Wednesday, November 19, 2014

A Meal More Powerful Than The NFL

Biology concepts – genetic code, neurotransmitters

A turkey dinner with all the fixins can lead to a
satisfying nap. But the meal usually takes a little
longer than this to have an effect. This fellow might
be more affected by last night’s activities than today’s
Turkey dinner at Thanksgiving brings the family together, celebrates the bountiful harvest, and puts you to sleep just as the NFL games are ready to start. Many people think that if you eat less turkey and fill up on the other goodies you can escape the post-Thanksgiving meal sleepiness. Other people look forward to eating seconds and thirds and then stretching out on the couch for a long nap, forcing Aunt Ethel to sit in the chair with the spring that surprises you every once in a while.

The culprit, or the hero, in this eat and sleep saga is said to be the tryptophan in the turkey. Other people think that it is simply how much you eat, not the turkey's tryptophan, but it isn’t quite that simple. What is tryptophan, and is it indeed responsible for the snoring that follows Thanksgiving dinner?  Some background will help.

Tryptophan is an amino acid, one of the twenty standard building blocks of proteins. Each amino acid has a similar basic structure, as shown in the picture below. The central carbon has an amino group (NH3) on one side and a carboxylic acid (COO-) moiety on the other; hence the name – amino acid. The third side group is a simple hydrogen (H), while the fourth side (R) refers to any of several different side groups and is what makes one amino acid different from one another.

Tryptophan is an aromatic amino acid, meaning that its side group contains a six-sided carbon ring structure (each corner represents a carbon). It also has a second ring group of four carbons and a nitrogen. As such, it is the largest and most massive of all the standard amino acids. However, tryptophan is the least abundant amino acid in plant and animal proteins; it accounts for only 1-1.5% of the total number of amino acids in proteins.

Amino acids are the building blocks of proteins. The NH3
is the amino part and the COO is the acid part. The R is
different for each amino acid. On the left, you see that
tryptophan’s R group is a big structure with two different
rings (each angle where two lines meet stands for a carbon,
they just don’t write in each “C”). Two lines means a double
bond. In producing the protein, the COO of the last amino acid
added gets connected to the NH3 of the next amino acid to be
connected. Which amino acid it is determine by the mRNA
and the genetic code.

Tryptophan’s large structure and intricate rings make it costly to produce in terms of ATP invested. In fact, it takes so much energy to make that we have stopped making tryptophan all together. Tryptophan is abundant in a number of food sources commonly available to humans, so over evolutionary time we have turned it into an essential amino acid. True, it is essential for life, but here the word “essential” means that we MUST get it from our diet, we cannot produce it ourselves.

Of the 20 standard amino acids, 10 are essential in humans (9 that we must eat and 1 that we make from an essential amino acid), but bacteria make them all just fine - although the parents of newborns may wish it wasn’t so. Gut bacteria make tryptophan or use the tryptophan we eat. They transform it into molecules they need to survive, but the byproducts of these reactions are skatole and indole – these are the precious little molecules that give dirty diapers that wonderful smell!

Tryptophan is different from many other amino acids in another way as well; it gets no respect from the genetic code. Each amino acid is coded for by a group of three RNA bases, together called a codon. Since there are four different bases in mRNAs (A, C, G, and U – remember that T is used in DNA but not RNA), then there are 64 different codons (4 x 4 x 4). This is more than the 20 amino acids that the codons code for, so most amino acids have two or three codons that signals that they should be added to the growing peptide. But tryptophan is encoded by only one codon (UGG).

It may make sense that an amino acid that is not used often in proteins might rate only one codon, but the amino acid methionine is used much more often than tryptophan, and it's only coded for by one codon as well (AUG). You know nature must have a reason why tryptophan has a single codon, we just don't know it yet.

The genetic code is how mRNA codons (3 bases sequences)
get translated into a signal to build proteins from specific amino
acids. The first base of the codon is represented by the biggest
letters (ACGU), the middle base is the middle size letters, while
the third position (wobble position) is usually where you see an
amino acid coded for by more than one codon. For instance,
serine is coded for by UCU, UCC, UCA, or UCG. But tryptophan is
only coded for by UGG. Three codons signal the protein to stop
growing, called stop codons (UAG, UAA, and UGA).
Even though it is used sparingly in proteins, tryptophan is an essential amino acid - don’t eat enough of it and you die. This is because tryptophan’s most essential functions have nothing to do with protein synthesis or structure – tryptophan is important to your brain function. The crucial neurotransmitter, serotonin, is synthesized only from tryptophan.

