Showing posts with label cytoskeleton. Show all posts
Showing posts with label cytoskeleton. Show all posts

Wednesday, October 28, 2015

It’s All in the Numbers - Sizes in Nature


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

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


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

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


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


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




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

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


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

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

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

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



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



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

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


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


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


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

Wednesday, January 28, 2015

Crawling To The Top


Biology concepts – characteristics of animals, undulipodia, gametes, nematodes, roundworms,


Yes, a sponge is an animal – just like a barracuda, a
platypus or a that weird nephew of yours. They are
multicellular, loosely organized into a couple tissues,
and eat other organisms. You can see how they filter
feed in this demonstration. Not so different from
that nephew.
Sponges and birds – they’re both animals, but would you know it to look at them? Sponges are sessile (except for the exceptions), and birds can’t breathe under water (no exceptions). Birds eat worms and lay eggs – most people don’t know what the heck sponges do. Yet they’re both animals. Are there characteristics that all animals have in common?

Yes there are, thanks for asking. Animals are all eukaryotic and diploid (2 of each chromosome). For the most part, our cells have nuclei and organelles and all but our gametes have two copies of each chromosome.

Animals are all multicellular - a unicellular organism that acts like an animal is still called a protist. Because they are multicellular, animals have the capability to have cells of different types that organize themselves into tissues and organs, like we have discussed before as a characteristic of life.

Another attribute of animals is that they can move. True, sponges are sessile when attached to rocks or coral reefs, but they do have motile cells and motile life cycle stages. Birds are very motile unless dead.

One other thing animals have in common is how the male gamete finds the female egg. Male gametes have a flagellum that allows them to swim toward the chemical signals that show them where the egg is located. True, we have learned that protists and some lower plants also have gametes that swim with flagella or cilia, but animals characteristically have flagellated male gametes. But of course, given the nature of this blog, there must be an exception.


Nematodes are round worms; helminthes are just
one group of parasitic roundworms. They represent a
turning point in animal development. They sort of have
an internal body cavity (they are pseudocoelomates),
they sort of have a head (start of cephalization) and
they sort of have body symmetry (starting to be
bilateral).
The roundworms, phylum Nematoda, are our exception for the day. Their male gametes can’t swim! But who cares, it hasn’t seemed to slow them down. Which makes us ask why everyone else goes to the trouble of producing gametes with flagella – it’s expensive. Shall we investigate?

In every other phylum of animals, male gametes use the eukaryotic flagellum to swim their way to the egg. Using exactly the same structure that we have talked about before, male gamete flagella have basal bodies and axonemes made of microtubules. The microtubule filaments slide past one another to produce their beating movement.

Look as hard as you want, but round worms don’t have basal bodies or flagella. They do have centrioles and centrosomes used for mitosis, but none of them mature into basal bodies for flagellar assembly, In fact, the male gametes of nematodes carry one centrosome (with its centriole pair) to the egg and form the basis of all centrioles in the baby roundworm. Weird - why no basal bodies? – I have no idea, but evolution approved it.

Instead of flagella for male gamete swimming, nematodes use an amoeboid movement to crawl to the egg. O.K., so they crawl instead of swim. That’s exceptional, but is it really that weird? Well… yes, considering that they don’t contain the most important protein that most cells use to make amoeboid movements.

Actin is one of the major proteins of the cytoskeleton. Actin works mostly in protrusion and contraction of parts of the cell, while intermediate filaments hold the cell’s shape and give it rigidity and microtubules are primarily for movement of proteins and structures throughout the cell.


This short video shows you the movement of C. elegans
male gametes. They are shaped like typical animal male
gametes, they don’t move like typical male gametes, and
they don’t have the same proteins as typical ones. Yet, the
nematode is the most numerous type of animal on Earth.
Actin comes on a two main forms. G-actin is the globular form; it's the monomer. When the monomers are induced to form filaments, like tubulin monomers monomers form microtubules, it's now called F-actin. Quick assembly and disassembly of F-actin polymers from G-actin monomers allows for movement of selected parts of the cell membrane.

So amoeboid cells use F-actin as the way they extends and retracts its pseudopodia. Thus, they crawls along. Nematodes do have cells with G- and F-actin, but the male gametes don’t have any (or very little). But it’s the male gametes that need it to move! What gives?

Instead, male gametes of nematodes use the MSP protein (major sperx protein; my posts get blocked by schools if I use the whole word, so I use gamete whenever possible). A 2014 study shows that MSP proteins are abundant in the male gamete (40% of total soluble protein), and change its distribution and volume as the gamete matures and is activated. When fully activated and in the female oviduct, the MSP of the male gamete assembles and creates pseudopodia just as actin would in any other amoeboid cell. Another 2014 study shows how it then senses the egg.

Does the inability of nematode male gametes to swim to the egg cost them in terms of reproductive advantage and evolution? Heck no.

Nematodes, ie. roundworms, are the most successful animals on Earth. They live inside every other living thing, and just about everywhere on Earth. There are free living worms, parasitic worms, and worms that eat decaying tissue. There are roundworms that eat nothing but other roundworms.


Nematodes are famous for the parasitic infections they
cause. On the left is a root knot worm. Nematodes are
responsible for more than 15% of crop loss each year.
On the top is one of the filarial worms that cause river
blindness. On the bottom is a grasshopper worm (Mermis
nigrescens) that grows to fill the entire body cavity.
In strictly numerical terms, it’s amazing that we aren’t nematodes. In truth, four out of every five animals are Earth are roundworms! Long ago in classification, all the roundworms used to be lumped together; later on they were grouped according to head size. With the advent of molecular typing, there are more than 25,000 species, and estimates are for more than a million. Compare that to 5000 known mammal species.

