"Life...finds a way"

Echoing Jeff Goldblum's famous quote from Jurassic Park, scientists discovered bacterial life in one of Antarctica subglacial lakes!

Antarctic subglacial lakes: Lake Vostok was reached earlier this month, Lake Ellsworth is planned next. 

Lake Vida: this super salty lake sits under 27 m of ice at its thickest point (not a subglacial lake but it is the thickest layer of ice recorded); in 2002, researchers found and thawed microbes that were locked away in ice cores collected in 1996.

--------- Now these are the main subglacial lakes:

Lake Whillans: under 800 meters of ice it is the first subglacial lake discovered to have life! Big finding! It was reached January 28 2013.

Lake Ellsworth: subglacial (~3,400 meters of ice on top!);they started drilling this winter but had to call it off Dec 27th due to technical problems...the equipment needs to be reserviced and who knows how long that will take. Drilling this deep has never been done before and the procedure/technology completely new. What's crazy is that if things had gone according to plan, they would have just about 60 hours to collect all the water/sediment/ice they wanted! After that the hole they made would've frozen completely over...

Lake Vostok: the largest subglacial lake known in Antarctica it sits under a staggering 4,000 meters of ice; in Feb 2012 researchers reached the surface of the lake, no life has been found as of yet but it is still early in the hunt*...

http://feeds.nature.com/~r/news/rss/newsblog/~3/JUXIjXo87pQ/antarctic-researchers-find-life-in-subglacial-lake.html

--------------------------------------------
*News update!
March 7, 2013

I had this entry as a draft for quite some time but this came across my radar today: 

Antarctic Lake Vostok yields 'new bacterial life'

http://www.bbc.co.uk/news/science-environment-21709225

Well, they have found bacterial (what looks to be bacterial at least) life! Lots of press about it, now we wait to see what more the scientific team offers...Where does it fall on the tree of life? What might it be living on? Articles say it has 86% similarity with its closest sequenced relative...is this enough to make a new branch on the bacterial tree? What is it eating down there?

Bacteria do it better

The Economist hath written an interesting article about a recent discovery from a lab here in OSU. The Giovanonni lab studies marine bacteria. Cool enough right? Well, it gets even cooler - with PARASITES!!!

The main bacterium they study, Pelagibacter ubique (pelagi = ocean, bacter = bacteria, ubique = everywhere (ubiquitous), is the most popular member of a larger group of bacteria called SAR11. I can give you all the statistics or you can believe that it's given scientific name is true and that there are more of them than anything else in the ocean. Anyways, a funny thing some people noticed since this bacterial group was described, was that there didn't seem to be any bacteriophages (bacterio = bacteria, phage = to consume) associated with it...

From BIOS Oceanic Microbial Observatory

You may think, Well they are quite small for bacteria so maybe they just avoid encountering phages or Maybe being incredibly minute makes P. ubique hard to infect? But no no no, there are so many of them out there and there are others of similar size with plenty of phages that eat away at them...

Well, rest easy folks, they found them! Now we know it's not that SAR11 has magic anti-infection powers. It's just that no one has found them until now. These researchers did an ingenious study, the methods of which are concisely explained in this Economist piece. They used P. ubique and found it does indeed have phages - and since their are lots of P. ubique (and their SAR11 cousins) out there, there are lots of their phages too. How might this work?

Remember the mid-14th century? Under plague conditions, people whose immune systems could not handle infection died in the masses, taking their genes with them. Those with the fortunate cocktail of immune genes would survive the outbreak, have babies, and continue the human race. A very dramatic case of natural selection. Why am I talking about the Black Death? Why, to bring up The Red Queen Hypothesis. This evolutionary theory (RIP Leigh Van Valen) posits that "it takes all the running you can do, to keep in the same place." And so, immunity traits must keep changing and evolving in order for its host to stay one step ahead of parasites and pathogens. Humans recombine genes during sex and make a kid. Way to go for the kid but the parents are still stuck with the same genes they were born with for the rest of their life -> bummer! Bacteria don't play that. They can swap DNA with each other (conjugation) or just absorb it from the environment around them (transformation)! What a wild and crazy world, huh? As you would imagine, this means a community of bacteria can evolve to adapt rapidly to stressful conditions. And that is exactly what this paper suggests. They suggest that rapid* coevolution in the SAR11 group in response to phage predation has helped lead them to successful dominance of the ocean!