It takes two enzymes to turn tryptophan into serotonin (also called 5-HT).  First is tryptophan hydroxylase; hydroxylase means it splits water, here it adds an OH to tryptophan. Next, the amino acid decarboxylase removes a carboxylic acid (COOH), producing serotonin.

Amongst the many functions of serotonin are a few that are not brain related. Serotonin is released by enterochromaffin cells that line your gut to tell your gut to move. The movement helps push the food along your digestive tract, but serves a protective function.

If you eat something toxic, the enterochromaffin cells produce more serotonin – your gut moves much faster, and you get diarrhea. If even more serotonin is made and released, it moves through the bloodstream to your stomach and esophagus and causes you to vomit.

But it is in the CNS that serotonin has its significant activities. As a neurotransmitter, it is responsible for controlling how electric messages are passed from one neuron to another. When serotonin is released in the synapse (the gap between the upstream and downstream neurons) and is taken up by adjacent neurons, it produces a sense of well-being.

Where one neuron ends and others begin there is
a gap called the synaptic cleft. Different types of
neurons use different neurotransmitters, of which
serotonin is one. It is released into the synapse, and
adjacent neurons with serotonin receptors can be
stimulated to conduct a nerve impulse. The serotonin
is broken down in the synapse by MAO’s and taken
back up to produce more serotonin.
It isn’t surprising that depressed individuals often have low blood levels of tryptophan, as well as reduced serotonin. Classic treatments for depression include increased tryptophan intake, monoamine oxidase (MAO) inhibitors, and serotonin reuptake inhibitors (SSRI). With more tryptophan, you make more serotonin – problem solved. On the other hand, MAO’s break down serotonin, so their inhibitors enhance the action of tryptophan. SSRI’s prevent the reuptake, this leaves serotonin in the synapse longer. Both types of drugs make tryptophan more likely to be taken up by downstream neurons.

Unfortunate, but interesting, is the study showing that the suicidal thoughts that sometimes accompany anti-depressant therapies (TESI – treatment enhances suicidal ideation) use may be related to polymorphisms in one form of the tryptophan hydroxylase enzyme that starts the serotonin production from tryptophan.

When non-suicidal patients were compared to those with TESI or those who were suicidal without treatment, a pattern emerged. Only those with TESI showed a polymorphism pattern in the tryptophan hydroxlyase 2 (TPH2) gene. This polymorphism had previously been associated with suicide victims and major depressive disorder. It seems that a slight alteration in function of TPH2 due to a single nucleotide change can contribute to the genetic background of treatment induced suicidal thoughts.

The feeling of general well being induced by serotonin also participates in the sleep/wake cycle. So is tryptophan – through serotonin – responsible for the post-Thanksgiving nap? Well… yes and no, it's an accomplice in a larger conspiracy.

Serotonin is use to produce the hormone melatonin, and melatonin promotes sleep, so you could say turkey dinner promotes sleep. But turkey doesn’t have that much tryptophan! Tofu has much more tryptophan than turkey, but you don’t get a post-Chinese takeout urge to sleep, so what gives?

Melatonin is made from serotonin in the pineal
gland. Sunlight stimulates the suprachiasmatic
nucleus (SCN) which inhibits the pineal from
making melatonin. As the sun goes down,
inhibition is reduced, more melatonin is made
and released from the pineal, and sleep is
The melatonin effect has to do more with how much of everything else you eat at Thanksgiving dinner, especially carbohydrates. Here is how it works – eating lots of carbohydrates causes a release of insulin into the blood (to reduced blood glucose levels). Another function of insulin is to promote the uptake of some amino acids (but not tryptophan) into muscle cells. This leaves the blood higher in tryptophan as compared to other amino acids than it would normally be.

The brain takes in amino acids through a neutral amino acid transporter, which now finds more tryptophan than other neutral amino acids, so the brain level of tryptophan goes up. More tryptophan in the brain, more serotonin – more serotonin, more melatonin. More melatonin = nap time! So if you want to avoid the post-Thanksgiving nap, eat the turkey and skip the mashed potatoes.

