them radiation or chemicals. They wouldn’t have any idea which flies were mutated, or what the mutations were, it was just a shotgun method. They would then study the flies, looking for abnormal anatomy, abnormal behavior, or abnormal responses to stimuli. In some cases, the mutations were spontaneous, not caused by radiation or the chemicals, but finding them was done the same way, and the ionizing radiation or mutagenic chemicals just made the mutation rate much higher. When they found a fly with a change, then they would go to work and identify the mutation.

One mutation they noticed was that some flies wouldn’t avoid things that should have been painful. Before they knew what gene was involved, they decided to call it painless. Comparing it to known genes, they found it was the drosophila homolog to a mammalian TRP called TRPA1 or ANKTM1. TRPV’s and TRPM8 were already known, and they all have ankyrin repeats, so I don’t know why TRPA1 got the “A” for ankyrin.

Ankyrin is just one of thousands of known protein domains, meaning short sequences of amino acids that are known to have specific functions. Ankyrin is often found to mediate protein folding and protein-protein interactions, even though its own folding is a little out of the ordinary. Most proteins with ankyrin domains have about 4-6 repeats of the 33 amino acid sequence, but the parasite Giardia lamblia has a protein with 34 repeats.


This is a computer generated image based on ankyrin repeat
morphology. The different repeats are good for building a protein
interaction domain. The interesting thing is that although
most ankyrin repeats have this shape, they bind different
protein structures and induce different functions. Where's
the specificity? Good question - could win you a Nobel Prize.
As for the “1” in TRPA1, all I can say is that they must be anticipating the discovery of more TRPs of this type, although right now it stands alone. It’s kind of weird though, you don’t call a dad “Sr.” if there is no “Jr.” so why is there a TRPA1 if there are no other TRPA’s?

So, flies with broken painless(TRPA1) genes didn’t respond to pain; therefore, TRPA1 must be a gene that codes for a protein that confers a pain signal. This meshed well with the information from mammals showing that TRPA1 stimulated pain signals from some chemicals. But was this all?

This is where the controversy began and still continues. Some studies find that TRPA1 is a noxious chemical receptor, some say it's a noxious cold receptor. Some experiments show it to be both, a receptor for pain from cold and a receptor for pain from chemicals. And then there are those that show it to be a heat receptor! More on those studies in a couple of weeks – they’re cool… I mean hot!

Even within mammals, the results can sometimes be very different. Old studies suggested that TRPA1 was a noxious cold sensor (below 15˚C) in humans, but newer research (2013) shows that while TRPA1 does sense cold in rats and mice, it isn’t affected by cold in humans or monkeys. Many of the older reports suggesting that TRPA1 is a noxious cold sensor were based on studies in mice, so maybe they do act differently in humans.

The other possibility is that they don’t sense intense cold directly, but work with other TRPs to respond with pain when cold is sensed. A 2014 study showed that TRPA1 modulates TRPV1 activity. The two are often co-expressed on the same neurons, and they are also activated by many of the same chemicals. This study shows sensitization of TRPV1 by activation of TRPA1 – so maybe this is why your hands burn when you go out in to the cold for a long time.


Here is a cartoon comparison of TRPV1 and TRPA1. The parts
that go through the membrane (transmembrane domains)
look very similar, but you can see many differences
in the intracellular tails of each. Remember that TRPV1 and
TRPA1 bind many of the same chemical agonists, but look at
the difference in the ankyrin repeats and the other domains
of the tails, as well as the cytoplasmic sides of the TM
domains. These are where specificity occurs.
An earlier study (2012) also showed that activity from TRPV1-4 receptors could modulate the activity of TRPA1. Gentle warm temperatures could desensitize TRPA1 and therefore keep pain from being felt. Could this be one of the ways that warm compresses work against pain?

So, if TRPA1 modulates TRPV1 and vice versa for pain sensation, maybe TRPA1 works with TRPM8 to induce noxious cold pain. There have been papers that suggest TRPM8 does sense cold temperatures below 15˚C and when those cells are lost, mice have no aversion to painfully cold stimuli. It is probable that TRPA1 works with TRPM8 and TRPV1 to elicit pain to cold temperatures.

Maybe we could get some insights into the cold sensing of TRPA1 if we could find out if it participates in warming the body when it is cold. TRPV1 is a heat sensor and initiates cooling programs. TRPM8 sense cool and starts to warm the body – so what about TRPA1?

Well, it looks like we get no help there at all. Even in the species that are most likely to have noxious cold sensation via TRPA1 (rats and mice), the channel doesn’t look to be calling for warming responses. In fact, a 2014 study suggests that when TRPA1 ion channels are knocked out in mice, cold temperatures induced physiologic changes just as if the TRPA1 was there – TRPA1 was not a participant in inducing warming activities.


This cartoon gives you an idea of how TRPA1 can work with
other TRPs in order to increase pain or bring pain when other
signals alone might not. This example is with injury and
inflammation. Some things trigger TRPV1 but the activation
of TRPV1 can influence TRPA1 activity. This would sensitize
for more pain. Perhaps this is how pain is generated from
intense cold, even if TRPA1 doesn’t respond to cold on its
own. TRPM8 does respond to cold, so maybe it or TRPV1
are the triggers needed for TRPA1 to bring pain from cold.
In the same set up, blocking TRPM8 channels did result in a hypothermia (mouse bodies did not initiate a warming response to cold temperatures). So, the authors concluded that while TRPA1 does cause pain in response to cold, it doesn’t start or participate in a program to warm the mice.

Oh well, like we said at the beginning of the post, the more we know, the less we seem to know for sure. I think TRPA1 is probably involved in cold pain, even if it doesn’t sense it directly. But I can’t wait to see what they find out next.

What we do know is that TRPA1 is intimately involved with pain. Migraine headaches probably have a TRPA1 component. A 2013 paper summarized the evidence by saying that many migraine triggers are now known to be TRPA1 activators. Many of the endogenous stress activators of TRPA1, like oxidative damage, electrophilic stress, etc. also act to induce pain. Finally, many of the drugs and analgesics that work on migraines are being identified as TRPA1 antagonists.

Since it’s evident that TRPA1 doesn’t work in thermoregulation (see above), maybe we can use antagonists of TRPA1 as pain drugs without worrying about the hyperthermias and hypothermias associated with TRPV1 antagonists and TRPM8 antagonists. And wouldn’t you know it, a new antagonist for TRPA1 has just been discovered in a weird place.
           

Meet the Peruvian green velvet tarantula. It does have a
green hue on its legs and it is soft and velvety. But it isn’t
from Peru. It actually lives in northern Chile, south of the
Peruvian border. Its venom contains a TRPA1 antagonist,
but the problem is that even though it is not likely to bite
the hand that feeds it, it will fling urticating hairs at the
drop of a hat. This is important, as we discussed here.
The Peruvian green velvet tarantula (Thrixopelma puriens) has a peptide in its venom that is the first identified peptide (protein) TRPA1 antagonist. What’s it doing in venom? One of the purposes of venom is to cause pain – pain is a great teacher – enough pain and you won’t attack that spider again. But here is a potential pain killer in the venom, maybe the green velvet tarantula is trying to kill its prey, but doesn’t want to cause undue stress to its victim. Is that how evolution works?

One last tidbit about TRPA1 – it could save your life in the middle of the night. If you block mouse nasal activity of TRPA1, they won’t wake up in response to formalin, acrolein, or other noxious stimuli that should generate an avoidance response. Would a house fire be something you need to wake up from – you bet. Another recent study found that TRPA1 sensors in upper airway cells are important for sensing smoke from wood fires. Don’t hate the TRPA1 because it gives you pain – enjoy the pain – it’s keeping you safe.

Next week – prepare to throw TRPA1 a party; it’s saving your life in many more ways.



de Oliveira, C., Garami, A., Lehto, S., Pakai, E., Tekus, V., Pohoczky, K., Youngblood, B., Wang, W., Kort, M., Kym, P., Pinter, E., Gavva, N., & Romanovsky, A. (2014). Transient Receptor Potential Channel Ankyrin-1 Is Not a Cold Sensor for Autonomic Thermoregulation in Rodents Journal of Neuroscience, 34 (13), 4445-4452 DOI: 10.1523/JNEUROSCI.5387-13.2014

Spahn V, Stein C, & Zöllner C (2014). Modulation of transient receptor vanilloid 1 activity by transient receptor potential ankyrin 1. Molecular pharmacology, 85 (2), 335-44 PMID: 24275229

Benemei S, Fusi C, Trevisan G, & Geppetti P (2014). The TRPA1 channel in migraine mechanism and treatment. British journal of pharmacology, 171 (10), 2552-67 PMID: 24206166

Gui J, Liu B, Cao G, Lipchik AM, Perez M, Dekan Z, Mobli M, Daly NL, Alewood PF, Parker LL, King GF, Zhou Y, Jordt SE, & Nitabach MN (2014). A tarantula-venom peptide antagonizes the TRPA1 nociceptor ion channel by binding to the S1-S4 gating domain. Current biology : CB, 24 (5), 473-83 PMID: 24530065




For more information or classroom activities, see:

Albert Schweitzer –

Protein domains/motifs –

Pervian green velvet tarantula –





Getting High On Life

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Biology concepts – bacteria, climate, respiratory, birds, arthropods, astrobiology, clouds


Carl Sagan wasn’t just the host of the original Cosmoson TV.
He solved the riddles of Venus’ high temperature, the seasons
on Mars, and the color of Titan. He also wrote one of my
favorite speculative fiction novels, Contact. The movie is
good; the book is better.
The astrophysicist Carl Sagan said, “There are naive questions, tedious questions, ill-phrased questions, questions put after inadequate self-criticism. But every question is a cry to understand the world. There is no such thing as a dumb question.” A cry to understand the world – so keep asking the questions, even if they seem silly.

Today’s question might seem a little naive – Is there any life that could escape Earth?But I assure you, there’s more to it than you might think – and no, the answer isn’t an astronaut. Let’s put it another way - is there any living organism that could get high enough on its own to leave our atmosphere?

Well, I guess the first prerequisite for escaping our atmosphere would be an organism that could get really, really high. Some birds can fly at absurd altitudes.

The Ruppell’s Griffon Vulture (Gyps rueppellii) has the highest recorded flight. On November 29, 1975, a Ruppell’s vulture was sucked into the jet engine of a plane flying at 39,700 ft (12.1 km, Mt. Everest is 9.0 km) over the Ivory Coast in Africa. A unfortunate flight plan for the bird, but amazingly the plane landed safely after ingesting a bird with a 10-foot wingspan.


These two pictures are not at the same scale. The Ruppell’s
vulture on the left has a wing span of about 10 ft (3 m),
while the bar headed goose on the right (see the bars?) has
a span of about half that. They should not box one another,
it’s be a slaughter. But still, these are both much bigger than
most birds. Is their longer wing span part of their success at
high altitudes? Songbirds rarely fly above 2000 feet.
We don’t know how often the vultures venture that high, but the bar headed goose (Anser indicus) makes a habit of flying over Mt. Everest. This is a migratory bird that flies over the Himalayas twice a year, sustaining 8-hr flights at more than 28,000-29,000+ feet (8.8 km).

The real question is why birds would fly so high. As you ascend, the air becomes thinner; fewer molecules make the atmosphere less dense. Since bird flight is basically supported by the air, thinner air makes flying much more difficult.

