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 –



Wednesday, October 29, 2014

Almost This Or Almost That? Must Be The Other


Biology concepts – Protista, taxonomy, phylum, kingdom, monophyletic, paraphyletic, cladistics, algae, diatom, dinoflagellate


Euglena gracilis is an organism in the Kingdom Protista. It has
one long flagellar undulipodium, but it can also move by
amoeboid movement. It has chloroplasts and can do
photosynthesis, but it also can eat other organisms. Is it any
wonder that classifying protists is so hard?
Classifying living organisms is self-perpetuating job. Imagine if the dentist sold candy in his/her office, “Here’s your root canal and your Laffy Taffy.” Scientists try their best, but whenever you start sorting things out, you always have that pile left over that doesn’t seem to fit anywhere. So you have to rethink your categories and try again.

The best example of the inanity of classification is Kingdom Protista. The word means, “the very first,” probably because it is supposed that these were the first eukaryotes. How do we define the organisms of this Kingdom? The best we can manage is to say that they are the eukaryotes that aren't animals, plants, or fungi. Really, is that the best we can do?

In a perfect system, all the organisms of one kingdom would be descended from a single common ancestor (be monophyletic, mono = one, and phulon = tribe). But it don’t work like that. And this is where Kingdom Protista serves as a good example.

There are protists that look a lot like animals, those that resemble plants, and those that share features of fungi. No way did they all come from a single ancestor. Protista is a paraphyletic (para = near) kingdom, the group may exclude a member with a common ancestor. As such, the protists are a catch-all, those that don’t fit in some other kingdom. Protists are like pornography – hard to define, but you know it when you see it.


Classification isn’t perfect, some groups come from
different ancestors. A shows a group (in yellow) that
is monophyletic, they all come from one ancestor.
The paraphyletic group (B) shows that some groups
can’t include all descendents of a common ancestor.
And if a group is made from descendents of different
ancestors, it is called polyphyletic (C).
We already said that some behave like animals, plants, or fungi. Some are unicellular, some are multicellular, and some can be either. Some do photosynthesis, while some eat other organisms. How can you break these up into phyla, classes, orders, families, genera, and species when they are all so different?

You might do it by common ancestor; let their genes do the talking. We are learning more and more about who begot who – this is the study of cladistics. But if you break down protists into their clades – they don’t seem to make sense. Organisms that look or act similar might be in different clades, with wildly different organisms linked close together.

Alternatively, you might divide them up based on the characteristics, as Linneaus did - the animal-like protists in one phylum, the plant-like protozoans in another. But this may separate genetically related organisms into very different phyla. Same problem. How about by the way they get around? Some use flagella-like undulipodia, some use undulipodia called cilia, some use cytoplasmic crawling called pseudopodia, and others are immotile. Again, disparate organisms may be lumped together just based on their preferred mode of travel.

The idea of the "phylum" is to place the organisms in categories so that they are “more related to each other than they are to any other group.” Wow, that sounds scientific. Related based on what? We just discussed motility, genetics, and physical characteristics or behaviors.


The Kingdom Protista sits between the modern plants,
animals, and fungi, and the ancient prokaryotes. As such,
they end up being a catch all group. The right image
shows how some people group the protists based on
undulipodia characteristics, not ancestry.
And this assumes that we even know how related they are to each other and to organisms outside each phylum. Genome studies haven’t even begun to get close to establishing the ancestral relationships between all the organisms.

So we guess. And then we change things as new information becomes available. The work never ends, and the students never get to just memorize the categories.

As of today, some scientists classify protists based on a combination of the characteristics above. In the system I like best, there are 15 phyla, and we can roughly divide them as we show below. But there are six different phyla just for the protists that perform photosynthesis! The reason I like this system best -it roughly mimics the way they use undulipodia. And this is what we’re interested in today.

Kingdom Protista contains the organisms that seem to have made the most obvious uses of undulipodia. Eukaryotic flagella and cilia abound, some protists have both, and some have them only part of the time. There are six phylums of plant-like protists. Many have flagella, none that I could find have cilia. Here are some examples:


Pyrrophyta organisms will bloom and then bioluminesce
in order to scare predators away. Movement in the water
causes vesicles in the dinoflagellate to rupture via action
potential and release the reagents to make light. It’s exactly
the same system that fireflies use.
Phylum Pyrrhophyta The dinoflagellates are in this phylum; they have two flagella, one from that side that beats and one on the posterior that whips more traditionally. Some species of this protist are responsible for the red tides that poison fish and can (and have) killed humans who eat the fish. Other dinoflagellates are bioluminescent and make the water appear to be on fire (hence the phylum pyrro = fire).
             
Phylum Euglenophyta This phylum includes the Euglena gracilis organism shown in the animation at the beginning of the post. These protists also have two flagella, but one of them is reduced and doesn’t stick out. They have an eyespot, perhaps the genesis of our own eye. The eyespot helps them to move away from strong light sources, sources that would overheat them.

Euglena are common model organisms, on this world and in (near) space. They traveled on the parabolic flights to have their flagellar motions studied in zero gravity. The 2010 publication that resulted from the experiments showed that the process of beating is regulated and physiologic, as the change from hypergravity to microgravity stopped the flagellum from moving. The opposite change in gravity reoriented the cells and they started swimming to the bottom of their tank again.