You didn’t know how much tryptophan controlled your daily life, did you? Well, there’s more. Tryptophan is also important in synthesizing niacin, a.k.a. vitamin B3 or nicotinic acid. Niacin is important in production of NAD/NADH for energy metabolism, for production of steroid hormones and balance of lipid forms in the blood, and as an anti-convulsant.

The tryptophan-niacin connection is made stronger by recent evidence that high dietary tryptophan can prevent epileptic seizures in mice. In this study, a whey protein called alpha-lactoalbumin (ALAC) was found to have much tryptophan, much higher levels than in most proteins. Feeding epileptic mice ALAC resulted in reduced numbers of seizures.

So even if you don’t want to sleep or think happy thoughts, you still need to eat food that contain tryptophan or niacin. And many of those foods are plants, because plants use tryptophan to control their own activities. Tryptophan is easily converted to auxins, a type of plant hormone. Auxins are responsible for several different plant behaviors, namely the falling leaves in autumn and ripe fruits all year long.

Here is an interesting attempt to get kids to read
history. During the spring, captive warriors were
killed by cutting out their hearts, then their skin was
flayed off their body, and the priests would wear them
around for 20 days. This was meant to celebrate the
god who sacrificed himself to allow a new growing
season to begin. This time period corresponds
 to when they would have had the lowest amount of
 tryptophan in their daily die. No - I wouldn't want
to be an Aztec sacrifice!
Having dietary choices for tryptophan is good, and plants provide our major source. However, cooking grains and corn reduces usable tryptophan and niacin levels dramatically, so poorer environments where corn is the staple food need also to have additional dietary sources of tryptophan. A deficiency of this amino acid leads to some disturbing conditions. Low tryptophan leads to low serotonin levels and agitation, insomnia, and depression. A study in the Archives of General Psychiatry stated that chronically low levels of tryptophan led to relapses of purging behaviors in bulimics.

More amazingly, studies in the 1970’s to 1990’s suggest that low tryptophan levels can lead to increases in religious fanaticism. Several studies from a single author correlate the Aztec human sacrificial ceremonies to the times of year when their diets depended more on foods that had less tryptophan. Think of all the lives that could have been saved by tofu!

But turkey is more than just tryptophan. You have to love an animal that has caruncles, a wattle, and a snood! What's a snood? Come back next week.

Musil, R., Zill, P., Seemüller, F., Bondy, B., Meyer, S., Spellmann, I., Bender, W., Adli, M., Heuser, I., Fisher, R., Gaebel, W., Maier, W., Rietschel, M., Rujescu, D., Schennach, R., Möller, H., & Riedel, M. (2012). Genetics of emergent suicidality during antidepressive treatment—Data from a naturalistic study on a large sample of inpatients with a major depressive episode European Neuropsychopharmacology DOI: 10.1016/j.euroneuro.2012.08.009

Russo, E., Scicchitano, F., Citraro, R., Aiello, R., Camastra, C., Mainardi, P., Chimirri, S., Perucca, E., Donato, G., & De Sarro, G. (2012). Protective activity of α-lactoalbumin (ALAC), a whey protein rich in tryptophan, in rodent models of epileptogenesis Neuroscience, 226, 282-288 DOI: 10.1016/j.neuroscience.2012.09.021

For more information or classroom activities, see:

Genetic code –

Neurotransmitters –


Wednesday, November 12, 2014

A Goat For Thanksgiving

Biology concepts – cornucopia, goat, nutrition, sustainability, browser/grazer, Cassandra hypothesis

The image on top is the traditional cornucopia, filled with
foods or riches. The bottom image is the version form the
Hunger Games movies, filled with survival gear and weaponry.
Boy, did they go the other way with that idea. I prefer a
different Horn of Plenty, the Dizzie Gillespie album from 1953.
Thanksgiving is a traditional time to remember the work of planting and tending, and to be grateful for the harvest. In a larger sense, it’s a time to be grateful for life’s unending bounty, both the good and the challenging.

As a symbol of the gifts of the Earth, the ancient Greek cornucopia (comes to us as the Latin cornu = horn, and copiae = plenty) has been adopted as a symbol of this holiday in the USA. Not every country has a specific date set aside for celebrating the harvest, but almost every culture has a version of the cornucopia.