Difficult flying means that more energy is required. Birds live right on the edge of oxygen debt all the time; flying is tough at any altitude. But high in the air, it becomes even harder and requires more energy. And what’s needed to make energy in the form of ATP – oxygen (see this post) – the very thing there is less of at high altitude.

The bar headed goose and his compatriot avians breaks some rules in order to become a high flier. Birds in general are better at oxygenating their muscles, because they can exchange oxygen for carbon dioxide on both their inhalation and their exhalation (this will be the focus of s series soon). But that isn’t all.

Birds can also pant better than mammals. Panting is way to get more oxygen to the muscles, but it comes at a cost - it brings blood vessel constriction in the brain (an attempt to prevent oxidative damage). This makes for poor control, focus and decision making. But birds can pant much longer and harder without constricting brain vessels, so they don’t make stupid decisions - birds aren't bird brained.

Bar headed geese go even further (a 2013 study). The blood vessels in their muscles penetrate deeper and are more extensive. This can supercharge their muscles with oxygen so they can make more ATP and flap more energetically. Finally, the hemoglobin (oxygen-carrying molecule) of bar headed goose red blood cells is slightly different than that of other birds. It grabs onto oxygen molecules easier and quicker, so it does a better job of transporting the maximum amount of oxygen to the muscles.

We humans may not want to flap at high altitudes, but we could learn a lot from the bar headed goose about maximizing oxygen utilization. That’s where we get most of our best ideas – we steal them from nature’s rule breakers.


Many species of spiders, mites, and small caterpillars use
kiting as a means of dispersal. Remember that these are
newborns, and are usually of the smaller species, so these
fellows are awfully small. That makes it possible for a breeze
to catch the silk they spin straight up into the air and carry
them off to new neighborhoods. This is thought to be one of
the primary ways arthropods colonize newly formed islands.
But we shouldn’t restrict our discussion to birds, there may be other things that get high (pun intended). The winds can help out. Some small arthropods disperse themselves as youngsters by ballooningwith silk. Spiderlings (newly hatched spiders) risk being eaten by siblings if they hang around after hatching, and too many spiders in one area makes it hard to find food, so they get as high as they can and then shoot out a strand of silk.

The wind picks up the youngsters and deposits them somewhere else. However, the wind sometimes doesn’t want to let them go. They've been know to travel into the jet stream, and have been noted living in weather balloons at more than 16,000 ft (4.9 km).

Bees too have been found on the slopes of Mt. Everest (5.6 km). A 2014 study says bees could theoretically fly at almost 30,000 ft.; they could look down at Mt. Everest if they chose to. The researchers reduced the density of air and the oxygen concentration to match what would be found on top of the world and the bees flew just fine. They compensated not by beating their wings faster, but by widening and lengthening their stroke. Pretty good for an organism that many mistakenly believe shouldn’t be able to fly at all. But just because they could fly at that altitude, doesn’t mean that they do.

For one thing, bees and other arthropods go dormant when temperatures dip into the 40’s ˚F (7-10˚C) they become immobile and if they stay that way, they die. Not a good candidate for escaping Earth, where the temperature approaches -40˚C as you travel through the clouds.


These are the major types of clouds and their average altitudes.
They carry dust, water, chemicals, and apparently a whole lot of
bacteria and fungi. The 2013 paper says the bacteria act as seeds
for cloud formation and can therefore affect the weather.
Powerful beings.
The clouds are up there, could they harbor life? They contain water; life needs water. There are several types of clouds and they sit at various altitudes based on type, topping out at about 13 km (8 mi). The highest clouds are at about the same altitude that the griffon vulture has been known to fly (see picture).

Do all clouds have a living lining? You betcha. A 2013 study has shown that the clouds are actually their own biological environment. Bacteria, some from the ground, some from the ocean, and perhaps some from the air, are living and dividing up in the clouds. The study sampled air at 10,000 feet and found that air over water, had more marine organisms, while air over land had more soil organisms. They also found that hurricane air had many more organisms, so they hypothesize that strong winds pull up more organisms into the upper atmosphere.

But wait you say, the vulture was at 39,000 feet, and these bacteria were only at 10,000 ft. Well, let’s go higher. A 2009 study from Indiashowed that microbes were living as high as 25 miles (41 km) in the stratosphere. This shames the vulture and he makes him feel inadequate. What’s more, the 2009 study found three strains of bacteria in the clouds that are not found on the surface of the Earth!


Meteorites are one way that life might travel from planet to
planet. The organisms would have to survive the jolt that
speeds them to escape speed (bacteria can), and they have to
survive the temperatures of reentry. Interestingly, studies
show that even though the surface of a meteor entering the
atmosphere is several thousand degrees, it feels like a warm
summer day just a few centimeters deeper.
Bacteria are particularly well suited for life in the atmosphere. There are bacteria that can withstand intense radiation, can live in extreme cold temperatures, and can live nearly without water. These sound like good candidates for something that could escape Earth altogether.

A 2012 draft genome of one of these bacteria, Janibacter hoylei, confirms that it is different from any organism found previously on Earth. These bugs might be living their entire existences in the upper reaches of the atmosphere.

But we could look at this from the other direction as well. Could J. hoylei have come from space and is just living in the clouds because it liked the first place it saw when it got here? Astrobiologists are excited to study these high altitude bacteria in terms of whether they could seed other planets or whether life could come here from other places.

The hiccup in all our hypothetical space entering organisms is something called escape speed. In order to leave Earth’s gravitational pull, an object on the ground must travel at 11.2 km/sec. The escape speed decreases as you travel away from the center of mass, but even at 9000 km, an object must travel at 7.1 km/sec. A bullet fired from a rifle travels at about 1.7 km/sec, so you get the idea. It ain’t easy to leave Earth behind, even if you happen to be rugged enough to survive space (as some bacteria and lichens can, see this post and this post).


The Earth’s magnetic field protects life on the planet from many
types of deadly radiation. Near the poles, the earth’s magnetic field
lines bend to pass through the center of the planet. It is here at the
poles that the radiation can interact with the field lines in a position
for us to see. These are the Northern and Southern Lights.
One theory holds that bacteria living in the high atmosphere could be affected by the magnetic field lines of the Earth and sort of ride along a magnetic railway. Tom Dehel, an electrical engineer for the FAA, proposed in 2006 that electromagnetic fluxes, like the solar flares and fields that produce the auroras in the northern and southern hemispheres, could provide charged bacteria with enough energy that they could escape Earth’s gravitational pull. Not one scientist I could find has signed on to this idea. But still, there are no silly hypotheses, they’re all just a cry for the truth.

Next week, another question with a more fascinating answer than you would expect - why is it so hard to catch or swat a fly?





Pawar SP, Dhotre DP, Shetty SA, Chowdhury SP, Chaudhari BL, & Shouche YS (2012). Genome sequence of Janibacter hoylei MTCC8307, isolated from the stratospheric air. Journal of bacteriology, 194 (23), 6629-30 PMID: 23144385
 
Dillon ME, & Dudley R (2014). Surpassing Mt. Everest: extreme flight performance of alpine bumble-bees. Biology letters, 10 (2) PMID: 24501268

Hawkes LA, Balachandran S, Batbayar N, Butler PJ, Chua B, Douglas DC, Frappell PB, Hou Y, Milsom WK, Newman SH, Prosser DJ, Sathiyaselvam P, Scott GR, Takekawa JY, Natsagdorj T, Wikelski M, Witt MJ, Yan B, & Bishop CM (2013). The paradox of extreme high-altitude migration in bar-headed geese Anser indicus. Proceedings. Biological sciences / The Royal Society, 280 (1750) PMID: 23118436

Because He Is The One

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Biology Concepts – ommatidia, reflex, fly, arthropod, sensory receptors, sensilla, metabolic rate, life span


Neo (Keanu Reeves) learned that he could dodge bullets
at one point in The Matrix. This was before he learned he
didn’t have to. Was he speeding himself up so the bullets
looked to be going slower, or was he actually slowing
down time?
Neo from the Matrixfilms had the ability, once he learned to accept it, to react so fast that everything around him seemed to be moving slowly. It made for cool cinema, but could it be real? It can seem so, athletes in “the zone” describe their situation as if everything else is moving slower and their task becomes much easier.

Let’s look at a case of this in nature. Today’s question – Why is it so hard to catch or swat a fly? The answer involves fighter jets, optical illusions, and yes, time manipulation.

Ever try to catch a fly? It ain’t easy. Even swatting them can be frustrating; most fly swatters have an area that is more than 350x bigger than the fly itself. It’s even hard to catch or hit them with your hand, and it’s as big or bigger than a fly swatter. We aren’t all as skilled as Pat Morita and his chopsticks in The Karate Kid.

One big reason that it’s hard to catch or swat a fly is because they know you’re coming. It’s not mental telepathy or a glimpse into the Matrix; it’s just that house flies (Musca domestica) and fruit flies (Drosophila melanogaster) as well as many other types of flies have sensory apparatus to let them know something big and powerful is coming at them.

First of all, look at their heads. They are almost all eyes. Each eye is not a single sensory organ, but is made up of 4000 individual ommatidia (omma = eye and tidium= small). Each ommatidium faces a slightly different direction, so all together, they give the fly a 360˚ field of vision. You can’t sneak up on them unless they’re asleep or dead.


The fly eye is a wonder to behold. Technology is using their
design (stealing really) to make smaller, cheaper magnifying
camera lens, to make better robotic eyes, solar panels, and to
reduce glass fogging on windows. The ommatidium on the
right is the basic unit. Fruit flies have about 800 in each eye,
house flies have about 4000.
Each ommatidium senses light changes or objects, so a large moving object (like a fly swatter) will be picked up by several thousand eyes and will alert the fly. The ommatidia aren’t particularly good at resolving objects, but the fact that there are so many of them makes the fly very good at detecting movement. So the fly flies away and you curse under your breath.

Even if you do swing at a distracted, contemplative, or sleeping fly with your rolled up newspaper, book, or hand – you’re still most likely to miss. Flies have sensilla (see this post) on their bodies that contain sensitive mechanoreceptors. The object moving toward them creates an air pressure wave that distorts the receptors. This sends a neural impulse through the giant fibers that make up much of the fly’s reflex arcs, and they immediately fly away.

This is why fly swatters are usually made of plastic or metal mesh. The little holes reduce the amount of air that the swatter pushes toward the fly, so that he's less likely to sense his coming doom. This is also one of the reasons it’s harder to hit them with your hand. Your hand is solid, so it pushes more air toward the fly. But also, the lever arm of the fly swatter (the long handle) creates a greater angular velocity, so it's traveling faster toward the fly than you could move your hand alone.


This is a weird illustration, but work with me. When a
band marches around a corner, they guys on the outside
part of the turn have to march much faster to stay in line.
Now, when swatting a fly, your hand is the guy on the
inside of the turn, and the tuba on the outside, running to
keep up, is the flyswatter. See why it’s easier to hit a
fly with a swatter – more speed.
The quick reaction due to visual or mechanical stimuli is even more amazing when you consider the tarsal reflex. Wing movements are inhibited when the fly is resting on your egg salad. It can't flap when its legs a resting on a surface. A startled fly has to overcome the tarsal reflex inhibition before it can fly away.

