Showing posts with label human. Show all posts
Showing posts with label human. Show all posts

Wednesday, May 11, 2016

Viva La Evolution

Biology concepts – evolution, reproductive advantage, natural selection, co-dominance, X-linked genes

Last week we learned how less aggressive strains of malaria were used to treat neurosyphilis and how they may be useful in treating HIV infection. This week, we will turn 180˚ and see if other diseases can help prevent or lessen the effects of malaria. In the process, much can be learned about natural selection and reproductive advantage.

Plasmodium-infected red blood cells develop knobs,
the surface protrusions seen on the left erythrocyte.
These knobs are covered in a certain protein that
inhibits the immune system’s ability to recognize this
cell as infected and respond to it. The cell on the right
is also infected with P. falciparum, but has a mutation
that prevents knob formation. Image credit: Ross
Waller and Alan Cowman.
As you undoubtedly remember from last week, malaria is a parasite-caused infectious disease that is transmitted from human to human by mosquitoes. The parasite, Plasmodium falciparum, takes up residence in the red blood cells (RBC) to reproduce. The red cells burst to release the organisms, and this brings fever and weakness.

As far back as the 15th and 16th centuries, quinine, made from the bark of the cinchona tree, was being used in Peru to treat malaria. Chloroquine, mefloquine, and quinine all work against malaria in similar fashion. Because of their neutral pH, they move across membranes easily including the lysosome membrane. Once inside the lysosome, they become charged and can’t get out. This includes the trophozoite-containing lysosomes. In the RBC, trophozoites consume hemoglobin to obtain amino acids, and the heme is digested in the lysosomes to form a black malaria pigment. The quinine drugs in the lysosome bind up the heme and produce a toxic product (cytotoxic heme) that kills the parasite.

There are other classes of drugs that are useful against P. falciparum. Primaquine and the artemisinin drug, artesunate, act by a completely different mechanism from that the quinine drugs. Artesunate is excellent for treating P. falciparum malaria, while primaquine is often used in conjunction with quinine to treat P. vivax or P. ovale forms of the disease.

These drugs work by breaking down – weird, but this is how many drugs work. It isn’t what you swallow that kills the organism, it's the metabolites (the products made by your biochemistry breaking down the drug) that are active. In the case of artesunate and primaquine, the heme molecule in the red blood cells releases peroxide from the parent compound (the drug you take). This is just like the peroxide you use to wipe out cut in order to prevent infection.

Artusenate comes from the sweet wormwood
plant. Chinese herbal medicine has used it for
thousands of years. A recipe for an Artemisia
based malaria medicine was found on a tablet
from the Han Dynasty (206 BCE to 20 CE). It is
now being investigated as a treatment for breast
cancer, also based on its ability to form radicals.
Oxygen is crucial for cellular function because it can gain electrons and can react with many other atoms. Unfortunately, this also makes it harmful to your cells as well. Without proper supervision, forms of oxygen that have picked up an extra electron or two (peroxide, superoxide, nitric oxide) can react with many important molecules in your cells and leave the cell impossibly damaged.

The cell has defenses against free radical damage, but higher than normal concentrations render the RBC fragile; on the tipping point of destruction. Treatment with primaquine or artesunate makes the cell inhospitable for the parasite, the red blood cells become flop houses instead of five star hotels. The parasite’s operating instructions are to survive and reproduce, but these drugs pull up the erythrocyte welcome mat and the parasite seeks moves on to seek friendlier accommodations.

Unfortunately, some strains of P. falciparum have become resistant to some quinine drugs, especially chloroquine. The free radical generating drugs are still useful, but scientists in Western Cambodia recently reported artesunate drug resistance there. The parasite has evolved – evolutionary pressure is everywhere. The actions of humans have put pressure on the organism to evolve; those parasites with mutations to resist the drugs have a reproductive advantage, and those mutations get passed on. We had better have something else on our plate to combat malaria – we're working on it, but nature has provided some help as well.

There are natural defenses against malaria. We have seen that a fragile red blood cell helps in preventing are lessening the disease course of malaria. What else might do that? This is where human genes come into play.

Sickle cell disease creates a very fragile RBC. The mutation is just a single DNA base change in the hemoglobin beta chain peptide, but the result is a hemoglobin molecule that becomes pointy and can tear the red blood cell apart, or can get stuck in small blood vessels and prevent good blood flow. Reduced blood flow starves the downstream tissues of oxygen.