Looking at the horn of plenty in a little more detail, we will see that it fits more nicely with the American holiday tradition, and perhaps the American future.

From Greek mythology, there are a few stories about how the horn of plenty came to be. My favorite is that when Zeus was born, he had to be hidden from his father Chronos. Dad had a nasty habit of eating his young, so Zeus was whisked away to a mountain cave on Crete where he was suckled by Almathea, a lesser god that took the form of a goat.

Zeus, being the he-man god that he was, accidentally broke off one of Almathea’s horns while playing. Of course he blamed it on his sister ….. wait, that’s what used to happen at my house. No, Zeus felt bad about his rude feat of strength, so he enchanted the horn so that it would provide Almathea with whatever she desired. I imagine that for a goat that would be anything edible, and goats will eat almost anything.

Other versions of the myth say that Almathea was a nymph that fed goat’s milk to Zeus and he subsequently blessed one of the goat’s horns to provide her with unlimited bounty as a way of thanking her – but either way it didn’t end well for for the goat. A teenage Zeus showed his appreciation by killing and skinning the goat. The skin was used to make his shield, the aegis, and is shown in many depictions of Zeus. But the horn was still around, spewing forth sustenance for the holder.

This is from the 1555-1556 painting, Infancy of Jupiter, by
Giorgio Vasari. It shows the god being suckled by the divine
goat Amalthea. Notice we said Jupiter, not Zeus. Roman and
Greek myths often stole from one another, the same stories
can be found in each traditions; only the names have been
changed to protect the copyright.
This brings us to the goat horn and the American Thanksgiving. The goat just may have been a part of the first Thanksgiving, and it may have implications for future Thanksgivings, speaking biologically.

The first Thanksgiving wasn’t too much of feast; it looked nothing like the table we look over as we watch football and stuff ourselves. The pilgrims had it rough, but they were thankful for the harvest that they did manage and the wisdom that the native Americans had passed on to them about finding food in their new home.

They might have had some turkey, but they certainly didn’t have a big steak. The pilgrims had not brought any cows with them on their journey, and they weren’t native to this country. They may have had some pork, as they did have a few pigs, but they may also have had another meat – goat.

It's true, goats are not native to the Americas. No, the Rocky Mountain goats (Oreamnos americanus) that grace the crags and cliff faces so majestically are not really goats, they’re actually members of the antelope family. And it turns out that they aren’t even native to the Rocky Mountains, at least not the lower Rockies. They were originally found in Alaska, and were introduced to Colorado, Montana, and South Dakota much later.

Check out the nutritional values for goat meat. If you, unlike
most Americans, can stomach the idea, you should be adding
it to your diet in place of some other red meat.
The pilgrims had at least some goats with them in 1621, they were remarked upon in one person’s journal. They certainly used them for milk and cheese at the first Thanksgiving, but they may have eaten goat meat as well. Does that sound weird to you?

True American’s don’t eat goat to any great degree. But in this instance, we’re the exception. Over 70% of all the red meat consumed worldwide is goat! I don’t remember trying it, but I am sure going to try and procure some now – not just for the novelty of it, goat meat (sometimes called chevon) is really good for you.

Chevon has greater vitamin and lower fat content than other red meats, even fewer calories and fat than chicken. People around the world haven't necessarily known about the nutritional value of goat meat for centuries; goats lived there and they ate them. Even south of the border in Mexico and Latin America they eat lots of goat (and I don’t just mean the cryptozoologic chupacabra).

All across Asia they eat goat, especially northern China, but as many of my Chinese friends say, the only thing with four legs the Chinese won’t eat is the kitchen table. Andrew Zimmern, he of the bizarre foods shows, says that goat is like soccer - it’s popular everywhere but the US.

Despite the fact that we don’t eat it nowadays, our story tells us that goat might have a bit more to do with Thanksgiving that one might think. Is there more – you bet. Along with their meager harvest and maybe some roast goat, the pilgrims enjoyed native American foods, things that were grown, hunted and/or gathered.