Interestingly, the reflex problem for the fly turns into a problem for you. To overcome the tarsal reflex, the mesothoracic (middle) legs push off and the fly jumps. Now it isn’t in contact with a surface and can therefore flap its wings. But the jump is always away from your impinging deathblow. Take a look at this video to see the jump. A 2008 paper showed that the fly plans the jump up to 200 milliseconds (0.002 sec) before its flight, so that it will jump directly away from the approaching object. He’s evading you even before he really starts trying.

Fruit flies and house flies can avoid most attempts at assassination just through these actions, but they have other tools at their disposal as well. For one thing, they can turn away from an approaching object and head off in another direction in only 0.03 seconds. The same group that conducted the 2008 study also showed in 2014 paper how a flying fly avoids visually perceived objects.


Count how few wing beats it takes for these flies to turn
almost 180 degrees –it’s about one and a half. In the top
right turn, you can see how they almost do a loop de
loop, and they all show the subtle changes in wing and
body position need to pull off the turn.
They saw that the fly can bank and turn all the way over or pull up and fly back over its own head in a flipping motion in order to change direction. They move their body, and they counter with subtle wing movements to reorient themselves within just 1.5 wing beats - and they beat their wings over 200 times a second. (see video)

And now we get to the relationship between flies and Neo (other than the observation that Mr. Anderson can fly). To a fly, we mere mortals seem to be moving slow motion. This phenomenon has to do with their metabolic rate.

It was observed long ago that bigger animals tend to live longer than smaller animals. It was also known that smaller animals had faster heart rates and faster metabolic rates (they make and used energy faster) than larger animals. This led to the rate of living (ROL) hypothesis of life span. The faster your metabolism, the shorter your lifespan. This hypothesis fell out of vogue as oversimplified, but has made a remarkable comeback in the last decade.

In fact, a 2011 study showed that people with slower heart rates and lower resting metabolic rates tend to live longer than people with faster resting metabolic rates. It seems that, “Live fast and die young,” is more than just a macho platitude.


Knock On Any Door was the book and movie that
introduced the phrase, “Live fast, die young, and leave a
good-looking corpse.” Bogart didn’t say the line; he was
the attorney for the kid who did. But “live fast, die young”
has been the title for two movies, three pop songs, and
biography of James Dean.
A 2013 study has taken this observation even further. Small animals with higher metabolic rates tend to process stimuli faster as well. They can sense, process, interpret, and react to a stimulus in the same amount of time a human needs to sense the snowball that is coming at his head.

It’s as if (not really) time moves slower for the smallest animals as compared to us. This is yet another reason that the fly is likely to escape the torment of reading your People magazine from very close up. Like Neo seeing the bullets in flight or the coming head butt from Agent Smith, flies sense and react on a completely different time scale.

This makes me feel better. Some mayflies live only 5 minutes as a flying adult (see this post), and house flies have a life span of about three weeks regardless of whether you hunt them or not, but this doesn’t have to be so sad. If time passes slower for them, then maybe their life is long enough. They might have time to fulfill all their dreams and learn about love, loss, and which wine goes with which meat. What’s important is not the years in their life, but the life in their years.



Muijres FT, Elzinga MJ, Melis JM, & Dickinson MH (2014). Flies evade looming targets by executing rapid visually directed banked turns. Science (New York, N.Y.), 344 (6180), 172-7 PMID: 24723606

Healy K, McNally L, Ruxton GD, Cooper N, & Jackson AL (2013). Metabolic rate and body size are linked with perception of temporal information. Animal behaviour, 86 (4), 685-696 PMID: 24109147

Jumpertz R, Hanson RL, Sievers ML, Bennett PH, Nelson RG, & Krakoff J (2011). Higher energy expenditure in humans predicts natural mortality. The Journal of clinical endocrinology and metabolism, 96 (6) PMID: 21450984



Let’s Chew The Fat

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Biology concepts – lipid, saturation, fruit, vegetable, drupe, berry, mesocarp, cotyledon, tuber, fatty acid, triglyceride


To try and get blood from a stone dates back to the 1600’s,
meaning to try and do the impossible. It was first used in a
book by Giovanni Toriano called The Second Alphabet. As far
as the turnip goes, it may relate to a story in the Bible of Cain
and Abel making sacrifices – one a vegetable and one an animal.
The vegetable sacrifice was not as appropriate since it could
not drip blood. Now we often use the phrase for the inability of
getting someone to pay money.
Did you ever hear or use the phrase, “You can’t get blood from a stone?” Sometimes the phrase goes, “You can’t squeeze blood from a turnip.” Item one - gross. Item two, where did the phrases come from? (see picture caption) Basically, they both mean the same thing. You can’t harvest something that wasn’t there to begin with. I use it with creditors – they can’t get money from me if I don’t have any.

You can’t harvest what isn’t there, so that leads to today’s question. If plants are low fat sources of nutrition, how can we use them for cooking oils? There’s corn oil, sunflower oil, cottonseed oil, canola oil, rapeseed oil, olive oil, even coconut oil. How can such low fat organisms provide us with so much fat?

Of course every cell has fats – there are the phospholipids in the cell membrane, and phytophormones made from lipids help the cells communicate and the plant respond to stimuli. Thylakoid membranes for photosynthesis have a lipid (MGDG) that normally doesn’t form a bilayer, but does in the thylakoid. Please refer to this post to show that lipids have a role in almost every cellular activity.

Unfortunately, we don’t get oil from the whole plant, just a little part of it. And even more amazing, the part we get oil from only exists for a short time in the plant’s yearly cycle. When we say vegetable oil, we really mean fruit oil.

The fruit is the part of the plant that grows from the flower after fertilization, including the seed(s). The vegetable is all the other parts of the plant, including the flower bud before it is fertilized. Now you know the true difference between fruits and vegetables.

The fat in plants is almost always associated with its attempt to reproduce itself. Part of the fruitmay be fatty, the seed of the fruit may be fatty, or even the germinating plant inside the fruit could be the source of the fat.


The upper image shows the different parts of the berry fruit
avocado. The mesocarp is the part we eat and contains the
fats. The same is true for the olives below. These have had
their seeds removed and replaced with a piece of pimento.
Maybe they thought we wouldn’t notice. No, they can’t grow
them with the pimento there already, but it might be
something Bill Blazejowski could work on, like his idea to
feed mayonnaise to the tuna in the 1982 movie, Nightshift.
Let’s start with the easiest – fruits that are high fat. The oldest is the most famous – olives. The fleshy part of the fruit, the part we eat, is called the mesocarp. In olives, up to 85% of the weight of the mesocarp is fat in the form of triglycerides. Olives have been grown for eating and pressing oil since about 6000 BCE. Olive cultivation predates written language and even teenage vampire movies.

Avocados are also pressed for oil. In locales where olives are harvested part of the year, avocados can be harvested year round, so many olive oil producer make avocado oil when the olives aren’t in season. Even though we use the mesocarp of each fruit for oil, the olive is a type of fruit called a drupe, while the avocado is actually a single-seeded berry. The avocado is just about the only berry from which we harvest edible oil.

In people with metabolic and liver function changes due to diabetes or other parts of a metabolic syndrome, it is known that the monounsaturated fatty acids in olive oil help to normalize many biochemical markers of liver function in people with metabolic syndrome. A 2014 study now expands that to avocado oil. It contains many monosaturated fatty acids, and the researchers found that it has similar positive effects on biochemical metabolic markers as compared to olive oil.

Oil palm (Elaeis guineensis or E. oleifera) fruit are also high in fat. The mesocarp is pressed to make palm oil that is used for eating and cooking, especially in Africa. The seed (kernel) can also be harvested for oil, and this is called palm kernel oil. The differences between the oil from the mesocarp and from the kernel lie in their color (the fruit oil is reddish while the kernel oil is colorless) and the percentage of saturated fats. The kernel oil is higher in saturated (no double bonds) fat.

These differences have an good side for us. Palm kernel oil esters have been shown to pass the blood brain barrier (BBB, see this post) better than other oil esters. So in a 2013 study, the palm kernel esters were combined with the antibiotic chloramphenicol. The resulting emulsion showed properties that could make it useful for treating bacterial meningitis, because more of the antibiotic could be carried across the BBB.


The mesocarp of the coconut is not edible. See the fibrous
stuff being cut away from the coconut? That’s the mesocarp,
or coir. It does have other uses though. You can make good
rope from it, or perhaps you would be more interested in some
biodegradable flower pots – all made with coir.
Another type of palm oil is also used in cooking. Coconut palm oil is pressed from the flaky coconut meat that makes german chocolate cake so irresistible. But the meat isn’t the mesocarp of the coconut fruit. You wouldn’t want to eat the mesocarp of a coconut; it’s the fibrous brown covering that has to be peeled away to get to the nut.
The coconut meat is the endosperm of the seed – the more it grows, the more of the liquid endosperm (coconut milk) turns solid. It turns solid because it is more saturated fat, and like most saturated fats it is more likely to be solid at room temperature. Coconut oil is sometimes used in place of butter.
Other “vegetable” oils come from different parts of the fruit. Sunflower oil uses the entire seed, including the embryonic plant, the endosperm and skin layers – outer (exocarp) and inner (endocarp).
Canola oil is pressed from the seeds of the canola plant. Canola is a plant bred from a type of rapeplant, a member of the mustard family. Therefore, there's a really no difference between rapeseed oil and canola oil. The name "canola" was thought up in the 1970’s, using “Can” from Canada, because that is where it was developed, and “ola” as a term for oil. The word “rape” didn’t seem to help sales.

The top cartoon shows how the cotyledons can have different
fates. The brown oval cotyledons can become the first leaves in
epigeal growth, or can stay below ground in hypogeal growth.
Either way, they help the germinating plant get a good start. The
peanuts below show the cotyledons, the big parts we eat, as well
as the germinating plant. The red arrows point to the peanut
nibs; they’re actually the plumule and radicle (stems and root) of
the embryonic plant.
Drupe fruits like olives seem to make good oil. Drupes also include plants like peanuts and soybeans. However, these are different than olives. The fat from most drupes and whole seeds are found in the embryonic leaves, called cotyledons. They often serve as the first leaves of the baby plant, but they also store fat and carbohydrates for the germinating plant.
It occurs to me that the examples above are equal and opposite. On one hand, the fat of peanuts, soybeans, sunflowers, rapeseeds, and coconut serve to nourish the embryonic plant. Fat is a great idea for this function because it stores a large amount of energy in a small volume. Carbohydrates require water for storage, so they take up more room.
On the other hand, the fat of avocados, palm oil fruits and olives are enticements to other animals to eat the fruit. Why do the fruits “want” to be eaten, anthropomorphism aside? The answer - to disperse the seeds held within or on the fruits.
New plants do better when they are far enough away from the parent plant that they will not have to compete with them for resources and sunlight, especially since they will be smaller and in the shade. This is why seeds need to be dispersed. Nourishment for itself or nourishment for a predatory animal, these are two completely different functions for the fat, but both are held in the fruit.


The corn kernel is the fruit of the maize plant. There is starch
(glucose chains), gluten (protein) and the germ, which is the
germinating plant with a single cotyledon. The bottom drawing
shows the difference in constituents of different varieties of corn.
Sweet corn has more sugar, while dent corn has a higher germ to
endosperm ratio.
Given the high enough fat contents of the plant components described above, it makes sense that we could use them for oils. But what’s one of the most common “vegetable” oils used for both cooking and biodiesel? I’ll give you a hint – you probably enjoy some of this fat at the movies.