You get one gene for hemoglobin beta chain from each parent. The disease comes when an individual receives mutated genes from both parents. But that doesn’t mean that sickle cell anemia is a recessive trait. If you have one copy of the mutated gene, then you will have sickling problems when oxygen concentrations are low, like during exercise or at high altitude.
Sickle cell disease or a sickle cell trait episode can result in red blood
cells clogging up vessels and organs. On the left is an absolutely
HUGE spleen from a sickle cell patient. On the right is a normal sized
spleen, about 20% the size of the injured spleen on the left. A normal 
spleen is about the size of your hand, maybe a little skinnier.

If sickle cell anemia was a recessive disease, then a single wild type (normal) gene would be dominant, and you would show no disease. Instead, sickle cell anemia is co-dominant, one mutated allele (copy of the gene) is like having half the disease; it only shows up in certain circumstances.

This can still be a pebble in your shoe, just ask Ryan Clark, the Pro-Bowl safety for the Pittsburgh Steelers. In a 2007 game in Denver (altitude 5300 ft, 1616 m), Ryan almost died from a sickling attack during the game, and ended up having his spleen and gall bladder removed (remember that sickled RBCs can clog blood vessels, especially in blood rich organs like the spleen).

When Pittsburgh next played Denver, Clark didn’t even make the trip. This just happened to be the 2011 playoff game in which Tim Tebow threw a long touchdown pass in overtime to the receiver being covered by Clark’s replacement. Sometimes disease can change how sports evolve as well.

Thalassemia is another example. This is a group of inherited disorders wherein there is reduced production of one of the subunits of hemoglobin (hemoglobin is made from 2 alpha and 2 beta subunits). Alpha-thalassemias have mutations in the alpha subunit; likewise for beta-thalassemia.

Reduced subunit number means reduced hemoglobin number; the blood won’t carry enough oxygen, and the patient is constantly oxygen-poor in his/her tissues. Having two mutated alpha genes is lethal in the very young (called hydrops fetalis), but you can live with one mutated alpha gene, one mutated beta gene, or even two mutated beta genes.

This the broad bean, or fava bean in opened pod
and out of the pod in a bowl. The ancient Greeks
used to vote with fava beans, a young white bean
meant yes, and old black one meant no.
Sickle cell trait (one mutated allele), and thalassemias result in fragile erythrocytes. This makes them poor hosts for malaria, and confer a resistance to the disease - bad genes aren’t bad in every case. And just for good measure here is another example.

Favism, better called glucose-6 phosphate dehydrogenase deficiency (G6PDH), is an X-linked genetic disease; the gene is on the X chromosome. A female (XX) has two copies, so having one mutant copy is no problem, but a male (XY) has only one, so getting a mutated copy from your mother means that you ONLY have the mutated gene – this brings the disease.

The enzyme G6PDH works in several pathways; in your red blood cells, it is the only source of reduced glutathione, an important antioxidant. This means that things that trigger free radical formation in your red blood cells will trigger the disease – lots of weakness and lack of energy. If there is enough erythrocyte destruction, one could die.

Triggers include broad beans (fava beans), hence the name favism. Other triggers include many drugs, including primaquine and artesunate, the anti-malaria drugs that induce free radicals. Having G6PDH-deficiency is like having your own artesunate pharmacy right in your cells - you naturally have higher oxygen radical levels in your RBCs, so the malarial parasite can't live there.

Not by accident, sickle cell mutation is more prevalent in people of Sub-Saharan African descent, thalassemia mutation is more common in people from the warm, moist Mediterranean, and G6PDH-deficiency is found most commonly in the Mediterranean and Southeast Asia. These just happen to be the areas where malaria-carrying mosquitoes are most abundant. Evolutionary biologists make the argument that natural selection has maintained these genes in the populations because they provide a reproductive advantage to the species.

Left image: dark green is where there is thalassemia and yellow and red are where there is sickle cell. Right image, light green is where there is favism, and inside the light blue outline is duffy antigen mutation. It is
interesting that these areas are also where malaria is endemic.


You might die from sickle cell disease, but probably not from sickle cell trait or beta-thalassemia. Learning not to eat fava beans makes the G6PDH mutation less lethal. One might very well live to an age where one could mate and pass on his/her genes. The diseases might still kill the patient, just not as soon as malaria would.

