Showing posts with label psychrophile. Show all posts
Showing posts with label psychrophile. Show all posts

Wednesday, December 9, 2015

Snow Saves Lives

Biology concepts – subnivean zone, chionophiles, antifreeze proteins, UV vision, snow blindness, photokeratitis


Rudolph the red nosed reindeer didn’t start as a song or
even a Rankin and Bass stop motion special. It was a story
published by the Montgomery Ward Stores.  The author’s
brother-in-law was Johnny Marks, the king of Christmas
songs. He adapted the story into a song that was recorded
by Gene Autry in 1949. Then it went viral. The TV
special didn’t appear until 1964.
Rudolph with his nose so bright – only he could lead Santa’s sleigh through the snowstorm. What a great mutation, a beaming red nose – although that might be quite the draw for predators. In real life, reindeer have indeed evolved to overcome the snow, but also to rely on it. You could even speculate that Rudolph would die without the snow.

This leads a biologist to ask, "Just who and what is depending on the snow; how does snow affect the living world?" Many animals have snow in their name, but that isn’t always a good clue. The snowy egret and the snow crab are examples.

The snowy egret is called that only because of its white plumes, while the snow crab is so named because its hunting season is when the snow is the deepest. Mike Rowe, the hardest working man in show business since James Brown, taught watchers of The Deadliest Catch that the snow crab is better called the opilio crab (Chionoecetes opilio). Fisherman that go to sea to put them on your table are a breed unto themselves.

Egrets and crabs don’t help us to investigate the question of the effects of snow on life. The easy observation is that snowy winters are something that organisms have evolved to overcome or even use to their advantage. They have developed ways to survive the harsh conditions of the snowy season or to exploit the white stuff.


The snow leopard is unique amongst cats. It has blue-green or
gray eyes, while most other cats have yellow or black eyes. It
also can’t roar. It has a partially ossified (turned to bone)
hyoid cartilage, which was thought to be the key to cat roars,
but it just can’t manage more than a screech. Maybe it just
doesn’t feel like roaring – or maybe it fears an avalanche.
The snow leopard (Panthera uncia) is an animal that overcomes snow. It has evolved large paws to act as snowshoes. The snow leopard can easily stalk prey and run in snow as deep as 36 in (1 m). Their paws also have fur on all surfaces, to insulate their footpads from the cold and wet snow.

On the other hand, their markings are better suited for their preferred living and hunting grounds. They aren’t nearly as white as you would expect. They like to live on rocky ledges and they descend into the forests to hunt prey when the weather gets really cold (because that’s where the prey are), so their brown tints and spots help them blend in to both habitats.

The lemming is an example of a small mammal that exploits the snow for cover, others being mice, voles, and shrews. The Norway lemming (Lemmus lemmus) moves from the low mountainsides up to higher elevations (opposite of the snow leopard for obvious reasons) as the snow falls. They don’t live underground, although they may nest there, but they don’t live on top of the snow either.

The lemmings dig vast networks of tunnels in the snow where it meets the ground. This is called the subnivean environment (sub = below, and niveus is Latin for snow), and they race around looking for vegetation to eat and other lemmings with which to mate. The many openings in the snow may seem to be doors to the subnivean environment, but the lemmings rarely come out of the snow. They are more likely vents to release carbon dioxide from lemming breath and plant decomposition.

Lemmings don’t jump off cliffs in large numbers when they
get older. That is a myth. However, they may be a little
challenged when they run for new feeding grounds in great
numbers – some seem to find their way to cliffs and accidently
go over head first. They are solitary except for mating times,
as is seen here. He’s taking flowers to his girl.

Some animals, like some big cats and large owls have evolved a hearing sense that allows them to pinpoint lemmings under the snow, but the subnivean tunnels work well enough that lemming populations usually skyrocket every 3-4 years, and then plummet as resources become scarce. Their success is in some ways their downfall.