Yes, corn it is, both as your popcorn and the margarine you slather all over it. We already know that corn is amazing (see this post), but only 10% of corn is fat (dry it and 20% is fat). The sweet corn you eat is a special hybrid that contains more endosperm and less fat, but dent corn is the one used for making oil and feeding livestock. The corn kernel is mostly starch and glucose, but the embryonic plant has the fat. This is called the corn germ and is the only part used to make oil. The germ contains the cotyledon (called a scuttelum for corn) that stores fat for the germinating plant (get it? Germ = germinating plant)

Look at the bottom picture to see how small the germ of the corn kernel is. Because of this, it takes 40 bushels of dried dent corn kernels (at 56 pounds/bushel) to make 500 ml (0.85 lb) of corn oil! It must be cheap to grow corn because that isn’t a very good ratio, yet corn oil isn’t that expensive.


Tiger nut sedge looks a lot like a grass and is considered a weed
in many places. It was cultivated as far backs as 3000 years ago
in Egypt and has been used in cooking for just as long. The tubers
on top left can be eaten as a root vegetable, and are high in
monounsaturated fats. The dried tubers (bottom) can be ground
into flour or used as a spice. However, we might just start to grow
them for biodiesel. I’d line up to buy a tiger nut fueled car – that’s
really putting a tiger in your tank! (a 1960’s Esso gasoline slogan)
Even though this is a summer post, there’s no reason we can’t talk about an exception. Today, it’s sedge oil. The tiger nut sedge (Cyperus esculentus) is being considered as a viable source for biodiesel, but it's used in African cooking as well. Sedge plants reproduce in several ways. They have fruits, but they aren’t significantly high in fat. They have rhizomes and well, but we’re interested in their tubers (serves the same function as a potato).

The tubers are fairly high fat, and they’re a heck of a lot larger than corn germ. On a per plant basis, sedge produce much more oil, which will make C. esculentus a cheaper source of fuel if farmed on a global scale. In truth, since sedge oil comes from a part of the plant other than the fruit, it’s the only true “vegetable” oil we talked about today. I wonder - could we get oil from a turnip? Maybe that’s the blood we should be looking for.

Next week, we'll start a series of posts on just how bacteria get around using flagella. Can flagella be used to prove the existence of a universal designer?



Carvajal-Zarrabal O, Nolasco-Hipolito C, Aguilar-Uscanga MG, Melo Santiesteban G, Hayward-Jones PM, & Barradas-Dermitz DM (2014). Effect of dietary intake of avocado oil and olive oil on biochemical markers of liver function in sucrose-fed rats. BioMed research international, 2014 PMID: 24860825
 
Musa SH, Basri M, Masoumi HR, Karjiban RA, Malek EA, Basri H, & Shamsuddin AF (2013). Formulation optimization of palm kernel oil esters nanoemulsion-loaded with chloramphenicol suitable for meningitis treatment. Colloids and surfaces. B, Biointerfaces, 112, 113-9 PMID: 23974000


Sneaking Up On A Snake

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Biology concepts – thermosensor, sight-hunters, snake hearing, mutation, TRPA1, pit vipers

We have been talking about taste sense for many weeks. I
remember a 1975 movie called, A Boy And His Dog, starring a
very young Don Johnson. It was a post-apocalyptic story of a
guy, his dog, and cannibalism. The best line of the movie? “Well,
she might not have had good taste, but she sure tasted good.”
Of course, this isn’t the kind of tastes we have been talking about.
We’ve come a long way since we started talking about taste sense. We have learned about how TRPV1 capsaicin receptors sense pain and heat. We have also learned that TRPV1 capsaicin receptors have cousins that sense cold - TRPM8 and TRPA1. They may generate pain, and they certainly help to warm us when we are cold.

We have even learned that in rare cases, the cold receptors can be heat sensors, like in chickens and insects where TRPA1 sense hot instead of cold. And this leads us to today’s exception. It’s time to talk about how these relatives of taste receptors help animals to become better hunters and to better sense their environment. Today let’s focus on snakes.

Snakes have a number of ways to catch prey (see this post). Some lie in wait, blending in with the jungle or background until a moving potential dinner catches their eye and moves across their path. Vision is their primary way of finding dinner. As a consequence, most sight-hunting snakes are diurnal (active in daylight).

Here is the southern black racer. You can see it has big eyes with
round pupils so lots of light can enter – it’s a sight hunter. Many
grow to be 5 ft. (1.5 m) long, so they can look intimidating. But
they are not venomous and will usually exit the seen if disturbed.
The non-venomous Southern black racer (Coluber constrictor priapus) is a sight-hunting snake of North and Central America. It’s called a racer because it is quick, reaching 4 mph (1.8 kph) in a very short time. Even though it is a constrictor, it typically doesn’t coil around the lizard, mole, or bird (I said they were quick) that it catches. It prefers to crush them into the ground to suffocate them. Sometimes nature can be a little rough around the edges.

Other snakes use the combination of scent and taste that we talked about a while back. The Jacobson organ (more scientifically called the vomeronasal organ, VNO) in their mouth can sense the molecules that the tongue pulls in from the air. Like it or not, every organism has molecules floating off of them continuously. Snakes' VNO can pick these up. See this post for more on the VNO.

Some snakes “hear” their prey coming. True, snakes don’t have an outer ear opening or the small bones that convert sound waves into mechanical waves in our middle ear (see this post for an explanation). But they do have a cochlea, the organ for sensing the vibrations and converting them to a nerve signal. Many snakes can sense the vibrations that their prey generate when they move through the environment using this cochlea and their lower jaw.

Similar to something called bone conduction hearing in animals with ears like ours, vibrations that travel through the bone can also cause movement in the hairs of the cochlea. As we discussed previously, the bending of the sensory hairs of the cochlea are transduced to chemico-electrical signals that travel to the hearing centers of the brain.

This is from a scientific paper showing the bone hearing of a python.
The red is the lower jawbone. The bark blue is the quadrate bone
and the green is the equivalent to our stapes bone of the middle
ear. The light blue is the inner ear space and the purple is where
the cochlea is housed. Vibrations go from red, to blue, to green to
light blue, to purple. You can see how sound waves would find it
tough to get to the cochlea.
A 2008 study showed that many snakes rest their jaw bones against the ground. The vibrations caused by moving animals are transferred from the ground to the bone, and from the bone to the buried cochlea. The sensation in the brain is a lot like muffled knocks, not unlike the bass that is turned up too loud in peoples’ cars.

This was followed by a 2012 study that showed pythons have very sensitive vibratory hearing, but poor sound pressure hearing. Almost all their hearing input comes from the vibrations they sense in the ground or tree, or whatever they happen to be lying on. So be on tip toes, that snake may hear you coming.

But how does any of this relate to a receptor for painful cold and controls mammalian breathing rate? Well, another way some snakes find their prey is by sensing the heat they give off – even from a few meters away.

Pit vipers are a subfamily of the Viperdae family, called Crotalinae.There are two types of vipers; all of them have hinged fangs, the ones that are folded up into the upper jaw when the mouth is closed, but protrude for striking as the mouth is opened. Pit vipers differ from true vipers in that they have pits (duh!); more about these below. True vipers live exclusively in Africa and tropical Europe and Asia.

In America, where I live, there are a lot of pit vipers. Cottonmouths, rattlesnakes (all 30 species), water moccasins, copperheads – these are all pit vipers. From southern Canada to Argentina, and from Eastern Europe to parts of Asia, pit vipers are not rare. Eyelash vipers (Bothriechis schlegelii) of South America are arboreal (live in the trees). They have bright coloring, but sit still and wait for their prey to happen by. They strike from above, so they scare the heck out of jungle hikers.

On the left is the eyelash viper. You can see it doesn’t mean business
because its hinged fangs aren’t extended. In the middle is the two-striped
forest pit viper. It is protecting it’s young, so the fangs are extended. On
the right is a sidewinder rattlesnake. Sidewinders are amazing and will
get their own post soon.
The amazing thing is that there aren’t any pit vipers or true vipers in Australia. The land of a million weird and painful deaths has nothing to offer in the way of hinged fang venomous snakes. I’m sure there’s a movement to import some.

But it’s specific part of the pit viper that we are interested in today – namely the pit. The pit organ is located between the eye and the nostril, on each side of the snake’s head. It is a hollow pit, so the actual business end of the pit organ is inside the snake’s skull.

The pit is lined with epithelium, but it also has a membrane that is stretched across the base. As a consequence of the location membrane, there are air pockets on each side of the membrane. The trigeminal nerve innervates the membrane and there are thermosensors in the cells of the membrane.

So, the pit organ is a thermosensor that helps them locate prey animals (or predators). But wait you say. Sure, pit vipers may use a thermosensitive ion channel to sense the heat given off by passing prey animals. But we just said they use a COLD sensing ion channel, TRPA1. What gives?

The pit on a pit viper is located between the nostril and the eye.
It would be easy to mistake the pit for the nostril. The cartoon
shows the pit anatomy. The air chamber helps cool the air
quickly and stops the TRPA1 receptors from firing again. This
is so the snake won’t get a residual image of something warm,
when the target may have moved in the interim period.
The explanation is two fold. 1) We said a couple of weeks ago that TRPA1 might sense painful cold on its own, or may work with other TRP’s to respond to very cold temperature. But whichever way it works, it is very similar to TRPV1 for heat sensing and TRPM8 for cold sensing. 2) Remember that in birds, lizards, and many insects, TRPA1 actually senses heat, not cold.

So maybe it’s not so terribly bizarre that pit vipers use TRPA1 to sense their prey. But before they touch it??? We eat chili peppers and we react to the capsaicin in our mouths and noses. We go out on a summer day, and the heat activates our TRPV receptors in skin and other tissues. We eat something cold (or menthol) and we feel the cold sensations it touches or tissues. But snakes feel the heat of their prey before they eat, from a distance away! There must be more at work.

And there is. The TRPA1 ion channels in the pit organs of pit vipers have a mutated version of TRPA1. Here’s how things work according to a 2010 study that identified TRPA1 as the heat sensor. The pit is a hole with a membrane stretched toward the back. Consequently, there is an air chamber on both sides of the membrane.  The membrane is highly vasculature and has the sensitive nerve endings with the TRPA1 channels.

The TRPA1 receptors are always firing, but at a low rate. Neutrally warm objects don’t change the firing rate, but warmer objects (as little as 0.001 ˚C warmer than background) will increase the firing rate. The receptor is mutated according to a 2011 study, with 11 amino acids of the pit TRPA1 divergent on only pit-containing snakes. These changes make the receptor so sensitive that it can react to infrared light signals (heat) from several feet away. That would be like our mouth burning over a chili pepper that we walked past in the supermarket.

Since the sensors are spread across the entire membrane, the effect on locating the source is sort of like vision or a pinhole camera. Light passes through the pupil and diverges before it hits the retina. This provides for a larger spread of the “image” across the membrane and allows for precise two-dimensional map of the target. The difference in heat between the target and the background gives a “picture” of the object that is warm.
The Taylor’s Cantil viper will play dead and then strike, but this
brings up an important point. DON’T get near a pit viper, even if
you are sure it’s dead. The pit is wired directly to the brain and
muscles. A dead snake, even one with a severed head, can still
strike as long as there is any residual neural electrical flow. People
die every year from snake bites from dead snakes.