It will be very interesting to see what new research comes of this discovery. Being one of the most abundant things out there in the marine landscape, SAR11 plays a huge role in the microbial food web and in regulating geochemical cycles.



* the Nature article also mentioned studies in which they found recombination rates in the SAR11 group were also freakishly high!

Zhao Y et al. Abundant SAR11 viruses in the ocean. 13 Feb 2013. Nature <http://www.nature.com/nature/journal/vaop/ncurrent/full/nature11921.html>

Leaf Miners

If anyone can tell me what critter made these I would appreciate it! The trail is light pink with a shimmer to it :)

I found this suspicious trail on a hike this past weekend. It looks like someone took one of those glittery gel markers and drew all over a leaf! My botanically-inclined companion informed me this is the work of a leaf miner. The term loosely refers to the larvae of any insect that lives within the leaf and eats the cellulose material. That way, the little critters are somewhat protected from predators and any chemical plant defenses that may exist on the outer layers. Pretty sneaky of them...

The Wikipedia page cited a 2009 BBC article mentioning the discovery of a plant from Ecuador that has suspicious leaf miner markings... but not caused by an insect at all! One of the first things we learn in biology class is that chlorophyll allows plants to make energy from the sun and gives them their green color, right? So, if a plant has splotches of white on the leaves, that just decreases the area on which photosynthesis can occur...non bueno right? Not so! These researchers from Germany found those splotches might be doing good in another sense...

Traipsing around the Ecuadorian forest they noticed a plant that sometimes had fully green leaves and sometimes had leaves with white splotches:

"A leaf damaged by mining moths (left) compared to one faking it (right)."

They also noticed that the fully green leaves seemed to be infected by leaf miners more often than the splotchy one. A hypothesis was born. They hypothesized that plants 'faking' leaf miner infestations would have less damage from actual leaf miners (in this case it was a type of moth) because insects prefer to lay their larvae in uninfected leaves (duh, more food and no damage). They did some experiments with green leaves, splotchy leaves, and hand-painted splotchy leaves (they used white-out!) and found that moths indeed preferred to infect fully green leaves. (By the way, they did tests to see if the chemicals in the white-out affected moth behavior and it didn't.)

This is the official scientific paper but if you just want a cursory look the BBC article does a good job casually pinning down the main points. So, that's how a quick internet search on the pretty pink  leaf trail ended up being a blog post! Pretty cool huh? If enough of these plants start faking it I wonder if the moths will wise up and start using more non-visual cues to assess infection...


Soltau, Ulf, Stefan Dötterl, and Sigrid Liede-Schumann. "Leaf variegation in Caladium steudneriifolium (Araceae): a case of mimicry?." Evolutionary Ecology23.4 (2009): 503-512.

Bats and viruses, a continuing love affair

Bats continue to be an intriguing player in the field of wildlife disease. Beside the fact that they carry disease pathogens, they can carry human disease pathogens - and crazy fatal ones to boot! Most of us don't have to worry about this, but if you are a horse rancher in Australia  or a pig farmer in Malaysia or Singapore - be careful! Two of the most deadly and thus fascinating human diseases (in my opinion) to erupt in recent years have taken hold in these areas. Hendra and Nipah viruses are current examples of what disease researchers call spillover events. In short, this refers to the 'fuzziness' of the boundaries separating humans, domesticated animals, and wildlife. As our worlds come into more contact with each other, it makes sense that we all start swapping pathogens and start getting new diseases from them.

The tricky thing is, you can't just say, 'Oh this animal has no visible disease symptoms, I'll be safe, my contact with it won't result in me catching anything bad." We are becoming more aware that some pathogens, while living just fine in one type of animal , can inflict surprisingly detrimental harm as soon as it "spills over" into a new animal host. It's like seeing the mild-mannered Dr. Jekyll turn into a violent, inflammatory Mr. Hyde! The term researchers use for the animal host that physically tolerates and harbors the pathogen is reservoir species. A lake reservoir holds water much like a reservoir host stores (and transmits) the pathogen.
When the pathogen is transmitted to a new/different host, i.e. a host who has never encountered this pathogen in its evolutionary history, its body can basically flip out and go bananas. The new host will likely get sick from having this foreign invader and in the most dire scenario, might even die from it. The cascade of these events are varied and dependent on A LOT of things. Many people spend their whole research careers trying to tease apart this puzzle so I won't try to here. But what is it about bats that make them so special? There are plenty of ideas: http://cmr.asm.org/content/19/3/531.abstract, http://onlinelibrary.wiley.com/doi/10.1111/zph.12000/abstract (from my labmate, Paul Bradley). Bats hang out in large groups, are highly social, eat a variety of plant/animal/bug material, can fly (!), all the while being warm-blooded mammals like us! It will be interesting to see what comes of this line of disease research...