And speaking of falling, the lemmings are also responsible for some human tragedies. When the temperatures fluctuate and the tunnels remodel with ice and snow, the layers of snow can become unstable. The dense snow above the tunnel system will crush and slide off the subnivean layer and …. look out below, here comes the avalanche. And I thought skiers that flock to resorts in order to fall off the mountain repeatedly were the lemmings!

You wouldn’t expect it, but some small arthropods (insects and such) have found ways to live in the snow. When a warmer winter day pops up, so do the snow fleas (Hypogastrura nivicola). You will see them as black specks on the snow – appearing in the thousands at the bases of trees. They aren’t really fleas at all, but a species of springtail (see picture). The reason they come out is not known exactly, but I think that any snow melt due to warmth might drown them in their below ground hiding places.

On the left is a convention of snow fleas discussing the merits
of elm leaves as decaying foliage – or maybe that’s the buffet.
On the right is a single snow flea, called a springtail. The back
legs can apply a load and then are released. They spring from
place to place, but they aren’t “fleaing.”

Snow fleas have an antifreeze protein that keeps them alive over the winter. This isn’t an exception, many animals have chemical mechanisms to prevent freezing, but the protein in snow fleas is unlike any other. The snow flea anti-freeze protein (sfAFP) may serve humans as well. See the post here for more on anti-freezing mechanisms, and here to show that snow midges are the largest animals in many parts of cold Antarctica.

A 2008 project produced the protein in a laboratory and showed that it may be possible to use it to preserve organs for transplant a longer time. Storage at cooler temperatures would allow for longer shelf lives for organs, but they can become damaged by ice crystal formation. The researchers also made a version of the protein using D-amino acids. We have talked about these before – but here they work to our advantage, by making the protein less susceptible to enzymatic degradation, while still providing antifreeze function.           

Snow melt mosquitoes, on the other hand, are winged. Living from northern California up to the arctic tundra, snowpool Aedes mosquitoes (many species) lay their eggs and their larvae develop in the pools of melted snow as the weather warms. This gives them a head start on the rest of the mosquito world. It would seem many forms of life have found ways to exploit snow.

Watermelon snow is caused by an alga that grows in the
snow. Chlamydomonas nivalis is a green algae, but it also
produces a lot of anthocyanins (red) pigments. They
absorb the sunlight and generate heat. This melts some
of the snow and gives the algae the water it needs to grow.
The algae serves as a food source for other animals
during the winter, including the snow fleas.

Then there are the chionophiles (chioni is Greek for snow, and phile = lover). We have talked about the psychrophiles, organisms that prefer cold temperatures, but chionophiles need the snow to survive.

It may seem counterintuitive, but many organisms need the snow to keep them warm. It’s the wind that blows heat away from around the skin, so a layer of snow actually helps trap heat and protect form the wind. Lemmings give snow a big thumbs up (if they have thumbs) for snow as an insulator.

It isn’t just animals that need a “blanket” of snow to retain heat and protect from the wind. Winter wheat needs the snow, but for several reasons. Sure, the snow provides insulation for the young shoots that were planted in the late fall and go dormant until the spring. Nothing worse than frozen wheat.

But the snow also provides a source of water when it melts. This loosens the ground to give the wheat plants strength to push through the earth, and for early water for growth. Snow also gives stability to the young plants out on the plains. Lots of wind out there, enough to knock down and break the fragile plants when they are young. A cast of snow surrounding the stem helps keep them upright. The wise man says, “ Rain versus snow, the wheat doesn’t know the difference, but the farmer wants snow in the winter.”


Winter wheat is susceptible to grey snow mold, even though
it can produce antifungal compounds. This can decimate
entire crops of wheat, especially if the snow fall lasts deep
into the spring. The bottom image shows a close up of pink
snow mold on grass. This is a particular problem on golf
courses – I’m not going to cry over that.
Growing in the snow has also created a problem for wheat, a problem caused by another snow grower. Snow molds (gray or pink) remains dormant in the summer, and only start growing when covered by a layer of snow. As the snow melts in the spring, the damage is down, causing circular patches of gray or brown grass, including wheat, which is a grass.