The picture generated is also a little like hearing, since the heat will reach one pit earlier or more strongly. By comparing the timing and the strength of the signals from each pit, the distance and direction to the target can be detected by the brain (see this post for localization of sound waves).

Because the heat “picture” pit vipers pick up is based on the difference between the temperature of target and background, most pit vipers hunt when coolest, so temperature gradient between environment and prey is greatest. Prey will stick out the most.

Snakes can also use the pit more conventionally, as a thermosensor for its whole body. The basal rate of firing will tell the snake when to move to shade if it’s too warm or move to sun if it’s too cold. This is how it regulates its body temperature.

Pythons and boas can also have heat-sensing pits, but they are
5-10 times less sensitive because of their differing anatomy.
The amazing thing is that they evolved the same special power
independently from pit vipers, although they both use mutated
versions of TRPA1. The nostril has a black arrow and the pits
have red arrows.
The exception to today’s exception: some non-pit vipers have pits. In terms of evolution, pits evolved once in pit vipers, but they have sprung up several times in boas and pythons. These pits are less sophisticated (no membrane or air chambers), are less sensitive, and are located in different places.

Boas and pythons with pits have 3-4 simple pits in their upper lips. They don’t have the suspended membrane for sensing temperature, the TRPA1 sensors are housed within the epidermal cells at the back of the pit.

Next week – vampire bats and mosquitoes get into the mutated thermosensor act as well.



Christensen CB, Christensen-Dalsgaard J, Brandt C, & Madsen PT (2012). Hearing with an atympanic ear: good vibration and poor sound-pressure detection in the royal python, Python regius. The Journal of experimental biology, 215 (Pt 2), 331-42 PMID: 22189777

Gracheva EO, Ingolia NT, Kelly YM, Cordero-Morales JF, Hollopeter G, Chesler AT, Sánchez EE, Perez JC, Weissman JS, & Julius D (2010). Molecular basis of infrared detection by snakes. Nature, 464 (7291), 1006-11 PMID: 20228791

Geng J, Liang D, Jiang K, & Zhang P (2011). Molecular evolution of the infrared sensory gene TRPA1 in snakes and implications for functional studies. PloS one, 6 (12) PMID: 22163322



For more information or classroom activities, see:
Pit vipers –

Bone conduction hearing –

VNO (Jacobson organ) -

Bacteria Are Intelligent Designers

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Biology concepts – nature of science, flagella, intelligent design, irreducible complexity, motility, Gram+, Gram -, ion gradient

You don’t believe it now, but in the weeks ahead we’re going to discuss how bacterial motility, plant reproduction, intelligence, and the location of your heart are all related to whips and eyelashes. Sounds preposterous, but give me a few posts and a little leeway and you’ll be amazed.


Cheetahs can cover about 25 body lengths in a second, but
some Salmonella can move 60-80 of their own lengths in the
same time! See this post for finding out what the fastest
organisms are. Salmonella typhi is the bacterium that causes
typhoid fever and is spread in contaminated water or touch.
Mary Mallon was blamed for 51 cases of typhoid fever as a
carrier (no symptoms but still sheds bacteria). A 2013 study
shows that the bacteria turn on a fat regulator, PPAR-delta, in
macrophages which lets them live inside the cells forever.
Let’s get right to it. Bacteria are small, but they’re quick little devils. They have inboard motors – or are they outboard? – I can never keep those straight. This piece of machinery is so complex and fascinating that some people use it as a sign that someone or something had a hand in designing life on Earth.

The bacterial motor is called the flagellum, but it's so much more than just a way to get around, it’s often the means to saving their own lives. The word flagellum comes from the Latin word flagrum meaning whip, so you can see we are already starting to work on our challenge for these posts. Flagrum could also mean scourge, and this seems to be prophetic, since many flagella (the plural) we study have a hand in causing disease.

In typhoid fever, a potentially deadly disease that affects more than 20 million people each year, flagella are important not just for putting the bacterium, Salmonella enterica typhi, in the correct place to cause disease, but for attaching the bacterium to the gut wall and for invasion of the gut. A study in 1984 showed that even flagella that couldn’t move were still needed for S. typhi to produce disease. More about this in a couple of weeks.

A flagellum is very much like a boat propeller, it spins to produce force along its axis. This is possible because flagella aren’t perfectly straight. One of the main components of the flagellum is called the hook. This hook is located just outside the cell wall and lies in between the basal body and the filament. The basal body is the engine and is what attaches the flagellum to the cell, while the filament is the long whip like end that sticks out into the world.


A cartoon of the bacterial flagellum shows the structures,
filament, hook, and the entire lower part is the basal body
(motor). The filament is hollow and sends new flagellin
subunits up through it to be added on to the end. The electron
microscope image shows the basal body. It looks like art or
engineering.
The hook turns at about 90 degrees, but the degree of turn is different for different bacteria. This means that that filament, when spun by the motor in the basal body whips around in a circle, bigger at the bottom where the hook is located. So instead of rotating like a straight pencil and not generating any forward force, it spins like a propeller.

The basal body attaches the filament and hook to the cell, and is made up of several rings. In Gram+ bacteria there are two basal body rings that anchor the flagella apparatus, the M ring which attaches to the membrane and the P ring which is anchored in the peptidoglycan layer. In Gram- bacteria, the basal body is longer and has more rings since it must anchor the flagella into the LPS (the L ring) and the M ring has a buddy in the inner membrane called the S ring. All these rings support the rod, which is turned by the rotor and then spins the hook and the filament.

The filament is pretty cool. It’s either a left- or right-handed helix of subunits of a protein called flagellin. The filament is a prescribed length in each bacterium, but we aren’t exactly sure how the length is regulated. Scientists know that it grows faster at first and then slows down, but if broken it will start to grow again at the faster pace.


The filament of the bacterial flagella is capped by a small
protein called FLiD. This is an amazing protein that
regulates and mediates the assembly of the filament
subunits of flagellin at the tip of the growing filament.
The flagellin units are straight as they travel through the
middle of the filament, but their final shape is bent. The
FliD mediates this folding at the tip.
The amazing thing is that the filament grows from the tip, not the base where it attaches to the hook. The flagellin filament is hollow, and subunits of the protein travel from the cytoplasm up through the basal body and hook and then through the existing filament out to the end. Then they are attached to make the filament longer. That’s a pretty neat system because it alleviates the need for a way of exporting the parts, regulating their movement to the end of the filament and then attaching them. Sometimes, but only sometimes, evolution finds the simpler way to do something.

The energy for the motion of the flagellum comes from the movement of ions across the membrane of the cell. We have seen before how protons (or other ions) being pumped out and then allowed to enter through a pore can create the force needed to do work. That’s how ATP is made, how the neural action potential works, and how photosynthesis proceeds. But here, the proton motive force is used to spin the hook and the filament, driving the bacterium forward.

The flagella spin one way to move forward, but when they spin the other way, the bacterium just sort of tumbles around. We’ll talk more about this next time. We’re just now starting to learn how the motor can go from spinning counter clockwise (forward motion for a left handed filament) to spinning clockwise in no time whatsoever and without slowing down. Nothing looks very different in the basal body, the hook or the filament, but the direction of spin is reversed.


This is a complicated picture so stick with me. A) is the shape
of the FLiG protein from a certain bacterium. The end we are
interested in is red, it holds the charge for interacting with the
ion gradient across the membrane. B) shows the positive and
negative bubbles of charge in the helix. Below, see the ring of
FLiG proteins of the rotor. When spinning different directions,
the positive and negative bubbles are reversed, one shape
makes it go clockwise, the other, counterclockwise. It all has to
do with the pushing and pulling by same and opposite charges
as the ions pass through the membrane.
I can hear you thinking out there, “Well, just reverse the direction that the protons move, instead of outside to inside, go inside to outside.” Nope, when a flagellum switches direction, the protons keep moving the same direction. We do have information that one of the proteins that connect the motor (electrochemical gradient) to the physical turning (rotor), a protein called FLiG, can change shape.

Several studies have shown this change, and it is hypothesized that the change moves charged amino acids of FLiG around in relation to the cation gradient. By changing them, it changes the direction of the turning of the rotor (see the picture to the right). This might be akin to reversing the poles of a mag-lev train by flipping the electrical charge can make the train go the opposite direction.

Different bacteria have flagella that look similar but they have small differences. Nevertheless, it can be seen that this is a very complex machine for such a supposedly “primitive” domain of organisms. We have to remember that bacteria have been here the longest; they must be doing something right. There are over 40 genes that are required to build a flagellum, and they all fit together just so.

This complexity and order leads some people to declare that flagella couldn’t have evolved on their own. The concept is called irreducible complexity. People who support the idea of intelligent design (ID) say that some biologic components are so complex and have so many working parts that they could not arise through a series of mutations.

All the parts of a flagellum must be present for it to work (therefore they say it is irreducible) and must be assembled all at once which suggests it could not be random (complex in ID means improbably occurs by chance). Therefore, a flagellum could not have evolved over time and, ipso facto, it must have been designed as one unit by someone or something.

ID proponents haven’t always focused on the flagellum. They first talked of the blood coagulation cascade as irreducibly complex, but then it was shown that portions of the cascade were not necessary for function – whales don’t have factor XII and jawless fishes only use about half the proteins that vertebrates use. It was also shown how the cascade evolved over time.


A vibrio bacterium can make two different flagella types,
signified by the two sides of the dotted line above. The ions are
different that run the gradient, and the genes are different for
the motor/rotor. Are there two different irreducibly complex
flagella or did one modify into the other – then they aren’t
“complex.” Vibrio vulnificus is shown on the bottom. It has been
unusually numerous this summer (2014) and causes a disease
that looks like flesh eating disease, but isn’t.
Over the years, ID has proposed that the eye, the immune system, the flagellum and the eukaryotic cilia and its production system were irreducibly complex.  But each time, the ideas of specified, irreducible and complex (must have all come together at once) have been refuted for each example.

For the bacterial flagellum, arguments against ID include the facts that different bacteria use different systems, although they are all variations on a theme. One exception is the Vibrio. They use two different kinds of flagella on the same cells, each needing its own genes. Likewise some bacteria don’t use protons for the gradients, they use Na+ ions. The bacterium Vibrio parahemolyticus is an exception in both cases.

It uses a single flagellum at its end (polar) to swim in liquid water, but many flagella all around its cell when in something thicker. The polar flagellum uses Na+ ions to drive the rotor, while the lateral ones use protons. The genes are different for each flagellar type and mutations in one don’t hurt the other.


The top cartoon shows that when a gene duplicates (and they
do, often) one copy can drift and acquire mutations without
hurting the cell. This can lead to better function or new
function. Over generations, one set of genes for a function
can be replaced with another set – this would hardly be
called irreducibly complex. On the bottom, you see the type III
secretory system for injecting bacterial toxins on the left and
the flagellum on the right. They are very similar, so why is the
flagellum irreducibly complex and the not the type III system?
Lastly, only some Vibrio and other bacteria have a protein sheath over their flagellar filaments. These protein sheaths cover the filament and aid in sensing changes in chemicals outside the cell. So which flagellar type is irreducibly complex and which is not?