Malaria is a killer, and significantly, a killer of the young. In East Africa, children are bitten by the anopheles mosquito on average 50-80 times each month. They very well might not reach an age to reproduce. Therefore, having sickle cell trait, thalassemia, or favism provides a reproductive advantage in these environments and natural selection has resulted in these alleles remaining in the populations in these areas.

The Duffy antigen (DARC) is important for P. vivax
entrance into the red blood cell. The Duffy binding
protein (DBP) interacts with DARC, the yellow parts
of the DBP are variable, and can be used to bind an
antibody. These variable areas overlap the binding
site, and can be used to make a vaccine for P. vivax.
Evolution maintains some diseases in order to combat others. It isn’t by design, it's by biology; no big plan is involved, as exemplified by the Duffy antigen. All your cells have proteins on their surfaces. One, called DARC (Duffy Antigen Receptor for Chemokines, or Duffy antigen) helps your cells receive signals from your immune system. In those people with a specific single nucleotide polymorphism (SNP) for Duffy Ag, the antigen is not present on red blood cells (though it is still present on all other cells).

Since P. vivax uses Duffy Ag as a way to enter the red blood cells, those with the Duffy SNP are resistant to P. vivax malaria – they don’t even have to suffer with some other disease; just a simple case of chance.  And the prepared mind exploits chance – the Duffy antigen binding protein is now a candidate for use as a P. vivax vaccine.

Next week, how the plague was defeated by a genetic disease.


Chootong P, Panichakul T, Permmongkol C, Barnes SJ, Udomsangpetch R, et al. (2012). Characterization of Inhibitory Anti-Duffy Binding Protein II Immunity: Approach to Plasmodium vivax Vaccine Development in Thailand. PLoS ONE , 7 (4) DOI: 10.1371/journal.pone.0035769

For more information or classroom activities, see:

Malaria –

sickle cell mutation –

thalassemia –

favism –

duffy antigen –

Wednesday, June 24, 2015

The CPU In Your Head

Biology concepts – homeostasis, neuroendocrine system, hormone, pituitary, hypothalamus



Let’s face it, everything I know about computers I
learned from Tron and Tron Legacy. What I learned
most from the sequel is that we still can’t make a
decent avatar for Jeff Bridges. But I did learn about
the CPU and programs and users. I like to think there
are small motorcycle races going on in my laptop
while I write. It makes it more interactive.
A computer can be a wonderful tool. It can facilitate learning, entertain you, store information for future retrieval, and manage menial tasks to free your mind for higher thinking. But a computer can also create problems; it makes facts look like knowledge, it presents all content equally so it can be hard to discern validity, and it can distract you from true accomplishment or learning.

Basically, a computer is like any other tool, its worth depends on how it is used. But its a very complex tool with many parts that are easily broken or can wear out. A computer is like your brain in some ways; let’s look at one specific system in your body that can be likened to part of your computer.

The central processing unit (CPU) of your computer controls most of what your machine can do, but it’s functions fall into two broad categories – 1) calculations and information storage, and 2) monitoring the machine itself. The CPU has programs to manipulate information and present information in different forms, but it also has sensory and feedback systems to keep the machine working at optimum levels.

It is this second function that we’re interested in today. Let’s say you use your laptop for an extended time and it starts to heat up. Sooner or later you'll hear the fan turn on; this is your computer’s attempt to maintain the temperature within a small window of values so that function is maintained and there is no damage to the machine. Your body does the same thing.

Another example – you let your computer sit for a while without doing anything. Sooner or later the screen will go black and the machine will go into a sleep mode to save energy and not burn out the screen. Once you start to use it again, it will draw more power; if you stream a movie or 100 videos of cats playing the piano, it will draw a lot more energy and the battery will wear down faster.


Homeostasis is a little like riding a Segway. If you
stand perfectly still and upright, nothing moves; all
the sensors are working but they don’t have to make
any adjustments. If you lean forward, the gyroscopes
recognize it and move the Segway forward so that you
stay balanced; the same thing if you lean backwards.
Everything works to keep your body systems in
balance even when, especially when, something
changes in the system.
Your body also has a system for controlling how much energy is made and used by your body, depending on the demands you are placing on it. In your computer, a portion of the CPU is dedicated to these functions of maintenance and there are peripherals in the machine (the fan, the temperature sensors, the screen saver, the virus software) that carry out the maintenance functions called for by the CPU.