Snow mold doesn’t attack plants on exposed soil – but they may be killed by the more extreme temperature. They do attack where there is snow, and there is more damage in the deeper snow banks – it seems they do their damage under cover of snow only – more snow, longer time for complete melt, more damage.

The snow mold excretes its antifreeze proteins, not to prevent itself from freezing, but to keep ice crystals from forming or altering around the fungus. Perhaps they are protecting their food to keep it growing and a good source of nutrients; often that food is wheat. But wheat also has tricks. A 2002 study shows that winter wheat produces several proteins that inhibit the growth of the mold.

Now back to Rudolph. To understand his exception with snow, we first need to talk about photokeratitis (photo = light, keratin = the protein found in cornea, and it is = inflammation), better known as snow blindness. For Eskimos and other humans, the 90% of the sunlight’s UV waves bouncing off the snow is enough to burn the cornea and lead to fuzzy vision or even blindness. The cornea is a protective structure, keeping the UV rays from injuring the retina.


This is part of the study that discovered UV vision in
reindeer. I get the part where they examine the retina,
but what I need to know is how they get them to read
the lines of letters on the eye chart.
Other animals are prone to snow blindness as well. Polar bears have a nictating membrane to protect the eye, but the reindeer have gone much further. Of all the mammals, only the reindeer actually sees in the UV range.

Their cornea doesn’t stop UV rays from entering the eye, yet they don’t suffer damage. The pigments of their retina absorb the energy and convert it into images, just like our eye does with visible light only. A good study would determine how they are protected – you work on that. It might be related to a new study that shows that reindeer eyes change color with the seasons, becoming blue in winter.

Being able to see in the UV range is what saves the reindeer. Predators that blend in with the snow still show up easily in UV, and well as urine stains in the snow that mark the territories of predators or other reindeer. Using his UV vision, the reindeer is better protected from predation. And it only works because of the snow – no snow, no reflected UV light. And thus we learn…. snow saved Christmas.

Next week, the biology of one of the original Christmas gifts.



Hogg C, Neveu M, Stokkan KA, Folkow L, Cottrill P, Douglas R, Hunt DM, & Jeffery G (2011). Arctic reindeer extend their visual range into the ultraviolet. The Journal of experimental biology, 214 (Pt 12), 2014-9 PMID: 21613517

Kondo H, Hanada Y, Sugimoto H, Hoshino T, Garnham CP, Davies PL, & Tsuda S (2012). Ice-binding site of snow mold fungus antifreeze protein deviates from structural regularity and high conservation. Proceedings of the National Academy of Sciences of the United States of America, 109 (24), 9360-5 PMID: 22645341

Pentelute BL, Gates ZP, Dashnau JL, Vanderkooi JM, & Kent SB (2008). Mirror image forms of snow flea antifreeze protein prepared by total chemical synthesis have identical antifreeze activities. Journal of the American Chemical Society, 130 (30), 9702-7 PMID: 18598026

Kuwabara C, Takezawa D, Shimada T, Hamada T, Fujikawa S, & Arakawa K (2002). Abscisic acid- and cold-induced thaumatin-like protein in winter wheat has an antifungal activity against snow mould, Microdochium nivale. Physiologia plantarum, 115 (1), 101-110 PMID: 12010473



For more information or classroom activities, see:

A great book on the mechanisms of survival in the winter and how cold and snow affect life is entitled
           Winter World, The Ingenuity of Animal Survival
           Bernd Heinrich
           2003
           ecco publishing, an imprint of Harper-Collins
           ISBN 0-06-019744-7

Snow blindness –

Reindeer –

Subnivean layer –

Winter wheat –

Snow mold –

Watermelon snow -



Wednesday, November 13, 2013

Covering All Our Bases

Biology concepts – nucleoside, tRNA, RNA editing, nonstandard bases, DNA oxidation


Specialized pieces are needed to best build special Lincoln
Log structures, like this castle. This is much like how
specialized nucleosides are needed to carry out special
functions of RNAs. Really – a log castle? Wouldn’t the
Black Knight just burn it?
Last week, we used Lincoln Logs as a model for the different nucleic acids. The small logs mean little until you put them together in an order of which you can make – a cabin, for example. This week we can take the analogy a little further.