Spirochetes don’t even have flagella that protrude from the cell, they’re located between the inner and out membranes (endoflagella). This is a different system and again argues against irreducible complexity in flagella, unless different systems were designed differently. More about spirochete motion next week.

Please read more about ID and decide for yourself if it holds up to the tenets of science - that something that is true must be observable, repeatable, and able to be refuted if incorrect. Irreducible complexity is refutable, and has been for every example proffered by ID. But the conclusion that ID draws – that a designer must be involved, is a belief not a hypothesis – you can’t refute a belief, it doesn’t rely on observable evidence, therefore ID is not science. It doesn't make it wrong - it just makes it faith, not science.

Next week, let’s look at the different ways flagella help bacteria move, and some exceptions in bacterial motility.




Eisele NA, Ruby T, Jacobson A, Manzanillo PS, Cox JS, Lam L, Mukundan L, Chawla A, & Monack DM (2013). Salmonella require the fatty acid regulator PPARδ for the establishment of a metabolic environment essential for long-term persistence. Cell host & microbe, 14 (2), 171-82 PMID: 23954156

Lee LK, Ginsburg MA, Crovace C, Donohoe M, & Stock D (2010). Structure of the torque ring of the flagellar motor and the molecular basis for rotational switching. Nature, 466 (7309), 996-1000 PMID: 20676082

Minamino T, Imada K, Kinoshita M, Nakamura S, Morimoto YV, & Namba K (2011). Structural insight into the rotational switching mechanism of the bacterial flagellar motor. PLoS biology, 9 (5) PMID: 21572987

Carsiotis M, Weinstein DL, Karch H, Holder IA, & O'Brien AD (1984). Flagella of Salmonella typhimurium are a virulence factor in infected C57BL/6J mice. Infection and immunity, 46 (3), 814-8 PMID: 6389363




For more information or classroom activities, see:
Bacterial flagella –
   You must be careful to vet the source of material on flagella, much “science” is actually put out by Intelligent Design proponents, masking it as science.

Intelligent design –

Typhoid fever and Typhoid Mary –

Vibrio bacteria -




Bacteria Can Really Get Around

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Biology concepts – motility, microbiology, bacteria, evolution, gliding, twitching, flagella, pilus


The Giant Devil Ray, or mobula ray (Mobula mobular) can reach
18 ft. (5.4 m) wide. It’s not so much that they fly or glide, they
just breach the waves and look like they are trying to flap wings.
They were almost fished to extinction in the 1970’s. Their meat
was sold as scallops after they cut it out with a round cookie cutter!
How many different ways can humans move about? Walk, crawl, run, hop, swim, dance - you could say walk on hands or do the worm but I don’t think they count as normal modes of locomotion. Birds can fly, walk, or swim. Fish can swim and at least two think they can fly – flying fish and mobula rays. But the winners are……bacteria, again. They basically move forward, backward or turn, but they have several unique ways of accomplishing this.

The most common type of movement for bacteria is called run and tumble. Sounds a little like a toddler learning to walk; however, the bacteria aren’t falling down, it’s more like run and wander for them. The run is easy enough to explain; the flagella we talked about last week spin and the bacteria swims forward in its fluid environment like a little torpedo.

It’s not quitethat simple, but close. We explained last time that a flagellum is made of subunits of the flagellin protein and that these are joined together into a hollow helix. The helix is most often left-handed (as you rise, the curve moves to the left). So when these bacteria spin their flagella counterclockwise (looking from behind the flagellum), the helix is pressed tight together and spins efficiently – lots of forward movement. For those bacteria with right-handed helices in their flagella, a clockwise spin is for forward movement, but this is less common.

When the flagellum/flagella rotate the opposite direction, you might think they would go backwards, but not so much. Many bacteria have more than one flagellum and they work together when all spinning one for forward motion (more next week). They bundle together like the trailing hair of a girl who is swimming forward in a pool. But what happens when she stops or turns around quickly? Her hair ends up in a tangled mess and she has to brush it out of her eyes – that is unless she starts swimming again, then it trails behind in a bundle again.


The run of a bacterium uses flagella that are all rotating the same
direction and work together. The tumble occurs when the turn
differently and work against each other. On the bottom, the left
side shows a random path with runs and tumbles, but the right
shows how a bacterium can get closer to a food source when run
goes up gradient but every tumble is completely random.
This is similar to the flagellar movement, except that with bacteria the flagella are the source of the movement, not just passive followers. When they switch from forward direction spinning, the bundles fall apart and they each start pushing in a different direction. This is why the bacterium tumbles, it just jerks around turning in random directions.

For a bacterium with a single flagellum, the reversal of spin pushes the bacterium backwards, but then it runs into the flagellum and all efficiency is gone. In a motor boat, the propeller is fixed a certain distance from the back of the hull, so when it reverses direction, the movement may be less efficient, but the boat doesn’t run into its own propeller. But with a flagellum, the bacterium gets pulled right into the flagellum and movement is hampered severely. The tumble begins.

Tumbling is just a random turning based on the various places the flagella are inserted into the bacterial cell, the nature of the flow of the fluid the bacterium is in, and the efficiency of the movement. However, after a small tumble time, they will spin forward direction and the bacterium will take off running forward again, probably in a new direction. The purpose the run and tumble is to move toward something good (source of food) or away from something bad (predator or chemical). More on this in a couple of weeks.

Of course, there are exceptions. Some marine bacteria (those that swim in salt water) have one flagellum and can reverse direction by rotating their flagellum the opposite direction. This works for a while and actually works better for reversing motion than having several flagella would. However, a new study shows that they don’t reverse for long, they quickly execute a trick called a flick. Their flagellum flicks in one direction, turning them so that when they run again, it will be in a new direction.

The researcher’s paper shows that this "reverse and flick" is a very efficient way of turning. Some of these bacteria can move up gradients toward food faster than bacteria that use the run and tumble method. "Reverse and flick" is a good strategy, just like the “bend and snap maneuver from the movie Legally Blonde.


The axial filaments of spirochetes are really several flagella
that lie in a ribbon. They work together to rotate under the
“skin” of a bacterium, which causes a helical wave that
propels the organism along. Scientists didn’t have this
mechanism for a long time because when they prepared
bacteria for electron micrograph, the flagella would pile up
on one another and the coordinated rotation hypothesis just
wouldn’t work that way. It was a preparation artifact that s
topped our learning for a couple of decades.
Spirochete bacteria use flagella to move as well, but they use them differently. We talked about this a bit last week. Spirochetes have internal flagella (called endoflagella) that run the length of their corkscrew shape in their periplasm (between inner and outer membranes).

According to a 2005 paper, these 7-11 flagella lie in a ribbon that wraps around the cell body. By rotating counterclockwise, the flagella put a torque into the cell body that makes it spin the opposite direction, this drives the spirochete forward. See the image to the right and this movie to get a better picture.

If most bacteria use flagella to move, you just know that some have to be finding a different way. Twitchingis a kind of bacterial motility that doesn’t need flagella at all. Even though I could probably come up with several movie references for twitching, I will refrain. Twitching makes use of small appendages that project from bacteria cells called pili (pilus is the singular, it comes from Latin for hair). We have talked about them before in terms of trading DNA back and forth in lateral gene transfer, but here that are used to move the bacteria along.

Pseudomonas aerguinosa bacteria are famous for twitching, but a surface has to be involved, it isn’t possible in a liquid medium only. The proteins in type IV pili are coiled like a slinky. They stretch out, attach to a surface, and then retract forcefully. This jerks the bacterium forward. This was discovered in the very late 1990’s, but they didn’t know how they turned until 2011.


Have you ever had a twitch in your eyelid? You swear everyone
can see it. It occurs because of a spasm in the palpebral
portion of the occularis occuli muscle. That short fast
movement looks a little like the twitch of bacteria, except
they do it by snapping back a pilus instead of contracting
a muscle.
A 2011 PNAS paper showed that they slingshot themselves. Some pili stretch out and attach. Others stretch out in another direction and then instead of retracting to pull the bacterium in that direction, they release at the tip. This shoots the organism in the other direction. It’s the moral equivalent of a tumble, just not using flagella.

Another kind of surface motility is called gliding. This type of motion is more of a mystery than twitching ever was. There’s more than one way to glide. The first example of gliding can really be considered elegant twitching. It uses type IV pili that stretch out and then retract, but it is much smoother than the jerky movement created when twitching.

Another type of gliding is used by some cytophagia (cell-eating) and flavobacterial organisms. This movement might work a little like a conveyor belt, where proteins attach to the surface and then move along the cell’s surface from front to back. As the proteins are moved backwards, the cell moves forward. Many show a helical track along the surface of the bacterium, so that as the proteins dislocate toward the back, the cell goes both forward and rotates around its long axis – efficient, but they may get dizzy. A 2014 minireview paper shows that very different bacteria use the same mechanism, but the proteins and force for motility are different.


Slimer from Ghostbusters left slime where he had been, but I don’t
know that he used it to push him along – he flew. Bacteria that use
slime have to be on a surface. Is it just me, or does Slimer look a lot
like the snot monsters from the Mucinex commercials? Bacterial
slime is a little like snot, but is made of most sugars, not mucin proteins.
In a third form of gliding, the bacterium produces a slime that it then travels over, sort of like a snail or slug, maybe more like Slimer in Ghostbusters. In this form of gliding on a surface, a mix of polysaccharides is secreted from pores in the cell wall and membranes of the bacterium. The force of the release in one direction pushes the cell in the other direction. Think of it as very slow motion rocket propulsion.

Finally, one of the fastest bacteria on surfaces is called Mycoplasma mobile. It may use a mechanism of motility previously unseen and evolutionarily stunning. A 2005 paper showed that if you lyse the M. mobile with a detergent, but provide the resulting fragments with the proper ions, they will still move along a surface. This suggested that the mechanism was ion gradient driven and confined to the membrane.

More recent studies (here and here) suggest that the protein mechanism in the membrane might look very similar to the cytoskeleton of a eukaryotic cell. This would be either an evidence of an endosymbiotic origin of the cytoskeleton or that very different organisms had the same great idea, called convergent evolution. Either way, it’s cool.


Myxococcus gets around. When alone, he forms a slime trail
that actually pushes him forward. When he is with his buds,
he might push out pili and retract them to pull himself
forward, he might use a conveyor belt system to spin himself
along, or he might use both. The signals that control which
he uses still need to be worked out – anyone out there
feel up to that task?
All these mechanisms just go to prove that bacteria have more ways of moving than we could ever dream up on our own. They have propellers, finger proteins to pull them along, conveyor belts, cytoskeletons, and even snot rockets. It must be important to get from on place to another if they have developed so many mechanisms. Some even combine their modes of transportation.

Several strains of bacteria together known as Myxococcus use different types of gliding at different times. When M. xanthus is with other bacteria of his kind, they move using something called social gliding, which is of the conveyor belt type OR the elegant twitching type. But when he’s alone, he performs adventurous gliding, which uses slime extrusion. Humans call this social climbing, but sliminess is certainly involved in both.

Speaking of social motility - bacteria working with other bacteria; this just happens to be our topic for next week.