Sure there are many species, but that number is dwarfed by the number of individuals of some species. One 2013 study from England gives us a clue. In just the city of Bristol, dogs drop about four tons of doo-doo each day. That four tons holds an astounding 3.7 billion Toxicara eggs. Every two days the dogs of that one city squat out the equivalent of the human population of the entire world. Man, is that a bizarre visual.

This isn’t useless information, considering that the eggs become worms that can cause blindness in people who accidentally eat contaminated dirt, or those who eat dirt on purpose for that matter. Indeed, many nematodes are parasites of humans and cause much disease, but this isn't our focus today. If you like that sort of weird disease stuff (and I most certainly do), I suggest you Google ascariasis, hookworm, onchocerciasis, strongyloidiasis, filariasis, or trichinosis.

Nathan Cobb of the U.S. Bureau of Plant Industry gave a very apt description of the numbers and distribution of nematodes in 1915. He said that if you eliminated every bit of matter on Earth other than nematodes, an onlooker could still recognize our world.

There are enough nematodes in the dirt that we could distinguish mountains and valleys. There are more in the cities, so we would know where they had been. Nematodes are numerous enough in living things that we could identify where every living thing had once stood. And yes, the onlooker could see humans, we ingest billions over our lifetime and more than two billion people are infected with Ascaris lumbricoides at any one moment.


At least 2 billion people are infected with this worm
(Ascaris lumbricoides) at any one time. The pictures of
the infection are just too gruesome, so I show his smile
instead. Look can up the pictures for yourself if you
haven’t eaten recently.
A. lumbricoides is the largest nematode by mass which infects humans. Females can be 40 cm long and the diameter of a No. 2 pencil. The worm takes quite the tour through you. From your stomach to your liver to your lung move the young larva. You cough them up and swallow them, and they mature in the gut. There they grow, fall in love, and mate. Yep—pretty gross.

The smallest nematodes are in marine sediment. Desmoscolex sp. and Greeffiella sp. are only 80 µm long, which means that if 30 of them stood on each other’s shoulders, they would only be as tall as a dime is thick.

At the other end of the spectrum, the largest known nematode is Placentonema gigantissima, which can reach around 30 feet long in the placenta of its host, the sperm whale.

The placenta of a whale, tree root balls, in water, mud, fruit, nematodes literally live everywhere except in the skies – even though they do find themselves in the sky every day - inside birds. Roundworms have been found in the crevices of South African gold mines two miles below the Earth’s surface – at 48˚ C (118.5˚ F) and 1000x atmospheric pressure. No other animal has been found living in stone at these depths and conditions.

Many roundworms live in the soil, and perhaps the greatest number live in the sediment of ocean floors. Because there are some many different kinds of nematodes, it isn’t surprising that many have very developed specific niches.

Biologist Colin Tudge stated in his book, The Variety of Life that half the animal species on Earth have a nematode that lives only in that species. Even beyond animal hosts, there is evidence of a nematode species that lives one place on Earth – in the felt of German beer coasters.


The German beer mat worm doesn’t just live on the
bottoms of beer soaked coasters. But they do like yeast
for dinner. I like this one for Apostelbrau in Germany
because the brewery has been located in Worms, a city
between Frankfort and Stuttgart, since 1713.
The German beer mat nematode, Panagrellus redivivus, was first named Chaos redivivum by none other than Linnaeus himself. Its story is told in a nice 2009 commentary. While nematologist Cobb was aware of this worm only from felt beer mats, in truth they live in rotting peaches, in book binding paste and in other places as well.

Nematodes can be political was well. The giant kidney worm, Dioctophyma renale, is found in many different mammal species, such as dogs, cats, minks, humans, etc. But the infection is almost always just in the right kidney. Since this worm is usually ingested via contaminated fish, the right kidney might be more susceptible simply because it's closer to the liver and stomach – or maybe they’re Democrats.

All this talk about undulipodia and nematodes has been perhaps a little misleading. Nematodes do have cilia on a very small subset of the their neurons, but they aren’t motile cilia. These are sensory cilia, also called primary cilia. They are our topic for next week.




Smith HE (2014). Nematode sperm motility. WormBook : the online review of C. elegans biology, 1-15 PMID: 24715710

H. Ferris (2009). The beer mat nematode, Panagrellus The beer mat nematode, Panagrellus redivivus: A study of the connectedness of scientific discovery J. Nematode Morphol. Syst., 12 (1), 19-25

McKnight, K., Hoang, H., Prasain, J., Brown, N., Vibbert, J., Hollister, K., Moore, R., Ragains, J., Reese, J., & Miller, M. (2014). Neurosensory Perception of Environmental Cues Modulates Sperm Motility Critical for Fertilization Science, 344 (6185), 754-757 DOI: 10.1126/science.1250598

Morgan, E., Azam, D., & Pegler, K. (2013). Quantifying sources of environmental contamination with Toxocara spp. eggs Veterinary Parasitology, 193 (4), 390-397 DOI: 10.1016/j.vetpar.2012.12.034

Sepsenwol S, Ris H, & Roberts TM (1989). A unique cytoskeleton associated with crawling in the amoeboid sperm of the nematode, Ascaris suum. The Journal of cell biology, 108 (1), 55-66 PMID: 2910878


For more information or classroom activities, see:

Nematodes –

Characteristics of animals –

Cytoskeleton –