Some editions of Lincoln Logs have specialized pieces for building special buildings. These buildings have different purposes, like a sawmill or a bank, and the specialized pieces help them carry out their function of being that building.

Low and behold, there are special building blocks for building specialized nucleic acid structures; usually these are RNAs for which the usual building blocks just won’t do. These are the exceptions to the nucleotide rules of A, C, G, and T for DNA and A C, G, and U for RNA.

There are a few different nucleotides located in DNA molecules, but to date all these have been found to be damaged bases. Oxidized guanosine bases have been the most commonly identified mutations, because guanine is more susceptible to oxidation than the other bases. However, a recent study has identified a 6-oxothymidine in the placental DNA of a smoker.  

More than 20 oxidized DNA bases have been found at one time or another. Their importance lies in their inability to direct correct base pairing in a replicating DNA or a transcribed RNA. In particular, 8-oxoguanosine in a DNA molecule often base pairs with A instead of C, while an oxidized 8-oxoguanosine nucleotide (damaged before it is incorporated into a DNA) will often be put in where a T should rightfully have been placed.

Both of these problems would lead to mistakes in replication or transcription. Some of these mistakes could be in places that matter. If they change a codon, they might cause the wrong amino acid to be incorporated and the resulting protein might be nonfunctional. Or they could create or destroy a stop codon or a splice site. These would definitely alter the resulting protein. Mistakes like this spell disease or cancer.

The top left image shows how 8-oxoguanine is produced by
oxidative damage or radiation. The bottom left shows it
effects on DNA. There can be a miscmatch base pairing
between G and A instead of G and C when the G is damaged.
One possible result is shon on the right. Huntington’s
disease may involve the mismatching of unrepaired
8-oxoguanosines with adneosines. As a result, areas of the
brain are lost and the fluid filled sinuses are enlarged.

Oxoguanosine has been the most studied of the oxidized bases, and several diseases have been linked to this mutation. Many cancers have shown this mutation – leukemias, breast cancer, colorectal cancer, etc. But in addition, things like Parkinson’s disease, Huntington’s disease, Lou Gherig’s disease (ALS), and cystic fibrosis have been correlated with 8-oxoguanosine.

Don’t make the mistake of assuming that an 8-oxoguanosine is the cause of any or all of these diseases, most have many potential causes. The point is that this mutation may contribute to these diseases in some cases. The point then is to find out how to better prevent or repair them. However, your body is pretty good at doing this itself – if everything is behaving normally.

There are specific repair pathways dedicated to removing and replacing oxidized bases (base excision repair or BER) or for nucleotides that contain oxidized bases (nucleotide excision repair or NER) in DNA. In RNA, the major process to deal with 8-oxoguanosine is to destroy the damaged RNA. There are actually several overlapping and redundant repair pathways for 8-oxoguanosine, suggesting that this mutation is particularly damaging and must be dealt with for proper cell function.

It is when the body’s sensing and repair mechanisms don’t work that the problems begin. Therefore, science needs to find better ways to tell when the natural processes aren’t working and develop artificial ways to reverse the damage. A 2013 review is showing the way to detecting mutated guanines in bodily fluids and tissues.

Specifically, this study looked at methods of detecting 8-oxoguanosine levels in plasma, urine, and cerebrospinal fluid and what those changes might mean. The levels found represent a balance between the production and repair of the mutations, so an increase means that more mistakes are being made, or fewer are being repaired. Either way, it means that something must be done.