The remaining phyla of plant-like protists can be included in a supergroup called the Chromista (colored organisms).  In terms of their undulipodia, the chromists tend to have two flagella, one on each end. The forward flagellum is usually longer and has lateral growths called mastigonemes. The best description for this type of flagellum is that it looks like Christmas tinsel.  The back flagellum is shorter and smooth.


These are the phyla of the Chromista; the colored protists.
Problem is, not all of them are colored and some colored
protists aren’t included in this group. Top right and bottom
left are the chlorophyta, the green algae. These are the most
recognizable algae. The bottom right is the diatoms, they have
the most interesting shapes. Look them up.
The Chrysophyta are the golden algae and diatoms. The diatoms are only flagellated when undergoing sexual reproduction, and is just the male gametes that have the flagella, sounds like male gametes in mammals doesn’t it?
  
Green algae are the ones we recognize; they belong to the Chlorophyta phylum. These are the ancestors of the land plants, and some have flagella in all stages, while others only have flagellated gametes.  We will see soon how some land plants still have flagellated gametes.

Brown algae belong to the Phaeophyta phylum. They are exceptional amongst the protists because every organism in this phylum is multicellular. No brown algae live as individual cells. Kelp is an example of brown algae. Kelp forests are multicellular example of brown algae thalli, growing to 40-60 m (130-200 ft) in height! Kelp forests are some of the most productive ecosystems on earth.      
The gametes of the brown algae are flagellated like in most of the other chromists. A 2014 study has started to look at the flagella of the chromists, using brown algae as the model organism. The study found that the flagella have functions in motility, signal transduction, and even metabolic activities.  The two different types of flagella had common proteins and proteins specific to each form, for a total of 495 different proteins associated with flagellar function and structure. For instance, only the posterior flagellum has a protein that senses blue light, and may be used for steering the organism. 


The Rhodophyta are where we get food stuffs. On the left
represents agar that can be used to make things that are like
Jello, it fills the role of the gelatin. In the middle, agar is also
used as a polysaccharide source of nutrition for growing
bacteria in the lab. On the right, nori is a rhodophyta
seaweed used in sushi.
Finally, Phylum Rhodophyta is the last of the Chromists. They are known as red algae, but you may know this protist better as seaweed. We saved them for last because they are the biggest exception in the plant-like protists.

If you’ve eaten Japanese sushi rolls, then you’ve eaten red algae in the nori that the rice and fish are wrapped in. Nori is made from several species of red algae of the genus Porphyra. Not a sushi fan? How about ice cream? Carageenans that make ice cream smooth also come from red algae.

Ice cream is reason enough to love the red algae, but there’s more. A 2014 study indicates that one compound found in the Porphyra is a strong antibiotic. Studies of 1,8-dihydroxy-anthraquinone from this red algae genus can disrupt the cell wall of Staphylococcus aureus. This is hugely important, since many strains of S. aureus (like MRSA and VRSA) are now resistant to most existing antibiotics.

Rhodophyta algae are red because although they use some chlorophylls for photosynthesis, they also use phycoerythrins and phycocyanins. Interestingly, these are the same pigments that are present in the cyanobacteria. This suggests that there is an ancestral link. The link is supported by one other factoid. Both cyanobacteria and red algae lack undulipodia!


The seaweed Rhodophyta organisms often live in the tidal
pools. The spongy material in the stalks and “leaves” is the
agar and is related to the mucin product that attaches to the
male gametes as they are released. I couldn’t find a picture of
the gametes with their mucin tails, so this will have to do.
The male gametes of red algae are at a deficit; they don’t have flagella to swim toward the female eggs. They must relay on water movement to disperse them. An older study showed that when the male spermatia are released by the discharge from vesicles, the vesicle contents can hang on to the gametes and form mucin appendages. These are then more likely to be moved around by the water.

Whatever it is, the system seems to work. A 2014 study found that fertilization success was dependent on male organism biomass, but neared 100% when there were relatively few male gametes present. This was hypothesized to be possible because low tides in the tidal pools where the organisms live greatly increase the chances of male/female interaction and fertilization. Seaweed takes advantage of the moon’s effect on the tides to ensure reproductive success – who needs flagella!?

So far we have met protists that use flagella at some point in their life cycle (except for the red algae). Notice that none of them have used cilia. Next week, how about the animal-like protists? I bet there are some exceptions there as well.




Fu G, Nagasato C, Oka S, Cock JM, & Motomura T (2014). Proteomics Analysis of Heterogeneous Flagella in Brown Algae (Stramenopiles). Protist, 165 (5), 662-675 PMID: 25150613

Wei Y, Liu Q, Yu J, Feng Q, Zhao L, Song H, & Wang W (2014). Antibacterial mode of action of 1,8-dihydroxy-anthraquinone from Porphyra haitanensis against Staphylococcus aureus. Natural product research, 1-4 PMID: 25259418

Maggs CA, Fletcher HL, Fewer D, Loade L, Mineur F, & Johnson MP (2011). Speciation in red algae: members of the Ceramiales as model organisms. Integrative and comparative biology, 51 (3), 492-504 PMID: 21742776

Strauch SM, Richter P, Schuster M, & Häder DP (2010). The beating pattern of the flagellum of Euglena gracilis under altered gravity during parabolic flights. Journal of plant physiology, 167 (1), 41-6 PMID: 19679374




For more information or classroom activities, see:

Kingdom Protista –


Euglena –

Red tide –

Pyrrophyta –

Kelp –