In your body, the brain is your CPU. You’re cerebral cortex controls your higher functions, but each hemisphere has older parts that help maintain the body systems the hypothalamus and hippocampus (so do you have dual processors?). The peripherals that help control your body and keep things on normal are the endocrine glands and the neuroendocrine cells. Together, they’re called the neuroendocrine system and they maintain homeostasis (homeo = like and stasis = standing still).

Homeostasis is one of the characteristics of life. To be alive, an organism needs a system to resistant changes in itself when there are short-term changes in its environment. Like a computer overheating and turning on the fan, your body is constantly sensing internal temperature and turning on and off discrete systems to maintain a constant 98.6˚F.

You have homeostatic systems that control reproduction, temperature, energy consumption and production, hunger, sleep/wake cycles, basal metabolic rate, osmolarity, drinking, and blood pressure. Some of the sensory systems run straight to the brain via hardwiring (another computer analogy). These are the neurons of the peripheral and central nervous systems.

The outputs might be neural, but many times they aren’t. Imagine trying to send a neuron to each cell that needs to get a chemical message (via neurotransmitters released at the ends of the neurons). That would be very cumbersome to maintain and would require trillions more neurons.


“To whom it may concern,” is the introduction to
every hormone message sent throughout your body.
Like bulk e-mails, the hormones contact every cell
via the blood system, but only those that can and
need to respond (have the right receptors) will read
the message and do something about it.
Instead, your brain controls a system where messages can be sent to all cells of the body. Those that can receive the messages by having the correct receptors or gene control elements can then respond to the messages sent out. Those chemical messages controlled by your brain (mostly but not always) are called hormones (from Greek horman = to set in motion).

Hormones are the hallmark of the endocrine (endo = within, and crine = sift) system. When released into the bloodstream, they travel to every part of the body so that all cells have the opportunity to respond. Not all will, and you wouldn’t want them to. Specific cells and organs have the ability to respond to specific signals because they have the right hormone receptors.

There are eight endocrine glands in a human body. The adrenal glands (2 of them), the parathyroid glands (4), the thyroid gland (1), the pineal gland, the pancreas, the ovaries (2) or testes (2), the hypothalamus, and the pituitary gland. They can be stimulated to release hormones by either neurons, other hormones, or other chemicals. Besides these well known glands, a few tissues will release hormones in specific situations. The placenta will release progesterone and estrogen, and the stomach can release gastrin to stimulate gastric juice (acid) and ghrelin to stimulate hunger.

In addition to endocrine glands, there are also some cells that can be directly stimulated by neurons to release hormones into the blood. These are the neuroendocrine cells. There’s a lot more of them you think, and they’re just about everywhere in your body.


The upper image shows the PNEC’s in your respiratory
tract (NE). They can be alone or be grouped into neuro-
endocrine bodies (NEBs). A 2008 study, and several
before it, has correlated a hyperplasia and hypertrophy
of PNECs with Sudden Infant Death Syndrome. Too
many and your respiratory control may get thrown out
of whack; it may just stop working. It might be good to monitor
the PNEC system in youngsters to try and predict
susceptibility to SIDS.
It’s hard to explain what neuroendocrine cells are and aren’t. They aren’t neurons, but they can look and act a lot like neurons. They can release hormones into the blood (endocrine) or to local cells (paracrine) but they aren't exactly endocrine cells. In other cases, they can release neurotransmitters that act on neurons – this often occurs in sensory situations, like with the Merkel cells in your skin that sense touch.

For one example, there are pulmonary neuroendocrine cells (PNEC) in every part of your respiratory tract, from your nose to your alveoli. While they seem to act like neurons in many respects, they are derived from epithelial tissue, not the neural crest tissue that all neurons come from.

Each PNEC spans the distance from basement membrane to the air conducting space. On the luminal side, they have microvilli that stick out into the lumen and sample the air as it passes. On the basal side (bottom) they communicate with neurons. Just what are they doing there?

They have several functions, including regulating the development of the respiratory system in the fetus. They also regulate the function of the respiratory cells by sensing oxygen levels, controlling the muscular tone of the bronchi, regulating pulmonary blood flow and modulating immune responses. The origin and function of PNEC’s is reviewed in a 2012 paper, which also highlights a problem with them – when PNEC’s go bad, they cause a deadly small cell cancer.

In response to what the cell senses, it will release a variety of chemicals, many of which can act as neurotransmitters – hence the reason they are considered neuroendocrine cells. But the PNEC’s may have another function, one hinted at in a 2014 study. The results of these experiments indicated that PNEC’s can detect chemicals in the air as it passes over their microvilli – they quite literally can smell the air, as their microvilli were found to have olfactory (smell) receptors, just like in your nose!