This is a cartoon showing RNA processing. IT IS NOT TO BE
CONFUSED WITH RNA EDITING!! In processing of eukaryotic
mRNAs, the front end (5’ terminus) is capped so it will last
longer. Then the end is augmented with a bunch of A’s, called
the poly-A tail. Finally, the introns are removed and the
exons (the parts that code for a protein) end up in a
continuous sequence.
But what about nonstandard bases that are actually supposed to be in nucleic acids? The vast majority of these are found in the RNAs and help to point out yet another exception. You think that the RNA transcribed from DNA is the same RNA that functions or is translated to protein? Not always.

RNA editing takes place all the time, where RNA bases are changed after the RNA is transcribed from DNA. In the majority of cases, the RNA editing modifies a standard nucleoside to another standard nucleoside, or add/subtract nucleotides.

Insertion/deletion edits for uracils can increase or decrease the length of the transcript. The mRNA is paired with a guide RNA (gRNA) and base-pairing takes place. For insertion, when there is a mismatch between the mRNA and the gRNA, the editosome inserts a U, so the mRNA transcript gets longer. In deletion editing, if there is an unpaired U in the mRNA, it gets cut out, so the transcript gets shorter.

This was first discovered in a parasite called Trypanosoma brucei, the causative agent of African Sleeping Sickness. There are so many positions at which these insertions/deletions take place that it has come to be known as pan-editing.

In other cases, the editing takes the form of C being replaced by a U. In some cases this results in a protein sequence different than that coded for by the DNA - on purpose!! If that isn’t an exception, I don’t know what is. Other times, the changing of a C to a U creates a stop codon.

In the human apolipoprotein B transcript, the intestinal version undergoes the C to U editing and creates a stop codon, so the apolipoprotein B is 48 kD in mass (B48). In the liver, no editing takes place, so the protein is much larger (B100).


Here are two examples of RNA editing. The top image
shows the insertion/deletion mechanism, where a guide
RNA binds to the mRNA and where there are mismatches
a U is inserted and where there are unmatched U’s, they
are removed. The bottom example is an example where
a base is changed, and this changes the codon, so a
different amino acid is inserted when translated.
There is a lot of C to U editing in plants – I mean, a lot. So much editing goes on that there is now a 2013 database and algorithm to do nothing but predict C to U and U to C edits. Yes, there are U to C edits as well, but only in plant mitochondria and plastids. As far as is known, U to C edits work to destroy stop codons.

Then there is A to I editing. Wait you say, there’s no I in nucleic acids (well, there are actually two “i”s, but you know what I mean). “I” stands for inosine, the first specialized Lincoln Log and our first nonstandard nucleoside. Adenosine (A) is deaminated to form an inosine (I).

There are many functions for inosine editing. Changes from A to I in mRNA alter the protein made since the inosines get read as G’s. Genomically coded A’s end up being read as G’s in the mRNA, and this it changes the gene product! We have many more inosine changes than other primates do. Many of these A to I edits in humans are related to brain development and are a big reason why we are smarter than chimps.

There is also A to I editing in regulatory RNAs called miRNAs (micro RNA). The miRNAs suppress (prevent) translation of some transcripts, but editing of the pre-miRNA makes it bind less well to protein complexes that process the pre- to mature miRNA. More editing mean less binding of miRNAs, which leads to decreased regulation, more transcript translation, and increased protein. This may be one way A to I editing increases human brain power.


Micro RNA is important for controlling the amount of a
transcript that will be translated to protein. The miRNA
can be edited, which will change the amount that is
processed by the protein complex, and therefore changes
the amount that is incorporated into the complex
that will degrade mRNAs.
The search is on to discover the regulation of which A’s get turned to I’s in several types of RNAs ; called the inosome (like genome). The inosome is yet another code we haven’t figured out yet. But inosine doesn’t have to be in a nucleic acid to have an effect. Sometimes it functions just by itself.