The black trumpet mushroom lives in Europe across to Asia.
Avery closely related species lives in North America, still
called the black trumpet or horn of plenty. Recent studies
show that in America, the black trumpet lives in a symbiotic
relationship with several pine trees. This is interesting, since
goats are now being fed pine bark to make their meat taste
better. Everything is connected.
In southern Virginia, this would certainly have included many different species of mushroom. And wouldn’t you know it, one of the most bountiful mushrooms in this region is named Craterellus cornucopioides, or Craterellus fallax. Also called the black trumpet or the horn of plenty mushroom.

I have read that native American Indians didn’t eat a lot of mushrooms, but they did use them for medicines and as symbols. But the European pilgrims were certainly mushroom eaters, so it is likely they made good use of the horn of plenty mushrooms. I can see a big bowl of mushroom stuffing gracing the tables of the first Thanksgiving.

Maybe the Indians were on to something when they used the mushrooms in their medicine. Recent studies of the black trumpet mushrooms show have medicinal effects. A 2012 study indicated that several mushrooms related to, and including the black trumpet mushroom have the ability to regulate blood sugar levels so as to prevent hyperglycemia. I know my diabetic wife would be interested in that, even if she doesn’t like to eat mushrooms.

In addition to this, the same study showed that the mushrooms also have antioxidant activities. They could scavenge iron ions that can do damage to cells as well as oxygen radicals that can devastate cellular function, see this post for a discussion of oxygen radicals and antioxidants.

A newer 2014 study show that the black trumpet has significant anti-inflammatory properties. An alcohol extract of the black trumpet was able to prevent inflammatory cytokine and nitric oxide production in macrophages that were stimulated with LPS, a potent inflammatory agent.

We have seen that goat plays a role in the American Thanksgiving, perhaps in the symbol we use for the harvest, perhaps as a meat source, and even perhaps in the mushroom stuffing. Now we can see how it may represent the future as well.

Evolution is amazing. Some ruminants evolved as grazers, while
others became browsers. That way, they can live in the same
areas and they both still have enough to eat. Goats are browsers,
so they have to digest things that even cows can’t digest.
Goats are browsers, not grazers. This means that they don’t eat grasses down to the roots; they also feed on what ever is around. They eat bark, twigs, leaves, license plates, homework, just about anything laying around. As such, they have a smaller effect on the environment than do grazing livestock, like bovines. Cows can strip a pasture clear of grass and its roots, and this takes time to replenish.

So goats are better for the land, you can raise more goats on the same amount of land as cows, and you don’t need to grow as much grain for them to eat. The commercials should really be saying, “Eat More Goat.” Goat numbers in the US have doubled in the past few years, but they still pale in comparison to those of bovines. Given the nutritional and environmental advantages of goats, maybe they could use a marketing slogan – “Goat, the other green meat.” Maybe not.

All this environmental talk leads us into the last discussion for our Thanksgiving post. Is the horn of plenty really a good symbol for the Earth today? Are the resources of Earth limitless and will keep pouring forth no matter what we do to our home?

This is the issue in an argument about population growth referred to as the Cornucopia vs. Cassandra hypothesis. The cornucopia position is one that says that the Earth will be able to sustain human population no matter how much it grows, while the Cassandra hypothesis states that the Earth’s resources are limited and that uncontrolled population growth is untenable.

Alan AtKisson wrote Believing Cassandra in 1999. He
explains how working for sustainability is necessary but
possible. Global sustainability is explained via anecdote and
good science, unfortunately, his method for reaching
sustainability is abbreviated ISIS, not so good for late 2014.
I recommend the book highly.
Cassandra was another character from mythology. Apollo gave her the power of prophecy in hopes becoming her boyfriend, but she spurned his advances and he took revenge. He left her with the power to predict the future, but cursed her so that no one would believe her predictions. Ouch, that “hell hath no fury like a woman scorned” line might have to be amended to include Greek gods.

The argument seems odd to me. Of course the Earth can take what ever we throw at it, but we can’t. Population growth and climate change are untenable only to us. Life will change and go on, but we won’t be here to see it.

The key is to manage the growth so that we don’t destroy the Earth for ourselves and for the rest of the living organisms that we depend on. And we depend on them all in one way or another. Maybe we should give thanks that we still have time to embrace the goat. OK, that sounds bad too.

Next week - does Thanksgiving turkey really put you to sleep?