The hypothalamus is part of the diencephalon, a part
of the brain older than the cerebral cortex, but not as
old as the thalamus. The different nuclei each function
in different systems; the lateral nucleus senses
hormones and regulates thirst and hunger, the
dorsomedial nucleus regulates BP and HR. Several
nuclei are involved in making releasing hormones,
ADH and oxytocin.
The need to smell volatile chemicals in the lung may have something to do with responses to toxic chemicals; remember that the PNEC’s also regulate the pulmonary immune response. In chronic pulmonary diseases, like emphysema due to smoking, the PNECs are less responsive to volatile chemicals, maybe as a way to dampen the immune response.

So what controls much of this neuroendocrine system? Your brain of course. Well, a small part of your brain that's pretty old in terms of evolution (even primitive hagfish have a pituitary). The hypothalamus senses many of the inputs that tell your brain just how well your body is maintaining homeostasis. If something goes astray, or if there is a change in your environment that forces a change in your body chemistry, the hypothalamus will then spring into action (O.K., it’s always working, it will just work harder).

The hypothalamus has a neuroendocrine relationship with the pituitary gland (better named the hypophysis, where hypo = under and physis = growth – it is a growth under the brain). The hypophysis comes in two parts. Both parts release hormones, but where those hormones come from and the sources of the tissues of the two pituitary parts are very different.

The anterior pituitary isn’t part of the brain at all. The tissue for the adenohypophysis (anterior pituitary, adeno = secreting) comes from the roof of the embryonic mouth. It is epithelial in origin and has cells that produce hormones in response to signals from the hypothalamus (also hormones). Here’s how it happens.


The pituitary gland, or hypophysis, has two small
portal systems that carry blood from one place to
another instead of to a particular tissue and then
back to the heart. The anterior system carries
releasing hormones from the hypothalamus to the
ant. pituitary and then carries stimulating hormones
from the ant. pituitary to the rest of the body. The
posterior system moves hormones from the
hypothalamus directly to the rest of the body.
Image credit to Medicalook.
Some portions of the hypothalamus sense changes from the body and produce hormones called releasing hormones. These stimulate the epithelial cells of the adenohypophysis to produce hormones that then act on the endocrine glands throughout the body. Confusing, yes?

Well, it gets worse. There are six releasing hormones from the hypothalamus that stimulate production and release of seven hormones from the adenohypophysis that then act on at least 20 endocrine glands and neuroendocrine cell types. Hypothalamus to adenohypohysis to endocrine gland – it’s called an axis, and there are several of them.

On the other hand, the posterior pituitary (neurohypohysis) is derived from brain tissue. Instead of the neurons of the hypothalamus producing releasing hormones that then act on the neurohypophysis, the hypothalamic neurons project right into the posterior pituitary where they deposit their hormones (oxytocin and antidiuretic hormone).  The neurohypophysis doesn’t make any hormones itself, it just stores what the hypothalamic neurons produce and then releases them to the circulatory system.

That’s a heck of an exception- part of your brain isn’t actually part of your brain. Cells from your mouth control most functions in your body! Some people I know have mouths that completely ignore their brains! Next week, let’s talk more about the neuroendocrine system. Your thyroid gland size correlates to which hand you use to write – say what?




Gu, X., Karp, P., Brody, S., Pierce, R., Welsh, M., Holtzman, M., & Ben-Shahar, Y. (2014). Chemosensory Functions for Pulmonary Neuroendocrine Cells American Journal of Respiratory Cell and Molecular Biology, 50 (3), 637-646 DOI: 10.1165/rcmb.2013-0199OC

Song, H., Yao, E., Lin, C., Gacayan, R., Chen, M., & Chuang, P. (2012). Functional characterization of pulmonary neuroendocrine cells in lung development, injury, and tumorigenesis Proceedings of the National Academy of Sciences, 109 (43), 17531-17536 DOI: 10.1073/pnas.1207238109

Porzionato A, Macchi V, Parenti A, Matturri L, & De Caro R (2008). Peripheral chemoreceptors: postnatal development and cytochemical findings in Sudden Infant Death Syndrome. Histology and histopathology, 23 (3), 351-65 PMID: 18072092





For more information or classroom activities, see:

Homeostasis –

Neuroendocrine system –

Hypothalamus –

Pituitary –