For now, you can read more on:
- this Wikipedia page [http://en.wikipedia.org/wiki/Henipavirus]
- this CDC website [http://www.cdc.gov/ncidod/dvrd/spb/mnpages/dispages/nipah.htm]
 - this Nature piece from 2006 [http://www.nature.com/nrmicro/journal/v4/n1/abs/nrmicro1323.html]


UPDATE Feb-16-2013:
I just found out a group of researchers have evidence pinpointing bats as being the reservoir host for the Ebola virus in Bangladesh [http://www.sciencedaily.com/releases/2013/01/130116163819.htm]

And this just came in the recent issue of Nature: Bats as disease reservoirs. Let me know if you are interested in this article :)

Things that sometimes live in water and sometimes live on land

"Frog" is not included in the list of the 1000 most common English words.
Another graduate student in my program brought this website to my attention. It was born from this XKCD comic (http://xkcd.com/1133/). It's actually a really good 'elevator pitch' exercise. I could have written more but I got tired, here is mine:

http://bit.ly/SSIWfj

So polychaetes are funny looking eh?

When I was a lowly museum technician working on the Antarctic invertebrate collections, I remember the funny fat worms with copper-colored bristles. This was my first introduction to polychaetes, aka bristleworms:

Meet Hermadion magalhaensi, an Antarctic representative. I don't know if we are looking at the bottom or top...

Poly + chaetae = many bristles, they always reminded me of those bristly brushes one would use on horses or someone with really fine thick hair. That would be one expensive brush because these critters live mainly in the deep ocean and you would need a lot to make a full brush. Polychaeta is a Class within the larger Phylum Annelida (segmented worms; not to be confused with non-segmented worms, the Nematoda, which include your intestinal parasites!*). Anyways, they are a pretty adaptable group of critters, some live in the uber-hot, chaotic cities of hydrothermal vents, others settle on the cold cold lonely abyssal plains. Some live in self-secreted tubes! Some are free-living! Some are parasitic! You get the picture, very diverse. The ones most people will be familiar with are the christmas tree worms:

"Cuz dey purdy!"

But if you look at one real close up it is a completely different animal:

This one looks like a hungry baby.

This one looks worried. Are those sensors of some sort? The picture is more amusing if I pretend they are eyes. Unfortunately, you don't get much in the way of actual information in this online gallery, still amazing SEM images.

Animal mouths are so weird. The incisor-like teeth and puffy cheeks of the former image actually made me flashback to a critter we had our students learn in Vertebrate Biology lab: pocket gophers!

Family Geoymidae. Look at those claws!

In the Order Rodentia, blah blah blah...burrowing, yup yup....ruining vegetable gardens.....external cheek pouches....Excuse me, what was that last one?? I had to do a double back when I came across this curious aspect of their anatomy. Turns out the 'pocket' in pocket gopher refers to cheek pouches they stuff food in on the outside of their mouths! Being so, they are lined with fur!

Nota bene: see how the lips close behind the front incisors as to not let dirt get into their mouths whilst digging.

I saw an old paper laying out how this might have happened: a particularly deep-dimpled ancestor gopher might have had a nice life because it was able to haul more food. It's babies also had this trait which was carried down through more descendants becoming augmented to the pouches we see today. Evolution leads to some weird forms doesn't it? While grading final exams earlier this month one student had a good zinger that went kind of like this: "Evolution is acting upon all of us, and frankly, I don't think it has any idea what it's doing."
So true :)


* Have you ever looked up how many animal phyla there are? A number like 14 or 20 sounds reasonable right? WRONG! There are currently 35!

Things around me 1

Am home for Winter Break and today I took a long overdue walk in the neighborhood. This isn't an area I grew up in so I had no idea I lived right behind a park! I left my binoculars AND camera in Oregon so all I have is my iPhone...but I am constantly surprised at the crisp images I can take from it. Here are some from my walk:

Who made these tracks?