O'Callaghan YC, O'Brien NM, Kenny O, Harrington T, Brunton N, & Smyth TJ (2014). Anti-Inflammatory Effects of Wild Irish Mushroom Extracts in RAW264.7 Mouse Macrophage Cells. Journal of medicinal food PMID: 25136763

Liu YT, Sun J, Luo ZY, Rao SQ, Su YJ, Xu RR, & Yang YJ (2012). Chemical composition of five wild edible mushrooms collected from Southwest China and their antihyperglycemic and antioxidant activity. Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association, 50 (5), 1238-44 PMID: 22300772

For more information or classroom activities, see:

Cornucopia in myth –

First Thanksgiving meal –

Browser versus grazer –

Cassandra and population growth –

Wednesday, November 5, 2014

Doing More With Less

Biology concepts – protists, complexity, undulipodia, flagella, cilia, amoebas,

Emotions are one of the things that make humans so complex.
Memories attached to associations, stimulated by
individualized brain chemistry makes it so you can’t predict
how any one person might feel about a particular stimulus.
But perhaps we are not so complex. A new study suggests that
there are really only four human emotions, happy, sad, afraid,
and mad. The other two commonly held states, disgusted and
surprised are just sides of mad and afraid, respectively. Read
the study and feel…… something.
Are humans the most complex animals? Humans have cells, tissues, organs, and organ systems that allow us to do things that no other organism can do – like invent doughnuts.

Indeed, this makes us complex and hard to understand, especially when we mumble. But on the other hand, wouldn’t it be more amazing if an organism could do complex things without the benefit of all that organization and without all those trillions of cells doing different jobs?

What if an organism did many complex things but was only made of one cell? I think this blog has shown on many occasions that bacteria are capable of some pretty astounding feats, and they don’t even have a nucleus! True, they don’t have structures as complex as ours, most of their behaviors are responses to chemical signals from other cells, and they can’t make doughnuts.

But there are other single celled organisms that might match us for complexity, or even exceed our level of complexity, and they do it all within the confines of a single cell. Of course I’m talking about the ciliate protists. If don't know them, stick around and meet them and their kin. Sometimes, less is more.

We have been talking about the undulipodia in the last few weeks, and our last story started to describe the great catch-all kingdom, the protists. They use cilia and eukaryotic flagella (these being the undulupodia), but this is just one characteristic that can be used to separate them into groups.

The last post talked about the plant-like protists and how they can use flagella to either move around or to have their gamete cells move around. Today let’s discuss the animal-like protists; they use undulipodia in more ways.

There are six phylums of animal-like protists, just like there were six phylums of plant-like protists – but I think that was just a happy accident. The animal-like protists have more diversity amongst their phyla than did the plant-like protists; some use flagella, some use cilia, some use neither. Each phylum is amazing, but we’ll save the most complex – or is that most simple – for last.

The radiolaria are counted amongst the actinopoda. They
have intricate mineral skeletons. What you can’t appreciate from
these photomicrographs is that also have an inner skeleton that
divides them into an endoplasm and ectoplasm. Some house
algae in there ectoplasm to harvest their photosynthetically-
produced carbohydrates.
We start with the Phylum Actinopoda – their pictures are very impressive. No, I don’t mean that they are good photographers. Seeing them shows you how delicate and complex they are. The have silica (glass-like) coverings that protect them from the outside world. Though many of these organisms are among the zooplankton (zoo = animal-like, and plankton = drifter) that are in the oceans; remember that plankton don’t have to be microorganisms; many species of jellyfish are zooplanktonic as well.

The radiolaria are amongst the actinopoda and are quite complex. They're one celled, but the cell has two parts, an endoplasm that contains the nucleus and organelles, and the ectoplasm, that has frothy bubbles to control their buoyancy.

Radiolaria are floaters, which would suggest that they don’t use undulipodia for motility. In fact, the only time that flagella have been observed in radiolarians is in some swarmer cells. Scientists think these represent sexual reproductive gametes that might be released from a swelling in the adult cell. Sexual reproduction has not been confirmed; scientists must be too embarrassed to ask them about it.

The swarmers are very small, as a new study shows and can move in the water column. This may be why we often find radiolarian DNA at depths where they don’t live – it’s their swarmers. And they do seem to get around. A Russian cosmonaut just reported having sampled the windows on the space station and found plankton! They think they have escaped the atmosphere on the wind. If true, that certainly changes our post about life moving from Earth to space.