Inosine and adenosine accumulate extracellularly during hypoxia/ischaemia (lack of oxygen or blood flow) in the brain and may act as neuroprotectants. A new study extends this protective action to the spinal cord in rats in a hypoxic environment. To characterize hypoxia-evoked A and I accumulation, they examined the effect of hypoxia on the extracellular levels of adenosine and inosine in isolated spinal cords from rats. "Isolated" means the rats and their spinal cords were not necessarily in the same room at the time - so it could be a while before this helps humans.

But perhaps the most common use for I is to alter tRNA binding to amino acids and to the target codons. A to I editing can occur in the anticodon, and change which amino acid is placed in the growing peptide. This is especially true in many organisms for the amino acid isoleucine. Many tRNAs will insert an isoleucine into the protein only when the anticodon of the tRNA has been edited to contain an I in the first position (equivalent to the wobble position of the mRNA codon).


This menacing creature is a worm that lives at the bottom
of the Ocean in the Sea of Cortez. It thrives in the methane
ice on the ocean floor, making it a psychrophile. It can’t
even survive or reproduce if keep above freezing.
What is more, there are other nonstandard nucleosides that serve similar functions, usually with isoleucine or methionine amino acids. Agamantidine is present in many archaeal anticodons and codes for isoleucine. Agamantidine is also present at other points in the tRNA for isoleucine and is important for adding the isoleucine amino acid to the tRNA.

Other nonstandard (modified) nucleosides also work in tRNAs. Lysidine, dihydrouridine, and pseudouridine are some of the more common specialized Lincoln Logs – or maybe we should stick to calling them nonstandard nucleosides. They can be found in the tRNAs of organisms from each of the three domains of life (archaea, bacteria, and eukaryotes). For example, psycrophiles – organisms that grow at very low temperatures – have 70% more dihydrouridines because they help the tRNAs to flex as they need to, even at subfreezing temperatures.

Found mostly in tRNAs, but not exclusively in tRNAs, there are over 100 non-standard nucleosides. Many times they function to increase tRNA binding to transcripts via the anticodon-codon, or increase the binding of the amino acid to the tRNA. They ultimately work to increase translation efficiency. They are weird and are exceptions, but we can’t live without them.

Next week we can spend some time talking about exceptions in the realm of lipids, the last of our four biomolecules.


Paz-Yaacov N, Levanon EY, Nevo E, Kinar Y, Harmelin A, Jacob-Hirsch J, Amariglio N, Eisenberg E, & Rechavi G (2010). Adenosine-to-inosine RNA editing shapes transcriptome diversity in primates. Proceedings of the National Academy of Sciences of the United States of America, 107 (27), 12174-9 PMID: 20566853

Takahashi T, Otsuguro K, Ohta T, & Ito S (2010). Adenosine and inosine release during hypoxia in the isolated spinal cord of neonatal rats. British journal of pharmacology, 161 (8), 1806-16 PMID: 20735412

Lenz H, & Knoop V (2013). PREPACT 2.0: Predicting C-to-U and U-to-C RNA Editing in Organelle Genome Sequences with Multiple References and Curated RNA Editing Annotation. Bioinformatics and biology insights, 7, 1-19 PMID: 23362369

Poulsen HE, Nadal LL, Broedbaek K, Nielsen PE, & Weimann A (2013). Detection and interpretation of 8-oxodG and 8-oxoGua in urine, plasma and cerebrospinal fluid. Biochimica et biophysica acta PMID: 23791936

Wang P, Fisher D, Rao A, & Giese RW (2012). Nontargeted nucleotide analysis based on benzoylhistamine labeling-MALDI-TOF/TOF-MS: discovery of putative 6-oxo-thymine in DNA. Analytical chemistry, 84 (8), 3811-9 PMID: 22409256



For more information or classroom activities, see:

RNA editing –