Balish MF (2014). Giant steps toward understanding a mycoplasma gliding motor. Trends in microbiology, 22 (8), 429-31 PMID: 24986074

Kinosita Y, Nakane D, Sugawa M, Masaike T, Mizutani K, Miyata M, & Nishizaka T (2014). Unitary step of gliding machinery in Mycoplasma mobile. Proceedings of the National Academy of Sciences of the United States of America, 111 (23), 8601-6 PMID: 24912194

Jin F, Conrad JC, Gibiansky ML, & Wong GC (2011). Bacteria use type-IV pili to slingshot on surfaces. Proceedings of the National Academy of Sciences of the United States of America, 108 (31), 12617-22 PMID: 21768344

Stocker R (2011). Reverse and flick: Hybrid locomotion in bacteria. Proceedings of the National Academy of Sciences of the United States of America, 108 (7), 2635-6 PMID: 21289282



For more information or classroom activities, see:

A great site from Harvard University with movies of many types of bacterial motility:
http://www.rowland.harvard.edu/labs/bacteria/movies/

Bacterial motility -

Run and tumble –

Pili –

Gliding –
http://www.molecularmovies.com/showcase/

Should I Stay Or Should I Go

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Biology concepts – bacteria, motility, flagella, quorum sensing, bacterial swarming, biofilms, pathogenesis


Nomads are wanderers. They come in different flavors.
Hunter-gatherers follow the animals as they graze in
different places. Pastoral nomads have animal herds and
move them around to where the grazing is best. But the
interesting ones are the peripatetic nomads. These are
people that move around within cities and other
populated areas, often to sell services or trades. Romanis,
or gypsies as they are sometimes called, are a
group of peripatetic nomads.
We humans have complex interactive behaviors with one another - these can make things better or, oh so much worse. We form herds as nomadic tribes, or we settle to form cities. Each has its own set of niches and behaviors that must be fulfilled by members of the group. But, it's important that we realize that we aren’t doing anything new, apparently bacteria have been roaming and settling for billions of years.

Our current series has been talking about flagella and how they help bacteria become motile (amongst other things). A relatively new discovery has opened our eyes to an exceptional movement by flagellated bacteria, swarming.

Swimming is when a bacterium on a liquid/surface interface or in liquid moves around by itself using its flagella as a propeller. But groups of bacteria can use their flagella to create a swarm; a mass of bacteria moving as one unit, often faster than the individuals can move on their own.

Bacteria moving as a unit is like tribes of humans moving from one place to another. But there are also those bacteria that choose to hunker down in one location and build a “city.” This prokaryotic Gotham is called a biofilm. We should do a whole series on biofilms, but for now let’s just talk about them in general.

When a number of bacteria of the same type, or sometimes even of different types, are in the same place at the same time, they may begin to form a biofilm. Certain bacteria will secrete proteins as filaments, polysaccharides in the form of slime, and some other structures. All of these together form a network of tunnels, tubules, cavities, and surfaces onto which the bacteria adhere. The biofilm also adheres to whatever surface is nearby. It’s a bacterial city.


The plaque on your teeth is a biofilm. The saliva and
crevicular fluid (between root and gum) provides some
proteins and sugars to build the film. Above is a
photomicrograph of plaque showing that yeast and
bacteria are both involved in mature plaque.
The biofilm matures over time, and different bacteria will have different jobs. The bacteria are stronger together than they are on their own, since the biofilm can prevent antibacterial agents from working. Biofilms are turning out to be important virulence factors (structures that enhance an organism’s ability to cause disease) and are crucial for pathogenesis (patho = disease, and genesis= beginning or course).

Some bacterial colonies settle to form cities and some move on en masse to another location – it really does sound like humans tribes. But biofilms and swarming are not mutually exclusive, in some cases you will see the bacteria at the edge of a biofilm start to swarm and expand, just like urban sprawl creates bigger cities.

There's organization to the swarm as well. Swarming isn’t an, “Everybody run!” kind of movement. Swarming requires controls, regulation, and numerous gene products spread out over the colony. Even though they work as a group, the bacteria might not all go the same direction.

Since bacteria divide by binary fission (one form of asexual reproduction), they tend to form masses in one location, often circular. When they give the signal(s) to swarm, some may take off in this direction, and some in another, based on where they are in the circle. Look at the picture below and right. Pretty, but it shows that colony swarm has multiple leading edges that will travel out into the unknown, and part of the colony will follow behind each.

Every once in a while, a new leading edge might branch off and swarm in a different direction, taking some followers with it. Other types of bacteria seem to swarm equally in all directions, forming concentric circles of new colonies.


This is a false color image showing the branching of a
bacteria colony in a swarm. Dr. Eshel Ben-Jacob from
Tel Aviv University produces these images as science
and art. See many of his images at this site.
The disease-causing bacteria Pseudomonas aeruginosa branches when it swarms, but even this is coordinated. A 2014 paper used a computer to model the branches seen in P. aeruginosa. They occur over a very narrow range of parameters. This means that the bacteria are limiting their activities and conducting themselves within a finely adapted range of behaviors and signals. Bottom line - their movement isn’t random.

Many behaviors occur in swarming bacteria that don’t occur in swimming bacteria. The leading edge cells may secrete surfactant, a combination of chemicals that reduce the surface tension on the plane so that the bacteria can move with less resistance.

The leading edge bacteria grow extra flagella, become elongated, and secrete slime for easy movement - but only the leading edge cells. They band together, becoming like rafts; in fact that’s what they’re called, rafts. The movement of the leading edge plows a furrow in the material they're moving across. This is partly due to the leading edge cells, but it has more to do with the cells behind them. The following cells form roiling masses, and together they push the leading edge along, like pushing a plow to form a ditch for planting seeds.

The furrows are then followed and expanded by the cells behind the leading edge, growing larger and easier to follow. That way, they can push the leading edge better. All these changes and functions lead to faster movement, which is why the swarm can move faster than individuals.

One amazing thing discovered in a 2013 series of experiments was that the leading edge cells secrete DNA. This nucleic acid doesn’t function as genetic material, but is apparently important for keeping the leading edge cells together and moving in the same direction, as well as stimulating movement at all. In experiments where this DNA was chewed by enzymes, the swarming movement stopped completely. Amazing - if they were a marching band in a parade, the DNA would be the banner carried by the drum majors that's emblazoned with their school and nickname. Everybody follows the banner and the drum major.

Integral to the concepts of swarming and biofilm development is the idea of multicellularity in bacteria. They're all clones of one another (except for mutation and any lateral gene transfer), but they work together and may take on different jobs, structures, and morphologies. They are working together to accomplish more than they could on their own. That sounds a lot like a multicellular organism where the different cell specialize into different types in order to perform different functions.


On the left is a cartoon that illustrates how the electron
donor hydrogen sulfide can’t donate electrons unless
something is available to accept them. The oxygen is the
acceptor, and the bacteria provide the cable to connect
them. The filaments of bacteria are shown on the right.
Photocredit to Nils Risgaard-Petersen.
One example comes from a 2012 study. Sea floor bacteria that bridge an area of high oxygen and low hydrogen sulfide to one of low oxygen and high hydrogen sulfide actually form filaments that act as power cables. Electron pass long a length of millions of cells to complete a circuit between the two sets of cells and this provides the energy to make ATP. Bacteria seem to work together in tough environments better than humans do on our best day.

We don’t know all the bacteria that are capable of swarming, but it's probably many more than we have found so far. And we aren't sure just why do they do it. Perhaps it's to leave an area of poor food value behind and strike out for better hunting grounds. Moving faster than they would as individuals might be important when trying to find, and then take advantage of a new food source. Eat up before someone else finds it.

Perhaps swarming is for protection. Like for biofilms, there is evidence that bacteria are less susceptible to antibiotics when swarming. Or it may have something to do with the best way to achieve full biochemical development. There are many studies that suggest that infectious organisms must swarm in order to create disease. Please remember, they aren’t trying to cause disease, but it shows that swarming must be important in their colonial development and a byproduct of this may be disease.


Three colonies of the same bacteria that were not clonal (not
from same exact ancestor - A, B, and C) were grown on the same
plate and they expanded in a swarm-like behavior. Where the
different colonies meet is the Dienes line. On the right is a false
color close up of a Dienes line, showing the battlefield. The
black line is 50 µm long.
They may also swarm to protect a new environment. Bacteria from one colony that grow and begin to swarm can tell their brethren apart. They can even discriminate between bacteria of the same type that have come from separate colony. When the two colonies swarm, they set a boundary between them, called a Dienes Line. A 2013 study showed that in Proteus mirabilis, a bacterium that causes urinary tract infections (UTIs), this boundary is really a battleground.

P. mirabilis has the ability to produce a type VI secretion system that acts as a needle. It punctures an adjacent bacterium and injects toxins. When a swarming colony invades another colony, they all start to produce their type VI secretion needles.

They attack any cell that makes contact with them, in a preemptive sort of fashion. There are many friendly fire incidents, but kin will survive the attack while cells from the other colony will be killed (they aren't immune to the specific toxin). The deeper invader is usually the dominant colony and will kill off the other colony, even though they may be of the same strain. Man - bacteria can be ruthless.

The key to both biofilm development and swarming is quorum sensing (quorum is from Latin qui meaning who, it means the number of members that must be present to transact business). The bacteria sense when their numbers reach a certain tipping point because the levels of certain chemicals reach critical concentrations.

We aren’t sure just why one behavior happens instead of the other, the situations that will induce either biofilm formation or swarming, but the number of bacteria and the state of their environment is key. Therefore, if you can stop the quorum sensing, you can stop swarming or biofilm formation, or both. This would be key to battling some pretty nasty infectious organisms since we said they are often important for pathogenesis.


Proteus mirabilis is a bacteria that swarms in concentric
circles. It causes urinary tract infections in both men and
women. In the lower image you can see the many flagella
of the organism – and this is before it starts to swarm and
leading edge organisms differentiate.
Several recent studies (here and here for example) have shown that certain natural or man made chemicals have the ability to interrupt quorum sensing or swarming/biofilms. Even cranberries seem to do the job.

We have discussed in prior posts about the amazing ability of cranberry to prevent UTIs. A 2013 paper shows that at least part of the cranberry's action on UTI-causing P. mirabilis is through the prevention of swarmer cell differentiation. Work with other bacteria shows that it is quorum sensing that is disrupted by the cranberry compounds, so the swarm in P. mirabilis might be stopped via the bacteria not knowing how many of their brothers are around. Bacteria won't pick a fight unless they know their gang is big enough - it's West Side Story in your bladder.

Next week - some prokaryotes don't move. Just like couch potatoes, they wait for someone to bring them their dinner.