Phylum Foraminifera – these organisms have tests, shells of calcium carbonate with little holes in them from which they stick out a pseudopod (we'll see more of this below) and walk.  The foarminifera look like and are closely related to the actinopoda. Some wonder if they shouldn’t be lumped together, but we all know that arguments about protist classification are the rule, not the exception. Like actinopoda, they only show flagella on their gametes, and like actinopoda, the gametes are biflagellated.

The foraminifera are protists with calcium carbonate shells. I
wonder if the RAF pilots returning during WWII knew that the
White Cliffs of Dover are chalk formed from these protists.
Likewise, the limestone quarries in Bloomington, IN where they
filmed Breaking Away in 1979 are also made from the tests
of these protists.
While radiolarian zooplantokton skeletons are responsible for a lot of the sediment at the bottom of the ocean and over time – forming rock called radiolarite, the tests of foraminifera organisms go to form limestone and chalk.

Oil spills and other such disasters are having an effect on the ability of foraminifera to maintain their calcium tests, and this affects us beyond just having some pretty cliffs to look at. We may be using foraminifera in the future to repair bone injuries.

A 2014 study showed that using foraminifera exoskeletons is a good way to promote bone growth in skull defects in rats. The hope is that we can use these for bone grafts and for bone repair in the future. As long as we don’t destroy all the formanifera.

Phylum Apicomplexa – We could talk about the best known apicomplexans for years and just touch the surface of their biology. Why do we know so much about them? Because they kill us. Plasmodium falciparum is an apicomplexan – it causes malaria. Toxoplasma gondii is an apicomplexan; it causes toxoplasmosis that can chew holes in your brain and kill you as well.

Apicomplexans are immotile, a lot like the planktonic foraminifera and actinopoda. But in this case they're usually carried around from place to place inside a living host. The vast majority of them are parasites. Since they get carried around, they don’t need flagella to move, but some of the species have gametes that have three flagella on their back ends. Even though I’m breaking my parasitology friend Bill’s heart, I am going to leave the apicomplexa here and move on.  Don’t worry Bill, we’ll come back to them soon.

Phylum Rhizopoda - These are the amoebas; most don’t have cilia or flagella. They move by pseudopodia (pseudo = false, podia = feet), oozing their membrane and cytoplasm in one direction and then pulling the rest along. Of course, this means they need a surface to move across, you don’t use pseudopodia to move in water. But this phylum also includes the ameoboflagellates,

Naegleria fowleri lives in warm waters. It enters the body
through the nose and travels straight to the brain. The
feeding structures look like a clown face, which makes it
double frightening for my daughter. The infection is almost
always fatal. Must be a sad clown.
Amoeboflagelleates are the exception, and can switch back and forth from amoeba form to flagellated form, depending on their environment. When in a liquid environment, amoeboflagellates use flagella to move about. But when in dry environment or a surface, the resorb their undulipodia and move by amoeboid mechanism. One amoeboflagellate in particular gets my attention.

Naegleria fowleri is the brain-eating protozoan that is transmitted through contaminated drinking or swimming water. It may not happen often, but I hate to think about something swimming (or would they crawl?) around my brain and feasting. Primary amoebic meningioencephalitis from N. fowleri is fatal in about 95% of cases, and though it is rare worldwide, most cases occur in the U.S.

A 2014 study in Arizona found that N. fowleri in five of 33 lakes studied. That’s scary enough, but the researchers also found that the protozoa were present in the cooler months, when it had been supposed that the cooler water temperatures were lethal to the organism. I am not retiring to Arizona.

Choanoflagellates look so much like the choanocyte cell
type in sponges. They are both collared and have a
flagellum sticking out. Since sponges are the basal phylum
of kingdom Animalia, it is believed that choanocyte protists
are the ancestor to all animal cells. But a new study says don’t
be so hasty. They resemble each other, but it could be parallel
evolution not straight descent.
Phylum Sarcomastigophora – this group of protists includes the most animal-like organisms that aren’t officially animals. The trichonympha have over 1000 flagella, but more species are like the choanoflagellates (means collared flagellar cells). These are believed to be the ancestor of all animal cells. They are very similar to the choanocytes of sponges, the most basal of the animals. However, a 2014 study warns against assuming that they are the same. The bending of the modified cilium that marks the choanocyte functions differently in the protists as compared to the sponges. The two diverged more than 600 million years ago, so similarities are there, but so are differences.