Of course I ran into some Canada geese and some mallards. Oh the silly squishy sounds of their bills pokin' around the mud.

I was attracted to the shininess of the beetle shell but, alas, it had no head.

These thorny branches grew through this white shelf fungus!

Some kind of little puffball mushroom, there were tons covering this fallen tree. The little holes in their heads means they have released their spores! How cool would it bee to see it like this (!):

This is from Wikipedia

I have no idea what this is. It is kind of hard to look up these tree infections online. The bark itself is not split open, the growth just makes it look like it is. You'd think there would be some "Common tree diseases of Virginia" website...however after much sleuthing I did figure out the following enigma:

So these cork-like growths are quite common for a type of tree called a hackberry. They are pretty common elm-like deciduous trees and apparently grow these when they are young but smooth them out later. I like how the conical ones look like limpets.

Anyways, looking up hackberry was pretty interesting. I had never heard of it before but it is pretty common in northern temperate areas. Super low maintenance in terms of soil type, weather, rainfall, shade, etc. It's got soft bark so its not really used commercially for furniture or building though it is sometimes used for cheap furniture. It is in the elm family (Ulmaceae) and the overall shape/size/leaf is like an elm:

I keep seeing it referred to as a good 'urban tree' though it's features (especially the warty growths!) are not that spectacular. It is a pretty easy-going tree though in terms of living conditions. What a polite, homely tree!

Haiku inspired by National Geographic photos

National Geographic's Photo of the Day: Best of October 2012 (Dragon's Blood Trees, Socotra)

The soft moon rises
The trees stretch, sigh heavenly
Blanketed by light

----------

National Geographic's Photo of the Day: Sep 30, 2012 (Muckross Lake, Ireland)

Thin glassy water

To sink slowly, completely

Cool still - dark silent

*Update Dec 18, 2012 -- "Haiku" is the singular and plural form! I forget who mentioned this to me but the title has thus been changed

The romantic twist of beta sheets

Thomas Cole's Romantic Landscape with Ruined Tower

So I am going further and further into the genomics rabbit hole and I am loving what I am finding! The genetics I remember encountering in undergrad was so dry, so static, so...lacking in dynamism!
How does one compete with the image of an Ecologist, that adventurous, jungle/island/mountain/tundra/desert/reef/volcano/ocean-bound Earth trekker? Any bench-bound Molecular Biologist pipetting fluids from one tube into another tube would seem rather tame, right? I certainly thought so.
But little by little, the more I scratched at the surface the more wonders and curiosities I uncovered. And now, years later (eons it feels like!), I am discovering how completely wrong I was. Somewhere in between learning about the mysterious structure of chromatin and reading about the puzzling habits of enhancers...I think I fell in love.
This world is moodier and more chaotic than a westbound journey 'round Cape Horn!

But I digress. The reason I even thought to post tonight was because I uncovered a delightful bit of protein trivia:
So first off you need to understand that the ability for a protein to function depends on how they fold. There are many different levels of folding which I will not get into too much now, but know that this folding ultimately occurs due to the sequence of amino acids that make up that protein*. As you would imagine, there are tons and tons of proteins that perform diverse activities (some recognizable ones: hemoglobin, insulin, collagen, etc). You would think that there must be a seemingly infinite number of ways to fold a protein in order for it to carry out its specific task - and you are right...but fear not, for there is order in the madness! Those complicated bunches of amino acids can actually be divvied up into many smaller, recognizable structures called structural motifs. Some structural motifs are more common than others and thus can be seen in many different kinds of proteins. One of these is called a Greek key motif:

A snapshot of a segment of amino acids in this protein show us there are 4 connecting beta sheets**. This looping pattern is reminiscent of the common Greek design, the Greek key and is thus aptly named:

Added Oct 12, 2012

This was described and named by Dr. Jane S. Richardson*** who has been a pioneer in the field of protein structure since the 1970s. Lovely, eh? I have to wait til I get on the school network to download the paper but I can't wait to read it! I love finding things like this in science, especially in a field that is not known for quirks. Things like this are just so delightful to find. Obviously this is a reflection on how much I love etymology and taxonomy, there are always so many hidden relationships in words and names. Maybe one day I will discover something and get to name it after some semi-obscure thing students in the future will be compelled to look up and spend over an hour researching!