Gloag ES, Turnbull L, Huang A, Vallotton P, Wang H, Nolan LM, Mililli L, Hunt C, Lu J, Osvath SR, Monahan LG, Cavaliere R, Charles IG, Wand MP, Gee ML, Prabhakar R, & Whitchurch CB (2013). Self-organization of bacterial biofilms is facilitated by extracellular DNA. Proceedings of the National Academy of Sciences of the United States of America, 110 (28), 11541-6 PMID: 23798445

Deng P, de Vargas Roditi L, van Ditmarsch D, & Xavier JB (2014). The ecological basis of morphogenesis: branching patterns in swarming colonies of bacteria. New journal of physics, 16, 15006-15006 PMID: 24587694

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

Alteri CJ, Himpsl SD, Pickens SR, Lindner JR, Zora JS, Miller JE, Arno PD, Straight SW, & Mobley HL (2013). Multicellular bacteria deploy the type VI secretion system to preemptively strike neighboring cells. PLoS pathogens, 9 (9) PMID: 24039579


For more information or classroom activities, see:

Quorum sensing –

Biofilms –

Bacterial swarming -



Chase The Good, Evade The Bad

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Biology concepts – motility, flagella, bacteria, chemotaxis, magnetotactic, monotrichous, amphitrichous, lophotrichous, peritrichous, run and tumble, coccus


The Princess Bride had everything – good guys, bad guys,
rodents of unusual size, ex-professional wrestlers. Vizzini
was supposed to be brilliant, so why didn’t he cure his own
speech impediment? Inconceivable!
Proximity is a good relative indicator of danger or benefit. As Vizzini said to Wesley in The Princess Bride, “As a student you must have learned that man is mortal and you would therefore put the poison as far from you as possible.” We tend to move toward things we need or want, and away from those things that could harm us – except for doughnuts of course.

A couple of weeks ago we started to talk about flagellar movement and the how a bacterium will “run” up a positive gradient or “down” a negative gradient. More detail will show us how amazing this chemotaxis (chemo = chemical, and taxis= arrangement) is.

The “run” in run and tumble movement is in a particular direction, while the tumble is a mess, just turning randomly before the run continues in another direction. What directs a run or a tumble? Well, they’re either running toward or running away from something.

There are receptor proteins on the surface of bacteria that sense different things. Some sense food; if food is to the left, receptors on the left will start to pick up more signals. As long the concentration keeps going up, the cell is directed to continue a run (positive chemotaxis). If the concentration starts to decrease (less signal for receptors), then a tumble is in order.

Random walking by run and tumble in bacteria.
Since the tumble is a random turn, the result doesn’t necessarily turn the bacterium toward food. If the concentration doesn’t start to increase as the next run starts, another tumble will commence and maybe then the organism will be faced the right direction (see animation). This works for twitches, glides, and rolls as well, and is particularly effective even if part of it is random.

Chemotaxis works the other direction as well. If a negative chemical is sensed, such as a predator or toxin, a run will continue as long as the concentration of the chemical keeps going down (negative chemotaxis). If the concentration stays the same or increases, a tumble will hopefullyreorient the direction of movement down the gradient.

Remember that the movements for runs and tumbles are controlled by the flagella.  Not surprisingly, there are several different flagellar possibilities. Having one flagella is called monotrichous (mono = one, and trichous = hair), it’s usually at the long end of a bacterium.


A new paper has started to describe the symbiotic relationship
between the bobtail squid and Vibrio fischeri. The bacterium is
bioluminescent, and lights up the squid when it is in the
moonlight so it doesn’t cast a shadow from below (predators
would find it that way). It turns out that flagella of the bacteria
give off LPS a toxin, and the concentration tells the squid when
to alter the biochemistry of its light organ to accommodate the
needs of the bacteria. They work together to keep them both alive.
For example, many Vibrio organisms are monotrichous. They have one flagellum located on one end of their cell body, and it propels tem forward or in a tumble. One organism, Vibrio cholerae, is especially important to humans as it causes the disease cholera. This organism has a sheathed flagella (cell membrane covers the flagellin protein polymer on the outside). It has been hard to study this since unsheathed mutants are nonfunctional. See the caption at right for more.

Lophotrichous bacteria (lopho = crested or tufted) have tufts of multiple flagella at one (polar lophotrichous) or both ends of the organism. Spirillum volutans is lophotrichous - but not always. When it divides, each of the progeny has just one tuft of flagella, since each daughter gets one end of the parent. As they grow longer and older, they develop the second tuft of flagella at the opposite end.
           

S. volutans was first described in 1900's. The unusually large
flagella made them visible by light microscopy, the only type they
had at the time. Most other flagella had to wait for electron
microscopy to be discovered. S. volutans is a spirillum, shaped sort
of like a spirochete, and the flagella make the body spin in the
opposite direction, just like the spirochetes. But the spirochete has
the flagella on the inside, and the spirillum has them on the outside.
I wonder if one evolved from the other.
The question then is how S. volutans regulates movement with a tuft at each end. An older study showed that there is a head type tuft and a tail tuft in terms of sensing chemicals. When the tufts reverse their rotation, the tail tuft becomes the head tuft. There are chemicals that can make each tuft rotate as the head, and then the organism doesn’t go anywhere. This could become important for stopping disease development.

If a bacterium has one flagellum at each end it is considered amphitrichous (amphi = both). A good example is Campylobacter jejuni, the causative organism of the most common type of gastroenteritis (diarrhea). C. jejuni causes more disease each year than Shigella and salmonella combined, about 3 million cases – mostly from poorly cooked chicken.
           
A 2014 study on C. jejuni flagella show that it has necessary genes that are not found in other types of bacteria. Campylobacter flagella are some of the most complex and the motility they control is very important for pathogenesis. This flagellar system is just another example of how flagella can’t be seen as evidence for intelligent design.
           
Peritrichous (peri = around) bacteria are hippies. They have flagella that stick out in all directions; no sense of order or grooming. The quintessential peritrichous organism is E. coli. All the flagella turn the same direction in a run, but when just one or a few switch direction, they start a tumble. Since these organisms sense chemicals from all directions, they switch from runs to tumbles quicker and more often. As a result, peritrichous organisms are often faster in both + and – chemotaxis.


Selenomonad bacteria are bean shaped, with a long axis. But their
tuft of flagella is located on the long side, not on an end. So why
do they travel along their long axis? It might have something to
do with the degree of turn in their hook, or the curve of the
bacterial cell.
Notice that we've been talking about bacteria that have a long axis and a short axis. Their flagella are usually on their end(s). But there are exceptions. Selenomonad bacteria are polar lophotrichous, but the flagella aren’t on a long end. It’s weird, because they still move along their long axis. You need to figure out how they do that.

And what about the cocci? A coccus type microorganism is round (coccus= berry in Greek). Most cocci are immotile, they get moved around instead of moving around. But it hasn’t hurt them, as cocci are found everywhere the other shaped bacteria are found.

Being round may have something to do with their immotility. Round objects aren’t best designed for movement in a single direction. Think about it, almost all animals are motile (except some sponges and the Tribbles on Star Trek), but have you ever seen a spherical animal?

Things that are longer than wide are usually best equipped for linear movement. And if you aren’t going to move linearly (up or down a gradient), what’s the point of moving at all? Therefore, most cocci are flagella-less. Fortunately for us, there are exceptions to the exceptions. Some cocci do have flagella and are motile. Often, the flagellated cocci are polar lophotrichous - like a bald guy with a ponytail.

I was surprised to find that the term “coccus” doesn’t just apply to bacteria, archaea can be coccal as well. This may not seem like a big deal, but remember that archaea and bacteria are as divergent from one another as we are from bacteria. The point is that “coccus” is just a description of a shape, it doesn’t have to mean bacteria. Coccolithophores are eukaryotic phytopklankton, and the genus “coccus” plants are berry-forming vines or shrubs.


On the top is an electron microscopic image of the magnetosome
chain inside a magnetotactic bacterium. See how they line up along
a field line? The bottom cartoon is one hypothesis of why they
developed this skill. Perhaps they can find the right concentration of
oxygen to sulfur by traveling just along the field line, not in three
dimensions. This is sort of like the electrical cable bacteria we talked
about last week.
Pyrococcus furiosus (rushing fireball) is a lophotrichous archaea with up to 50 flagella. They swim very fast when in their optimum temperature water, around 100˚C, hence their name. A 2006 paper showed that the flagella aren’t just for swimming, but also for cell-cell adhesion and adhering to surfaces, but more about this in the future.

In terms of the flagellated cocci, the most interesting exceptions are the magnetotactic cocci. Magnetotactic bacteria come in many shapes and sizes, and examples can be found in many different bacterial family trees.

What these differently shaped magnetotactic bacteria have in common is that they contain tiny magnetic organelles (yes, bacteria can have organelles, see this post). There are basically two types of magnetic organelles, based on what metal they contain, but both are generated by the bacterium sequestering the metal and then storing it in a granule.

Because they contain magnets, magnetotactic bacteria line up along the magnetic field lines of the Earth. This was noticed as early as 1963 when an Italian scientist studying some bacteria on slides noticed that certain types of them always pointed north/south.

Since we're talking about cocci at the moment, you may ask how something that is spherical can line up in a direction. Well, some of them are flagellated, so you can see a direction, some of them string together to form streptococci (strepto = line) along a magnetic line, and some that don’t attach to each other will still line up by the hundreds according to magnetic lines introduced by a strong, close magnet.

A recent study has found what might be the first peritrichous coccus, and it's magentotactic as well. This paper refers to them as MMP– multicellular magnetotactic prokaryotes. These particular microorganism are always found in strings of a dozen to three dozen and have flagella sticking out on all sides.


So last week and above we see that some bacteria can generate an
electrical current in oxygen and sulfur. A new study shows that
altering magnets can turn magnetotactic bacteria, which might
then be like the logic gates or 0/1 switches of a computer. I think
someone should be looking into building a completely bacterial
computer, with bacteria supplying the power and the circuitry.
Also a novelty, these new bacteria are the first magnetotactic bacteria known to have both types of magnetic granules; all others have one type or the other. The question - why have either type? What good does it do a bacterium to be aligned along the magnetic fields of the planet?

All the known magnetotactic bacteria, including all the coccal examples, are flagellated; therefore, it must be important for them to be motile. What’s the point of lining up with magnetic field lines if you just sit there, it should be involved in helping you get somewhere faster or better or putting you in a position to take advantage of something - so they’re all flagellated. The current hypothesis is that lining up with the field takes one plane of movement decision away from them, so they can move quickly toward food or oxygen. Sounds plausible.

Next week – not every flagellum is the same, so we need another name. Ever hear of an undulipodium?




Gao B, Lara-Tejero M, Lefebre M, Goodman AL, & Galán JE (2014). Novel components of the flagellar system in epsilonproteobacteria. mBio, 5 (3) PMID: 24961693

Zhang R, Chen YR, Du HJ, Zhang WY, Pan HM, Xiao T, & Wu LF (2014). Characterization and phylogenetic identification of a species of spherical multicellular magnetotactic prokaryotes that produces both magnetite and greigite crystals. Research in microbiology PMID: 25086260
 
Brennan CA, Hunt JR, Kremer N, Krasity BC, Apicella MA, McFall-Ngai MJ, & Ruby EG (2014). A model symbiosis reveals a role for sheathed-flagellum rotation in the release of immunogenic lipopolysaccharide. eLife, 3 PMID: 24596150
 
Khalil, I., & Misra, S. (2014). Control Characteristics of Magnetotactic Bacteria: Magnetospirillum Magnetotacticum Strain MS-1 and Magnetospirillum Magneticum Strain AMB-1 IEEE Transactions on Magnetics, 50 (4), 1-11 DOI: 10.1109/TMAG.2013.2287495




For more information or classroom activities, see:

A great video of chemotaxis, a neutrophil chasing a bacterium. One using chemotaxis to find, the other using it try and escape.

Magnetotactic bacteria –

Bacterial flagellar chemotaxis –

Flagellar arrangements-




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