Phylum Ciliophora – The ciliates are those “less is more” organisms we described at the beginning of this post. These organisms have cilia all over their bodies, and they use them for feeding, motility (swimming and crawling), attachment and for sensing chemicals and perhaps sensing mates. These are all very complex behaviors for single-celled organisms. But wait, they do more.

Vorticella is one of the ciliates. It uses it’s cilia to shovel prey into
its oral groove, but the adult doesn’t use cilia to move. They
anchor to one spot and duck predators. The myoneme doesn’t
spring them up, it coils them down when something tries to eat them.
Some modified cilia funnel food into an oral groove, something that looks supiciously like a mouth to you and me. This is just the start of how they look like animals, they also get rid of waste in just one place, like our backside.

They have a complex cytoskeleton, made of connections between all those cilia. They have contractile vacuoles that control their water content. They even carry spears called trichocysts for defense against predators. These are like the cnidocytes of the jellyfish, and are a trick that we, with all our complexity, can't come close to matching

So do they go beyond us, even though they only have one cell? Yep, you have seen anything yet. Ciliates have up to six life cycle stages, they all have two nuclei, and they go through an insanely complex sexual reproduction that uses seven different sexes – with all our complexity, we only manage two - or are there more? That could be a good series of posts as well.

Ciliates are free living and cause us no problem. But in a great show of disrespect to their inferiors, Balantidium coli can be a horrible problem for us. It's the exception among ciliates in that it causes a disease, Balantidiasis, in primates. The organism usually lives in the guts of pigs, but if it gets into our gut, and we then become immunocompromised – watch out.

This is B. coli, the only know ciliate to cause disease in mammals.
You see all the cilia, that is how it moves around. It is transmitted
via the oral-fecal route, but might also be transmitted by
undercooked pork. Some people say fecal-oral, but that sounds
more gross to me.
Balantidiasis is characterized by explosive diarrhea, as much as one explosion every 20 minutes. Don’t think that "explosion" is too extreme a word. In some cases, the colon can literally have a hole blown in it (perforated) by the action of this ciliate. All that is bad enough, but a 2013 case study showed that B. coli infected an immunocompetent man’s spine, led to a pinching of the cervical nerves, and caused a temporary quadriplegia! Ciliates are complex, yes – and apparently one of them is mean.

We haven’t talked about the fungus-like protists. We’ll include them when we talka bout the undulipodia of the plants and fungi. Some plants cells have flagella for movement. Is my salad going to crawl off my plate?

But next week we'll start some Thanksgiving posts. Should we really be eating goat for Thanksgiving?

Jack, R., Garrod, O., & Schyns, P. (2014). Dynamic Facial Expressions of Emotion Transmit an Evolving Hierarchy of Signals over Time Current Biology, 24 (2), 187-192 DOI: 10.1016/j.cub.2013.11.064
Dhawan S, Jain D, & Mehta VS (2013). Balantidium coli: an unrecognized cause of vertebral osteomyelitis and myelopathy. Journal of neurosurgery. Spine, 18 (3), 310-3 PMID: 23259539

Chou J, Hao J, Kuroda S, Ben-Nissan B, Milthopre B, & Otsuka M (2014). Bone regeneration of calvarial defect using marine calcareous-derived beta-tricalcium phosphate macrospheres. Journal of tissue engineering, 5 PMID: 24808939

Yuasa T, & Takahashi O (2014). Ultrastructural morphology of the reproductive swarmers of Sphaerozoum punctatum (Huxley) from the East China Sea. European journal of protistology, 50 (2), 194-204 PMID: 24447698

Sifuentes LY, Choate BL, Gerba CP, & Bright KR (2014). The occurrence of Naegleria fowleri in recreational waters in Arizona. Journal of environmental science and health. Part A, Toxic/hazardous substances & environmental engineering, 49 (11), 1322-30 PMID: 24967566

Mah JL, Christensen-Dalsgaard KK, & Leys SP (2014). Choanoflagellate and choanocyte collar-flagellar systems and the assumption of homology. Evolution & development, 16 (1), 25-37 PMID: 24393465

For more information or classroom activities, see:

Plankton –

N. fowleri –

Ciliates –