*So proteins all start of with their DNA sequence which gets transcribed into RNA, spliced [edited] into mRNA, which then feeds into a ribosome that then translates that string of nucleotide bases into a string of amino acids which then scrunch up and twist and fold according to how they came out!

** beta sheets are flat configurations (contrast that to the alpha helix structure)

*** Remember seeing all those 3-D ribbon images of proteins from your textbooks? Well, you can thank Dr. Richardson for those! She created those ribbon diagrams that are now ubiquitous in science textbooks:

Triose phosphate isomerase hand-drawn by Jane Richardson in 1981

Richardson, J. S. 1977. B-sheet topology and the relatedness of proteins. Nature 268: 495-500.

My darling Darlingtonia

For a kid, animals rule. Animals fly, run, hunt, sing, dance, hiss, attack, nap, swim, learn, and even snowboard. Plants are just there for landscape and food*. However, there are certain plants children love because they break the typical mold of what they think a plant should be...

CARNIVOROUS PLANTS!

Ok, maybe not anything like what Rick Moranis encountered on the streets of New York in the 1980s but still, quite striking in their own right:

                   

                     

But let's start at the very beginning, with names. 

King              Philip         Came      Over        From         Geneva    Switzerland. 

Kingdom -> Phylum -> Class -> Order -> Family -> Genus -> species

Carnivorous plants fall into three families: Sarraceniaceae, Nepenthaceae, and Droseraceae

Droseraceae: seen worldwide, these are your venus fly traps (photo: above left)

Nepenthaceae: Old World family (South China, Indonesia, Australia, Philippines, etc), tropical pitcher plants (photo: above right)

and....

Sarraceniaceae: New World family (that's where we are!) with 3 genera; two are in North America and they are roughly split east + west coast. Plants in the Sarracenia genus live on the east coast and has about 8-11 species while Darlingtonia is the west coast representative with just one species...

Do you love my dramatic lighting? It looks as though it might move! Also called the Cobra Lilly for obvious reasons. 

Darlingtonia california, the moody only child of the genus, is a rare find in the field. It was initially stumbled up on by the a certain William Brackenridge, assistant botanist of the U.S. Exploring Expedition on Mount Shasta, California in 1841 (but let's face it, he was pretty much the botanist on the voyage...)! My former supervisor when I was interning for the Wilkes Expedition project told me that his journals revealed he had thought he found a new species of Sarracenia, not realizing he was "collecting the most iconic new species of the U.S.Ex.Ex."

It grows in northern CA and southern OR but the very tip top northernmost reaches of its range can slip past the halfway point up the coast of OR. It was this northernmost population I paid a visit to recently with my botanically inclined friend.

These plants are weird and pretty high maintenance:
- prefer serpentine soils (rich in heavy metals and lacking in nitrogen, phosphorous, potassium)
- needs cool running water (probably from a mountain)
- and likes ample sunshine

You can find them in bogs with the afore mentioned properties. The little population we found did not have that much sunlight (but enough) so their characteristic red color was not present. They still proved beautiful specimens:

This whole thing is actually a modified leaf! What you don't see is the whole plant which consists of many stalks radiating out of the center.

The mustache tips secrete a sugary concoction irresistible to insects! They travel up and into the dome of despair looking for more! Note the 'skylights'...

The 'skylights' are areas of thin plant tissue. A bug might try to leave through these false exits but will eventually tire and fall into the murky depths below... 

The skylights are really nice huh? Love how they attenuate down. 

You can't tell form this picture but the stalks grow in a way so that they don't overlap each other. They twist left or right as they extend upward and lean outward. Some stalks I saw were over a foot tall!

The fun thing about this particular species of pitcher plant is that it does not collect rain water to fill its pitcher. Other pitcher plants you see have an open container while this one takes water from its roots depending on how much dead organic stuff is inside. It also does not have its own digestive enzymes to eat the insects but instead relies on bacteria living in the pitcher to do the job.
So...kind of the opposite of what other pitcher plants do I guess? They just have to be different. Anyways I am discovering there is so much more to these plants but this post is getting a little long in the tooth as it is so I will stop. But if you want more Darlingtonia reading go here and here and here.

Til next time!

* My views on plants have changed since 1993.